diff --git a/docs/paper_spaeth_krumm_app.pdf b/docs/paper_spaeth_krumm_app.pdf new file mode 100755 index 0000000..0b5ed6a Binary files /dev/null and b/docs/paper_spaeth_krumm_app.pdf differ diff --git a/src/__init__.py b/src/__init__.py new file mode 100755 index 0000000..e69de29 diff --git a/src/data/aaindex1.txt b/src/data/aaindex1.txt new file mode 100755 index 0000000..0a83cad --- /dev/null +++ b/src/data/aaindex1.txt @@ -0,0 +1,10296 @@ +H ANDN920101 +D alpha-CH chemical shifts (Andersen et al., 1992) +R LIT:1810048b PMID:1575719 +A Andersen, N.H., Cao, B. and Chen, C. +T Peptide/protein structure analysis using the chemical shift index method: + upfield alpha-CH values reveal dynamic helices and aL sites +J Biochem. and Biophys. Res. Comm. 184, 1008-1014 (1992) +C BUNA790102 0.949 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 4.35 4.38 4.75 4.76 4.65 4.37 4.29 3.97 4.63 3.95 + 4.17 4.36 4.52 4.66 4.44 4.50 4.35 4.70 4.60 3.95 +// +H ARGP820101 +D Hydrophobicity index (Argos et al., 1982) +R LIT:0901079b PMID:7151796 +A Argos, P., Rao, J.K.M. and Hargrave, P.A. +T Structural prediction of membrane-bound proteins +J Eur. J. Biochem. 128, 565-575 (1982) +C JOND750101 1.000 SIMZ760101 0.967 GOLD730101 0.936 + TAKK010101 0.906 MEEJ810101 0.891 ROSM880104 0.872 + CIDH920105 0.867 LEVM760106 0.865 CIDH920102 0.862 + MEEJ800102 0.855 MEEJ810102 0.853 ZHOH040101 0.841 + CIDH920103 0.827 PLIV810101 0.820 CIDH920104 0.819 + LEVM760107 0.806 NOZY710101 0.800 GUYH850103 -0.808 + PARJ860101 -0.835 WOLS870101 -0.838 BULH740101 -0.854 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.61 0.60 0.06 0.46 1.07 0. 0.47 0.07 0.61 2.22 + 1.53 1.15 1.18 2.02 1.95 0.05 0.05 2.65 1.88 1.32 +// +H ARGP820102 +D Signal sequence helical potential (Argos et al., 1982) +R LIT:0901079b PMID:7151796 +A Argos, P., Rao, J.K.M. and Hargrave, P.A. +T Structural prediction of membrane-bound proteins +J Eur. J. Biochem. 128, 565-575 (1982) +C ARGP820103 0.961 KYTJ820101 0.803 JURD980101 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.18 0.20 0.23 0.05 1.89 0.72 0.11 0.49 0.31 1.45 + 3.23 0.06 2.67 1.96 0.76 0.97 0.84 0.77 0.39 1.08 +// +H ARGP820103 +D Membrane-buried preference parameters (Argos et al., 1982) +R LIT:0901079b PMID:7151796 +A Argos, P., Rao, J.K.M. and Hargrave, P.A. +T Structural prediction of membrane-bound proteins +J Eur. J. Biochem. 128, 565-575 (1982) +C ARGP820102 0.961 MIYS850101 0.822 NAKH900106 0.810 + EISD860103 0.810 KYTJ820101 0.806 JURD980101 0.800 + PUNT030101 -0.810 MIYS990102 -0.814 MIYS990101 -0.817 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.56 0.45 0.27 0.14 1.23 0.51 0.23 0.62 0.29 1.67 + 2.93 0.15 2.96 2.03 0.76 0.81 0.91 1.08 0.68 1.14 +// +H BEGF750101 +D Conformational parameter of inner helix (Beghin-Dirkx, 1975) +R LIT:1309065 PMID:50789 +A Beghin, F. and Dirkx, J. +T Une methode statistique simple de prediction des conformations proteiques +J Arch. Int. Physiol. Biochim. 83, 167-168 (1975) +C KANM800103 0.893 AURR980113 0.857 ROBB760103 0.852 + CHOP780201 0.841 QIAN880105 0.833 AURR980109 0.821 + QIAN880107 0.815 PALJ810102 0.811 AURR980108 0.810 + CHOP780101 -0.803 CHOP780210 -0.804 CRAJ730103 -0.812 + ROBB760108 -0.819 ROBB760113 -0.826 CHAM830101 -0.854 + PALJ810106 -0.859 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1. 0.52 0.35 0.44 0.06 0.44 0.73 0.35 0.60 0.73 + 1. 0.60 1. 0.60 0.06 0.35 0.44 0.73 0.44 0.82 +// +H BEGF750102 +D Conformational parameter of beta-structure (Beghin-Dirkx, 1975) +R LIT:1309065 PMID:50789 +A Beghin, F. and Dirkx, J. +T Une methode statistique simple de prediction des conformations proteiques +J Arch. Int. Physiol. Biochim. 83, 167-168 (1975) +C CORJ870105 0.878 CORJ870106 0.853 PRAM900103 0.834 + LEVM780102 0.834 PALJ810110 0.834 NAGK730102 0.833 + CORJ870107 0.831 QIAN880120 0.829 QIAN880119 0.811 + ROBB760106 0.809 PTIO830102 0.807 LIFS790101 0.807 + MIYS850101 0.806 PONP800107 0.803 PALJ810104 0.801 + CORJ870108 -0.825 MEIH800101 -0.832 RACS770101 -0.840 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.77 0.72 0.55 0.65 0.65 0.72 0.55 0.65 0.83 0.98 + 0.83 0.55 0.98 0.98 0.55 0.55 0.83 0.77 0.83 0.98 +// +H BEGF750103 +D Conformational parameter of beta-turn (Beghin-Dirkx, 1975) +R LIT:1309065 PMID:50789 +A Beghin, F. and Dirkx, J. +T Une methode statistique simple de prediction des conformations proteiques +J Arch. Int. Physiol. Biochim. 83, 167-168 (1975) +C ROBB760113 0.924 ROBB760108 0.922 ROBB760110 0.903 + CHOP780101 0.885 CRAJ730103 0.874 PALJ810106 0.859 + TANS770110 0.834 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.37 0.84 0.97 0.97 0.84 0.64 0.53 0.97 0.75 0.37 + 0.53 0.75 0.64 0.53 0.97 0.84 0.75 0.97 0.84 0.37 +// +H BHAR880101 +D Average flexibility indices (Bhaskaran-Ponnuswamy, 1988) +R LIT:1414112 +A Bhaskaran, R. and Ponnuswamy, P.K. +T Positional flexibilities of amino acid residues in globular proteins +J Int. J. Peptide Protein Res. 32, 241-255 (1988) +C VINM940103 0.869 KARP850102 0.806 WERD780101 -0.803 + RICJ880111 -0.813 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.357 0.529 0.463 0.511 0.346 0.493 0.497 0.544 0.323 0.462 + 0.365 0.466 0.295 0.314 0.509 0.507 0.444 0.305 0.420 0.386 +// +H BIGC670101 +D Residue volume (Bigelow, 1967) +R LIT:2004108b PMID:6048539 +A Bigelow, C.C. +T On the average hydrophobicity of proteins and the relation between it and + protein structure +J J. Theor. Biol. 16, 187-211 (1967) (Asn Gln 5.0) +C GOLD730102 1.000 KRIW790103 0.993 TSAJ990101 0.993 + TSAJ990102 0.992 CHOC750101 0.990 GRAR740103 0.984 + FAUJ880103 0.972 CHAM820101 0.966 HARY940101 0.960 + CHOC760101 0.960 PONJ960101 0.950 FASG760101 0.919 + LEVM760105 0.913 ROSG850101 0.910 DAWD720101 0.903 + LEVM760102 0.896 ZHOH040102 0.884 LEVM760106 0.876 + CHAM830106 0.870 LEVM760107 0.863 FAUJ880106 0.860 + RADA880106 0.856 MCMT640101 0.814 RADA880103 -0.865 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 52.6 109.1 75.7 68.4 68.3 89.7 84.7 36.3 91.9 102.0 + 102.0 105.1 97.7 113.9 73.6 54.9 71.2 135.4 116.2 85.1 +// +H BIOV880101 +D Information value for accessibility; average fraction 35% (Biou et al., 1988) +R LIT:1413106b PMID:3237683 +A Biou, V., Gibrat, J.F., Levin, J.M., Robson, B. and Garnier, J. +T Secondary structure prediction: combination of three different methods +J Protein Engineering 2, 185-191 (1988) +C RADA880108 0.981 ROSG850102 0.981 NISK860101 0.972 + BIOV880102 0.968 MIYS850101 0.960 WERD780101 0.951 + FAUJ830101 0.942 ZHOH040103 0.941 NADH010103 0.939 + NADH010104 0.937 CASG920101 0.935 MEIH800103 0.934 + CIDH920104 0.933 BASU050103 0.926 PONP800103 0.926 + PONP800102 0.926 NADH010102 0.921 NISK800101 0.920 + PONP800101 0.918 CORJ870101 0.917 CIDH920105 0.912 + PONP930101 0.912 BASU050102 0.909 PONP800108 0.907 + PLIV810101 0.899 MANP780101 0.899 ROBB790101 0.890 + CORJ870107 0.889 CIDH920103 0.887 BASU050101 0.883 + DESM900102 0.878 CORJ870103 0.876 JANJ780102 0.875 + ROSM880105 0.874 CORJ870106 0.870 CORJ870104 0.867 + NADH010105 0.867 CIDH920102 0.864 EISD860103 0.864 + CORJ870105 0.859 MEEJ810101 0.855 BAEK050101 0.853 + JANJ790102 0.848 CIDH920101 0.847 JURD980101 0.840 + GUOD860101 0.839 SWER830101 0.839 NADH010101 0.838 + BLAS910101 0.838 CORJ870102 0.837 KYTJ820101 0.829 + EISD860101 0.828 JANJ790101 0.827 ZHOH040101 0.825 + MEEJ810102 0.824 CHOC760103 0.823 PONP800107 0.816 + EISD840101 0.811 DESM900101 0.807 KRIW710101 -0.813 + PARS000101 -0.819 FUKS010102 -0.820 KARP850101 -0.825 + JANJ780103 -0.829 WOEC730101 -0.829 ROSM880101 -0.830 + LEVM760101 -0.831 KUHL950101 -0.834 FUKS010103 -0.840 + GUYH850104 -0.844 HOPT810101 -0.848 WOLS870101 -0.854 + ROSM880102 -0.854 RACS770103 -0.856 OOBM770101 -0.858 + KRIW790102 -0.869 FUKS010104 -0.873 VINM940102 -0.876 + PUNT030102 -0.878 KARP850102 -0.880 PUNT030101 -0.883 + CORJ870108 -0.886 PARJ860101 -0.889 GUYH850103 -0.890 + KIDA850101 -0.893 RACS770101 -0.893 VINM940103 -0.901 + GRAR740102 -0.910 KRIW790101 -0.910 OOBM770103 -0.920 + GUYH850102 -0.922 GUYH850101 -0.929 RACS770102 -0.937 + VINM940101 -0.941 MIYS990101 -0.947 MIYS990102 -0.948 + MEIH800101 -0.949 MEIH800102 -0.956 MIYS990103 -0.962 + MIYS990104 -0.965 MIYS990105 -0.975 FASG890101 -0.982 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 16. -70. -74. -78. 168. -73. -106. -13. 50. 151. + 145. -141. 124. 189. -20. -70. -38. 145. 53. 123. +// +H BIOV880102 +D Information value for accessibility; average fraction 23% (Biou et al., 1988) +R LIT:1413106b PMID:3237683 +A Biou, V., Gibrat, J.F., Levin, J.M., Robson, B. and Garnier, J. +T Secondary structure prediction: combination of three different methods +J Protein Engineering 2, 185-191 (1988) +C BIOV880101 0.968 ROSG850102 0.960 RADA880108 0.942 + NISK860101 0.939 MIYS850101 0.930 WERD780101 0.929 + CASG920101 0.919 MEIH800103 0.916 NADH010102 0.914 + NADH010103 0.913 FAUJ830101 0.911 NADH010104 0.900 + ZHOH040103 0.891 CIDH920104 0.890 CIDH920105 0.882 + CORJ870101 0.882 PONP800103 0.879 PONP930101 0.877 + DESM900102 0.876 NISK800101 0.873 ROSM880105 0.871 + BASU050103 0.868 PONP800102 0.867 JANJ780102 0.862 + PONP800101 0.860 CIDH920103 0.860 PLIV810101 0.858 + JANJ790102 0.856 PONP800108 0.854 WARP780101 0.853 + CORJ870107 0.850 MANP780101 0.847 EISD860103 0.845 + CORJ870103 0.840 BASU050102 0.838 CIDH920102 0.837 + EISD860101 0.832 NAKH900110 0.829 CORJ870105 0.823 + MEEJ810101 0.822 DESM900101 0.821 ROBB790101 0.821 + CIDH920101 0.819 CORJ870106 0.818 GUOD860101 0.817 + CORJ870104 0.815 PONP800107 0.814 EISD840101 0.814 + BASU050101 0.812 BLAS910101 0.809 JURD980101 0.805 + NADH010101 0.804 KARP850101 -0.804 KUHL950101 -0.809 + JANJ780101 -0.809 FUKS010102 -0.810 PARS000101 -0.813 + GUYH850103 -0.818 WOEC730101 -0.819 ROSM880101 -0.824 + VINM940102 -0.826 CORJ870108 -0.831 ROSM880102 -0.837 + WOLS870101 -0.842 LEVM760101 -0.847 GUYH850104 -0.855 + KARP850102 -0.859 JANJ780103 -0.860 PUNT030102 -0.860 + HOPT810101 -0.864 PARJ860101 -0.875 RACS770101 -0.875 + KRIW790101 -0.876 OOBM770101 -0.877 KRIW790102 -0.878 + GRAR740102 -0.881 GUYH850101 -0.885 FUKS010104 -0.887 + PUNT030101 -0.888 VINM940103 -0.889 KIDA850101 -0.892 + MIYS990101 -0.901 MIYS990102 -0.902 GUYH850102 -0.903 + RACS770103 -0.906 MIYS990103 -0.923 OOBM770103 -0.925 + FASG890101 -0.928 VINM940101 -0.929 MIYS990104 -0.932 + RACS770102 -0.932 MEIH800101 -0.937 MIYS990105 -0.947 + MEIH800102 -0.951 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 44. -68. -72. -91. 90. -117. -139. -8. 47. 100. + 108. -188. 121. 148. -36. -60. -54. 163. 22. 117. +// +H BROC820101 +D Retention coefficient in TFA (Browne et al., 1982) +R LIT:0809229 PMID:7125223 +A Browne, C.A., Bennett, H.P.J. and Solomon, S. +T The isolation of peptides by high-performance liquid chromatography using + predicted elution positions +J Anal. Biochem. 124, 201-208 (1982) +C BROC820102 0.925 ZIMJ680105 0.896 MEEJ800102 0.877 + TAKK010101 0.836 GUOD860101 0.832 NAKH900110 0.830 + NOZY710101 0.829 MEEJ810102 0.820 RADA880102 0.811 + BULH740101 -0.815 PARJ860101 -0.849 WOLS870101 -0.871 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 7.3 -3.6 -5.7 -2.9 -9.2 -0.3 -7.1 -1.2 -2.1 6.6 + 20.0 -3.7 5.6 19.2 5.1 -4.1 0.8 16.3 5.9 3.5 +// +H BROC820102 +D Retention coefficient in HFBA (Browne et al., 1982) +R LIT:0809229 PMID:7125223 +A Browne, C.A., Bennett, H.P.J. and Solomon, S. +T The isolation of peptides by high-performance liquid chromatography using + predicted elution positions +J Anal. Biochem. 124, 201-208 (1982) +C BROC820101 0.925 ZIMJ680105 0.865 MEEJ800102 0.857 + MEEJ800101 0.840 TAKK010101 0.839 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 3.9 3.2 -2.8 -2.8 -14.3 1.8 -7.5 -2.3 2.0 11.0 + 15.0 -2.5 4.1 14.7 5.6 -3.5 1.1 17.8 3.8 2.1 +// +H BULH740101 +D Transfer free energy to surface (Bull-Breese, 1974) +R PMID:4839053 +A Bull, H.B. and Breese, K. +T Surface tension of amino acid solutions: A hydrophobicity scale of the amino + acid residues +J Arch. Biochem. Biophys. 161, 665-670 (1974) +C WOLS870101 0.929 PARJ860101 0.909 MIYS990101 0.884 + MIYS990102 0.880 GRAR740102 0.822 GUYH850103 0.820 + COWR900101 -0.804 ROBB790101 -0.813 BROC820101 -0.815 + LEVM760106 -0.818 ZHOH040103 -0.828 CIDH920104 -0.829 + FAUJ830101 -0.830 BASU050103 -0.833 EISD860101 -0.833 + MIYS850101 -0.838 WILM950101 -0.845 BASU050102 -0.845 + CIDH920103 -0.848 CIDH920102 -0.851 JOND750101 -0.853 + ARGP820101 -0.854 BASU050101 -0.854 RADA880102 -0.856 + ZHOH040102 -0.860 BLAS910101 -0.860 TAKK010101 -0.865 + CIDH920105 -0.871 GOLD730101 -0.874 MEEJ800102 -0.875 + ZHOH040101 -0.876 MEEJ810101 -0.876 ZIMJ680105 -0.879 + MEEJ810102 -0.880 ROSM880104 -0.884 NOZY710101 -0.892 + SIMZ760101 -0.894 VENT840101 -0.907 PLIV810101 -0.912 + GUOD860101 -0.922 SWER830101 -0.923 CORJ870102 -0.923 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.20 -0.12 0.08 -0.20 -0.45 0.16 -0.30 0.00 -0.12 -2.26 + -2.46 -0.35 -1.47 -2.33 -0.98 -0.39 -0.52 -2.01 -2.24 -1.56 +// +H BULH740102 +D Apparent partial specific volume (Bull-Breese, 1974) +R PMID:4839053 +A Bull, H.B. and Breese, K. +T Surface tension of amino acid solutions: A hydrophobicity scale of the amino + acid residues +J Arch. Biochem. Biophys. 161, 665-670 (1974) (Tyr !) +C COHE430101 0.923 ZIMJ680102 0.825 GOLD730101 0.825 + SIMZ760101 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.691 0.728 0.596 0.558 0.624 0.649 0.632 0.592 0.646 0.809 + 0.842 0.767 0.709 0.756 0.730 0.594 0.655 0.743 0.743 0.777 +// +H BUNA790101 +D alpha-NH chemical shifts (Bundi-Wuthrich, 1979) +R LIT:0503064b +A Bundi, A. and Wuthrich, K. +T 1H-nmr parameters of the common amino acid residues measured in aqueous + solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH +J Biopolymers 18, 285-297 (1979) (Pro !) +C BLAM930101 0.945 ONEK900101 0.902 ROBB760104 0.823 + FAUJ880113 0.818 CHOP780213 -0.822 ISOY800104 -0.842 + MUNV940104 -0.865 TANS770104 -0.867 MUNV940105 -0.874 + GEOR030109 -0.901 AVBF000104 -0.922 ONEK900102 -0.949 + FINA910102 -0.992 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.249 8.274 8.747 8.410 8.312 8.411 8.368 8.391 8.415 8.195 + 8.423 8.408 8.418 8.228 0. 8.380 8.236 8.094 8.183 8.436 +// +H BUNA790102 +D alpha-CH chemical shifts (Bundi-Wuthrich, 1979) +R LIT:0503064b +A Bundi, A. and Wuthrich, K. +T 1H-nmr parameters of the common amino acid residues measured in aqueous + solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH +J Biopolymers 18, 285-297 (1979) +C ANDN920101 0.949 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 4.349 4.396 4.755 4.765 4.686 4.373 4.295 3.972 4.630 4.224 + 4.385 4.358 4.513 4.663 4.471 4.498 4.346 4.702 4.604 4.184 +// +H BUNA790103 +D Spin-spin coupling constants 3JHalpha-NH (Bundi-Wuthrich, 1979) +R LIT:0503064b +A Bundi, A. and Wuthrich, K. +T 1H-nmr parameters of the common amino acid residues measured in aqueous + solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH +J Biopolymers 18, 285-297 (1979) (Met Pro Trp !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.5 6.9 7.5 7.0 7.7 6.0 7.0 5.6 8.0 7.0 + 6.5 6.5 0. 9.4 0. 6.5 6.9 0. 6.8 7.0 +// +H BURA740101 +D Normalized frequency of alpha-helix (Burgess et al., 1974) +R LIT:2004075b +A Burgess, A.W., Ponnuswamy, P.K. and Scheraga, H.A. +T Analysis of conformations of amino acid residues and prediction of backbone + topography in proteins +J Isr. J. Chem. 12, 239-286 (1974) +C CHOP780201 0.917 TANS770101 0.917 ROBB760101 0.912 + CRAJ730101 0.900 PALJ810102 0.900 NAGK730101 0.883 + GEIM800101 0.858 KANM800101 0.855 MAXF760101 0.852 + PALJ810101 0.850 ISOY800101 0.839 LEVM780104 0.833 + GEIM800104 0.819 KANM800103 0.810 RACS820108 0.809 + AURR980108 0.808 PRAM900102 0.805 LEVM780101 0.805 + NAGK730103 -0.830 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.486 0.262 0.193 0.288 0.200 0.418 0.538 0.120 0.400 0.370 + 0.420 0.402 0.417 0.318 0.208 0.200 0.272 0.462 0.161 0.379 +// +H BURA740102 +D Normalized frequency of extended structure (Burgess et al., 1974) +R LIT:2004075b +A Burgess, A.W., Ponnuswamy, P.K. and Scheraga, H.A. +T Analysis of conformations of amino acid residues and prediction of backbone + topography in proteins +J Isr. J. Chem. 12, 239-286 (1974) +C ROBB760105 0.821 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.288 0.362 0.229 0.271 0.533 0.327 0.262 0.312 0.200 0.411 + 0.400 0.265 0.375 0.318 0.340 0.354 0.388 0.231 0.429 0.495 +// +H CHAM810101 +D Steric parameter (Charton, 1981) +R LIT:2004112b PMID:7300379 +A Charton, M. +T Protein folding and the genetic code: An alternative quantitative model +J J. Theor. Biol. 91, 115-123 (1981) (Pro !) +C FAUJ880102 0.881 LEVM760104 -0.818 KIMC930101 -0.848 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.52 0.68 0.76 0.76 0.62 0.68 0.68 0.00 0.70 1.02 + 0.98 0.68 0.78 0.70 0.36 0.53 0.50 0.70 0.70 0.76 +// +H CHAM820101 +D Polarizability parameter (Charton-Charton, 1982) +R LIT:0902079b PMID:7183857 +A Charton, M. and Charton, B.I. +T The structural dependence of amino acid hydrophobicity parameters +J J. Theor. Biol. 99, 629-644 (1982) (Pro 0.018) +C FAUJ880103 0.992 CHOC750101 0.982 TSAJ990102 0.978 + TSAJ990101 0.977 GOLD730102 0.967 CHOC760101 0.966 + BIGC670101 0.966 KRIW790103 0.963 FASG760101 0.962 + GRAR740103 0.951 PONJ960101 0.938 HARY940101 0.933 + ROSG850101 0.917 LEVM760102 0.915 LEVM760105 0.915 + FAUJ880106 0.902 CHAM830106 0.899 LEVM760107 0.891 + MCMT640101 0.871 DAWD720101 0.865 RADA880106 0.847 + ZHOH040102 0.826 LEVM760106 0.818 HUTJ700102 0.815 + CHAM830105 0.809 SNEP660103 0.808 RADA880103 -0.912 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.046 0.291 0.134 0.105 0.128 0.180 0.151 0.000 0.230 0.186 + 0.186 0.219 0.221 0.290 0.131 0.062 0.108 0.409 0.298 0.140 +// +H CHAM820102 +D Free energy of solution in water, kcal/mole (Charton-Charton, 1982) +R LIT:0902079b PMID:7183857 +A Charton, M. and Charton, B.I. +T The structural dependence of amino acid hydrophobicity parameters +J J. Theor. Biol. 99, 629-644 (1982) (Asn His Lys Thr !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.368 -1.03 0. 2.06 4.53 0.731 1.77 -0.525 0. 0.791 + 1.07 0. 0.656 1.06 -2.24 -0.524 0. 1.60 4.91 0.401 +// +H CHAM830101 +D The Chou-Fasman parameter of the coil conformation (Charton-Charton, 1983) +R LIT:0907093b PMID:6876837 +A Charton, M. and Charton, B. +T The dependence of the Chou-Fasman parameters on amino acid side chain + structure +J J. Theor. Biol. 111, 447-450 (1983) +C CHOP780101 0.946 CHOP780216 0.942 PALJ810106 0.939 + GEIM800111 0.938 CHOP780203 0.931 QIAN880132 0.925 + TANS770110 0.917 GEIM800108 0.916 QIAN880133 0.913 + LEVM780103 0.909 PRAM900104 0.909 CHOP780210 0.905 + LEVM780106 0.900 ISOY800103 0.881 QIAN880131 0.860 + NAGK730103 0.857 ROBB760113 0.841 QIAN880134 0.841 + PALJ810105 0.826 CRAJ730103 0.821 QIAN880135 0.814 + ROBB760108 0.812 ROBB760110 0.804 AVBF000102 -0.803 + QIAN880105 -0.803 PALJ810102 -0.808 FAUJ880102 -0.809 + ISOY800101 -0.815 RICJ880109 -0.826 CHOP780201 -0.828 + AURR980113 -0.828 ROBB760101 -0.828 AURR980108 -0.834 + PTIO830101 -0.841 AURR980114 -0.842 BEGF750101 -0.854 + QIAN880106 -0.856 QIAN880107 -0.858 ROBB760103 -0.878 + KANM800103 -0.889 SUEM840101 -0.891 AURR980109 -0.896 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.71 1.06 1.37 1.21 1.19 0.87 0.84 1.52 1.07 0.66 + 0.69 0.99 0.59 0.71 1.61 1.34 1.08 0.76 1.07 0.63 +// +H CHAM830102 +D A parameter defined from the residuals obtained from the best correlation of + the Chou-Fasman parameter of beta-sheet (Charton-Charton, 1983) +R LIT:0907093b PMID:6876837 +A Charton, M. and Charton, B. +T The dependence of the Chou-Fasman parameters on amino acid side chain + structure +J J. Theor. Biol. 111, 447-450 (1983) (Pro !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.118 0.124 0.289 0.048 0.083 -0.105 -0.245 0.104 0.138 0.230 + -0.052 0.032 -0.258 0.015 0. 0.225 0.166 0.158 0.094 0.513 +// +H CHAM830103 +D The number of atoms in the side chain labelled 1+1 (Charton-Charton, 1983) +R LIT:0907093b PMID:6876837 +A Charton, M. and Charton, B. +T The dependence of the Chou-Fasman parameters on amino acid side chain + structure +J J. Theor. Biol. 111, 447-450 (1983) (Pro !) +C AVBF000101 0.843 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 1. 1. 1. 1. 1. 1. 0. 1. 2. + 1. 1. 1. 1. 0. 1. 2. 1. 1. 2. +// +H CHAM830104 +D The number of atoms in the side chain labelled 2+1 (Charton-Charton, 1983) +R LIT:0907093b PMID: +A Charton, M. and Charton, B. +T The dependence of the Chou-Fasman parameters on amino acid side chain + structure +J J. Theor. Biol. 111, 447-450 (1983) (Pro !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 1. 1. 1. 0. 1. 1. 0. 1. 1. + 2. 1. 1. 1. 0. 0. 0. 1. 1. 0. +// +H CHAM830105 +D The number of atoms in the side chain labelled 3+1 (Charton-Charton, 1983) +R LIT:0907093b PMID:6876837 +A Charton, M. and Charton, B. +T The dependence of the Chou-Fasman parameters on amino acid side chain + structure +J J. Theor. Biol. 111, 447-450 (1983) (Pro !) +C CHAM830106 0.874 LEVM760102 0.843 FASG760101 0.839 + CHOC760101 0.833 LEVM760105 0.829 FAUJ880103 0.813 + CHAM820101 0.809 RADA880103 -0.808 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 1. 0. 0. 0. 1. 1. 0. 1. 0. + 0. 1. 1. 1. 0. 0. 0. 1.5 1. 0. +// +H CHAM830106 +D The number of bonds in the longest chain (Charton-Charton, 1983) +R LIT:0907093b PMID:6876837 +A Charton, M. and Charton, B. +T The dependence of the Chou-Fasman parameters on amino acid side chain + structure +J J. Theor. Biol. 111, 447-450 (1983) (Pro !) +C LEVM760102 0.962 LEVM760105 0.958 FASG760101 0.943 + CHOC760101 0.937 FAUJ880103 0.927 RADA880106 0.922 + PONJ960101 0.917 CHOC750101 0.906 CHAM820101 0.899 + TSAJ990102 0.896 HARY940101 0.894 GRAR740103 0.890 + TSAJ990101 0.889 KRIW790103 0.876 CHAM830105 0.874 + BIGC670101 0.870 GOLD730102 0.869 OOBM770102 0.858 + FAUJ880106 0.845 FAUJ880104 0.817 RADA880103 -0.901 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 5. 2. 2. 1. 3. 3. 0. 3. 2. + 2. 4. 3. 4. 0. 1. 1. 5. 5. 1. +// +H CHAM830107 +D A parameter of charge transfer capability (Charton-Charton, 1983) +R LIT:0907093b PMID:6876837 +A Charton, M. and Charton, B. +T The dependence of the Chou-Fasman parameters on amino acid side chain + structure +J J. Theor. Biol. 111, 447-450 (1983) (Pro !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 0. 1. 1. 0. 0. 1. 1. 0. 0. + 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. +// +H CHAM830108 +D A parameter of charge transfer donor capability (Charton-Charton, 1983) +R LIT:0907093b PMID:6876837 +A Charton, M. and Charton, B. +T The dependence of the Chou-Fasman parameters on amino acid side chain + structure +J J. Theor. Biol. 111, 447-450 (1983) (Pro !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 1. 1. 0. 1. 1. 0. 0. 1. 0. + 0. 1. 1. 1. 0. 0. 0. 1. 1. 0. +// +H CHOC750101 +D Average volume of buried residue (Chothia, 1975) +R PMID:1118010 +A Chothia, C. +T Structural invariants in protein folding +J Nature 254, 304-308 (1975) (Arg missing) +C TSAJ990102 0.996 TSAJ990101 0.995 FAUJ880103 0.990 + BIGC670101 0.990 GOLD730102 0.989 CHAM820101 0.982 + KRIW790103 0.982 CHOC760101 0.981 GRAR740103 0.973 + PONJ960101 0.966 HARY940101 0.961 FASG760101 0.956 + LEVM760105 0.939 LEVM760102 0.933 ROSG850101 0.908 + CHAM830106 0.906 DAWD720101 0.901 FAUJ880106 0.888 + RADA880106 0.867 LEVM760107 0.858 ZHOH040102 0.856 + LEVM760106 0.841 MCMT640101 0.822 HUTJ700102 0.802 + RADA880103 -0.892 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 91.5 202.0 135.2 124.5 117.7 161.1 155.1 66.4 167.3 168.8 + 167.9 171.3 170.8 203.4 129.3 99.1 122.1 237.6 203.6 141.7 +// +H CHOC760101 +D Residue accessible surface area in tripeptide (Chothia, 1976) +R LIT:2004094b PMID:994183 +A Chothia, C. +T The nature of the accessible and buried surfaces in proteins +J J. Mol. Biol. 105, 1-14 (1976) +C FAUJ880103 0.985 CHOC750101 0.981 FASG760101 0.978 + LEVM760102 0.972 TSAJ990102 0.972 LEVM760105 0.968 + TSAJ990101 0.968 CHAM820101 0.966 PONJ960101 0.961 + GOLD730102 0.960 BIGC670101 0.960 KRIW790103 0.948 + HARY940101 0.946 GRAR740103 0.945 CHAM830106 0.937 + DAWD720101 0.901 FAUJ880106 0.898 RADA880106 0.875 + WOLS870102 0.845 ROSG850101 0.842 FAUJ880104 0.835 + CHAM830105 0.833 OOBM770102 0.824 HUTJ700102 0.819 + MCMT640101 0.809 LEVM760107 0.807 RADA880103 -0.924 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 115. 225. 160. 150. 135. 180. 190. 75. 195. 175. + 170. 200. 185. 210. 145. 115. 140. 255. 230. 155. +// +H CHOC760102 +D Residue accessible surface area in folded protein (Chothia, 1976) +R LIT:2004094b PMID:994183 +A Chothia, C. +T The nature of the accessible and buried surfaces in proteins +J J. Mol. Biol. 105, 1-14 (1976) +C JANJ780101 0.973 GUYH850104 0.970 JANJ780103 0.959 + GUYH850105 0.946 OOBM770101 0.925 FAUJ880109 0.872 + ROSM880102 0.845 MEIH800102 0.839 PRAM900101 0.826 + ENGD860101 0.826 PUNT030101 0.809 RACS770102 0.809 + GUYH850101 0.807 KIDA850101 0.804 MEIH800103 -0.802 + EISD860103 -0.802 JACR890101 -0.803 NADH010104 -0.809 + JANJ790101 -0.809 RADA880101 -0.814 ROSG850102 -0.819 + DESM900102 -0.823 RADA880104 -0.830 WOLR790101 -0.834 + KYTJ820101 -0.838 WOLR810101 -0.840 NADH010103 -0.840 + CHOC760104 -0.845 WARP780101 -0.849 JURD980101 -0.851 + OLSK800101 -0.886 EISD840101 -0.892 NADH010102 -0.893 + CHOC760103 -0.912 RADA880107 -0.925 JANJ780102 -0.935 + JANJ790102 -0.969 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 25. 90. 63. 50. 19. 71. 49. 23. 43. 18. + 23. 97. 31. 24. 50. 44. 47. 32. 60. 18. +// +H CHOC760103 +D Proportion of residues 95% buried (Chothia, 1976) +R LIT:2004094b PMID:994183 +A Chothia, C. +T The nature of the accessible and buried surfaces in proteins +J J. Mol. Biol. 105, 1-14 (1976) +C OLSK800101 0.981 JURD980101 0.967 KYTJ820101 0.964 + JANJ780102 0.950 NADH010102 0.910 CHOC760104 0.907 + JANJ790102 0.905 EISD860103 0.892 JANJ790101 0.887 + EISD840101 0.885 NADH010101 0.881 DESM900102 0.877 + NADH010103 0.875 WOLR810101 0.873 RADA880107 0.870 + MEIH800103 0.865 MANP780101 0.859 WOLR790101 0.857 + RADA880101 0.853 ROSG850102 0.851 NADH010104 0.848 + PONP800103 0.837 PONP800102 0.836 PONP800101 0.830 + RADA880108 0.830 WARP780101 0.824 NAKH920108 0.824 + BIOV880101 0.823 CORJ870101 0.822 RADA880104 0.821 + COWR900101 0.820 PONP930101 0.816 PONP800107 0.813 + MIYS850101 0.810 LIFS790102 0.810 PONP800108 0.809 + BASU050103 0.805 MIYS990101 -0.803 MIYS990102 -0.805 + FAUJ880109 -0.806 ENGD860101 -0.813 PRAM900101 -0.814 + ROSM880101 -0.819 FASG890101 -0.849 GUYH850101 -0.856 + PUNT030101 -0.859 KUHL950101 -0.865 ROSM880102 -0.869 + RACS770102 -0.875 JANJ780103 -0.888 JANJ780101 -0.892 + MEIH800102 -0.894 OOBM770101 -0.902 GUYH850104 -0.907 + CHOC760102 -0.912 GUYH850105 -0.933 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.38 0.01 0.12 0.15 0.45 0.07 0.18 0.36 0.17 0.60 + 0.45 0.03 0.40 0.50 0.18 0.22 0.23 0.27 0.15 0.54 +// +H CHOC760104 +D Proportion of residues 100% buried (Chothia, 1976) +R LIT:2004094b PMID:994183 +A Chothia, C. +T The nature of the accessible and buried surfaces in proteins +J J. Mol. Biol. 105, 1-14 (1976) (normalized by the total number) +C CHOC760103 0.907 JANJ780102 0.903 KYTJ820101 0.889 + JANJ790101 0.886 OLSK800101 0.872 JURD980101 0.870 + WOLR810101 0.868 WOLR790101 0.851 PONP800104 0.844 + JANJ790102 0.835 DESM900102 0.824 NADH010102 0.817 + WARP780101 0.815 NADH010101 0.804 GUYH850105 -0.822 + CHOC760102 -0.845 GUYH850104 -0.845 JANJ780103 -0.851 + JANJ780101 -0.854 OOBM770101 -0.857 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.20 0.00 0.03 0.04 0.22 0.01 0.03 0.18 0.02 0.19 + 0.16 0.00 0.11 0.14 0.04 0.08 0.08 0.04 0.03 0.18 +// +H CHOP780101 +D Normalized frequency of beta-turn (Chou-Fasman, 1978a) +R LIT:2004003a PMID:354496 +A Chou, P.Y. and Fasman, G.D. +T Empirical predictions of protein conformation +J Ann. Rev. Biochem. 47, 251-276 (1978) +C PALJ810106 0.977 TANS770110 0.956 CHAM830101 0.946 + CHOP780203 0.940 CHOP780216 0.929 CHOP780210 0.921 + ROBB760113 0.907 GEIM800108 0.899 QIAN880133 0.897 + QIAN880132 0.896 LEVM780103 0.893 PRAM900104 0.891 + LEVM780106 0.890 ROBB760108 0.887 BEGF750103 0.885 + ISOY800103 0.885 CRAJ730103 0.882 GEIM800111 0.878 + PALJ810105 0.868 ROBB760110 0.863 NAGK730103 0.827 + QIAN880131 0.824 AURR980114 -0.803 BEGF750101 -0.803 + QIAN880107 -0.809 KANM800103 -0.824 AURR980109 -0.837 + SUEM840101 -0.845 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.66 0.95 1.56 1.46 1.19 0.98 0.74 1.56 0.95 0.47 + 0.59 1.01 0.60 0.60 1.52 1.43 0.96 0.96 1.14 0.50 +// +H CHOP780201 +D Normalized frequency of alpha-helix (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C PALJ810102 0.981 ROBB760101 0.969 ISOY800101 0.959 + MAXF760101 0.956 KANM800101 0.956 TANS770101 0.947 + BURA740101 0.917 GEIM800101 0.912 KANM800103 0.912 + NAGK730101 0.886 LEVM780104 0.886 PALJ810101 0.881 + QIAN880106 0.874 PRAM900102 0.873 LEVM780101 0.873 + GEIM800104 0.868 RACS820108 0.868 AURR980108 0.867 + AURR980109 0.859 AURR980112 0.856 CRAJ730101 0.851 + QIAN880107 0.843 BEGF750101 0.841 QIAN880105 0.835 + AURR980114 0.828 AURR980115 0.816 AURR980110 0.814 + PALJ810109 0.814 AURR980111 0.813 ROBB760103 0.806 + MUNV940101 -0.802 CRAJ730103 -0.808 ROBB760113 -0.811 + MUNV940102 -0.812 CHAM830101 -0.828 NAGK730103 -0.837 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.42 0.98 0.67 1.01 0.70 1.11 1.51 0.57 1.00 1.08 + 1.21 1.16 1.45 1.13 0.57 0.77 0.83 1.08 0.69 1.06 +// +H CHOP780202 +D Normalized frequency of beta-sheet (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C PALJ810104 0.970 LIFS790101 0.947 KANM800102 0.945 + PALJ810103 0.937 ROBB760106 0.931 LEVM780105 0.930 + GEIM800107 0.929 QIAN880120 0.915 PTIO830102 0.913 + QIAN880121 0.911 LIFS790103 0.908 GEIM800105 0.890 + ROBB760105 0.885 BASU050101 0.883 BASU050103 0.874 + PONP930101 0.867 NAGK730102 0.858 QIAN880119 0.855 + CHOP780208 0.851 BASU050102 0.841 KANM800104 0.839 + GEIM800106 0.839 LEVM780102 0.833 PRAM900103 0.833 + NISK860101 0.832 SWER830101 0.823 CORJ870102 0.822 + CHOP780209 0.822 CORJ870101 0.815 PALJ810112 0.815 + PONP800108 0.809 PALJ810110 0.808 MANP780101 0.805 + VENT840101 0.805 MIYS990102 -0.801 PUNT030102 -0.803 + VINM940102 -0.810 OOBM770103 -0.820 GEIM800110 -0.824 + MIYS990103 -0.825 MIYS990104 -0.829 VINM940101 -0.831 + MUNV940103 -0.892 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.83 0.93 0.89 0.54 1.19 1.10 0.37 0.75 0.87 1.60 + 1.30 0.74 1.05 1.38 0.55 0.75 1.19 1.37 1.47 1.70 +// +H CHOP780203 +D Normalized frequency of beta-turn (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C CHOP780216 0.979 CHOP780101 0.940 TANS770110 0.940 + LEVM780106 0.935 GEIM800111 0.933 ISOY800103 0.933 + CHAM830101 0.931 PRAM900104 0.928 QIAN880132 0.928 + LEVM780103 0.927 GEIM800108 0.925 CHOP780210 0.918 + QIAN880133 0.915 PALJ810106 0.907 PALJ810105 0.878 + QIAN880131 0.861 QIAN880134 0.838 RACS770101 0.827 + QIAN880135 0.811 CORJ870106 -0.813 QIAN880119 -0.814 + CORJ870105 -0.815 PONP800107 -0.818 SUEM840101 -0.892 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.74 1.01 1.46 1.52 0.96 0.96 0.95 1.56 0.95 0.47 + 0.50 1.19 0.60 0.66 1.56 1.43 0.98 0.60 1.14 0.59 +// +H CHOP780204 +D Normalized frequency of N-terminal helix (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C ROBB760102 0.911 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.29 0.44 0.81 2.02 0.66 1.22 2.44 0.76 0.73 0.67 + 0.58 0.66 0.71 0.61 2.01 0.74 1.08 1.47 0.68 0.61 +// +H CHOP780205 +D Normalized frequency of C-terminal helix (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C ROBB760104 0.841 QIAN880109 0.806 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.20 1.25 0.59 0.61 1.11 1.22 1.24 0.42 1.77 0.98 + 1.13 1.83 1.57 1.10 0.00 0.96 0.75 0.40 0.73 1.25 +// +H CHOP780206 +D Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.70 0.34 1.42 0.98 0.65 0.75 1.04 1.41 1.22 0.78 + 0.85 1.01 0.83 0.93 1.10 1.55 1.09 0.62 0.99 0.75 +// +H CHOP780207 +D Normalized frequency of C-terminal non helical region (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.52 1.24 1.64 1.06 0.94 0.70 0.59 1.64 1.86 0.87 + 0.84 1.49 0.52 1.04 1.58 0.93 0.86 0.16 0.96 0.32 +// +H CHOP780208 +D Normalized frequency of N-terminal beta-sheet (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C NAGK730102 0.860 CHOP780202 0.851 ROBB760106 0.846 + LIFS790101 0.820 QIAN880119 0.807 KANM800102 0.804 + QIAN880120 0.800 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.86 0.90 0.66 0.38 0.87 1.65 0.35 0.63 0.54 1.94 + 1.30 1.00 1.43 1.50 0.66 0.63 1.17 1.49 1.07 1.69 +// +H CHOP780209 +D Normalized frequency of C-terminal beta-sheet (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C PALJ810104 0.849 CHOP780202 0.822 VENT840101 0.817 + PTIO830102 0.814 QIAN880121 0.809 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.75 0.90 1.21 0.85 1.11 0.65 0.55 0.74 0.90 1.35 + 1.27 0.74 0.95 1.50 0.40 0.79 0.75 1.19 1.96 1.79 +// +H CHOP780210 +D Normalized frequency of N-terminal non beta region (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C CHOP780101 0.921 CHOP780203 0.918 PALJ810106 0.905 + CHAM830101 0.905 CHOP780216 0.896 GEIM800108 0.896 + GEIM800111 0.867 TANS770110 0.858 QIAN880132 0.852 + LEVM780103 0.852 PRAM900104 0.850 ISOY800103 0.829 + QIAN880131 0.826 QIAN880133 0.820 NAGK730103 0.814 + LEVM780106 0.812 PALJ810105 0.803 RICJ880111 -0.804 + BEGF750101 -0.804 RICJ880107 -0.818 PONP800107 -0.820 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.67 0.89 1.86 1.39 1.34 1.09 0.92 1.46 0.78 0.59 + 0.46 1.09 0.52 0.30 1.58 1.41 1.09 0.48 1.23 0.42 +// +H CHOP780211 +D Normalized frequency of C-terminal non beta region (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C ROBB760112 0.841 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.74 1.05 1.13 1.32 0.53 0.77 0.85 1.68 0.96 0.53 + 0.59 0.82 0.85 0.44 1.69 1.49 1.16 1.59 1.01 0.59 +// +H CHOP780212 +D Frequency of the 1st residue in turn (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C PALJ810106 0.801 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.060 0.070 0.161 0.147 0.149 0.074 0.056 0.102 0.140 0.043 + 0.061 0.055 0.068 0.059 0.102 0.120 0.086 0.077 0.082 0.062 +// +H CHOP780213 +D Frequency of the 2nd residue in turn (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C TANS770104 0.954 ISOY800104 0.916 QIAN880134 0.870 + QIAN880135 0.851 MUNV940104 0.836 FINA910102 0.832 + MUNV940105 0.826 GEOR030109 0.800 BUNA790101 -0.822 + BLAM930101 -0.824 PTIO830101 -0.835 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.076 0.106 0.083 0.110 0.053 0.098 0.060 0.085 0.047 0.034 + 0.025 0.115 0.082 0.041 0.301 0.139 0.108 0.013 0.065 0.048 +// +H CHOP780214 +D Frequency of the 3rd residue in turn (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C ISOY800105 0.923 TANS770105 0.862 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.035 0.099 0.191 0.179 0.117 0.037 0.077 0.190 0.093 0.013 + 0.036 0.072 0.014 0.065 0.034 0.125 0.065 0.064 0.114 0.028 +// +H CHOP780215 +D Frequency of the 4th residue in turn (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C ROBB760111 0.825 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.058 0.085 0.091 0.081 0.128 0.098 0.064 0.152 0.054 0.056 + 0.070 0.095 0.055 0.065 0.068 0.106 0.079 0.167 0.125 0.053 +// +H CHOP780216 +D Normalized frequency of the 2nd and 3rd residues in turn (Chou-Fasman, 1978b) +R PMID:364941 +A Chou, P.Y. and Fasman, G.D. +T Prediction of the secondary structure of proteins from their amino acid + sequence +J Adv. Enzymol. 47, 45-148 (1978) +C CHOP780203 0.979 GEIM800111 0.955 LEVM780106 0.953 + LEVM780103 0.952 PRAM900104 0.951 CHAM830101 0.942 + GEIM800108 0.942 QIAN880133 0.939 QIAN880132 0.931 + TANS770110 0.930 CHOP780101 0.929 ISOY800103 0.921 + PALJ810106 0.904 QIAN880134 0.900 CHOP780210 0.896 + QIAN880135 0.884 PALJ810105 0.881 QIAN880131 0.873 + NAGK730103 0.819 QIAN880120 -0.800 CORJ870106 -0.803 + FAUJ880102 -0.807 KANM800103 -0.808 QIAN880107 -0.808 + ROBB760103 -0.841 PTIO830101 -0.855 SUEM840101 -0.874 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.64 1.05 1.56 1.61 0.92 0.84 0.80 1.63 0.77 0.29 + 0.36 1.13 0.51 0.62 2.04 1.52 0.98 0.48 1.08 0.43 +// +H CIDH920101 +D Normalized hydrophobicity scales for alpha-proteins (Cid et al., 1992) +R LIT:1817105b PMID:1518784 +A Cid, H., Bunster, M., Canales, M. and Gazitua, F. +T Hydrophobicity and structural classes in proteins +J Protein Engineering 5, 373-375 (1992) +C CIDH920102 0.921 CIDH920105 0.921 NISK860101 0.882 + WERD780101 0.878 CIDH920103 0.872 RADA880108 0.858 + BASU050102 0.858 ZHOH040101 0.855 CORJ870102 0.855 + SWER830101 0.853 BIOV880101 0.847 ROBB790101 0.846 + ZHOH040103 0.845 CORJ870107 0.843 MIYS850101 0.843 + PLIV810101 0.843 CORJ870104 0.840 BASU050101 0.839 + CIDH920104 0.833 CORJ870106 0.832 ROSG850101 0.831 + CORJ870105 0.828 BASU050103 0.828 LEVM760106 0.826 + CORJ870103 0.825 BIOV880102 0.819 ZHOH040102 0.811 + PONP800101 0.805 VINM940103 -0.814 OOBM770103 -0.818 + KARP850102 -0.828 RACS770101 -0.837 MIYS990103 -0.838 + GUYH850102 -0.843 CORJ870108 -0.845 MIYS990102 -0.846 + MIYS990101 -0.847 MIYS990105 -0.849 VINM940101 -0.854 + FUKS010103 -0.854 GUYH850103 -0.854 MIYS990104 -0.860 + MEIH800101 -0.863 KARP850101 -0.864 PARJ860101 -0.871 + PARS000101 -0.877 VINM940102 -0.885 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.45 -0.24 -0.20 -1.52 0.79 -0.99 -0.80 -1.00 1.07 0.76 + 1.29 -0.36 1.37 1.48 -0.12 -0.98 -0.70 1.38 1.49 1.26 +// +H CIDH920102 +D Normalized hydrophobicity scales for beta-proteins (Cid et al., 1992) +R LIT:1817105b PMID:1518784 +A Cid, H., Bunster, M., Canales, M. and Gazitua, F. +T Hydrophobicity and structural classes in proteins +J Protein Engineering 5, 373-375 (1992) +C CIDH920105 0.969 ZHOH040101 0.939 CIDH920101 0.921 + BASU050102 0.914 CIDH920103 0.911 ZHOH040103 0.909 + CIDH920104 0.904 NISK860101 0.897 ROBB790101 0.896 + NOZY710101 0.889 MEEJ810101 0.887 PLIV810101 0.877 + LEVM760106 0.873 MIYS850101 0.873 CORJ870102 0.872 + WERD780101 0.871 SWER830101 0.870 ROSG850101 0.866 + BIOV880101 0.864 ZHOH040102 0.862 RADA880102 0.862 + ARGP820101 0.862 JOND750101 0.861 ROSM880104 0.859 + TAKK010101 0.859 BASU050101 0.858 MEEJ800102 0.856 + FAUJ830101 0.856 BASU050103 0.856 MEEJ810102 0.843 + BIOV880102 0.837 WIMW960101 0.837 RADA880108 0.833 + SIMZ760101 0.832 GUOD860101 0.831 GOLD730101 0.829 + PONP930101 0.820 EISD860101 0.819 ZASB820101 0.809 + LIFS790101 0.808 BLAS910101 0.805 CASG920101 0.802 + RACS770101 -0.825 VINM940103 -0.826 FUKS010103 -0.826 + GRAR740102 -0.842 MIYS990103 -0.845 BULH740101 -0.851 + GUYH850102 -0.855 MIYS990105 -0.859 MEIH800101 -0.867 + WOLS870101 -0.869 MIYS990102 -0.870 PARS000101 -0.871 + VINM940101 -0.872 MIYS990101 -0.872 KARP850101 -0.873 + MIYS990104 -0.877 OOBM770103 -0.877 GUYH850103 -0.904 + VINM940102 -0.925 PARJ860101 -0.930 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.08 -0.09 -0.70 -0.71 0.76 -0.40 -1.31 -0.84 0.43 1.39 + 1.24 -0.09 1.27 1.53 -0.01 -0.93 -0.59 2.25 1.53 1.09 +// +H CIDH920103 +D Normalized hydrophobicity scales for alpha+beta-proteins (Cid et al., 1992) +R LIT:1817105b PMID:1518784 +A Cid, H., Bunster, M., Canales, M. and Gazitua, F. +T Hydrophobicity and structural classes in proteins +J Protein Engineering 5, 373-375 (1992) +C CIDH920105 0.973 CIDH920104 0.955 CIDH920102 0.911 + NISK860101 0.909 MIYS850101 0.906 MANP780101 0.905 + PLIV810101 0.899 PONP930101 0.899 BASU050103 0.894 + BASU050101 0.894 RADA880108 0.891 BIOV880101 0.887 + BASU050102 0.887 ROBB790101 0.884 WERD780101 0.881 + ZHOH040103 0.881 PONP800101 0.876 CIDH920101 0.872 + FAUJ830101 0.868 CORJ870107 0.866 ROSM880104 0.866 + SWER830101 0.865 CORJ870102 0.864 BIOV880102 0.860 + CORJ870104 0.857 CORJ870103 0.856 NISK800101 0.855 + PONP800102 0.849 ROSG850102 0.846 GUOD860101 0.845 + PONP800108 0.841 BLAS910101 0.838 MEEJ810101 0.837 + CORJ870106 0.837 PONP800107 0.833 ROSM880105 0.832 + CORJ870105 0.832 ZHOH040101 0.829 CASG920101 0.827 + ARGP820101 0.827 JOND750101 0.826 PONP800103 0.823 + CORJ870101 0.822 EISD860101 0.821 RADA880102 0.819 + LIFS790101 0.815 PTIO830102 0.807 MEIH800103 0.802 + FUKS010103 -0.804 PUNT030102 -0.810 KRIW790101 -0.819 + PUNT030101 -0.819 PARS000101 -0.821 MEIH800102 -0.825 + RACS770102 -0.834 VINM940101 -0.837 FASG890101 -0.846 + BULH740101 -0.848 KARP850102 -0.852 VINM940102 -0.855 + OOBM770103 -0.863 CORJ870108 -0.864 MIYS990103 -0.870 + GRAR740102 -0.871 GUYH850102 -0.871 MIYS990105 -0.876 + WOLS870101 -0.879 RACS770101 -0.881 MIYS990104 -0.883 + GUYH850103 -0.890 MIYS990102 -0.899 MIYS990101 -0.900 + MEIH800101 -0.905 PARJ860101 -0.916 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.36 -0.52 -0.90 -1.09 0.70 -1.05 -0.83 -0.82 0.16 2.17 + 1.18 -0.56 1.21 1.01 -0.06 -0.60 -1.20 1.31 1.05 1.21 +// +H CIDH920104 +D Normalized hydrophobicity scales for alpha/beta-proteins (Cid et al., 1992) +R LIT:1817105b PMID:1518784 +A Cid, H., Bunster, M., Canales, M. and Gazitua, F. +T Hydrophobicity and structural classes in proteins +J Protein Engineering 5, 373-375 (1992) +C CIDH920105 0.970 CIDH920103 0.955 NISK860101 0.944 + ZHOH040103 0.941 BASU050103 0.941 BASU050102 0.934 + BIOV880101 0.933 PONP930101 0.930 FAUJ830101 0.922 + MANP780101 0.918 BASU050101 0.917 MIYS850101 0.915 + RADA880108 0.914 PONP800108 0.909 CIDH920102 0.904 + ROBB790101 0.903 CASG920101 0.903 NISK800101 0.900 + ROSG850102 0.896 CORJ870101 0.896 WERD780101 0.896 + PLIV810101 0.893 BIOV880102 0.890 PONP800101 0.888 + NADH010104 0.888 NADH010103 0.885 BLAS910101 0.881 + PONP800102 0.880 MEEJ810101 0.878 NADH010105 0.869 + NADH010101 0.865 PONP800103 0.863 SWER830101 0.862 + ROSM880104 0.860 CORJ870102 0.860 GUOD860101 0.860 + ZHOH040101 0.858 NADH010102 0.856 ROSM880105 0.855 + MEIH800103 0.853 PTIO830102 0.842 CORJ870103 0.841 + MEEJ810102 0.837 CORJ870107 0.835 EISD860103 0.834 + CIDH920101 0.833 PONP800107 0.832 JURD980101 0.832 + CORJ870104 0.832 LIFS790101 0.832 KYTJ820101 0.824 + ARGP820101 0.819 JOND750101 0.818 RADA880102 0.817 + EISD860101 0.812 BAEK050101 0.809 JANJ780102 0.803 + COWR900101 0.803 DESM900102 0.802 KARP850101 -0.801 + GUYH850101 -0.821 KUHL950101 -0.822 WOEC730101 -0.823 + PUNT030101 -0.827 ROSM880101 -0.828 BULH740101 -0.829 + CORJ870108 -0.829 ROSM880102 -0.831 KARP850102 -0.833 + VINM940103 -0.835 KIDA850101 -0.836 RACS770102 -0.854 + PUNT030102 -0.857 RACS770101 -0.864 KRIW790101 -0.867 + MEIH800102 -0.868 VINM940101 -0.883 VINM940102 -0.884 + WOLS870101 -0.891 GUYH850102 -0.894 MIYS990103 -0.902 + FASG890101 -0.903 GUYH850103 -0.906 OOBM770103 -0.912 + PARJ860101 -0.913 GRAR740102 -0.915 MIYS990101 -0.915 + MIYS990102 -0.916 MIYS990104 -0.916 MIYS990105 -0.916 + MEIH800101 -0.917 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.17 -0.70 -0.90 -1.05 1.24 -1.20 -1.19 -0.57 -0.25 2.06 + 0.96 -0.62 0.60 1.29 -0.21 -0.83 -0.62 1.51 0.66 1.21 +// +H CIDH920105 +D Normalized average hydrophobicity scales (Cid et al., 1992) +R LIT:1817105b PMID:1518784 +A Cid, H., Bunster, M., Canales, M. and Gazitua, F. +T Hydrophobicity and structural classes in proteins +J Protein Engineering 5, 373-375 (1992) +C CIDH920103 0.973 CIDH920104 0.970 CIDH920102 0.969 + NISK860101 0.938 BASU050102 0.931 ZHOH040103 0.926 + ROBB790101 0.921 CIDH920101 0.921 MIYS850101 0.916 + BASU050103 0.914 PLIV810101 0.914 BIOV880101 0.912 + BASU050101 0.907 WERD780101 0.905 ZHOH040101 0.904 + RADA880108 0.898 FAUJ830101 0.893 MEEJ810101 0.892 + PONP930101 0.891 SWER830101 0.890 CORJ870102 0.890 + ROSM880104 0.886 BIOV880102 0.882 MANP780101 0.879 + ARGP820101 0.867 JOND750101 0.866 RADA880102 0.861 + CASG920101 0.859 GUOD860101 0.858 ROSG850102 0.858 + NOZY710101 0.857 PONP800101 0.856 NISK800101 0.854 + BLAS910101 0.852 CORJ870107 0.848 MEEJ810102 0.844 + PONP800108 0.843 ROSM880105 0.843 MEEJ800102 0.840 + TAKK010101 0.840 EISD860101 0.839 CORJ870104 0.838 + CORJ870103 0.838 SIMZ760101 0.837 PONP800102 0.831 + LIFS790101 0.828 LEVM760106 0.828 CORJ870101 0.827 + CORJ870106 0.826 CORJ870105 0.822 GOLD730101 0.820 + ZHOH040102 0.818 PONP800107 0.818 NADH010104 0.817 + PTIO830102 0.813 VENT840101 0.813 NADH010103 0.810 + PONP800103 0.807 MEIH800103 0.804 NADH010105 0.800 + WOEC730101 -0.800 KIDA850101 -0.803 PUNT030101 -0.805 + KRIW790101 -0.816 FUKS010103 -0.821 PUNT030102 -0.822 + MEIH800102 -0.826 RACS770102 -0.830 VINM940103 -0.832 + KARP850102 -0.839 CORJ870108 -0.843 FASG890101 -0.860 + PARS000101 -0.860 KARP850101 -0.866 BULH740101 -0.871 + GRAR740102 -0.884 VINM940101 -0.885 MIYS990103 -0.886 + RACS770101 -0.887 GUYH850102 -0.892 WOLS870101 -0.899 + MIYS990105 -0.901 OOBM770103 -0.904 MIYS990104 -0.908 + VINM940102 -0.910 MIYS990102 -0.915 MIYS990101 -0.916 + MEIH800101 -0.923 GUYH850103 -0.927 PARJ860101 -0.948 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.02 -0.42 -0.77 -1.04 0.77 -1.10 -1.14 -0.80 0.26 1.81 + 1.14 -0.41 1.00 1.35 -0.09 -0.97 -0.77 1.71 1.11 1.13 +// +H COHE430101 +D Partial specific volume (Cohn-Edsall, 1943) +R +A Cohn, E.J. and Edsall, J.T. +T +J "Protein, Amino Acid, and Peptides", Reinhold, New York (1943) +C BULH740102 0.923 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.75 0.70 0.61 0.60 0.61 0.67 0.66 0.64 0.67 0.90 + 0.90 0.82 0.75 0.77 0.76 0.68 0.70 0.74 0.71 0.86 +// +H CRAJ730101 +D Normalized frequency of middle helix (Crawford et al., 1973) +R PMID:4510294 +A Crawford, J.L., Lipscomb, W.N. and Schellman, C.G. +T The reverse turn as a polypeptide conformation in globular proteins +J Proc. Natl. Acad. Sci. USA 70, 538-542 (1973) Reported values normalized by + the total percentage +C NAGK730101 0.925 BURA740101 0.900 PALJ810101 0.891 + PRAM900102 0.887 LEVM780101 0.887 ROBB760101 0.875 + PALJ810102 0.872 GEIM800101 0.870 LEVM780104 0.869 + CHOP780201 0.851 TANS770101 0.843 KANM800101 0.842 + ISOY800101 0.840 RACS820108 0.839 GEIM800104 0.838 + MAXF760101 0.826 PALJ810109 0.811 NAGK730103 -0.850 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.33 0.79 0.72 0.97 0.93 1.42 1.66 0.58 1.49 0.99 + 1.29 1.03 1.40 1.15 0.49 0.83 0.94 1.33 0.49 0.96 +// +H CRAJ730102 +D Normalized frequency of beta-sheet (Crawford et al., 1973) +R PMID:4510294 +A Crawford, J.L., Lipscomb, W.N. and Schellman, C.G. +T The reverse turn as a polypeptide conformation in globular proteins +J Proc. Natl. Acad. Sci. USA 70, 538-542 (1973) Reported values normalized by + the total percentage +C ROBB760106 0.865 PTIO830102 0.820 PALJ810104 0.817 + NAGK730102 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.00 0.74 0.75 0.89 0.99 0.87 0.37 0.56 0.36 1.75 + 1.53 1.18 1.40 1.26 0.36 0.65 1.15 0.84 1.41 1.61 +// +H CRAJ730103 +D Normalized frequency of turn (Crawford et al., 1973) +R PMID:4510294 +A Crawford, J.L., Lipscomb, W.N. and Schellman, C.G. +T The reverse turn as a polypeptide conformation in globular proteins +J Proc. Natl. Acad. Sci. USA 70, 538-542 (1973) Reported values normalized by + the total percentage +C ROBB760113 0.916 ROBB760108 0.912 ROBB760110 0.887 + PALJ810106 0.884 CHOP780101 0.882 BEGF750103 0.874 + TANS770110 0.859 CHAM830101 0.821 CHOP780201 -0.808 + PALJ810102 -0.809 BEGF750101 -0.812 QIAN880107 -0.840 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.60 0.79 1.42 1.24 1.29 0.92 0.64 1.38 0.95 0.67 + 0.70 1.10 0.67 1.05 1.47 1.26 1.05 1.23 1.35 0.48 +// +H DAWD720101 +D Size (Dawson, 1972) +R +A Dawson, D.M. +T +J In "The Biochemical Genetics of Man" (Brock, D.J.H. and Mayo, O., eds.), + Academic Press, New York, pp.1-38 (1972) +C TSAJ990102 0.905 GOLD730102 0.904 TSAJ990101 0.903 + BIGC670101 0.903 CHOC750101 0.901 CHOC760101 0.901 + HARY940101 0.900 LEVM760105 0.898 KRIW790103 0.893 + FAUJ880103 0.880 PONJ960101 0.873 LEVM760102 0.873 + CHAM820101 0.865 FAUJ880106 0.853 GRAR740103 0.853 + FASG760101 0.833 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.5 7.5 5.0 2.5 3.0 6.0 5.0 0.5 6.0 5.5 + 5.5 7.0 6.0 6.5 5.5 3.0 5.0 7.0 7.0 5.0 +// +H DAYM780101 +D Amino acid composition (Dayhoff et al., 1978a) +R +A Dayhoff, M.O., Hunt, L.T. and Hurst-Calderone, S. +T Composition of proteins +J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O., + ed.), National Biomedical Research Foundation, Washington, D.C., p.363 (1978) +C JUNJ780101 0.986 JUKT750101 0.975 CEDJ970101 0.970 + JOND920101 0.954 CEDJ970104 0.952 CEDJ970102 0.945 + NAKH900101 0.940 KUMS000102 0.925 FUKS010110 0.897 + NAKH900102 0.883 FUKS010111 0.882 NAKH920101 0.882 + KUMS000101 0.866 NAKH920107 0.861 FUKS010112 0.856 + NAKH920106 0.856 NAKH920103 0.851 CEDJ970105 0.839 + NAKH920104 0.819 CEDJ970103 0.807 NAKH920102 0.802 + FUKS010109 0.801 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.6 4.9 4.3 5.5 2.9 3.9 6.0 8.4 2.0 4.5 + 7.4 6.6 1.7 3.6 5.2 7.0 6.1 1.3 3.4 6.6 +// +H DAYM780201 +D Relative mutability (Dayhoff et al., 1978b) +R +A Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. +T A model of evolutionary change in proteins +J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O., + ed.), National Biomedical Research Foundation, Washington, D.C. pp. 345-352 + (1978) +C JOND920102 0.889 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 100. 65. 134. 106. 20. 93. 102. 49. 66. 96. + 40. 56. 94. 41. 56. 120. 97. 18. 41. 74. +// +H DESM900101 +D Membrane preference for cytochrome b: MPH89 (Degli Esposti et al., 1990) +R LIT:1612111b PMID:2364947 +A Degli Esposti, M., Crimi, M. and Venturoli, G. +T A critical evaluation of the hydropathy profile of membrane proteins +J Eur. J. Biochem. 190, 207-219 (1990) +C DESM900102 0.955 PONP800103 0.887 NADH010102 0.885 + PONP800102 0.871 CORJ870101 0.870 NADH010103 0.866 + ROSG850102 0.866 WARP780101 0.864 JANJ780102 0.853 + MEIH800103 0.853 PONP800101 0.847 NADH010104 0.843 + KYTJ820101 0.837 NISK800101 0.837 JURD980101 0.829 + NADH010101 0.825 BIOV880102 0.821 JANJ790102 0.818 + CORJ870107 0.815 CORJ870103 0.812 RADA880108 0.812 + BIOV880101 0.807 PONP930101 0.807 CASG920101 0.806 + PUNT030102 -0.801 RACS770102 -0.801 VINM940101 -0.806 + KRIW710101 -0.807 FASG890101 -0.808 CORJ870108 -0.809 + MEIH800102 -0.822 GUYH850104 -0.824 PUNT030101 -0.828 + MIYS990104 -0.828 KARP850102 -0.829 GUYH850101 -0.831 + MIYS990105 -0.832 KRIW790102 -0.835 RACS770103 -0.837 + JANJ780103 -0.838 KRIW790101 -0.847 MONM990101 -0.848 + MIYS990103 -0.854 OOBM770101 -0.894 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.56 0.59 0.51 0.23 1.80 0.39 0.19 1.03 1. 1.27 + 1.38 0.15 1.93 1.42 0.27 0.96 1.11 0.91 1.10 1.58 +// +H DESM900102 +D Average membrane preference: AMP07 (Degli Esposti et al., 1990) +R LIT:1612111b PMID:2364947 +A Degli Esposti, M., Crimi, M. and Venturoli, G. +T A critical evaluation of the hydropathy profile of membrane proteins +J Eur. J. Biochem. 190, 207-219 (1990) +C DESM900101 0.955 JANJ780102 0.935 NADH010102 0.933 + MEIH800103 0.924 ROSG850102 0.914 NADH010103 0.910 + NADH010101 0.905 CORJ870101 0.901 JURD980101 0.900 + KYTJ820101 0.898 JANJ790102 0.897 PONP800103 0.896 + NADH010104 0.886 WARP780101 0.882 RADA880108 0.881 + PONP800102 0.880 BIOV880101 0.878 CHOC760103 0.877 + BIOV880102 0.876 CASG920101 0.869 PONP800101 0.858 + JANJ790101 0.855 NISK800101 0.852 OLSK800101 0.849 + EISD860103 0.848 NISK860101 0.843 PONP930101 0.834 + PONP800108 0.833 MIYS850101 0.831 RADA880101 0.828 + EISD840101 0.828 ROSM880105 0.825 CHOC760104 0.824 + CORJ870107 0.819 BASU050103 0.818 MANP780101 0.816 + NADH010105 0.816 FAUJ830101 0.816 CORJ870103 0.815 + WERD780101 0.814 CIDH920104 0.802 VINM940104 -0.803 + MEIH800101 -0.804 MIYS990101 -0.809 CORJ870108 -0.811 + MIYS990102 -0.811 ROSM880101 -0.812 KARP850102 -0.815 + ROSM880102 -0.816 GUYH850105 -0.818 CHOC760102 -0.823 + VINM940103 -0.824 VINM940101 -0.829 WOEC730101 -0.847 + MONM990101 -0.850 KRIW790102 -0.852 MIYS990104 -0.854 + KRIW790101 -0.859 GRAR740102 -0.862 KUHL950101 -0.863 + RACS770102 -0.867 PUNT030102 -0.868 RACS770103 -0.868 + MIYS990105 -0.875 MIYS990103 -0.876 JANJ780101 -0.878 + FASG890101 -0.879 PRAM900101 -0.890 ENGD860101 -0.890 + GUYH850101 -0.895 GUYH850104 -0.896 MEIH800102 -0.898 + PUNT030101 -0.903 JANJ780103 -0.908 OOBM770101 -0.950 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.26 0.38 0.59 0.27 1.60 0.39 0.23 1.08 1. 1.44 + 1.36 0.33 1.52 1.46 0.54 0.98 1.01 1.06 0.89 1.33 +// +H EISD840101 +D Consensus normalized hydrophobicity scale (Eisenberg, 1984) +R LIT:2004004a PMID:6383201 +A Eisenberg, D. +T Three-dimensional structure of membrane and surface proteins +J Ann. Rev. Biochem. 53, 595-623 (1984) Original references: Eisenberg, D., + Weiss, R.M., Terwilliger, T.C. and Wilcox, W. Faraday Symp. Chem. Soc. 17, + 109-120 (1982) Eisenberg, D., Weiss, R.M. and Terwilliger, T.C. The + hydrophobic moment detects periodicity in protein hydrophobicity Proc. Natl. + Acad. Sci. USA 81, 140-144 (1984) +C RADA880101 0.968 JACR890101 0.938 RADA880107 0.927 + ROSM880105 0.923 WOLR810101 0.914 WOLR790101 0.909 + RADA880104 0.908 JANJ790102 0.900 JURD980101 0.895 + NADH010102 0.887 CHOC760103 0.885 BLAS910101 0.884 + EISD860101 0.884 KYTJ820101 0.878 FAUJ830101 0.875 + JANJ780102 0.874 OLSK800101 0.869 COWR900101 0.863 + NADH010101 0.861 NADH010103 0.840 NAKH900110 0.838 + EISD860103 0.837 DESM900102 0.828 RADA880108 0.817 + BIOV880102 0.814 BIOV880101 0.811 YUTK870101 0.809 + NADH010104 0.809 ROSG850102 0.806 BASU050103 0.806 + WOLS870101 -0.820 GRAR740102 -0.823 MEIH800102 -0.829 + HOPT810101 -0.846 GUYH850101 -0.849 PUNT030102 -0.854 + LEVM760101 -0.859 OOBM770101 -0.878 JANJ780103 -0.881 + FAUJ880109 -0.890 GUYH850104 -0.892 CHOC760102 -0.892 + KIDA850101 -0.900 JANJ780101 -0.907 KUHL950101 -0.907 + PUNT030101 -0.914 VHEG790101 -0.924 ROSM880102 -0.925 + ENGD860101 -0.936 PRAM900101 -0.936 ROSM880101 -0.947 + GUYH850105 -0.951 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.25 -1.76 -0.64 -0.72 0.04 -0.69 -0.62 0.16 -0.40 0.73 + 0.53 -1.10 0.26 0.61 -0.07 -0.26 -0.18 0.37 0.02 0.54 +// +H EISD860101 +D Solvation free energy (Eisenberg-McLachlan, 1986) +R LIT:2004121b PMID: 3945310 +A Eisenberg, D. and McLachlan, A.D. +T Solvation energy in protein folding and binding +J Nature 319, 199-203 (1986) +C ROSM880105 0.948 FAUJ830101 0.919 RADA880102 0.912 + BLAS910101 0.911 PLIV810101 0.904 ZIMJ680105 0.900 + RADA880101 0.891 MEEJ800102 0.890 EISD840101 0.884 + RADA880108 0.844 MIYS850101 0.842 GUOD860101 0.839 + CIDH920105 0.839 BIOV880102 0.832 BIOV880101 0.828 + JACR890101 0.827 SWER830101 0.824 CORJ870102 0.822 + NOZY710101 0.822 CIDH920103 0.821 NAKH900110 0.820 + CIDH920102 0.819 CIDH920104 0.812 NAKH900104 0.812 + NAKH900106 0.812 BASU050103 0.809 MEEJ810102 0.808 + MEEJ810101 0.805 GUYH850101 -0.823 MIYS990102 -0.824 + MIYS990101 -0.827 BULH740101 -0.833 KUHL950101 -0.835 + WOEC730101 -0.838 PRAM900101 -0.862 ENGD860101 -0.862 + VHEG790101 -0.862 ROSM880102 -0.868 PUNT030102 -0.869 + GRAR740102 -0.871 PARJ860101 -0.876 KIDA850101 -0.890 + PUNT030101 -0.890 HOPT810101 -0.905 ROSM880101 -0.917 + WOLS870101 -0.918 LEVM760101 -0.921 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.67 -2.1 -0.6 -1.2 0.38 -0.22 -0.76 0. 0.64 1.9 + 1.9 -0.57 2.4 2.3 1.2 0.01 0.52 2.6 1.6 1.5 +// +H EISD860102 +D Atom-based hydrophobic moment (Eisenberg-McLachlan, 1986) +R LIT:2004121b PMID: 3945310 +A Eisenberg, D. and McLachlan, A.D. +T Solvation energy in protein folding and binding +J Nature 319, 199-203 (1986) +C FAUJ880109 0.841 HUTJ700103 0.841 RADA880107 -0.837 + YUTK870103 -0.839 YUTK870104 -0.840 JACR890101 -0.871 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 10. 1.3 1.9 0.17 1.9 3. 0. 0.99 1.2 + 1.0 5.7 1.9 1.1 0.18 0.73 1.5 1.6 1.8 0.48 +// +H EISD860103 +D Direction of hydrophobic moment (Eisenberg-McLachlan, 1986) +R LIT:2004121b PMID: 3945310 +A Eisenberg, D. and McLachlan, A.D. +T Solvation energy in protein folding and binding +J Nature 319, 199-203 (1986) (Gly Ala missing) +C JURD980101 0.901 KYTJ820101 0.897 CHOC760103 0.892 + JANJ780102 0.883 OLSK800101 0.881 FAUJ830101 0.876 + RADA880108 0.873 NADH010102 0.872 MEIH800103 0.870 + NADH010101 0.868 COWR900101 0.868 BIOV880101 0.864 + MIYS850101 0.858 NADH010103 0.855 PLIV810101 0.852 + RADA880101 0.850 DESM900102 0.848 ROSG850102 0.846 + BIOV880102 0.845 PONP800103 0.842 NADH010104 0.840 + JANJ790102 0.838 EISD840101 0.837 CIDH920104 0.834 + BLAS910101 0.830 JANJ790101 0.829 MANP780101 0.826 + WARP780101 0.820 PONP800102 0.814 RADA880107 0.812 + NISK860101 0.811 ARGP820103 0.810 PONP800108 0.809 + CORJ870101 0.809 BASU050103 0.806 ROSM880105 0.801 + CHOC760102 -0.802 WOEC730101 -0.803 JANJ780101 -0.808 + MEIH800101 -0.810 GUYH850105 -0.812 MIYS990105 -0.815 + FAUJ880110 -0.815 JANJ780103 -0.819 PUNT030101 -0.829 + MIYS990101 -0.829 ENGD860101 -0.831 PRAM900101 -0.831 + MIYS990102 -0.831 GUYH850101 -0.832 KIDA850101 -0.832 + GUYH850104 -0.835 WOLS870101 -0.841 PUNT030102 -0.853 + RACS770102 -0.858 FASG890101 -0.863 ROSM880101 -0.871 + GRAR740102 -0.871 OOBM770101 -0.880 MEIH800102 -0.882 + KUHL950101 -0.894 ROSM880102 -0.943 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. -0.96 -0.86 -0.98 0.76 -1.0 -0.89 0. -0.75 0.99 + 0.89 -0.99 0.94 0.92 0.22 -0.67 0.09 0.67 -0.93 0.84 +// +H FASG760101 +D Molecular weight (Fasman, 1976) +R +A Fasman, G.D., ed. +T +J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume + 1, CRC Press, Cleveland (1976) +C FAUJ880103 0.979 CHOC760101 0.978 LEVM760102 0.966 + CHAM820101 0.962 CHOC750101 0.956 LEVM760105 0.951 + PONJ960101 0.945 CHAM830106 0.943 TSAJ990102 0.940 + TSAJ990101 0.935 BIGC670101 0.919 GOLD730102 0.918 + KRIW790103 0.910 HARY940101 0.910 GRAR740103 0.908 + FAUJ880106 0.899 RADA880106 0.870 WOLS870102 0.866 + MCMT640101 0.845 CHAM830105 0.839 ROSG850101 0.838 + DAWD720101 0.833 FAUJ880104 0.825 OOBM770102 0.821 + LEVM760107 0.815 RADA880103 -0.954 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 89.09 174.20 132.12 133.10 121.15 146.15 147.13 75.07 155.16 131.17 + 131.17 146.19 149.21 165.19 115.13 105.09 119.12 204.24 181.19 117.15 +// +H FASG760102 +D Melting point (Fasman, 1976) +R +A Fasman, G.D., ed. +T +J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume + 1, CRC Press, Cleveland (1976) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 297. 238. 236. 270. 178. 185. 249. 290. 277. 284. + 337. 224. 283. 284. 222. 228. 253. 282. 344. 293. +// +H FASG760103 +D Optical rotation (Fasman, 1976) +R +A Fasman, G.D., ed. +T +J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume + 1, CRC Press, Cleveland (1976) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.80 12.50 -5.60 5.05 -16.50 6.30 12.00 0.00 -38.50 12.40 + -11.00 14.60 -10.00 -34.50 -86.20 -7.50 -28.00 -33.70 -10.00 5.63 +// +H FASG760104 +D pK-N (Fasman, 1976) +R +A Fasman, G.D., ed. +T +J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume + 1, CRC Press, Cleveland (1976) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.69 8.99 8.80 9.60 8.35 9.13 9.67 9.78 9.17 9.68 + 9.60 9.18 9.21 9.18 10.64 9.21 9.10 9.44 9.11 9.62 +// +H FASG760105 +D pK-C (Fasman, 1976) +R +A Fasman, G.D., ed. +T +J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume + 1, CRC Press, Cleveland (1976) +C JOND750102 0.833 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.34 1.82 2.02 1.88 1.92 2.17 2.10 2.35 1.82 2.36 + 2.36 2.16 2.28 2.16 1.95 2.19 2.09 2.43 2.20 2.32 +// +H FAUJ830101 +D Hydrophobic parameter pi (Fauchere-Pliska, 1983) +R LIT:0912085 +A Fauchere, J.L. and Pliska, V. +T Hydrophobic parameters pi of amino-acid side chains from the partitioning of + N-acetyl-amino-acid amides +J Eur. J. Med. Chem. 18, 369-375 (1983) +C BIOV880101 0.942 ROSM880105 0.937 ZHOH040103 0.933 + RADA880108 0.932 PLIV810101 0.931 BLAS910101 0.923 + CIDH920104 0.922 EISD860101 0.919 MIYS850101 0.914 + BIOV880102 0.911 NISK860101 0.906 ROSG850102 0.904 + BASU050103 0.903 MEEJ810101 0.902 GUOD860101 0.900 + NADH010103 0.899 NADH010104 0.894 CIDH920105 0.893 + NADH010102 0.891 MEEJ810102 0.890 BASU050102 0.885 + COWR900101 0.876 EISD860103 0.876 CASG920101 0.875 + EISD840101 0.875 PONP800108 0.875 RADA880101 0.873 + ROBB790101 0.868 CIDH920103 0.868 PONP800103 0.863 + WERD780101 0.862 MEEJ800102 0.858 CIDH920102 0.856 + BASU050101 0.852 NISK800101 0.849 MEIH800103 0.849 + RADA880102 0.846 CORJ870101 0.845 MANP780101 0.843 + PONP930101 0.843 PONP800102 0.841 ZHOH040101 0.841 + NADH010101 0.837 SWER830101 0.833 JURD980101 0.833 + CORJ870102 0.831 JANJ790102 0.826 JANJ780102 0.825 + NADH010105 0.822 PONP800101 0.822 ZIMJ680105 0.816 + DESM900102 0.816 KYTJ820101 0.811 NOZY710101 0.803 + VINM940103 -0.804 FUKS010102 -0.805 GUYH850104 -0.816 + BULH740101 -0.830 OOBM770101 -0.832 FUKS010104 -0.832 + RACS770102 -0.843 VINM940102 -0.844 PRAM900101 -0.853 + ENGD860101 -0.853 GUYH850102 -0.857 GUYH850101 -0.863 + MEIH800101 -0.863 KUHL950101 -0.863 KRIW790101 -0.865 + GUYH850103 -0.870 VINM940101 -0.871 MEIH800102 -0.875 + PUNT030101 -0.876 WOEC730101 -0.880 MIYS990103 -0.893 + OOBM770103 -0.899 MIYS990104 -0.906 PARJ860101 -0.907 + ROSM880101 -0.907 MIYS990101 -0.907 PUNT030102 -0.908 + MIYS990102 -0.908 HOPT810101 -0.909 FASG890101 -0.911 + LEVM760101 -0.919 MIYS990105 -0.920 ROSM880102 -0.927 + WOLS870101 -0.928 KIDA850101 -0.946 GRAR740102 -0.948 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.31 -1.01 -0.60 -0.77 1.54 -0.22 -0.64 0.00 0.13 1.80 + 1.70 -0.99 1.23 1.79 0.72 -0.04 0.26 2.25 0.96 1.22 +// +H FAUJ880101 +D Graph shape index (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference: Kier, + L.B. Quant. Struct. Act. Relat. 6, 117-122 (1987) +C ZIMJ680102 0.888 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.28 2.34 1.60 1.60 1.77 1.56 1.56 0.00 2.99 4.19 + 2.59 1.89 2.35 2.94 2.67 1.31 3.03 3.21 2.94 3.67 +// +H FAUJ880102 +D Smoothed upsilon steric parameter (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro missing) Original + reference of these two data: Fauchere, L.J. In "QSAR in Design of Bioactive + Compounds", (Kuchar, M., ed.), Prous, Barcelona pp.135-144 (1984) +C AVBF000102 0.881 CHAM810101 0.881 PTIO830101 0.832 + CHOP780216 -0.807 CHAM830101 -0.809 GEIM800108 -0.819 + MUNV940104 -0.824 PRAM900104 -0.844 LEVM780103 -0.846 + QIAN880132 -0.849 QIAN880133 -0.851 QIAN880134 -0.852 + LEVM780106 -0.865 GEIM800111 -0.873 KIMC930101 -0.886 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.53 0.69 0.58 0.59 0.66 0.71 0.72 0.00 0.64 0.96 + 0.92 0.78 0.77 0.71 0. 0.55 0.63 0.84 0.71 0.89 +// +H FAUJ880103 +D Normalized van der Waals volume (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro !) Original reference of + these two data: Fauchere, L.J. In "QSAR in Design of Bioactive Compounds", + (Kuchar, M., ed.), Prous, Barcelona pp.135-144 (1984) +C CHAM820101 0.992 CHOC750101 0.990 CHOC760101 0.985 + TSAJ990102 0.985 TSAJ990101 0.983 FASG760101 0.979 + BIGC670101 0.972 GOLD730102 0.972 KRIW790103 0.965 + PONJ960101 0.963 GRAR740103 0.959 HARY940101 0.951 + LEVM760102 0.947 LEVM760105 0.945 CHAM830106 0.927 + FAUJ880106 0.908 ROSG850101 0.892 DAWD720101 0.880 + LEVM760107 0.875 RADA880106 0.869 MCMT640101 0.847 + ZHOH040102 0.816 WOLS870102 0.814 CHAM830105 0.813 + HUTJ700102 0.807 FAUJ880104 0.804 OOBM770102 0.801 + RADA880103 -0.923 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.00 6.13 2.95 2.78 2.43 3.95 3.78 0.00 4.66 4.00 + 4.00 4.77 4.43 5.89 2.72 1.60 2.60 8.08 6.47 3.00 +// +H FAUJ880104 +D STERIMOL length of the side chain (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro !) Original reference of + these three data: Verloop, A. In "IUPAC, Pesticide Chemistry", Vol.1 + (Miyamoto, J. and Kearney, P.C., eds.),Pergamon, Oxford pp.339-334 (1983) +C LEVM760105 0.896 LEVM760102 0.867 HUTJ700103 0.839 + CHOC760101 0.835 HUTJ700102 0.835 FASG760101 0.825 + CHAM830106 0.817 FAUJ880103 0.804 RADA880103 -0.806 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.87 7.82 4.58 4.74 4.47 6.11 5.97 2.06 5.23 4.92 + 4.92 6.89 6.36 4.62 4.11 3.97 4.11 7.68 4.73 4.11 +// +H FAUJ880105 +D STERIMOL minimum width of the side chain (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro !) Original reference of + these three data: Verloop, A. In "IUPAC, Pesticide Chemistry", Vol.1 + (Miyamoto, J. and Kearney, P.C., eds.),Pergamon, Oxford pp.339-334 (1983) +C AVBF000102 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.52 1.52 1.52 1.52 1.52 1.52 1.52 1.00 1.52 1.90 + 1.52 1.52 1.52 1.52 1.52 1.52 1.73 1.52 1.52 1.90 +// +H FAUJ880106 +D STERIMOL maximum width of the side chain (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference of these + three data: Verloop, A. In "IUPAC, Pesticide Chemistry", Vol.1 (Miyamoto, J. + and Kearney, P.C., eds.),Pergamon, Oxford pp.339-334 (1983) +C PONJ960101 0.913 HARY940101 0.909 FAUJ880103 0.908 + CHAM820101 0.902 LEVM760102 0.900 FASG760101 0.899 + CHOC760101 0.898 LEVM760105 0.889 CHOC750101 0.888 + TSAJ990102 0.882 TSAJ990101 0.879 WOLS870102 0.866 + BIGC670101 0.860 GOLD730102 0.857 DAWD720101 0.853 + KRIW790103 0.845 CHAM830106 0.845 GRAR740103 0.819 + HUTJ700102 0.806 RADA880103 -0.823 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.04 6.24 4.37 3.78 3.41 3.53 3.31 1.00 5.66 3.49 + 4.45 4.87 4.80 6.02 4.31 2.70 3.17 5.90 6.72 3.17 +// +H FAUJ880107 +D N.m.r. chemical shift of alpha-carbon (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference: Fauchere, + J.L. and Lauterwein, J. Quant. Struct. Act. Rel. 4, 11-13 (1985) +C AVBF000105 0.931 AVBF000107 0.884 AVBF000103 0.873 + AVBF000106 0.853 AVBF000108 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 7.3 11.1 8.0 9.2 14.4 10.6 11.4 0.0 10.2 16.1 + 10.1 10.9 10.4 13.9 17.8 13.1 16.7 13.2 13.9 17.2 +// +H FAUJ880108 +D Localized electrical effect (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro missing) Original + reference: Charton, M. and Charton, B.I. J. Theor. Biol. 102, 121-134 (1983) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.01 0.04 0.06 0.15 0.12 0.05 0.07 0.00 0.08 -0.01 + -0.01 0.00 0.04 0.03 0. 0.11 0.04 0.00 0.03 0.01 +// +H FAUJ880109 +D Number of hydrogen bond donors (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference of these + two data: IUPAC-IUB Joint Commission on Biochemical Nomenclature Eur. J. + Biochem. 138, 9-37 (1984) +C GUYH850105 0.927 CHOC760102 0.872 JANJ780101 0.850 + ROSM880101 0.846 EISD860102 0.841 KUHL950101 0.827 + ROSM880102 0.824 PRAM900101 0.815 ENGD860101 0.814 + GUYH850104 0.812 CHOC760103 -0.806 OLSK800101 -0.821 + JANJ790102 -0.822 RADA880101 -0.873 JACR890101 -0.889 + RADA880105 -0.889 EISD840101 -0.890 WOLR810101 -0.904 + WOLR790101 -0.920 RADA880104 -0.926 RADA880107 -0.957 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 4. 2. 1. 0. 2. 1. 0. 1. 0. + 0. 2. 0. 0. 0. 1. 1. 1. 1. 0. +// +H FAUJ880110 +D Number of full nonbonding orbitals (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference of these + two data: IUPAC-IUB Joint Commission on Biochemical Nomenclature Eur. J. + Biochem. 138, 9-37 (1984) +C KUHL950101 0.922 ROSM880101 0.888 WOEC730101 0.812 + ROSM880105 -0.803 SNEP660102 -0.804 NADH010101 -0.813 + EISD860103 -0.815 RADA880101 -0.838 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 3. 3. 4. 0. 3. 4. 0. 1. 0. + 0. 1. 0. 0. 0. 2. 2. 0. 2. 0. +// +H FAUJ880111 +D Positive charge (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) +C ZIMJ680104 0.813 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 1. 0. 0. 0. 0. 0. 0. 1. 0. + 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. +// +H FAUJ880112 +D Negative charge (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) +C RICJ880106 0.849 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 0. 0. 1. 0. 0. 1. 0. 0. 0. + 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. +// +H FAUJ880113 +D pK-a(RCOOH) (Fauchere et al., 1988) +R LIT:1414114 PMID:3209351 +A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. +T Amino acid side chain parameters for correlation studies in biology and + pharmacology +J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro missing) +C BLAM930101 0.839 ONEK900101 0.820 BUNA790101 0.818 + ROBB760103 0.802 MUNV940102 -0.826 MUNV940101 -0.836 + ONEK900102 -0.839 GEOR030109 -0.848 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 4.76 4.30 3.64 5.69 3.67 4.54 5.48 3.77 2.84 4.81 + 4.79 4.27 4.25 4.31 0. 3.83 3.87 4.75 4.30 4.86 +// +H FINA770101 +D Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977) +R LIT:2004052b PMID:843599 +A Finkelstein, A.V. and Ptitsyn, O.B. +T Theory of protein molecule self-organization. II. A comparison of calculated + thermodynamic parameters of local secondary structures with experiments +J Biopolymers 16, 497-524 (1977) (Pro 0.096) +C SUEM840101 0.883 AURR980114 0.875 AURR980113 0.849 + PTIO830101 0.826 KANM800103 0.823 QIAN880107 0.814 + QIAN880106 0.810 MAXF760101 0.810 AURR980109 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.08 1.05 0.85 0.85 0.95 0.95 1.15 0.55 1.00 1.05 + 1.25 1.15 1.15 1.10 0.71 0.75 0.75 1.10 1.10 0.95 +// +H FINA910101 +D Helix initiation parameter at posision i-1 (Finkelstein et al., 1991) +R LIT:1716158b PMID:1946339 +A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B. +T Physical reasons for secondary structure stability: alpha-helices in short + peptides +J Proteins 10, 287-299 (1991) In these four data, each of Arg, Asp, Glu, His + and Lys has two value. See comment lines. Arg pH < 12 ( 1 when pH > 12 ) Asp + pH > 4 ( 1.7 when pH < 4 ) Glu pH > 4.3 ( 1 when pH < 4.3 ) His pH > 6.3 ( + 0.7 when pH < 6.3 ) Lys pH < 10.5 ( 1 when pH > 10.5 ) +C MONM990201 0.812 AURR980104 0.804 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1. 0.70 1.70 3.20 1. 1. 1.70 1. 1. 0.60 + 1. 0.70 1. 1. 1. 1.70 1.70 1. 1. 0.60 +// +H FINA910102 +D Helix initiation parameter at posision i,i+1,i+2 (Finkelstein et al., 1991) +R LIT:1716158b PMID:1946339 +A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B. +T Physical reasons for secondary structure stability: alpha-helices in short + peptides +J Proteins 10, 287-299 (1991) In these four data, each of Arg, Asp, Glu, His + and Lys has two value. See comment lines. Arg pH < 12 ( 1 when pH > 12 ) Asp + pH > 4 ( 1 when pH < 4 ) Glu pH > 4.3 ( 1 when pH < 4.3 ) His pH > 6.3 ( 0.7 + when pH < 6.3 ) Lys pH < 10.5 ( 1 when pH > 10.5 ) (Pro !) +C ONEK900102 0.964 MUNV940105 0.911 AVBF000104 0.901 + MUNV940104 0.896 GEOR030109 0.890 TANS770104 0.876 + ISOY800104 0.844 CHOP780213 0.832 ROBB760104 -0.844 + ONEK900101 -0.920 BLAM930101 -0.961 BUNA790101 -0.992 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1. 0.70 1. 1.70 1. 1. 1.70 1.30 1. 1. + 1. 0.70 1. 1. 13. 1. 1. 1. 1. 1. +// +H FINA910103 +D Helix termination parameter at posision j-2,j-1,j (Finkelstein et al., 1991) +R LIT:1716158b PMID:1946339 +A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B. +T Physical reasons for secondary structure stability: alpha-helices in short + peptides +J Proteins 10, 287-299 (1991) In these four data, each of Arg, Asp, Glu, His + and Lys has two value. See comment lines. Arg pH < 12 ( 1 when pH > 12 ) Asp + pH > 4 ( 1 when pH < 4 ) Glu pH > 4.3 ( 1 when pH < 4.3 ) His pH > 6.3 ( 1.7 + when pH < 6.3 ) Lys pH < 10.5 ( 1 when pH > 10.5 ) +C ZIMJ680104 0.805 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.20 1.70 1.20 0.70 1. 1. 0.70 0.80 1.20 0.80 + 1. 1.70 1. 1. 1. 1.50 1. 1. 1. 0.80 +// +H FINA910104 +D Helix termination parameter at posision j+1 (Finkelstein et al., 1991) +R LIT:1716158b PMID:1946339 +A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B. +T Physical reasons for secondary structure stability: alpha-helices in short + peptides +J Proteins 10, 287-299 (1991) In these four data, each of Arg, Asp, Glu, His + and Lys has two value. See comment lines. Arg pH < 12 ( 1 when pH > 12 ) Asp + pH > 4 ( 1 when pH < 4 ) Glu pH > 4.3 ( 1 when pH < 4.3 ) His pH > 6.3 ( 1.7 + when pH < 6.3 ) Lys pH < 10.5 ( 1 when pH > 10.5 ) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1. 1.70 1. 0.70 1. 1. 0.70 1.50 1. 1. + 1. 1.70 1. 1. 0.10 1. 1. 1. 1. 1. +// +H GARJ730101 +D Partition coefficient (Garel et al., 1973) +R LIT:2004092b PMID:4700470 +A Garel, J.P., Filliol, D. and Mandel, P. +T Coefficients de partage d'aminoacides, nucleobases, nucleosides et + nucleotides dans un systeme solvant salin +J J. Chromatogr. 78, 381-391 (1973) +C LEVM760107 0.860 NOZY710101 0.821 OOBM850102 -0.877 + WEBA780101 -0.924 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.28 0.10 0.25 0.21 0.28 0.35 0.33 0.17 0.21 0.82 + 1.00 0.09 0.74 2.18 0.39 0.12 0.21 5.70 1.26 0.60 +// +H GEIM800101 +D Alpha-helix indices (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C PALJ810101 0.951 LEVM780104 0.950 KANM800101 0.942 + TANS770101 0.918 CHOP780201 0.912 NAGK730101 0.912 + PRAM900102 0.912 LEVM780101 0.912 PALJ810102 0.910 + GEIM800104 0.903 ISOY800101 0.903 ROBB760101 0.897 + MAXF760101 0.895 KANM800103 0.881 RACS820108 0.880 + CRAJ730101 0.870 BURA740101 0.858 PALJ810109 0.816 + AURR980115 0.804 AURR980112 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.29 1. 0.81 1.10 0.79 1.07 1.49 0.63 1.33 1.05 + 1.31 1.33 1.54 1.13 0.63 0.78 0.77 1.18 0.71 0.81 +// +H GEIM800102 +D Alpha-helix indices for alpha-proteins (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C PALJ810107 0.919 GEIM800109 -0.993 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.13 1.09 1.06 0.94 1.32 0.93 1.20 0.83 1.09 1.05 + 1.13 1.08 1.23 1.01 0.82 1.01 1.17 1.32 0.88 1.13 +// +H GEIM800103 +D Alpha-helix indices for beta-proteins (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.55 0.20 1.20 1.55 1.44 1.13 1.67 0.59 1.21 1.27 + 1.25 1.20 1.37 0.40 0.21 1.01 0.55 1.86 1.08 0.64 +// +H GEIM800104 +D Alpha-helix indices for alpha/beta-proteins (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C PALJ810109 0.937 KANM800101 0.916 LEVM780101 0.907 + PRAM900102 0.907 GEIM800101 0.903 MAXF760101 0.897 + ISOY800101 0.891 PALJ810102 0.886 LEVM780104 0.872 + CHOP780201 0.868 ROBB760101 0.855 RACS820108 0.851 + PALJ810101 0.841 TANS770101 0.841 CRAJ730101 0.838 + NAGK730101 0.828 BURA740101 0.819 AURR980112 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.19 1. 0.94 1.07 0.95 1.32 1.64 0.60 1.03 1.12 + 1.18 1.27 1.49 1.02 0.68 0.81 0.85 1.18 0.77 0.74 +// +H GEIM800105 +D Beta-strand indices (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C PALJ810103 0.945 LEVM780105 0.926 KANM800102 0.916 + GEIM800107 0.901 CHOP780202 0.890 ROBB760105 0.877 + KANM800104 0.861 PALJ810104 0.856 ROBB760106 0.856 + LIFS790101 0.855 TANS770103 0.850 ISOY800102 0.843 + LIFS790103 0.832 PALJ810112 0.830 QIAN880119 0.829 + QIAN880120 0.822 MAXF760102 0.819 QIAN880121 0.811 + PTIO830102 0.810 QIAN880118 0.810 MUNV940103 -0.841 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.84 1.04 0.66 0.59 1.27 1.02 0.57 0.94 0.81 1.29 + 1.10 0.86 0.88 1.15 0.80 1.05 1.20 1.15 1.39 1.56 +// +H GEIM800106 +D Beta-strand indices for beta-proteins (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C GEIM800107 0.878 PALJ810110 0.851 CHOP780202 0.839 + ROBB760106 0.838 QIAN880120 0.825 KANM800102 0.821 + LIFS790103 0.814 MUNV940103 -0.800 GEIM800110 -0.929 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.86 1.15 0.60 0.66 0.91 1.11 0.37 0.86 1.07 1.17 + 1.28 1.01 1.15 1.34 0.61 0.91 1.14 1.13 1.37 1.31 +// +H GEIM800107 +D Beta-strand indices for alpha/beta-proteins (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C KANM800102 0.955 CHOP780202 0.929 PALJ810104 0.928 + PALJ810112 0.905 GEIM800105 0.901 ROBB760106 0.899 + PALJ810103 0.890 LIFS790101 0.888 LEVM780105 0.884 + GEIM800106 0.878 KANM800104 0.876 QIAN880121 0.875 + PTIO830102 0.850 BASU050103 0.847 BASU050101 0.847 + QIAN880120 0.843 LEVM780102 0.842 PRAM900103 0.842 + PONP930101 0.838 ROBB760105 0.836 NAGK730102 0.830 + PALJ810110 0.826 LIFS790103 0.823 CORJ870101 0.821 + PONP800108 0.817 NISK860101 0.813 QIAN880119 0.807 + MIYS990103 -0.803 GEIM800110 -0.815 VINM940101 -0.819 + MUNV940103 -0.869 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.91 0.99 0.72 0.74 1.12 0.90 0.41 0.91 1.01 1.29 + 1.23 0.86 0.96 1.26 0.65 0.93 1.05 1.15 1.21 1.58 +// +H GEIM800108 +D Aperiodic indices (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C GEIM800111 0.967 CHOP780216 0.942 LEVM780106 0.932 + PRAM900104 0.931 LEVM780103 0.931 QIAN880133 0.930 + ISOY800103 0.930 CHOP780203 0.925 CHAM830101 0.916 + QIAN880132 0.906 CHOP780101 0.899 CHOP780210 0.896 + TANS770110 0.886 QIAN880134 0.884 QIAN880135 0.877 + PALJ810105 0.873 GEIM800110 0.870 PALJ810106 0.862 + QIAN880131 0.860 MUNV940103 0.806 ROBB760103 -0.802 + QIAN880120 -0.804 QIAN880119 -0.810 FAUJ880102 -0.819 + PTIO830101 -0.840 SUEM840101 -0.875 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.91 1. 1.64 1.40 0.93 0.94 0.97 1.51 0.90 0.65 + 0.59 0.82 0.58 0.72 1.66 1.23 1.04 0.67 0.92 0.60 +// +H GEIM800109 +D Aperiodic indices for alpha-proteins (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C PALJ810107 -0.909 GEIM800102 -0.993 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.80 0.96 1.10 1.60 0. 1.60 0.40 2. 0.96 0.85 + 0.80 0.94 0.39 1.20 2.10 1.30 0.60 0. 1.80 0.80 +// +H GEIM800110 +D Aperiodic indices for beta-proteins (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C MUNV940103 0.880 GEIM800108 0.870 GEIM800111 0.857 + QIAN880134 0.853 QIAN880135 0.842 PARS000101 0.831 + QIAN880133 0.822 LEVM780106 0.809 QIAN880121 -0.806 + CORJ870105 -0.807 CORJ870106 -0.812 KANM800102 -0.814 + GEIM800107 -0.815 ROBB760106 -0.819 CHOP780202 -0.824 + AVBF000101 -0.825 PALJ810110 -0.840 QIAN880119 -0.853 + LIFS790101 -0.862 LIFS790103 -0.889 QIAN880120 -0.898 + GEIM800106 -0.929 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.10 0.93 1.57 1.41 1.05 0.81 1.40 1.30 0.85 0.67 + 0.52 0.94 0.69 0.60 1.77 1.13 0.88 0.62 0.41 0.58 +// +H GEIM800111 +D Aperiodic indices for alpha/beta-proteins (Geisow-Roberts, 1980) +R LIT:0701087b +A Geisow, M.J. and Roberts, R.D.B. +T Amino acid preferences for secondary structure vary with protein class +J Int. J. Biol. Macromol. 2, 387-389 (1980) +C GEIM800108 0.967 CHOP780216 0.955 PRAM900104 0.954 + LEVM780103 0.952 LEVM780106 0.951 QIAN880133 0.943 + CHAM830101 0.938 CHOP780203 0.933 ISOY800103 0.929 + QIAN880132 0.929 QIAN880134 0.919 QIAN880135 0.895 + TANS770110 0.883 CHOP780101 0.878 CHOP780210 0.867 + QIAN880131 0.857 GEIM800110 0.857 PALJ810105 0.855 + PALJ810106 0.844 LIFS790101 -0.801 AVBF000101 -0.806 + KANM800103 -0.812 AURR980109 -0.814 QIAN880120 -0.816 + ROBB760103 -0.843 FAUJ880102 -0.873 PTIO830101 -0.876 + SUEM840101 -0.885 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.93 1.01 1.36 1.22 0.92 0.83 1.05 1.45 0.96 0.58 + 0.59 0.91 0.60 0.71 1.67 1.25 1.08 0.68 0.98 0.62 +// +H GOLD730101 +D Hydrophobicity factor (Goldsack-Chalifoux, 1973) +R LIT:2004110b PMID:4354159 +A Goldsack, D.E. and Chalifoux, R.C. +T Contribution of the free energy of mixing of hydrophobic side chains to the + stability of the tertiary structure +J J. Theor. Biol. 39, 645-651 (1973) (Asn Gln !) +C SIMZ760101 0.939 ARGP820101 0.936 JOND750101 0.935 + TAKK010101 0.872 MEEJ800102 0.866 LAWE840101 0.829 + CIDH920102 0.829 LEVM760106 0.827 BULH740102 0.825 + MEEJ810101 0.824 BLAS910101 0.821 ZIMJ680105 0.820 + CIDH920105 0.820 ZIMJ680102 0.818 ZHOH040101 0.817 + ROSM880104 0.808 MEEJ800101 0.808 MEEJ810102 0.806 + VENT840101 0.802 PARJ860101 -0.827 WOLS870101 -0.854 + BULH740101 -0.874 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.75 0.75 0.69 0.00 1.00 0.59 0.00 0.00 0.00 2.95 + 2.40 1.50 1.30 2.65 2.60 0.00 0.45 3.00 2.85 1.70 +// +H GOLD730102 +D Residue volume (Goldsack-Chalifoux, 1973) +R LIT:2004110b PMID:4354159 +A Goldsack, D.E. and Chalifoux, R.C. +T Contribution of the free energy of mixing of hydrophobic side chains to the + stability of the tertiary structure +J J. Theor. Biol. 39, 645-651 (1973) (Asn Gln 8.8) +C BIGC670101 1.000 KRIW790103 0.994 TSAJ990101 0.993 + TSAJ990102 0.991 CHOC750101 0.989 GRAR740103 0.984 + FAUJ880103 0.972 CHAM820101 0.967 CHOC760101 0.960 + HARY940101 0.959 PONJ960101 0.947 FASG760101 0.918 + LEVM760105 0.911 ROSG850101 0.909 DAWD720101 0.904 + LEVM760102 0.893 ZHOH040102 0.882 LEVM760106 0.875 + CHAM830106 0.869 LEVM760107 0.865 FAUJ880106 0.857 + RADA880106 0.854 MCMT640101 0.814 RADA880103 -0.864 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 88.3 181.2 125.1 110.8 112.4 148.7 140.5 60.0 152.6 168.5 + 168.5 175.6 162.2 189.0 122.2 88.7 118.2 227.0 193.0 141.4 +// +H GRAR740101 +D Composition (Grantham, 1974) +R LIT:2004143b PMID:4843792 +A Grantham, R. +T Amino acid difference formula to help explain protein evolution +J Science 185, 862-864 (1974) (Atomic weight ratio of noncarbons to carbons in + the side chain) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.00 0.65 1.33 1.38 2.75 0.89 0.92 0.74 0.58 0.00 + 0.00 0.33 0.00 0.00 0.39 1.42 0.71 0.13 0.20 0.00 +// +H GRAR740102 +D Polarity (Grantham, 1974) +R LIT:2004143b PMID:4843792 +A Grantham, R. +T Amino acid difference formula to help explain protein evolution +J Science 185, 862-864 (1974) +C WOEC730101 0.960 MIYS990105 0.928 PUNT030102 0.915 + MIYS990104 0.910 WOLS870101 0.910 MIYS990103 0.904 + MIYS990101 0.903 MIYS990102 0.903 OOBM770103 0.896 + PARJ860101 0.891 ROSM880101 0.887 KIDA850101 0.881 + HOPT810101 0.874 PUNT030101 0.873 FASG890101 0.872 + ROSM880102 0.870 VINM940101 0.869 LEVM760101 0.865 + KUHL950101 0.865 PRAM900101 0.855 ENGD860101 0.855 + KRIW790101 0.847 OOBM770101 0.841 CORJ870108 0.838 + VINM940102 0.837 MEIH800102 0.836 GUYH850103 0.831 + MONM990101 0.831 MEIH800101 0.824 BULH740101 0.822 + GUYH850101 0.818 GUYH850102 0.806 WIMW960101 -0.804 + JANJ780102 -0.809 MEEJ810102 -0.811 NADH010105 -0.812 + EISD840101 -0.823 WERD780101 -0.826 ROBB790101 -0.832 + CORJ870103 -0.836 MEEJ810101 -0.839 CORJ870107 -0.840 + CIDH920102 -0.842 PONP800101 -0.849 CORJ870104 -0.850 + CASG920101 -0.850 COWR900101 -0.854 GUOD860101 -0.855 + KYTJ820101 -0.859 NADH010101 -0.859 RADA880101 -0.861 + DESM900102 -0.862 JURD980101 -0.864 BASU050102 -0.864 + MEIH800103 -0.866 NADH010104 -0.868 MANP780101 -0.868 + PONP800102 -0.871 EISD860101 -0.871 EISD860103 -0.871 + CIDH920103 -0.871 PONP930101 -0.872 NISK800101 -0.879 + ROSG850102 -0.880 BIOV880102 -0.881 NADH010103 -0.881 + NADH010102 -0.881 CIDH920105 -0.884 PLIV810101 -0.888 + BASU050101 -0.889 CORJ870101 -0.890 CORJ870102 -0.893 + ZHOH040103 -0.895 MIYS850101 -0.895 SWER830101 -0.896 + PONP800103 -0.897 RADA880108 -0.899 NISK860101 -0.900 + BASU050103 -0.906 PONP800108 -0.907 BIOV880101 -0.910 + CIDH920104 -0.915 ROSM880105 -0.924 FAUJ830101 -0.948 + BLAS910101 -0.950 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.1 10.5 11.6 13.0 5.5 10.5 12.3 9.0 10.4 5.2 + 4.9 11.3 5.7 5.2 8.0 9.2 8.6 5.4 6.2 5.9 +// +H GRAR740103 +D Volume (Grantham, 1974) +R LIT:2004143b PMID:4843792 +A Grantham, R. +T Amino acid difference formula to help explain protein evolution +J Science 185, 862-864 (1974) +C KRIW790103 0.989 BIGC670101 0.984 GOLD730102 0.984 + TSAJ990101 0.979 TSAJ990102 0.978 CHOC750101 0.973 + FAUJ880103 0.959 CHAM820101 0.951 HARY940101 0.946 + CHOC760101 0.945 PONJ960101 0.937 ROSG850101 0.922 + RADA880106 0.920 FASG760101 0.908 LEVM760105 0.900 + CHAM830106 0.890 LEVM760102 0.885 ZHOH040102 0.872 + DAWD720101 0.853 LEVM760106 0.846 LEVM760107 0.841 + FAUJ880106 0.819 MCMT640101 0.817 RADA880103 -0.881 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 31. 124. 56. 54. 55. 85. 83. 3. 96. 111. + 111. 119. 105. 132. 32.5 32. 61. 170. 136. 84. +// +H GUYH850101 +D Partition energy (Guy, 1985) +R LIT:2004051b PMID:3978191 +A Guy, H.R. +T Amino acid side-chain partition energies and distribution of residues in + soluble proteins +J Biophys. J. 47, 61-70 (1985) +C MEIH800102 0.934 RACS770102 0.934 FASG890101 0.934 + PUNT030101 0.910 MIYS990103 0.907 MIYS990105 0.895 + MEIH800101 0.893 MIYS990102 0.892 MIYS990101 0.891 + MIYS990104 0.889 KRIW790101 0.885 VINM940103 0.865 + KRIW790102 0.864 GUYH850104 0.857 RACS770101 0.853 + CORJ870108 0.851 OOBM770101 0.848 GUYH850105 0.843 + KARP850102 0.840 ROSM880102 0.837 PUNT030102 0.836 + KIDA850101 0.834 KRIW710101 0.831 VINM940101 0.829 + JANJ780103 0.829 KUHL950101 0.827 JANJ780101 0.821 + PRAM900101 0.820 ENGD860101 0.820 GRAR740102 0.818 + RACS770103 0.816 CHOC760102 0.807 GUYH850102 0.805 + ROSM880101 0.803 HOPT810101 0.802 BASU050102 -0.801 + BASU050101 -0.807 CORJ870105 -0.810 NISK800101 -0.811 + YUTK870101 -0.813 CORJ870103 -0.813 RADA880101 -0.815 + CORJ870104 -0.815 PONP930101 -0.817 CORJ870101 -0.820 + CIDH920104 -0.821 OLSK800101 -0.823 EISD860101 -0.823 + PONP800106 -0.826 DESM900101 -0.831 EISD860103 -0.832 + ROSM880105 -0.832 CORJ870106 -0.833 CASG920101 -0.836 + PLIV810101 -0.836 MANP780101 -0.838 ZHOH040103 -0.839 + CORJ870107 -0.841 KYTJ820101 -0.843 EISD840101 -0.849 + NADH010105 -0.855 CHOC760103 -0.856 NADH010101 -0.862 + FAUJ830101 -0.863 JURD980101 -0.864 JANJ790102 -0.865 + BASU050103 -0.871 WERD780101 -0.871 JANJ780102 -0.872 + PONP800101 -0.877 NISK860101 -0.877 MEIH800103 -0.880 + PONP800102 -0.883 BIOV880102 -0.885 PONP800103 -0.887 + DESM900102 -0.895 MIYS850101 -0.909 NADH010104 -0.910 + NADH010102 -0.910 NADH010103 -0.916 BIOV880101 -0.929 + ROSG850102 -0.929 RADA880108 -0.948 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.10 1.91 0.48 0.78 -1.42 0.95 0.83 0.33 -0.50 -1.13 + -1.18 1.40 -1.59 -2.12 0.73 0.52 0.07 -0.51 -0.21 -1.27 +// +H HOPA770101 +D Hydration number (Hopfinger, 1971), Cited by Charton-Charton (1982) +R +A Hopfinger, A.J. +T +J "Intermolecular Interactions and Biomolecular Organizations", Wiley, New York + (1977) Cited by Charton-Charton (1982) (Cys !) +C WOEC730101 0.876 ZIMJ680103 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.0 2.3 2.2 6.5 0.1 2.1 6.2 1.1 2.8 0.8 + 0.8 5.3 0.7 1.4 0.9 1.7 1.5 1.9 2.1 0.9 +// +H HOPT810101 +D Hydrophilicity value (Hopp-Woods, 1981) +R LIT:0707598 PMID:6167991 +A Hopp, T.P. and Woods, K.R. +T Prediction of protein antigenic determinants from amino acid sequecces +J Proc. Natl. Acad. Sci. USA 78, 3824-3828 (1981) +C LEVM760101 0.985 WOEC730101 0.886 PUNT030102 0.886 + FUKS010104 0.884 ENGD860101 0.882 PRAM900101 0.881 + KIDA850101 0.881 GRAR740102 0.874 MIYS990105 0.862 + VINM940101 0.859 PUNT030101 0.858 FUKS010102 0.854 + VHEG790101 0.849 ROSM880101 0.848 MIYS990104 0.843 + OOBM770103 0.833 WOLS870101 0.830 MIYS990103 0.825 + PARJ860101 0.819 MIYS990102 0.804 MIYS990101 0.803 + GUYH850101 0.802 MIYS850101 -0.800 NADH010103 -0.805 + NAKH900110 -0.812 ZIMJ680105 -0.816 JACR890101 -0.816 + NADH010102 -0.820 NISK860101 -0.822 ROSG850102 -0.825 + MEEJ800102 -0.826 RADA880101 -0.829 ZHOH040103 -0.829 + BASU050103 -0.830 RADA880108 -0.831 CASG920101 -0.839 + EISD840101 -0.846 BIOV880101 -0.848 WIMW960101 -0.855 + RADA880102 -0.859 BIOV880102 -0.864 BLAS910101 -0.877 + EISD860101 -0.905 FAUJ830101 -0.909 ROSM880105 -0.955 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.5 3.0 0.2 3.0 -1.0 0.2 3.0 0.0 -0.5 -1.8 + -1.8 3.0 -1.3 -2.5 0.0 0.3 -0.4 -3.4 -2.3 -1.5 +// +H HUTJ700101 +D Heat capacity (Hutchens, 1970) +R +A Hutchens, J.O. +T Heat capacities, absolute entropies, and entropies of formation of amino + acids and related compounds +J In "Handbook of Biochemistry", 2nd ed. (Sober, H.A., ed.), Chemical Rubber + Co., Cleveland, Ohio, pp. B60-B61 (1970) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 29.22 26.37 38.30 37.09 50.70 44.02 41.84 23.71 59.64 45.00 + 48.03 57.10 69.32 48.52 36.13 32.40 35.20 56.92 51.73 40.35 +// +H HUTJ700102 +D Absolute entropy (Hutchens, 1970) +R +A Hutchens, J.O. +T Heat capacities, absolute entropies, and entropies of formation of amino + acids and related compounds +J In "Handbook of Biochemistry", 2nd ed. (Sober, H.A., ed.), Chemical Rubber + Co., Cleveland, Ohio, pp. B60-B61 (1970) +C HUTJ700103 0.867 LEVM760105 0.864 LEVM760102 0.835 + FAUJ880104 0.835 CHOC760101 0.819 CHAM820101 0.815 + FAUJ880103 0.807 FAUJ880106 0.806 CHOC750101 0.802 + RADA880103 -0.812 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 30.88 68.43 41.70 40.66 53.83 46.62 44.98 24.74 65.99 49.71 + 50.62 63.21 55.32 51.06 39.21 35.65 36.50 60.00 51.15 42.75 +// +H HUTJ700103 +D Entropy of formation (Hutchens, 1970) +R +A Hutchens, J.O. +T Heat capacities, absolute entropies, and entropies of formation of amino + acids and related compounds +J In "Handbook of Biochemistry", 2nd ed. (Sober, H.A., ed.), Chemical Rubber + Co., Cleveland, Ohio, pp. B60-B61 (1970) +C HUTJ700102 0.867 EISD860102 0.841 FAUJ880104 0.839 + LEVM760105 0.834 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 154.33 341.01 207.90 194.91 219.79 235.51 223.16 127.90 242.54 233.21 + 232.30 300.46 202.65 204.74 179.93 174.06 205.80 237.01 229.15 207.60 +// +H ISOY800101 +D Normalized relative frequency of alpha-helix (Isogai et al., 1980) +R LIT:2004053b PMID:7378550 +A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A +T Characterization of multiple bends in proteins +J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set + of proteins +C MAXF760101 0.982 PALJ810102 0.965 KANM800101 0.963 + CHOP780201 0.959 ROBB760101 0.957 KANM800103 0.931 + LEVM780101 0.929 PRAM900102 0.929 TANS770101 0.906 + LEVM780104 0.904 RACS820108 0.904 QIAN880106 0.903 + GEIM800101 0.903 AURR980109 0.894 GEIM800104 0.891 + QIAN880107 0.887 PALJ810101 0.882 PALJ810109 0.874 + AURR980112 0.870 NAGK730101 0.862 AURR980114 0.857 + AURR980108 0.856 AURR980110 0.855 AURR980115 0.844 + ROBB760103 0.841 CRAJ730101 0.840 BURA740101 0.839 + QIAN880105 0.828 AURR980113 0.815 AURR980111 0.801 + CHAM830101 -0.815 NAGK730103 -0.821 MUNV940101 -0.875 + MUNV940102 -0.877 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.53 1.17 0.60 1.00 0.89 1.27 1.63 0.44 1.03 1.07 + 1.32 1.26 1.66 1.22 0.25 0.65 0.86 1.05 0.70 0.93 +// +H ISOY800102 +D Normalized relative frequency of extended structure (Isogai et al., 1980) +R LIT:2004053b PMID:7378550 +A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A +T Characterization of multiple bends in proteins +J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set + of proteins +C MAXF760102 0.931 TANS770103 0.929 ROBB760105 0.847 + GEIM800105 0.843 PALJ810103 0.807 WOEC730101 -0.803 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.86 0.98 0.74 0.69 1.39 0.89 0.66 0.70 1.06 1.31 + 1.01 0.77 1.06 1.16 1.16 1.09 1.24 1.17 1.28 1.40 +// +H ISOY800103 +D Normalized relative frequency of bend (Isogai et al., 1980) +R LIT:2004053b PMID:7378550 +A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A +T Characterization of multiple bends in proteins +J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set + of proteins +C LEVM780106 0.941 PRAM900104 0.934 CHOP780203 0.933 + LEVM780103 0.932 GEIM800108 0.930 GEIM800111 0.929 + PALJ810105 0.928 CHOP780216 0.921 QIAN880133 0.908 + TANS770110 0.897 QIAN880132 0.892 CHOP780101 0.885 + CHAM830101 0.881 CHOP780210 0.829 QIAN880134 0.828 + PALJ810116 0.814 PALJ810114 0.809 PALJ810106 0.807 + ROBB760112 0.807 AVBF000102 -0.821 SUEM840101 -0.850 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.78 1.06 1.56 1.50 0.60 0.78 0.97 1.73 0.83 0.40 + 0.57 1.01 0.30 0.67 1.55 1.19 1.09 0.74 1.14 0.44 +// +H ISOY800104 +D Normalized relative frequency of bend R (Isogai et al., 1980) +R LIT:2004053b PMID:7378550 +A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A +T Characterization of multiple bends in proteins +J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set + of proteins +C TANS770104 0.918 CHOP780213 0.916 QIAN880134 0.893 + MUNV940104 0.866 FINA910102 0.844 MUNV940105 0.844 + QIAN880135 0.837 ONEK900102 0.828 GEOR030109 0.812 + ROBB760104 -0.817 ROBB760103 -0.830 PTIO830101 -0.832 + BUNA790101 -0.842 QIAN880108 -0.847 BLAM930101 -0.860 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.09 0.97 1.14 0.77 0.50 0.83 0.92 1.25 0.67 0.66 + 0.44 1.25 0.45 0.50 2.96 1.21 1.33 0.62 0.94 0.56 +// +H ISOY800105 +D Normalized relative frequency of bend S (Isogai et al., 1980) +R LIT:2004053b PMID:7378550 +A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A +T Characterization of multiple bends in proteins +J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set + of proteins +C CHOP780214 0.923 TANS770105 0.836 ISOY800108 0.812 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.35 0.75 2.12 2.16 0.50 0.73 0.65 2.40 1.19 0.12 + 0.58 0.83 0.22 0.89 0.43 1.24 0.85 0.62 1.44 0.43 +// +H ISOY800106 +D Normalized relative frequency of helix end (Isogai et al., 1980) +R LIT:2004053b PMID:7378550 +A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A +T Characterization of multiple bends in proteins +J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set + of proteins +C MAXF760106 0.849 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.09 1.07 0.88 1.24 1.04 1.09 1.14 0.27 1.07 0.97 + 1.30 1.20 0.55 0.80 1.78 1.20 0.99 1.03 0.69 0.77 +// +H ISOY800107 +D Normalized relative frequency of double bend (Isogai et al., 1980) +R LIT:2004053b PMID:7378550 +A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A +T Characterization of multiple bends in proteins +J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set + of proteins +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.34 2.78 0.92 1.77 1.44 0.79 2.54 0.95 0.00 0.52 + 1.05 0.79 0.00 0.43 0.37 0.87 1.14 1.79 0.73 0.00 +// +H ISOY800108 +D Normalized relative frequency of coil (Isogai et al., 1980) +R LIT:2004053b PMID:7378550 +A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A +T Characterization of multiple bends in proteins +J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set + of proteins +C MAXF760104 0.945 RICJ880115 0.889 RACS820109 0.848 + RACS820106 0.831 TANS770107 0.827 AURR980117 0.822 + TANS770109 0.816 ISOY800105 0.812 MAXF760105 0.810 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.47 0.52 2.16 1.15 0.41 0.95 0.64 3.03 0.89 0.62 + 0.53 0.98 0.68 0.61 0.63 1.03 0.39 0.63 0.83 0.76 +// +H JANJ780101 +D Average accessible surface area (Janin et al., 1978) +R LIT:0502087 PMID:731698 +A Janin, J., Wodak, S., Levitt, M. and Maigret, B. +T Conformation of amino acid side-chains in proteins +J J. Mol. Biol. 125, 357-386 (1978) +C GUYH850104 0.989 JANJ780103 0.985 CHOC760102 0.973 + OOBM770101 0.953 GUYH850105 0.923 PRAM900101 0.901 + ENGD860101 0.901 ROSM880102 0.853 FAUJ880109 0.850 + KIDA850101 0.843 MEIH800102 0.843 KUHL950101 0.839 + PUNT030101 0.824 ROSM880101 0.822 GUYH850101 0.821 + FASG890101 0.813 EISD860103 -0.808 BIOV880102 -0.809 + MEIH800103 -0.811 JANJ790101 -0.824 RADA880104 -0.825 + NADH010104 -0.832 ROSG850102 -0.836 RADA880101 -0.844 + KYTJ820101 -0.852 CHOC760104 -0.854 WOLR790101 -0.856 + OLSK800101 -0.858 JURD980101 -0.862 WOLR810101 -0.864 + JACR890101 -0.865 NADH010103 -0.868 WARP780101 -0.869 + DESM900102 -0.878 CHOC760103 -0.892 EISD840101 -0.907 + RADA880107 -0.917 NADH010102 -0.924 JANJ780102 -0.949 + JANJ790102 -0.989 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 27.8 94.7 60.1 60.6 15.5 68.7 68.2 24.5 50.7 22.8 + 27.6 103.0 33.5 25.5 51.5 42.0 45.0 34.7 55.2 23.7 +// +H JANJ780102 +D Percentage of buried residues (Janin et al., 1978) +R LIT:0502087 PMID:731698 +A Janin, J., Wodak, S., Levitt, M. and Maigret, B. +T Conformation of amino acid side-chains in proteins +J J. Mol. Biol. 125, 357-386 (1978) +C JANJ790102 0.966 CHOC760103 0.950 NADH010102 0.949 + JANJ790101 0.941 DESM900102 0.935 JURD980101 0.928 + NADH010103 0.923 KYTJ820101 0.922 ROSG850102 0.909 + OLSK800101 0.905 CHOC760104 0.903 NADH010104 0.898 + MEIH800103 0.897 NADH010101 0.892 CORJ870101 0.885 + EISD860103 0.883 PONP800103 0.882 WARP780101 0.878 + PONP800102 0.875 BIOV880101 0.875 EISD840101 0.874 + RADA880108 0.869 PONP800108 0.863 BIOV880102 0.862 + RADA880107 0.856 RADA880101 0.855 CASG920101 0.853 + DESM900101 0.853 NISK800101 0.853 PONP800101 0.851 + WOLR810101 0.851 MANP780101 0.842 WOLR790101 0.833 + PONP930101 0.825 FAUJ830101 0.825 NADH010105 0.814 + NISK860101 0.813 MIYS850101 0.806 BASU050103 0.803 + CIDH920104 0.803 GRAR740102 -0.809 MIYS990104 -0.811 + KRIW790102 -0.818 RACS770103 -0.828 KIDA850101 -0.828 + PUNT030102 -0.830 MIYS990103 -0.834 ROSM880101 -0.835 + KRIW790101 -0.837 MIYS990105 -0.846 PUNT030101 -0.848 + ENGD860101 -0.860 PRAM900101 -0.860 RACS770102 -0.869 + ROSM880102 -0.870 GUYH850101 -0.872 KUHL950101 -0.890 + GUYH850105 -0.898 FASG890101 -0.903 MEIH800102 -0.907 + CHOC760102 -0.935 JANJ780101 -0.949 JANJ780103 -0.957 + OOBM770101 -0.968 GUYH850104 -0.968 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 51. 5. 22. 19. 74. 16. 16. 52. 34. 66. + 60. 3. 52. 58. 25. 35. 30. 49. 24. 64. +// +H JANJ780103 +D Percentage of exposed residues (Janin et al., 1978) +R LIT:0502087 PMID:731698 +A Janin, J., Wodak, S., Levitt, M. and Maigret, B. +T Conformation of amino acid side-chains in proteins +J J. Mol. Biol. 125, 357-386 (1978) +C JANJ780101 0.985 GUYH850104 0.983 OOBM770101 0.965 + CHOC760102 0.959 GUYH850105 0.885 ENGD860101 0.884 + PRAM900101 0.884 MEIH800102 0.873 KRIW790102 0.848 + PUNT030101 0.848 RACS770103 0.847 KIDA850101 0.842 + FASG890101 0.838 ROSM880102 0.838 GUYH850101 0.829 + KUHL950101 0.826 RACS770102 0.823 MIYS990105 0.816 + VINM940104 0.811 ROSM880101 0.810 KRIW790101 0.805 + NADH010101 -0.804 RADA880108 -0.805 WOLR790101 -0.806 + JACR890101 -0.809 PONP800103 -0.812 RADA880101 -0.817 + EISD860103 -0.819 WOLR810101 -0.822 CASG920101 -0.825 + CORJ870101 -0.826 BIOV880101 -0.829 JANJ790101 -0.832 + DESM900101 -0.838 OLSK800101 -0.845 KYTJ820101 -0.845 + CHOC760104 -0.851 JURD980101 -0.853 RADA880107 -0.856 + BIOV880102 -0.860 NADH010104 -0.860 MEIH800103 -0.866 + ROSG850102 -0.879 EISD840101 -0.881 CHOC760103 -0.888 + WARP780101 -0.890 NADH010103 -0.892 DESM900102 -0.908 + NADH010102 -0.938 JANJ780102 -0.957 JANJ790102 -0.980 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 15. 67. 49. 50. 5. 56. 55. 10. 34. 13. + 16. 85. 20. 10. 45. 32. 32. 17. 41. 14. +// +H JANJ790101 +D Ratio of buried and accessible molar fractions (Janin, 1979) +R LIT:2004120b PMID:763335 +A Janin, J. +T Surface and inside volumes in globular proteins +J Nature 277, 491-492 (1979) +C JANJ780102 0.941 PONP800102 0.897 CORJ870101 0.891 + CHOC760103 0.887 CHOC760104 0.886 PONP800103 0.886 + PONP800108 0.881 NADH010103 0.879 NISK800101 0.875 + NADH010102 0.872 NADH010104 0.871 JURD980101 0.868 + KYTJ820101 0.867 PONP800101 0.866 JANJ790102 0.860 + ROSG850102 0.857 DESM900102 0.855 NADH010101 0.847 + NADH010105 0.843 MANP780101 0.842 MEIH800103 0.838 + EISD860103 0.829 OLSK800101 0.828 CASG920101 0.828 + BIOV880101 0.827 RADA880108 0.824 PONP930101 0.816 + CHOC760102 -0.809 KRIW790101 -0.810 KUHL950101 -0.811 + KRIW710101 -0.815 MEIH800102 -0.821 JANJ780101 -0.824 + JANJ780103 -0.832 GUYH850104 -0.862 OOBM770101 -0.871 + FASG890101 -0.885 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.7 0.1 0.4 0.4 4.6 0.3 0.3 1.8 0.8 3.1 + 2.4 0.05 1.9 2.2 0.6 0.8 0.7 1.6 0.5 2.9 +// +H JANJ790102 +D Transfer free energy (Janin, 1979) +R LIT:2004120b PMID:763335 +A Janin, J. +T Surface and inside volumes in globular proteins +J Nature 277, 491-492 (1979) +C JANJ780102 0.966 NADH010102 0.945 RADA880107 0.906 + CHOC760103 0.905 EISD840101 0.900 NADH010103 0.899 + DESM900102 0.897 ROSG850102 0.892 JURD980101 0.879 + WARP780101 0.877 OLSK800101 0.870 NADH010104 0.868 + KYTJ820101 0.866 JANJ790101 0.860 BIOV880102 0.856 + RADA880108 0.853 MEIH800103 0.853 BIOV880101 0.848 + PONP800103 0.844 JACR890101 0.840 RADA880101 0.839 + EISD860103 0.838 CHOC760104 0.835 WOLR810101 0.828 + FAUJ830101 0.826 CORJ870101 0.825 CASG920101 0.822 + PONP800102 0.822 DESM900101 0.818 WOLR790101 0.818 + NADH010101 0.808 ROSM880105 0.805 PONP800108 0.802 + MIYS990103 -0.804 MIYS990105 -0.820 FAUJ880109 -0.822 + ROSM880101 -0.824 KRIW790101 -0.825 RACS770103 -0.834 + KUHL950101 -0.844 PUNT030101 -0.846 KRIW790102 -0.847 + RACS770102 -0.851 KIDA850101 -0.858 GUYH850101 -0.865 + ROSM880102 -0.866 FASG890101 -0.875 ENGD860101 -0.890 + PRAM900101 -0.890 MEIH800102 -0.894 GUYH850105 -0.913 + OOBM770101 -0.963 CHOC760102 -0.969 JANJ780103 -0.980 + JANJ780101 -0.989 GUYH850104 -0.999 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.3 -1.4 -0.5 -0.6 0.9 -0.7 -0.7 0.3 -0.1 0.7 + 0.5 -1.8 0.4 0.5 -0.3 -0.1 -0.2 0.3 -0.4 0.6 +// +H JOND750101 +D Hydrophobicity (Jones, 1975) +R PMID:1127956 +A Jones, D.D. +T Amino acid properties and side-chain orientation in proteins: A cross + correlation approach +J J. Theor. Biol. 50, 167-183 (1975) +C ARGP820101 1.000 SIMZ760101 0.966 GOLD730101 0.935 + TAKK010101 0.906 MEEJ810101 0.891 ROSM880104 0.872 + CIDH920105 0.866 LEVM760106 0.864 CIDH920102 0.861 + MEEJ800102 0.855 MEEJ810102 0.852 ZHOH040101 0.841 + CIDH920103 0.826 PLIV810101 0.819 CIDH920104 0.818 + LEVM760107 0.806 GUYH850103 -0.807 PARJ860101 -0.834 + WOLS870101 -0.837 BULH740101 -0.853 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.87 0.85 0.09 0.66 1.52 0.00 0.67 0.10 0.87 3.15 + 2.17 1.64 1.67 2.87 2.77 0.07 0.07 3.77 2.67 1.87 +// +H JOND750102 +D pK (-COOH) (Jones, 1975) +R PMID:1127956 +A Jones, D.D. +T Amino acid properties and side-chain orientation in proteins: A cross + correlation approach +J J. Theor. Biol. 50, 167-183 (1975) Original reference of this data: McMeekin, + T.L., Groves, M.L. and Hipp, N.J. In "Amino Acids and Serum Proteins" + (Stekol, J.A., ed.), American Chemical Society, Washington, D.C., p. 54 + (1964) +C FASG760105 0.833 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.34 1.18 2.02 2.01 1.65 2.17 2.19 2.34 1.82 2.36 + 2.36 2.18 2.28 1.83 1.99 2.21 2.10 2.38 2.20 2.32 +// +H JOND920101 +D Relative frequency of occurrence (Jones et al., 1992) +R LIT:1814076 PMID:1633570 +A Jones, D.T., Taylor, W.R. and Thornton, J.M. +T The rapid generation of mutation data matrices from protein sequences +J CABIOS 8, 275-282 (1992) +C CEDJ970102 0.995 NAKH900101 0.993 CEDJ970104 0.983 + CEDJ970101 0.968 DAYM780101 0.954 JUKT750101 0.953 + FUKS010110 0.944 FUKS010112 0.943 JUNJ780101 0.932 + CEDJ970103 0.911 KUMS000102 0.909 NAKH920101 0.900 + NAKH920107 0.893 NAKH920106 0.889 NAKH920104 0.887 + NAKH920103 0.881 NAKH900109 0.878 KUMS000101 0.863 + FUKS010109 0.861 NAKH900102 0.846 CEDJ970105 0.834 + FUKS010111 0.832 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.077 0.051 0.043 0.052 0.020 0.041 0.062 0.074 0.023 0.053 + 0.091 0.059 0.024 0.040 0.051 0.069 0.059 0.014 0.032 0.066 +// +H JOND920102 +D Relative mutability (Jones et al., 1992) +R LIT:1814076 PMID:1633570 +A Jones, D.T., Taylor, W.R. and Thornton, J.M. +T The rapid generation of mutation data matrices from protein sequences +J CABIOS 8, 275-282 (1992) +C DAYM780201 0.889 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 100. 83. 104. 86. 44. 84. 77. 50. 91. 103. + 54. 72. 93. 51. 58. 117. 107. 25. 50. 98. +// +H JUKT750101 +D Amino acid distribution (Jukes et al., 1975) +R PMID:237322 +A Jukes, T.H., Holmquist, R. and Moise, H. +T Amino acid composition of proteins: Selection against the genetic code +J Science 189, 50-51 (1975) +C JUNJ780101 0.980 DAYM780101 0.975 CEDJ970101 0.973 + JOND920101 0.953 KUMS000102 0.948 CEDJ970104 0.942 + CEDJ970102 0.942 NAKH900101 0.941 FUKS010111 0.927 + FUKS010110 0.908 KUMS000101 0.879 FUKS010112 0.875 + NAKH920107 0.862 NAKH920101 0.849 NAKH920103 0.837 + CEDJ970103 0.835 NAKH920106 0.831 NAKH920104 0.827 + NAKH900109 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5.3 2.6 3.0 3.6 1.3 2.4 3.3 4.8 1.4 3.1 + 4.7 4.1 1.1 2.3 2.5 4.5 3.7 0.8 2.3 4.2 +// +H JUNJ780101 +D Sequence frequency (Jungck, 1978) +R LIT:2004107b PMID:691072 +A Jungck, J.R. +T The genetic code as a periodic table +J J. Mol. Evol. 11, 211-224 (1978) +C DAYM780101 0.986 JUKT750101 0.980 CEDJ970101 0.968 + JOND920101 0.932 KUMS000102 0.927 CEDJ970104 0.921 + CEDJ970102 0.920 NAKH900101 0.918 FUKS010111 0.906 + FUKS010110 0.868 NAKH920107 0.856 KUMS000101 0.854 + NAKH900102 0.853 FUKS010112 0.836 NAKH920106 0.829 + NAKH920101 0.826 NAKH920103 0.820 NAKH920104 0.807 + CEDJ970103 0.806 CEDJ970105 0.803 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 685. 382. 397. 400. 241. 313. 427. 707. 155. 394. + 581. 575. 132. 303. 366. 593. 490. 99. 292. 553. +// +H KANM800101 +D Average relative probability of helix (Kanehisa-Tsong, 1980) +R LIT:0611060 PMID:7426680 +A Kanehisa, M.I. and Tsong, T.Y. +T Local hydrophobicity stabilizes secondary structures in proteins +J Biopolymers 19, 1617-1628 (1980) +C ISOY800101 0.963 PALJ810102 0.962 LEVM780104 0.958 + CHOP780201 0.956 MAXF760101 0.950 ROBB760101 0.945 + GEIM800101 0.942 LEVM780101 0.942 PRAM900102 0.942 + PALJ810101 0.928 TANS770101 0.927 GEIM800104 0.916 + RACS820108 0.914 KANM800103 0.912 NAGK730101 0.883 + AURR980115 0.858 BURA740101 0.855 QIAN880106 0.854 + QIAN880107 0.854 AURR980109 0.852 AURR980114 0.852 + PALJ810109 0.849 AURR980112 0.847 CRAJ730101 0.842 + AURR980110 0.830 QIAN880105 0.827 MUNV940102 -0.843 + MUNV940101 -0.846 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.36 1.00 0.89 1.04 0.82 1.14 1.48 0.63 1.11 1.08 + 1.21 1.22 1.45 1.05 0.52 0.74 0.81 0.97 0.79 0.94 +// +H KANM800102 +D Average relative probability of beta-sheet (Kanehisa-Tsong, 1980) +R LIT:0611060 PMID:7426680 +A Kanehisa, M.I. and Tsong, T.Y. +T Local hydrophobicity stabilizes secondary structures in proteins +J Biopolymers 19, 1617-1628 (1980) +C GEIM800107 0.955 PALJ810104 0.948 CHOP780202 0.945 + LIFS790101 0.940 LEVM780105 0.938 ROBB760106 0.938 + PALJ810103 0.932 KANM800104 0.928 PTIO830102 0.917 + GEIM800105 0.916 QIAN880121 0.900 ROBB760105 0.898 + QIAN880120 0.896 QIAN880119 0.888 NAGK730102 0.878 + PALJ810112 0.869 BASU050103 0.869 PONP930101 0.866 + LIFS790103 0.863 AVBF000101 0.859 BASU050101 0.856 + LEVM780102 0.856 PRAM900103 0.856 PONP800108 0.849 + CORJ870101 0.839 PALJ810110 0.836 MANP780101 0.833 + PONP800101 0.829 GEIM800106 0.821 NISK860101 0.819 + PONP800102 0.815 NISK800101 0.809 CHOP780208 0.804 + PONP800103 0.803 LIFS790102 0.801 QIAN880118 0.801 + PUNT030102 -0.803 MIYS990104 -0.808 OOBM770103 -0.812 + GEIM800110 -0.814 MIYS990103 -0.823 MUNV940103 -0.916 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.81 0.85 0.62 0.71 1.17 0.98 0.53 0.88 0.92 1.48 + 1.24 0.77 1.05 1.20 0.61 0.92 1.18 1.18 1.23 1.66 +// +H KANM800103 +D Average relative probability of inner helix (Kanehisa-Tsong, 1980) +R LIT:0611060 PMID:7426680 +A Kanehisa, M.I. and Tsong, T.Y. +T Local hydrophobicity stabilizes secondary structures in proteins +J Biopolymers 19, 1617-1628 (1980) +C AURR980109 0.944 ISOY800101 0.931 PALJ810102 0.916 + AURR980114 0.916 KANM800101 0.912 CHOP780201 0.912 + QIAN880107 0.908 AURR980113 0.905 MAXF760101 0.901 + BEGF750101 0.893 QIAN880106 0.889 ROBB760103 0.887 + ROBB760101 0.886 GEIM800101 0.881 AURR980112 0.871 + LEVM780104 0.859 RACS820108 0.858 AURR980108 0.857 + PRAM900102 0.850 LEVM780101 0.850 TANS770101 0.843 + PALJ810101 0.836 RICJ880109 0.829 QIAN880108 0.829 + QIAN880109 0.824 FINA770101 0.823 QIAN880110 0.820 + SUEM840101 0.820 QIAN880105 0.820 BURA740101 0.810 + CHOP780216 -0.808 GEIM800111 -0.812 PRAM900104 -0.814 + LEVM780103 -0.816 MUNV940102 -0.823 CHOP780101 -0.824 + MUNV940101 -0.826 PALJ810106 -0.840 NAGK730103 -0.847 + CHAM830101 -0.889 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.45 1.15 0.64 0.91 0.70 1.14 1.29 0.53 1.13 1.23 + 1.56 1.27 1.83 1.20 0.21 0.48 0.77 1.17 0.74 1.10 +// +H KANM800104 +D Average relative probability of inner beta-sheet (Kanehisa-Tsong, 1980) +R LIT:0611060 PMID:7426680 +A Kanehisa, M.I. and Tsong, T.Y. +T Local hydrophobicity stabilizes secondary structures in proteins +J Biopolymers 19, 1617-1628 (1980) +C KANM800102 0.928 ROBB760105 0.885 ROBB760106 0.877 + GEIM800107 0.876 GEIM800105 0.861 PTIO830102 0.858 + PALJ810104 0.851 BASU050101 0.850 PONP800108 0.849 + BASU050103 0.848 LEVM780105 0.841 QIAN880119 0.841 + CHOP780202 0.839 LIFS790101 0.834 PONP930101 0.833 + CORJ870101 0.833 QIAN880121 0.829 MANP780101 0.827 + JURD980101 0.826 KYTJ820101 0.824 PALJ810103 0.823 + PONP800101 0.823 PALJ810112 0.813 PONP800102 0.813 + LIFS790102 0.809 QIAN880120 0.803 MUNV940103 -0.857 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.75 0.79 0.33 0.31 1.46 0.75 0.46 0.83 0.83 1.87 + 1.56 0.66 0.86 1.37 0.52 0.82 1.36 0.79 1.08 2.00 +// +H KARP850101 +D Flexibility parameter for no rigid neighbors (Karplus-Schulz, 1985) +R LIT:1110994 +A Karplus, P.A. and Schulz, G.E. +T Prediction of chain flexibility in proteins +J Naturwiss. 72, 212-213 (1985) +C VINM940102 0.874 VINM940103 0.837 RACS770101 0.837 + FUKS010103 0.834 MEIH800101 0.832 MIYS990104 0.822 + VINM940101 0.821 PARS000101 0.816 GUYH850102 0.811 + CIDH920104 -0.801 BIOV880102 -0.804 RADA880108 -0.804 + ROSG850101 -0.807 MIYS850101 -0.811 MEEJ810101 -0.818 + BASU050102 -0.819 BIOV880101 -0.825 NISK860101 -0.828 + ZHOH040101 -0.833 WERD780101 -0.842 ZHOH040103 -0.846 + CIDH920101 -0.864 CIDH920105 -0.866 CIDH920102 -0.873 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.041 1.038 1.117 1.033 0.960 1.165 1.094 1.142 0.982 1.002 + 0.967 1.093 0.947 0.930 1.055 1.169 1.073 0.925 0.961 0.982 +// +H KARP850102 +D Flexibility parameter for one rigid neighbor (Karplus-Schulz, 1985) +R LIT:1110994 +A Karplus, P.A. and Schulz, G.E. +T Prediction of chain flexibility in proteins +J Naturwiss. 72, 212-213 (1985) +C KRIW790101 0.917 MIYS990104 0.909 MIYS990103 0.901 + MIYS990105 0.888 VINM940101 0.885 MEIH800101 0.884 + GUYH850102 0.882 FASG890101 0.871 RACS770101 0.869 + CORJ870108 0.868 VINM940103 0.863 KRIW710101 0.855 + PARS000101 0.852 RACS770102 0.852 KRIW790102 0.843 + GUYH850101 0.840 MEIH800102 0.837 FUKS010103 0.835 + VINM940102 0.834 MIYS990102 0.828 MIYS990101 0.825 + FUKS010104 0.822 OOBM770103 0.820 BHAR880101 0.806 + PUNT030101 0.805 BASU050103 -0.806 NADH010102 -0.807 + DESM900102 -0.815 PONP800106 -0.820 BASU050102 -0.825 + CIDH920101 -0.828 DESM900101 -0.829 CORJ870104 -0.830 + CIDH920104 -0.833 NADH010103 -0.834 CORJ870105 -0.834 + NADH010104 -0.835 ZHOH040103 -0.836 CIDH920105 -0.839 + BAEK050101 -0.839 CORJ870103 -0.850 CIDH920103 -0.852 + BIOV880102 -0.859 MANP780101 -0.863 CORJ870101 -0.865 + CORJ870107 -0.866 PONP800103 -0.870 CORJ870106 -0.870 + MIYS850101 -0.878 RADA880108 -0.879 BIOV880101 -0.880 + NISK800101 -0.885 PONP800102 -0.887 PONP800101 -0.889 + PONP930101 -0.893 ROSG850102 -0.897 CASG920101 -0.901 + NISK860101 -0.901 WERD780101 -0.909 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.946 1.028 1.006 1.089 0.878 1.025 1.036 1.042 0.952 0.892 + 0.961 1.082 0.862 0.912 1.085 1.048 1.051 0.917 0.930 0.927 +// +H KARP850103 +D Flexibility parameter for two rigid neighbors (Karplus-Schulz, 1985) +R LIT:1110994 +A Karplus, P.A. and Schulz, G.E. +T Prediction of chain flexibility in proteins +J Naturwiss. 72, 212-213 (1985) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.892 0.901 0.930 0.932 0.925 0.885 0.933 0.923 0.894 0.872 + 0.921 1.057 0.804 0.914 0.932 0.923 0.934 0.803 0.837 0.913 +// +H KHAG800101 +D The Kerr-constant increments (Khanarian-Moore, 1980) +R LIT:0611050b +A Khanarian, G. and Moore, W.J. +T The Kerr effect of amino acids in water +J Aust. J. Chem. 33, 1727-1741 (1980) (Cys Lys Tyr !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 49.1 133. -3.6 0. 0. 20. 0. 64.6 75.7 18.9 + 15.6 0. 6.8 54.7 43.8 44.4 31.0 70.5 0. 29.5 +// +H KLEP840101 +D Net charge (Klein et al., 1984) +R LIT:1008055 PMID:6547351 +A Klein, P., Kanehisa, M. and DeLisi, C. +T Prediction of protein function from sequence properties: Discriminant + analysis of a data base +J Biochim. Biophys. Acta 787, 221-226 (1984) +C ZIMJ680104 0.941 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 1. 0. -1. 0. 0. -1. 0. 0. 0. + 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. +// +H KRIW710101 +D Side chain interaction parameter (Krigbaum-Rubin, 1971) +R LIT:2004046b PMID:5553983 +A Krigbaum, W.R. and Rubin, B.H. +T Local interactions as structure determinant for globular proteins +J Biochim. Biophys. Acta 229, 368-383 (1971) +C KRIW790101 0.908 FASG890101 0.865 MIYS990103 0.856 + KARP850102 0.855 KRIW790102 0.839 MIYS990104 0.837 + GUYH850101 0.831 GUYH850102 0.811 MIYS990105 0.801 + DESM900101 -0.807 CASG920101 -0.808 CORJ870101 -0.812 + BIOV880101 -0.813 JANJ790101 -0.815 WERD780101 -0.819 + NADH010102 -0.825 NISK800101 -0.831 PONP800106 -0.841 + NADH010105 -0.842 NADH010106 -0.846 RADA880108 -0.847 + PONP800101 -0.850 ROSG850102 -0.852 NADH010103 -0.860 + NADH010104 -0.874 PONP800102 -0.887 PONP800103 -0.890 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 4.60 6.50 5.90 5.70 -1.00 6.10 5.60 7.60 4.50 2.60 + 3.25 7.90 1.40 3.20 7.00 5.25 4.80 4.00 4.35 3.40 +// +H KRIW790101 +D Side chain interaction parameter (Krigbaum-Komoriya, 1979) +R LIT:0502056 PMID:760806 +A Krigbaum, W.R. and Komoriya, A. +T Local interactions as a structure determinant for protein molecules: II +J Biochim. Biophys. Acta 576, 204-228 (1979) +C MIYS990104 0.945 MIYS990103 0.944 MIYS990105 0.925 + KARP850102 0.917 FASG890101 0.914 KRIW790102 0.914 + KRIW710101 0.908 VINM940101 0.890 GUYH850101 0.885 + GUYH850102 0.878 MEIH800102 0.876 VINM940103 0.875 + MIYS990102 0.873 RACS770102 0.871 MIYS990101 0.870 + MEIH800101 0.869 OOBM770103 0.865 GRAR740102 0.847 + VINM940102 0.834 PUNT030101 0.833 CORJ870108 0.833 + MONM990101 0.830 RACS770101 0.828 FUKS010104 0.828 + PUNT030102 0.826 GUYH850104 0.822 OOBM770101 0.816 + JANJ780103 0.805 PARS000101 0.804 CORJ870104 -0.801 + PTIO830102 -0.801 QIAN880121 -0.803 KYTJ820101 -0.805 + JANJ790101 -0.810 CIDH920105 -0.816 CIDH920103 -0.819 + BASU050101 -0.821 JURD980101 -0.824 JANJ790102 -0.825 + CORJ870106 -0.825 NADH010101 -0.827 CORJ870103 -0.830 + CORJ870107 -0.832 JANJ780102 -0.837 DESM900101 -0.847 + MEIH800103 -0.850 DESM900102 -0.859 PONP800108 -0.860 + BAEK050101 -0.860 BASU050103 -0.860 NADH010106 -0.861 + FAUJ830101 -0.865 BASU050102 -0.867 CIDH920104 -0.867 + MANP780101 -0.870 BIOV880102 -0.876 PONP800101 -0.888 + NISK800101 -0.896 RADA880108 -0.897 NADH010105 -0.898 + WERD780101 -0.899 CORJ870101 -0.902 ZHOH040103 -0.905 + NISK860101 -0.907 PONP930101 -0.909 MIYS850101 -0.910 + BIOV880101 -0.910 CASG920101 -0.911 PONP800102 -0.915 + NADH010102 -0.929 PONP800103 -0.930 ROSG850102 -0.935 + NADH010103 -0.954 NADH010104 -0.958 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 4.32 6.55 6.24 6.04 1.73 6.13 6.17 6.09 5.66 2.31 + 3.93 7.92 2.44 2.59 7.19 5.37 5.16 2.78 3.58 3.31 +// +H KRIW790102 +D Fraction of site occupied by water (Krigbaum-Komoriya, 1979) +R LIT:0502056 PMID:760806 +A Krigbaum, W.R. and Komoriya, A. +T Local interactions as a structure determinant for protein molecules: II +J Biochim. Biophys. Acta 576, 204-228 (1979) +C KRIW790101 0.914 MIYS990103 0.899 MEIH800102 0.898 + RACS770102 0.895 RACS770103 0.889 MIYS990104 0.889 + MIYS990105 0.887 FASG890101 0.882 GUYH850101 0.864 + FUKS010104 0.853 VINM940101 0.853 GUYH850104 0.849 + JANJ780103 0.848 KARP850102 0.843 GUYH850102 0.841 + KRIW710101 0.839 VINM940103 0.836 MEIH800101 0.835 + MIYS990102 0.826 OOBM770103 0.824 OOBM770101 0.822 + MIYS990101 0.821 RACS770101 0.814 PUNT030101 0.811 + PONP800101 -0.804 CORJ870103 -0.812 CORJ870107 -0.816 + JANJ780102 -0.818 PONP930101 -0.821 PONP800102 -0.830 + DESM900101 -0.835 CORJ870101 -0.838 JANJ790102 -0.847 + DESM900102 -0.852 PONP800103 -0.853 NISK860101 -0.855 + RADA880108 -0.856 CASG920101 -0.865 BIOV880101 -0.869 + MIYS850101 -0.869 WERD780101 -0.875 BIOV880102 -0.878 + NADH010104 -0.882 MEIH800103 -0.885 NADH010103 -0.887 + NADH010102 -0.890 ROSG850102 -0.922 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.28 0.34 0.31 0.33 0.11 0.39 0.37 0.28 0.23 0.12 + 0.16 0.59 0.08 0.10 0.46 0.27 0.26 0.15 0.25 0.22 +// +H KRIW790103 +D Side chain volume (Krigbaum-Komoriya, 1979) +R LIT:0502056 PMID:760806 +A Krigbaum, W.R. and Komoriya, A. +T Local interactions as a structure determinant for protein molecules: II +J Biochim. Biophys. Acta 576, 204-228 (1979) (Gly Pro 7.8) +C GOLD730102 0.994 BIGC670101 0.993 GRAR740103 0.989 + TSAJ990101 0.988 TSAJ990102 0.987 CHOC750101 0.982 + FAUJ880103 0.965 CHAM820101 0.963 HARY940101 0.956 + CHOC760101 0.948 PONJ960101 0.943 ROSG850101 0.920 + FASG760101 0.910 LEVM760105 0.900 DAWD720101 0.893 + ZHOH040102 0.884 LEVM760102 0.884 RADA880106 0.883 + CHAM830106 0.876 LEVM760106 0.862 LEVM760107 0.860 + FAUJ880106 0.845 MCMT640101 0.810 RADA880103 -0.871 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 27.5 105.0 58.7 40.0 44.6 80.7 62.0 0.0 79.0 93.5 + 93.5 100.0 94.1 115.5 41.9 29.3 51.3 145.5 117.3 71.5 +// +H KYTJ820101 +D Hydropathy index (Kyte-Doolittle, 1982) +R LIT:0807099 PMID:7108955 +A Kyte, J. and Doolittle, R.F. +T A simple method for displaying the hydropathic character of a protein +J J. Mol. Biol. 157, 105-132 (1982) +C JURD980101 0.996 CHOC760103 0.964 OLSK800101 0.942 + JANJ780102 0.922 NADH010102 0.920 NADH010101 0.918 + DESM900102 0.898 EISD860103 0.897 CHOC760104 0.889 + NADH010103 0.885 WOLR810101 0.885 RADA880101 0.884 + MANP780101 0.881 EISD840101 0.878 PONP800103 0.870 + WOLR790101 0.869 NAKH920108 0.868 JANJ790101 0.867 + JANJ790102 0.866 BASU050103 0.863 PONP800102 0.861 + MEIH800103 0.856 NADH010104 0.856 PONP800101 0.851 + PONP800108 0.850 CORJ870101 0.848 WARP780101 0.845 + COWR900101 0.845 PONP930101 0.844 RADA880108 0.842 + ROSG850102 0.841 DESM900101 0.837 BLAS910101 0.836 + BIOV880101 0.829 RADA880107 0.828 BASU050101 0.826 + KANM800104 0.824 LIFS790102 0.824 CIDH920104 0.824 + MIYS850101 0.821 RADA880104 0.819 NAKH900111 0.817 + CORJ870104 0.812 NISK800101 0.812 FAUJ830101 0.811 + ROSM880105 0.806 ARGP820103 0.806 CORJ870103 0.806 + NADH010105 0.804 NAKH920105 0.803 ARGP820102 0.803 + CORJ870107 0.801 MIYS990104 -0.800 CORJ870108 -0.802 + KRIW790101 -0.805 MIYS990105 -0.818 MIYS990103 -0.833 + CHOC760102 -0.838 MIYS990101 -0.840 MIYS990102 -0.840 + MONM990101 -0.842 GUYH850101 -0.843 FASG890101 -0.844 + RACS770102 -0.844 ROSM880101 -0.845 JANJ780103 -0.845 + ENGD860101 -0.850 PRAM900101 -0.850 JANJ780101 -0.852 + GRAR740102 -0.859 PUNT030102 -0.862 GUYH850104 -0.869 + MEIH800102 -0.871 PUNT030101 -0.872 ROSM880102 -0.878 + KUHL950101 -0.883 GUYH850105 -0.883 OOBM770101 -0.899 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.8 -4.5 -3.5 -3.5 2.5 -3.5 -3.5 -0.4 -3.2 4.5 + 3.8 -3.9 1.9 2.8 -1.6 -0.8 -0.7 -0.9 -1.3 4.2 +// +H LAWE840101 +D Transfer free energy, CHP/water (Lawson et al., 1984) +R LIT:1004126 PMID:6699000 +A Lawson, E.Q., Sadler, A.J., Harmatz, D., Brandau, D.T., Micanovic, R. + MacElroy, R.D. and Middaught, C.R. +T A simple experimental model for hydrophobic interactions in proteins +J J. Biol. Chem. 259, 2910-2912 (1984) +C GOLD730101 0.829 SIMZ760101 0.815 ZIMJ680105 0.809 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.48 -0.06 -0.87 -0.75 -0.32 -0.32 -0.71 0.00 -0.51 0.81 + 1.02 -0.09 0.81 1.03 2.03 0.05 -0.35 0.66 1.24 0.56 +// +H LEVM760101 +D Hydrophobic parameter (Levitt, 1976) +R LIT:2004093b PMID:957439 +A Levitt, M. +T A simplified representation of protein conformations for rapid simulation of + protein folfing +J J. Mol. Biol. 104, 59-107 (1976) +C HOPT810101 0.985 KIDA850101 0.915 ENGD860101 0.881 + PRAM900101 0.881 ROSM880101 0.876 WOEC730101 0.872 + FUKS010104 0.869 GRAR740102 0.865 PUNT030102 0.848 + WOLS870101 0.845 FUKS010102 0.837 PUNT030101 0.835 + MIYS990105 0.828 VHEG790101 0.825 ROSM880102 0.823 + VINM940101 0.815 KUHL950101 0.807 PARJ860101 0.806 + OOBM770103 0.805 MIYS990104 0.801 PLIV810101 -0.801 + BASU050103 -0.808 ZHOH040103 -0.811 WIMW960101 -0.812 + RADA880108 -0.824 BIOV880101 -0.831 JACR890101 -0.832 + RADA880101 -0.838 RADA880102 -0.838 ZIMJ680105 -0.844 + BIOV880102 -0.847 MEEJ800102 -0.855 EISD840101 -0.859 + BLAS910101 -0.889 FAUJ830101 -0.919 EISD860101 -0.921 + ROSM880105 -0.954 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.5 3.0 0.2 2.5 -1.0 0.2 2.5 0.0 -0.5 -1.8 + -1.8 3.0 -1.3 -2.5 -1.4 0.3 -0.4 -3.4 -2.3 -1.5 +// +H LEVM760102 +D Distance between C-alpha and centroid of side chain (Levitt, 1976) +R LIT:2004093b PMID:957439 +A Levitt, M. +T A simplified representation of protein conformations for rapid simulation of + protein folfing +J J. Mol. Biol. 104, 59-107 (1976) +C LEVM760105 0.987 CHOC760101 0.972 FASG760101 0.966 + CHAM830106 0.962 FAUJ880103 0.947 CHOC750101 0.933 + PONJ960101 0.930 TSAJ990102 0.918 CHAM820101 0.915 + TSAJ990101 0.910 HARY940101 0.905 FAUJ880106 0.900 + BIGC670101 0.896 GOLD730102 0.893 GRAR740103 0.885 + KRIW790103 0.884 WOLS870102 0.881 DAWD720101 0.873 + RADA880106 0.871 OOBM770102 0.869 FAUJ880104 0.867 + CHAM830105 0.843 HUTJ700102 0.835 RADA880103 -0.913 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.77 3.72 1.98 1.99 1.38 2.58 2.63 0.00 2.76 1.83 + 2.08 2.94 2.34 2.97 1.42 1.28 1.43 3.58 3.36 1.49 +// +H LEVM760103 +D Side chain angle theta(AAR) (Levitt, 1976) +R LIT:2004093b PMID:957439 +A Levitt, M. +T A simplified representation of protein conformations for rapid simulation of + protein folfing +J J. Mol. Biol. 104, 59-107 (1976) (Gly missing) +C AVBF000102 0.816 RICJ880115 -0.829 LEVM760104 -0.840 + KIMC930101 -0.861 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 121.9 121.4 117.5 121.2 113.7 118.0 118.2 0. 118.2 118.9 + 118.1 122.0 113.1 118.2 81.9 117.9 117.1 118.4 110.0 121.7 +// +H LEVM760104 +D Side chain torsion angle phi(AAAR) (Levitt, 1976) +R LIT:2004093b PMID:957439 +A Levitt, M. +T A simplified representation of protein conformations for rapid simulation of + protein folfing +J J. Mol. Biol. 104, 59-107 (1976) +C KIMC930101 0.842 PRAM820102 0.812 CHAM810101 -0.818 + LEVM760103 -0.840 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 243.2 206.6 207.1 215.0 209.4 205.4 213.6 300.0 219.9 217.9 + 205.6 210.9 204.0 203.7 237.4 232.0 226.7 203.7 195.6 220.3 +// +H LEVM760105 +D Radius of gyration of side chain (Levitt, 1976) +R LIT:2004093b PMID:957439 +A Levitt, M. +T A simplified representation of protein conformations for rapid simulation of + protein folfing +J J. Mol. Biol. 104, 59-107 (1976) (Gly 0.089) +C LEVM760102 0.987 CHOC760101 0.968 CHAM830106 0.958 + FASG760101 0.951 FAUJ880103 0.945 CHOC750101 0.939 + PONJ960101 0.928 TSAJ990102 0.928 TSAJ990101 0.922 + HARY940101 0.919 CHAM820101 0.915 BIGC670101 0.913 + GOLD730102 0.911 GRAR740103 0.900 KRIW790103 0.900 + DAWD720101 0.898 FAUJ880104 0.896 FAUJ880106 0.889 + RADA880106 0.871 OOBM770102 0.868 HUTJ700102 0.864 + WOLS870102 0.836 HUTJ700103 0.834 CHAM830105 0.829 + RADA880103 -0.893 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.77 2.38 1.45 1.43 1.22 1.75 1.77 0.58 1.78 1.56 + 1.54 2.08 1.80 1.90 1.25 1.08 1.24 2.21 2.13 1.29 +// +H LEVM760106 +D van der Waals parameter R0 (Levitt, 1976) +R LIT:2004093b PMID:957439 +A Levitt, M. +T A simplified representation of protein conformations for rapid simulation of + protein folfing +J J. Mol. Biol. 104, 59-107 (1976) +C ZHOH040102 0.905 ROSG850101 0.896 ZHOH040101 0.883 + BIGC670101 0.876 GOLD730102 0.875 ZIMJ680102 0.873 + CIDH920102 0.873 ARGP820101 0.865 JOND750101 0.864 + KRIW790103 0.862 TSAJ990101 0.849 SIMZ760101 0.848 + GRAR740103 0.846 CHOC750101 0.841 TSAJ990102 0.841 + TAKK010101 0.841 PLIV810101 0.830 HARY940101 0.829 + CIDH920105 0.828 GOLD730101 0.827 MEEJ810101 0.827 + CIDH920101 0.826 CHAM820101 0.818 BASU050102 0.805 + ROBB790101 0.804 LEVM760107 0.804 BULH740101 -0.818 + GUYH850103 -0.822 FUKS010103 -0.829 PARJ860101 -0.832 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5.2 6.0 5.0 5.0 6.1 6.0 6.0 4.2 6.0 7.0 + 7.0 6.0 6.8 7.1 6.2 4.9 5.0 7.6 7.1 6.4 +// +H LEVM760107 +D van der Waals parameter epsilon (Levitt, 1976) +R LIT:2004093b PMID:957439 +A Levitt, M. +T A simplified representation of protein conformations for rapid simulation of + protein folfing +J J. Mol. Biol. 104, 59-107 (1976) +C CHAM820101 0.891 FAUJ880103 0.875 TSAJ990101 0.866 + GOLD730102 0.865 BIGC670101 0.863 TSAJ990102 0.861 + GARJ730101 0.860 KRIW790103 0.860 CHOC750101 0.858 + ZHOH040101 0.855 ROSG850101 0.852 NOZY710101 0.845 + ZHOH040102 0.843 GRAR740103 0.841 PONJ960101 0.827 + TAKK010101 0.819 SNEP660103 0.818 HARY940101 0.815 + FASG760101 0.815 CHOC760101 0.807 JOND750101 0.806 + ARGP820101 0.806 LEVM760106 0.804 WEBA780101 -0.923 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.025 0.20 0.10 0.10 0.10 0.10 0.10 0.025 0.10 0.19 + 0.19 0.20 0.19 0.39 0.17 0.025 0.10 0.56 0.39 0.15 +// +H LEVM780101 +D Normalized frequency of alpha-helix, with weights (Levitt, 1978) +R LIT:0411042 PMID:708713 +A Levitt, M. +T Conformational preferences of amino acids in globular proteins +J Biochemistry 17, 4277-4285 (1978) +C PRAM900102 1.000 LEVM780104 0.964 PALJ810101 0.943 + KANM800101 0.942 ISOY800101 0.929 MAXF760101 0.924 + ROBB760101 0.916 GEIM800101 0.912 GEIM800104 0.907 + RACS820108 0.904 PALJ810102 0.902 PALJ810109 0.898 + NAGK730101 0.894 CRAJ730101 0.887 CHOP780201 0.873 + TANS770101 0.854 KANM800103 0.850 QIAN880107 0.829 + QIAN880106 0.827 BURA740101 0.805 NAGK730103 -0.809 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.29 0.96 0.90 1.04 1.11 1.27 1.44 0.56 1.22 0.97 + 1.30 1.23 1.47 1.07 0.52 0.82 0.82 0.99 0.72 0.91 +// +H LEVM780102 +D Normalized frequency of beta-sheet, with weights (Levitt, 1978) +R LIT:0411042 PMID:708713 +A Levitt, M. +T Conformational preferences of amino acids in globular proteins +J Biochemistry 17, 4277-4285 (1978) +C PRAM900103 1.000 PALJ810112 0.913 LEVM780105 0.899 + PALJ810104 0.868 PTIO830102 0.865 LIFS790101 0.864 + QIAN880120 0.858 KANM800102 0.856 PALJ810103 0.846 + GEIM800107 0.842 BEGF750102 0.834 QIAN880119 0.834 + CHOP780202 0.833 AVBF000101 0.815 QIAN880121 0.805 + MUNV940103 -0.848 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.90 0.99 0.76 0.72 0.74 0.80 0.75 0.92 1.08 1.45 + 1.02 0.77 0.97 1.32 0.64 0.95 1.21 1.14 1.25 1.49 +// +H LEVM780103 +D Normalized frequency of reverse turn, with weights (Levitt, 1978) +R LIT:0411042 PMID:708713 +A Levitt, M. +T Conformational preferences of amino acids in globular proteins +J Biochemistry 17, 4277-4285 (1978) +C PRAM900104 1.000 LEVM780106 0.984 GEIM800111 0.952 + CHOP780216 0.952 QIAN880133 0.948 QIAN880134 0.935 + ISOY800103 0.932 QIAN880132 0.931 GEIM800108 0.931 + CHOP780203 0.927 CHAM830101 0.909 PALJ810105 0.909 + QIAN880135 0.906 CHOP780101 0.893 TANS770110 0.875 + CHOP780210 0.852 PALJ810106 0.848 RACS770101 0.808 + AURR980109 -0.814 KANM800103 -0.816 QIAN880108 -0.820 + QIAN880107 -0.834 AVBF000102 -0.834 ROBB760103 -0.843 + FAUJ880102 -0.846 QIAN880109 -0.848 PTIO830101 -0.860 + SUEM840101 -0.864 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.77 0.88 1.28 1.41 0.81 0.98 0.99 1.64 0.68 0.51 + 0.58 0.96 0.41 0.59 1.91 1.32 1.04 0.76 1.05 0.47 +// +H LEVM780104 +D Normalized frequency of alpha-helix, unweighted (Levitt, 1978) +R LIT:0411042 PMID:708713 +A Levitt, M. +T Conformational preferences of amino acids in globular proteins +J Biochemistry 17, 4277-4285 (1978) +C PALJ810101 0.988 PRAM900102 0.964 LEVM780101 0.964 + KANM800101 0.958 GEIM800101 0.950 NAGK730101 0.918 + ROBB760101 0.911 TANS770101 0.908 PALJ810102 0.906 + MAXF760101 0.904 ISOY800101 0.904 RACS820108 0.889 + CHOP780201 0.886 GEIM800104 0.872 CRAJ730101 0.869 + KANM800103 0.859 BURA740101 0.833 QIAN880107 0.822 + PALJ810109 0.819 AURR980115 0.818 QIAN880106 0.804 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.32 0.98 0.95 1.03 0.92 1.10 1.44 0.61 1.31 0.93 + 1.31 1.25 1.39 1.02 0.58 0.76 0.79 0.97 0.73 0.93 +// +H LEVM780105 +D Normalized frequency of beta-sheet, unweighted (Levitt, 1978) +R LIT:0411042 PMID:708713 +A Levitt, M. +T Conformational preferences of amino acids in globular proteins +J Biochemistry 17, 4277-4285 (1978) +C PALJ810103 0.980 KANM800102 0.938 CHOP780202 0.930 + LIFS790101 0.928 GEIM800105 0.926 PALJ810104 0.921 + QIAN880120 0.913 QIAN880119 0.903 PRAM900103 0.899 + LEVM780102 0.899 LIFS790103 0.897 PTIO830102 0.894 + GEIM800107 0.884 QIAN880121 0.876 PALJ810112 0.870 + ROBB760106 0.869 ROBB760105 0.842 KANM800104 0.841 + AVBF000101 0.824 QIAN880118 0.819 MUNV940103 -0.891 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.86 0.97 0.73 0.69 1.04 1.00 0.66 0.89 0.85 1.47 + 1.04 0.77 0.93 1.21 0.68 1.02 1.27 1.26 1.31 1.43 +// +H LEVM780106 +D Normalized frequency of reverse turn, unweighted (Levitt, 1978) +R LIT:0411042 PMID:708713 +A Levitt, M. +T Conformational preferences of amino acids in globular proteins +J Biochemistry 17, 4277-4285 (1978) +C LEVM780103 0.984 PRAM900104 0.983 QIAN880133 0.971 + CHOP780216 0.953 GEIM800111 0.951 QIAN880132 0.943 + ISOY800103 0.941 CHOP780203 0.935 QIAN880134 0.932 + GEIM800108 0.932 QIAN880135 0.902 PALJ810105 0.902 + CHAM830101 0.900 TANS770110 0.892 CHOP780101 0.890 + PALJ810106 0.850 MUNV940103 0.815 CHOP780210 0.812 + GEIM800110 0.809 AVBF000101 -0.805 LIFS790101 -0.806 + QIAN880119 -0.810 QIAN880107 -0.813 QIAN880109 -0.815 + QIAN880120 -0.831 PTIO830101 -0.854 AVBF000102 -0.860 + FAUJ880102 -0.865 SUEM840101 -0.878 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.79 0.90 1.25 1.47 0.79 0.92 1.02 1.67 0.81 0.50 + 0.57 0.99 0.51 0.77 1.78 1.30 0.97 0.79 0.93 0.46 +// +H LEWP710101 +D Frequency of occurrence in beta-bends (Lewis et al., 1971) +R PMID:5289387 +A Lewis, P. N., Momany, F.A. and Scheraga, H.A. +T Folding of polypeptide chains in proteins: A proposed mechanism for folding +J Proc. Natl. Acad. Sci. USA 68, 2293-2297 (1971) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.22 0.28 0.42 0.73 0.20 0.26 0.08 0.58 0.14 0.22 + 0.19 0.27 0.38 0.08 0.46 0.55 0.49 0.43 0.46 0.08 +// +H LIFS790101 +D Conformational preference for all beta-strands (Lifson-Sander, 1979) +R LIT:0512128 PMID:503185 +A Lifson, S. and Sander, C. +T Antiparallel and parallel beta-strands differ in amino acid residue + preference +J Nature 282, 109-111 (1979) +C QIAN880120 0.969 CHOP780202 0.947 LIFS790103 0.944 + PTIO830102 0.941 KANM800102 0.940 QIAN880121 0.930 + PALJ810104 0.929 QIAN880119 0.929 LEVM780105 0.928 + PALJ810103 0.912 PONP930101 0.908 ROBB760106 0.906 + GEIM800107 0.888 BASU050101 0.886 ROBB760105 0.867 + BASU050103 0.865 PRAM900103 0.864 LEVM780102 0.864 + BASU050102 0.861 MANP780101 0.859 NISK860101 0.859 + AVBF000101 0.857 GEIM800105 0.855 PALJ810112 0.845 + CORJ870106 0.836 KANM800104 0.834 CIDH920104 0.832 + CORJ870105 0.830 CIDH920105 0.828 PONP800108 0.828 + NISK800101 0.827 CORJ870101 0.826 PONP800101 0.823 + CHOP780208 0.820 CORJ870107 0.820 PALJ810110 0.817 + SWER830101 0.815 CIDH920103 0.815 CORJ870102 0.815 + ZHOH040103 0.815 VENT840101 0.814 CIDH920102 0.808 + BEGF750102 0.807 LIFS790102 0.803 PONP800107 0.801 + GEIM800111 -0.801 QIAN880134 -0.804 LEVM780106 -0.806 + QIAN880132 -0.806 MEIH800101 -0.809 PUNT030102 -0.809 + MIYS990101 -0.811 CORJ870108 -0.811 MIYS990102 -0.813 + VINM940101 -0.834 MIYS990103 -0.838 VINM940102 -0.843 + MIYS990104 -0.843 PARS000101 -0.844 QIAN880133 -0.848 + OOBM770103 -0.855 GEIM800110 -0.862 MUNV940103 -0.941 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.92 0.93 0.60 0.48 1.16 0.95 0.61 0.61 0.93 1.81 + 1.30 0.70 1.19 1.25 0.40 0.82 1.12 1.54 1.53 1.81 +// +H LIFS790102 +D Conformational preference for parallel beta-strands (Lifson-Sander, 1979) +R LIT:0512128 PMID:503185 +A Lifson, S. and Sander, C. +T Antiparallel and parallel beta-strands differ in amino acid residue + preference +J Nature 282, 109-111 (1979) +C PTIO830102 0.874 MANP780101 0.870 PONP800107 0.849 + PONP930101 0.833 JURD980101 0.824 KYTJ820101 0.824 + OLSK800101 0.818 CHOC760103 0.810 KANM800104 0.809 + PONP800101 0.804 LIFS790101 0.803 KANM800102 0.801 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.00 0.68 0.54 0.50 0.91 0.28 0.59 0.79 0.38 2.60 + 1.42 0.59 1.49 1.30 0.35 0.70 0.59 0.89 1.08 2.63 +// +H LIFS790103 +D Conformational preference for antiparallel beta-strands (Lifson-Sander, 1979) +R LIT:0512128 PMID:503185 +A Lifson, S. and Sander, C. +T Antiparallel and parallel beta-strands differ in amino acid residue + preference +J Nature 282, 109-111 (1979) +C LIFS790101 0.944 QIAN880120 0.939 CHOP780202 0.908 + LEVM780105 0.897 QIAN880121 0.882 PALJ810103 0.877 + QIAN880119 0.877 KANM800102 0.863 PALJ810104 0.860 + GEIM800105 0.832 ROBB760106 0.827 BASU050102 0.826 + GEIM800107 0.823 PTIO830102 0.822 GEIM800106 0.814 + AVBF000101 0.814 ZHOH040101 0.801 OOBM770103 -0.807 + VINM940101 -0.829 PARS000101 -0.861 VINM940102 -0.862 + GEIM800110 -0.889 MUNV940103 -0.902 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.90 1.02 0.62 0.47 1.24 1.18 0.62 0.56 1.12 1.54 + 1.26 0.74 1.09 1.23 0.42 0.87 1.30 1.75 1.68 1.53 +// +H MANP780101 +D Average surrounding hydrophobicity (Manavalan-Ponnuswamy, 1978) +R LIT:0411088 PMID:703834 +A Manavalan, P. and Ponnuswamy, P.K. +T Hydrophobic character of amino acid residues in globular proteins +J Nature 275, 673-674 (1978) +C PONP930101 0.967 PONP800101 0.963 PONP800102 0.945 + NISK800101 0.940 PONP800108 0.935 NISK860101 0.930 + BASU050101 0.925 BASU050103 0.923 CIDH920104 0.918 + CORJ870101 0.918 PONP800103 0.913 MIYS850101 0.909 + CORJ870107 0.908 CORJ870104 0.908 CORJ870103 0.906 + CIDH920103 0.905 ROSG850102 0.903 RADA880108 0.900 + BIOV880101 0.899 JURD980101 0.887 KYTJ820101 0.881 + BASU050102 0.879 CIDH920105 0.879 NADH010103 0.878 + NADH010104 0.873 PONP800107 0.871 LIFS790102 0.870 + CORJ870106 0.867 ZHOH040103 0.864 NADH010102 0.863 + PTIO830102 0.861 LIFS790101 0.859 CHOC760103 0.859 + PLIV810101 0.856 WERD780101 0.853 CORJ870105 0.853 + CASG920101 0.848 BIOV880102 0.847 NADH010101 0.847 + FAUJ830101 0.843 JANJ790101 0.842 NADH010105 0.842 + JANJ780102 0.842 MEIH800103 0.839 ROBB790101 0.834 + KANM800102 0.833 KANM800104 0.827 EISD860103 0.826 + ROBB760106 0.824 SWER830101 0.821 CORJ870102 0.818 + OLSK800101 0.817 DESM900102 0.816 GUOD860101 0.815 + PONP800106 0.813 QIAN880120 0.806 PALJ810104 0.805 + CHOP780202 0.805 ROBB760105 0.805 ROSM880105 0.803 + BLAS910101 0.802 QIAN880121 0.802 OOBM770101 -0.806 + WOLS870101 -0.809 MUNV940103 -0.815 VINM940102 -0.821 + PUNT030101 -0.824 GUYH850103 -0.833 VINM940101 -0.836 + GUYH850101 -0.838 PARJ860101 -0.841 GUYH850102 -0.850 + OOBM770103 -0.859 KARP850102 -0.863 RACS770102 -0.865 + MEIH800102 -0.865 GRAR740102 -0.868 KRIW790101 -0.870 + PUNT030102 -0.873 RACS770101 -0.878 MEIH800101 -0.897 + FASG890101 -0.904 MIYS990105 -0.906 MIYS990104 -0.909 + CORJ870108 -0.911 MIYS990101 -0.913 MIYS990102 -0.915 + MIYS990103 -0.918 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 12.97 11.72 11.42 10.85 14.63 11.76 11.89 12.43 12.16 15.67 + 14.90 11.36 14.39 14.00 11.37 11.23 11.69 13.93 13.42 15.71 +// +H MAXF760101 +D Normalized frequency of alpha-helix (Maxfield-Scheraga, 1976) +R LIT:2004036b PMID:990270 +A Maxfield, F.R. and Scheraga, H.A. +T Status of empirical methods for the prediction of protein backbone topography +J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different + set of proteins Reported values normalized by the total number +C ISOY800101 0.982 PALJ810102 0.959 CHOP780201 0.956 + ROBB760101 0.956 KANM800101 0.950 TANS770101 0.930 + PRAM900102 0.924 LEVM780101 0.924 LEVM780104 0.904 + KANM800103 0.901 GEIM800104 0.897 GEIM800101 0.895 + PALJ810101 0.889 QIAN880107 0.885 QIAN880106 0.881 + NAGK730101 0.877 PALJ810109 0.876 AURR980109 0.865 + AURR980110 0.860 RACS820108 0.860 AURR980114 0.853 + BURA740101 0.852 AURR980115 0.852 AURR980108 0.841 + AURR980112 0.838 CRAJ730101 0.826 QIAN880105 0.811 + AURR980111 0.811 FINA770101 0.810 NAGK730103 -0.801 + MUNV940102 -0.829 MUNV940101 -0.833 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.43 1.18 0.64 0.92 0.94 1.22 1.67 0.46 0.98 1.04 + 1.36 1.27 1.53 1.19 0.49 0.70 0.78 1.01 0.69 0.98 +// +H MAXF760102 +D Normalized frequency of extended structure (Maxfield-Scheraga, 1976) +R LIT:2004036b PMID:990270 +A Maxfield, F.R. and Scheraga, H.A. +T Status of empirical methods for the prediction of protein backbone topography +J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different + set of proteins Reported values normalized by the total number +C ISOY800102 0.931 TANS770103 0.891 GEIM800105 0.819 + RACS820111 0.815 WOEC730101 -0.842 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.86 0.94 0.74 0.72 1.17 0.89 0.62 0.97 1.06 1.24 + 0.98 0.79 1.08 1.16 1.22 1.04 1.18 1.07 1.25 1.33 +// +H MAXF760103 +D Normalized frequency of zeta R (Maxfield-Scheraga, 1976) +R LIT:2004036b PMID:990270 +A Maxfield, F.R. and Scheraga, H.A. +T Status of empirical methods for the prediction of protein backbone topography +J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different + set of proteins Reported values normalized by the total number +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.64 0.62 3.14 1.92 0.32 0.80 1.01 0.63 2.05 0.92 + 0.37 0.89 1.07 0.86 0.50 1.01 0.92 1.00 1.31 0.87 +// +H MAXF760104 +D Normalized frequency of left-handed alpha-helix (Maxfield-Scheraga, 1976) +R LIT:2004036b PMID:990270 +A Maxfield, F.R. and Scheraga, H.A. +T Status of empirical methods for the prediction of protein backbone topography +J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different + set of proteins Reported values normalized by the total number +C ISOY800108 0.945 RICJ880115 0.919 TANS770107 0.913 + MAXF760105 0.850 AURR980117 0.849 RACS820109 0.844 + TANS770109 0.821 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.17 0.76 2.62 1.08 0.95 0.91 0.28 5.02 0.57 0.26 + 0.21 1.17 0.00 0.28 0.12 0.57 0.23 0.00 0.97 0.24 +// +H MAXF760105 +D Normalized frequency of zeta L (Maxfield-Scheraga, 1976) +R LIT:2004036b PMID:990270 +A Maxfield, F.R. and Scheraga, H.A. +T Status of empirical methods for the prediction of protein backbone topography +J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different + set of proteins Reported values normalized by the total number +C TANS770109 0.878 MAXF760104 0.850 ISOY800108 0.810 + RICJ880115 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.13 0.48 1.11 1.18 0.38 0.41 1.02 3.84 0.30 0.40 + 0.65 1.13 0.00 0.45 0.00 0.81 0.71 0.93 0.38 0.48 +// +H MAXF760106 +D Normalized frequency of alpha region (Maxfield-Scheraga, 1976) +R LIT:2004036b PMID:990270 +A Maxfield, F.R. and Scheraga, H.A. +T Status of empirical methods for the prediction of protein backbone topography +J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different + set of proteins Reported values normalized by the total number +C ISOY800106 0.849 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.00 1.18 0.87 1.39 1.09 1.13 1.04 0.46 0.71 0.68 + 1.01 1.05 0.36 0.65 1.95 1.56 1.23 1.10 0.87 0.58 +// +H MCMT640101 +D Refractivity (McMeekin et al., 1964), Cited by Jones (1975) +R +A McMeekin, T.L., Groves, M.L. and Hipp, N.J. +T +J In "Amino Acids and Serum Proteins" (Stekol, J.A., ed.), American Chemical + Society, Washington, D.C., p. 54 (1964) +C CHAM820101 0.871 ROSG850101 0.857 FAUJ880103 0.847 + FASG760101 0.845 CHOC750101 0.822 GRAR740103 0.817 + BIGC670101 0.814 GOLD730102 0.814 KRIW790103 0.810 + CHOC760101 0.809 FUKS010111 -0.806 RADA880103 -0.833 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 4.34 26.66 13.28 12.00 35.77 17.56 17.26 0.00 21.81 19.06 + 18.78 21.29 21.64 29.40 10.93 6.35 11.01 42.53 31.53 13.92 +// +H MEEJ800101 +D Retention coefficient in HPLC, pH7.4 (Meek, 1980) +R LIT:0604247 PMID:6929513 +A Meek, J.L. +T Prediction of peptide retention times in high-pressure liquid chromatography + on the basis of amino acid composition +J Proc. Natl. Acad. Sci. USA 77, 1632-1636 (1980) +C MEEJ800102 0.886 ZIMJ680105 0.842 BROC820102 0.840 + WIMW960101 0.838 GOLD730101 0.808 PARJ860101 -0.806 + WOLS870101 -0.823 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.5 0.8 0.8 -8.2 -6.8 -4.8 -16.9 0.0 -3.5 13.9 + 8.8 0.1 4.8 13.2 6.1 1.2 2.7 14.9 6.1 2.7 +// +H MEEJ800102 +D Retention coefficient in HPLC, pH2.1 (Meek, 1980) +R LIT:0604247 PMID:6929513 +A Meek, J.L. +T Prediction of peptide retention times in high-pressure liquid chromatography + on the basis of amino acid composition +J Proc. Natl. Acad. Sci. USA 77, 1632-1636 (1980) +C ZIMJ680105 0.921 RADA880102 0.900 NOZY710101 0.895 + TAKK010101 0.891 EISD860101 0.890 MEEJ800101 0.886 + MEEJ810102 0.881 BROC820101 0.877 MEEJ810101 0.871 + PLIV810101 0.867 GOLD730101 0.866 GUOD860101 0.866 + SIMZ760101 0.861 FAUJ830101 0.858 BROC820102 0.857 + CIDH920102 0.856 ARGP820101 0.855 JOND750101 0.855 + BLAS910101 0.849 ROSM880105 0.841 CIDH920105 0.840 + ZHOH040101 0.838 WIMW960101 0.821 ZHOH040102 0.808 + ROBB790101 0.807 WEBA780101 -0.808 GUYH850103 -0.809 + KIDA850101 -0.823 HOPT810101 -0.826 LEVM760101 -0.855 + BULH740101 -0.875 PARJ860101 -0.902 WOLS870101 -0.925 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.1 -4.5 -1.6 -2.8 -2.2 -2.5 -7.5 -0.5 0.8 11.8 + 10.0 -3.2 7.1 13.9 8.0 -3.7 1.5 18.1 8.2 3.3 +// +H MEEJ810101 +D Retention coefficient in NaClO4 (Meek-Rossetti, 1981) +R LIT:0708201 +A Meek, J.L. and Rossetti, Z.L. +T Factors affecting retention and resolution of peptides in high-performance + liquid chromatography +J J. Chromatogr. 211, 15-28 (1981) +C MEEJ810102 0.987 ZHOH040101 0.935 GUOD860101 0.931 + ZHOH040103 0.921 PLIV810101 0.914 ROSM880104 0.911 + FAUJ830101 0.902 BASU050102 0.898 CIDH920105 0.892 + ARGP820101 0.891 JOND750101 0.891 CIDH920102 0.887 + NOZY710101 0.882 CIDH920104 0.878 MEEJ800102 0.871 + MIYS850101 0.863 ROBB790101 0.861 BIOV880101 0.855 + NISK860101 0.848 CIDH920103 0.837 SIMZ760101 0.836 + TAKK010101 0.836 BLAS910101 0.831 LEVM760106 0.827 + WERD780101 0.825 GOLD730101 0.824 COWR900101 0.823 + BIOV880102 0.822 VENT840101 0.813 BASU050101 0.810 + CORJ870102 0.807 SWER830101 0.806 EISD860101 0.805 + ZHOH040102 0.804 RADA880108 0.804 ROSM880105 0.802 + MEIH800101 -0.809 GUYH850102 -0.813 KARP850101 -0.818 + MIYS990104 -0.831 WEBA780101 -0.831 GRAR740102 -0.839 + VINM940102 -0.839 MIYS990105 -0.839 KIDA850101 -0.850 + OOBM770103 -0.861 GUYH850103 -0.864 MIYS990102 -0.866 + MIYS990101 -0.867 BULH740101 -0.876 WOLS870101 -0.906 + PARJ860101 -0.920 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.1 -0.4 -4.2 -1.6 7.1 -2.9 0.7 -0.2 -0.7 8.5 + 11.0 -1.9 5.4 13.4 4.4 -3.2 -1.7 17.1 7.4 5.9 +// +H MEEJ810102 +D Retention coefficient in NaH2PO4 (Meek-Rossetti, 1981) +R LIT:0708201 +A Meek, J.L. and Rossetti, Z.L. +T Factors affecting retention and resolution of peptides in high-performance + liquid chromatography +J J. Chromatogr. 211, 15-28 (1981) +C MEEJ810101 0.987 GUOD860101 0.949 ZHOH040101 0.922 + ZHOH040103 0.902 NOZY710101 0.899 PLIV810101 0.898 + FAUJ830101 0.890 ROSM880104 0.885 MEEJ800102 0.881 + BASU050102 0.871 ARGP820101 0.853 JOND750101 0.852 + WILM950101 0.849 COWR900101 0.849 MIYS850101 0.844 + CIDH920105 0.844 CIDH920102 0.843 CIDH920104 0.837 + VENT840101 0.831 BLAS910101 0.830 BIOV880101 0.824 + ROBB790101 0.821 BROC820101 0.820 TAKK010101 0.819 + RADA880102 0.813 NISK860101 0.810 WILM950102 0.809 + EISD860101 0.808 SIMZ760101 0.808 GOLD730101 0.806 + ROSM880105 0.804 MIYS990104 -0.807 GRAR740102 -0.811 + MIYS990105 -0.817 GUYH850103 -0.823 OOBM770103 -0.831 + KIDA850101 -0.851 MIYS990102 -0.853 WEBA780101 -0.854 + MIYS990101 -0.854 BULH740101 -0.880 PARJ860101 -0.897 + WOLS870101 -0.905 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.0 -2.0 -3.0 -0.5 4.6 -2.0 1.1 0.2 -2.2 7.0 + 9.6 -3.0 4.0 12.6 3.1 -2.9 -0.6 15.1 6.7 4.6 +// +H MEIH800101 +D Average reduced distance for C-alpha (Meirovitch et al., 1980) +R LIT:0702089 +A Meirovitch, H., Rackovsky, S. and Scheraga, H.A. +T Empirical studies of hydrophobicity. 1. Effect of protein size on the + hydrophobic behavior of amino acids +J Macromolecules 13, 1398-1405 (1980) Database taken from group C +C RACS770101 0.973 RACS770102 0.963 MEIH800102 0.952 + MIYS990102 0.941 MIYS990101 0.940 MIYS990104 0.925 + MIYS990103 0.923 FASG890101 0.919 MIYS990105 0.912 + PARJ860101 0.905 VINM940101 0.900 GUYH850102 0.899 + OOBM770103 0.897 GUYH850101 0.893 CORJ870108 0.889 + KARP850102 0.884 VINM940103 0.875 GUYH850103 0.873 + KRIW790101 0.869 PUNT030101 0.860 WOLS870101 0.852 + PUNT030102 0.837 RACS770103 0.837 KRIW790102 0.835 + VINM940102 0.833 KARP850101 0.832 FUKS010103 0.832 + GRAR740102 0.824 PARS000101 0.813 RICJ880111 -0.802 + ROSM880105 -0.802 DESM900102 -0.804 NADH010105 -0.806 + LIFS790101 -0.809 MEEJ810101 -0.809 EISD860103 -0.810 + RADA880102 -0.816 PONP800108 -0.825 ZHOH040101 -0.827 + PTIO830102 -0.828 CORJ870102 -0.829 SWER830101 -0.830 + BEGF750102 -0.832 GUOD860101 -0.833 NADH010102 -0.847 + NISK800101 -0.852 CORJ870101 -0.855 PONP800103 -0.856 + CORJ870104 -0.862 CIDH920101 -0.863 FAUJ830101 -0.863 + NADH010104 -0.867 CIDH920102 -0.867 NADH010103 -0.868 + ROBB790101 -0.868 PONP800102 -0.870 CORJ870103 -0.871 + CASG920101 -0.875 MEIH800103 -0.875 CORJ870106 -0.882 + CORJ870105 -0.883 BASU050101 -0.887 PONP800101 -0.888 + BASU050102 -0.892 PLIV810101 -0.896 MANP780101 -0.897 + CORJ870107 -0.897 ZHOH040103 -0.898 CIDH920103 -0.905 + BASU050103 -0.906 PONP800107 -0.909 PONP930101 -0.916 + CIDH920104 -0.917 CIDH920105 -0.923 ROSG850102 -0.930 + BIOV880102 -0.937 RADA880108 -0.940 WERD780101 -0.943 + BIOV880101 -0.949 MIYS850101 -0.957 NISK860101 -0.960 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.93 0.98 0.98 1.01 0.88 1.02 1.02 1.01 0.89 0.79 + 0.85 1.05 0.84 0.78 1.00 1.02 0.99 0.83 0.93 0.81 +// +H MEIH800102 +D Average reduced distance for side chain (Meirovitch et al., 1980) +R LIT:0702089 +A Meirovitch, H., Rackovsky, S. and Scheraga, H.A. +T Empirical studies of hydrophobicity. 1. Effect of protein size on the + hydrophobic behavior of amino acids +J Macromolecules 13, 1398-1405 (1980) Database taken from group C (Gly 0.067) +C RACS770102 0.987 MEIH800101 0.952 FASG890101 0.951 + GUYH850101 0.934 MIYS990103 0.917 MIYS990102 0.916 + MIYS990105 0.914 MIYS990101 0.913 RACS770101 0.905 + MIYS990104 0.903 RACS770103 0.903 PUNT030101 0.901 + KRIW790102 0.898 GUYH850104 0.892 OOBM770101 0.881 + KRIW790101 0.876 JANJ780103 0.873 VINM940101 0.872 + CORJ870108 0.860 ROSM880102 0.859 OOBM770103 0.859 + GUYH850102 0.856 PUNT030102 0.849 JANJ780101 0.843 + VINM940103 0.841 CHOC760102 0.839 KARP850102 0.837 + GRAR740102 0.836 KIDA850101 0.834 PARJ860101 0.831 + KUHL950101 0.822 FUKS010104 0.822 WOLS870101 0.813 + GUYH850105 0.811 VINM940104 0.808 NAKH900110 -0.802 + BASU050102 -0.812 NADH010101 -0.818 JANJ790101 -0.821 + ROSM880105 -0.821 DESM900101 -0.822 BASU050101 -0.825 + CIDH920103 -0.825 WARP780101 -0.826 CIDH920105 -0.826 + EISD840101 -0.829 CORJ870106 -0.835 PONP800108 -0.836 + CORJ870105 -0.839 CORJ870104 -0.840 NISK800101 -0.844 + ZHOH040103 -0.848 PLIV810101 -0.849 CORJ870103 -0.855 + OLSK800101 -0.858 PONP800107 -0.858 MANP780101 -0.865 + CIDH920104 -0.868 CORJ870107 -0.871 KYTJ820101 -0.871 + FAUJ830101 -0.875 PONP800101 -0.877 CORJ870101 -0.878 + CASG920101 -0.879 JURD980101 -0.879 BASU050103 -0.880 + PONP930101 -0.881 EISD860103 -0.882 PONP800102 -0.883 + PONP800103 -0.891 CHOC760103 -0.894 JANJ790102 -0.894 + DESM900102 -0.898 NADH010104 -0.900 WERD780101 -0.903 + JANJ780102 -0.907 NADH010103 -0.916 NISK860101 -0.920 + NADH010102 -0.928 MIYS850101 -0.934 MEIH800103 -0.941 + BIOV880102 -0.951 RADA880108 -0.953 BIOV880101 -0.956 + ROSG850102 -0.959 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.94 1.09 1.04 1.08 0.84 1.11 1.12 1.01 0.92 0.76 + 0.82 1.23 0.83 0.73 1.04 1.04 1.02 0.87 1.03 0.81 +// +H MEIH800103 +D Average side chain orientation angle (Meirovitch et al., 1980) +R LIT:0702089 +A Meirovitch, H., Rackovsky, S. and Scheraga, H.A. +T Empirical studies of hydrophobicity. 1. Effect of protein size on the + hydrophobic behavior of amino acids +J Macromolecules 13, 1398-1405 (1980) Database taken from group C (Gly 7.4) +C ROSG850102 0.948 BIOV880101 0.934 DESM900102 0.924 + RADA880108 0.916 BIOV880102 0.916 NISK860101 0.909 + MIYS850101 0.908 NADH010102 0.907 CORJ870101 0.902 + NADH010103 0.901 JANJ780102 0.897 WERD780101 0.895 + PONP800103 0.895 NADH010104 0.890 PONP800102 0.885 + CORJ870107 0.883 CASG920101 0.881 CORJ870103 0.880 + NISK800101 0.871 EISD860103 0.870 PONP800101 0.869 + CHOC760103 0.865 PONP930101 0.863 PONP800108 0.862 + JURD980101 0.861 KYTJ820101 0.856 CORJ870104 0.856 + CIDH920104 0.853 DESM900101 0.853 JANJ790102 0.853 + FAUJ830101 0.849 MANP780101 0.839 JANJ790101 0.838 + WARP780101 0.835 BASU050103 0.832 CORJ870105 0.827 + OLSK800101 0.826 NADH010101 0.824 CORJ870106 0.822 + ZHOH040103 0.820 NADH010105 0.816 PLIV810101 0.811 + CIDH920105 0.804 CIDH920103 0.802 ROBB790101 0.801 + BASU050102 0.801 WOEC730101 -0.802 CHOC760102 -0.802 + PARJ860101 -0.808 KUHL950101 -0.809 JANJ780101 -0.811 + KIDA850101 -0.813 PUNT030102 -0.815 ROSM880102 -0.829 + VINM940103 -0.830 RACS770101 -0.845 KRIW790101 -0.850 + GUYH850102 -0.854 GUYH850104 -0.854 VINM940101 -0.861 + GRAR740102 -0.866 OOBM770103 -0.866 JANJ780103 -0.866 + CORJ870108 -0.870 MEIH800101 -0.875 GUYH850101 -0.880 + PUNT030101 -0.882 KRIW790102 -0.885 MIYS990101 -0.891 + MIYS990102 -0.893 MIYS990104 -0.894 OOBM770101 -0.896 + MIYS990103 -0.906 RACS770102 -0.918 MIYS990105 -0.919 + RACS770103 -0.919 FASG890101 -0.924 MEIH800102 -0.941 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 87. 81. 70. 71. 104. 66. 72. 90. 90. 105. + 104. 65. 100. 108. 78. 83. 83. 94. 83. 94. +// +H MIYS850101 +D Effective partition energy (Miyazawa-Jernigan, 1985) +R LIT:2004114b +A Miyazawa, S. and Jernigan, R.L. +T Estimation of effective interresidue contact energies from protein crystal + structures: Quasi-chemical approximation +J Macromolecules 18, 534-552 (1985) +C BIOV880101 0.960 NISK860101 0.960 RADA880108 0.950 + PLIV810101 0.944 ROSG850102 0.937 WERD780101 0.934 + BIOV880102 0.930 CIDH920105 0.916 CIDH920104 0.915 + FAUJ830101 0.914 ZHOH040103 0.914 CORJ870107 0.911 + PONP930101 0.910 MANP780101 0.909 MEIH800103 0.908 + GUOD860101 0.908 CIDH920103 0.906 BASU050102 0.904 + BASU050103 0.899 PONP800103 0.898 NADH010104 0.897 + NADH010103 0.896 ROBB790101 0.895 CORJ870104 0.892 + PONP800101 0.892 CORJ870103 0.892 PONP800102 0.891 + SWER830101 0.889 BASU050101 0.888 CORJ870102 0.887 + CORJ870106 0.884 PONP800107 0.884 CORJ870105 0.879 + NADH010102 0.878 CIDH920102 0.873 NISK800101 0.864 + MEEJ810101 0.863 CASG920101 0.863 CORJ870101 0.861 + EISD860103 0.858 ZHOH040101 0.855 PONP800108 0.847 + MEEJ810102 0.844 NADH010105 0.844 ROSM880105 0.844 + CIDH920101 0.843 EISD860101 0.842 JURD980101 0.837 + DESM900102 0.831 BLAS910101 0.829 RADA880102 0.824 + COWR900101 0.824 ROSM880104 0.824 ARGP820103 0.822 + KYTJ820101 0.821 NADH010101 0.815 PONP800106 0.812 + CHOC760103 0.810 NOZY710101 0.810 PTIO830102 0.807 + BEGF750102 0.806 JANJ780102 0.806 NAKH900110 0.804 + HOPT810101 -0.800 KARP850101 -0.811 RACS770103 -0.818 + PARS000101 -0.821 ROSM880102 -0.825 FUKS010103 -0.828 + KIDA850101 -0.831 VINM940102 -0.832 BULH740101 -0.838 + VINM940103 -0.849 PUNT030102 -0.868 KRIW790102 -0.869 + KARP850102 -0.878 VINM940101 -0.883 GUYH850102 -0.884 + PUNT030101 -0.892 GRAR740102 -0.895 GUYH850103 -0.897 + WOLS870101 -0.899 GUYH850101 -0.909 OOBM770103 -0.910 + KRIW790101 -0.910 CORJ870108 -0.910 PARJ860101 -0.929 + MEIH800102 -0.934 FASG890101 -0.938 RACS770101 -0.940 + RACS770102 -0.943 MIYS990105 -0.951 MIYS990103 -0.952 + MIYS990104 -0.953 MEIH800101 -0.957 MIYS990101 -0.977 + MIYS990102 -0.978 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.36 1.92 1.70 1.67 3.36 1.75 1.74 2.06 2.41 4.17 + 3.93 1.23 4.22 4.37 1.89 1.81 2.04 3.82 2.91 3.49 +// +H NAGK730101 +D Normalized frequency of alpha-helix (Nagano, 1973) +R PMID:4728695 +A Nagano, K. +T Local analysis of the mechanism of protein folding. I. Prediction of helices, + loops, and beta-structures from primary structure +J J. Mol. Biol. 75, 401-420 (1973) +C PALJ810101 0.953 CRAJ730101 0.925 TANS770101 0.925 + LEVM780104 0.918 GEIM800101 0.912 ROBB760101 0.910 + PRAM900102 0.894 LEVM780101 0.894 CHOP780201 0.886 + KANM800101 0.883 BURA740101 0.883 MAXF760101 0.877 + PALJ810102 0.876 ISOY800101 0.862 GEIM800104 0.828 + RACS820108 0.820 NAGK730103 -0.870 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.29 0.83 0.77 1.00 0.94 1.10 1.54 0.72 1.29 0.94 + 1.23 1.23 1.23 1.23 0.70 0.78 0.87 1.06 0.63 0.97 +// +H NAGK730102 +D Normalized frequency of bata-structure (Nagano, 1973) +R PMID:4728695 +A Nagano, K. +T Local analysis of the mechanism of protein folding. I. Prediction of helices, + loops, and beta-structures from primary structure +J J. Mol. Biol. 75, 401-420 (1973) +C ROBB760106 0.887 KANM800102 0.878 PALJ810104 0.867 + CHOP780208 0.860 CHOP780202 0.858 BASU050103 0.837 + BEGF750102 0.833 GEIM800107 0.830 ROBB760105 0.815 + CRAJ730102 0.815 PTIO830102 0.811 PUNT030102 -0.836 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.96 0.67 0.72 0.90 1.13 1.18 0.33 0.90 0.87 1.54 + 1.26 0.81 1.29 1.37 0.75 0.77 1.23 1.13 1.07 1.41 +// +H NAGK730103 +D Normalized frequency of coil (Nagano, 1973) +R PMID:4728695 +A Nagano, K. +T Local analysis of the mechanism of protein folding. I. Prediction of helices, + loops, and beta-structures from primary structure +J J. Mol. Biol. 75, 401-420 (1973) +C CHAM830101 0.857 CHOP780101 0.827 CHOP780216 0.819 + CHOP780210 0.814 ROBB760113 0.811 PALJ810105 0.804 + TANS770101 -0.800 MAXF760101 -0.801 PALJ810101 -0.808 + LEVM780101 -0.809 PRAM900102 -0.809 PALJ810102 -0.818 + ISOY800101 -0.821 BURA740101 -0.830 CHOP780201 -0.837 + KANM800103 -0.847 CRAJ730101 -0.850 ROBB760101 -0.861 + NAGK730101 -0.870 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.72 1.33 1.38 1.04 1.01 0.81 0.75 1.35 0.76 0.80 + 0.63 0.84 0.62 0.58 1.43 1.34 1.03 0.87 1.35 0.83 +// +H NAKH900101 +D AA composition of total proteins (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C JOND920101 0.993 CEDJ970102 0.988 CEDJ970104 0.978 + CEDJ970101 0.954 FUKS010112 0.948 FUKS010110 0.946 + JUKT750101 0.941 DAYM780101 0.940 JUNJ780101 0.918 + CEDJ970103 0.908 NAKH920101 0.907 NAKH920106 0.900 + KUMS000102 0.894 FUKS010109 0.868 NAKH900109 0.866 + NAKH920107 0.863 CEDJ970105 0.860 NAKH900102 0.858 + NAKH920104 0.857 KUMS000101 0.856 NAKH920103 0.854 + FUKS010111 0.812 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 7.99 5.86 4.33 5.14 1.81 3.98 6.10 6.91 2.17 5.48 + 9.16 6.01 2.50 3.83 4.95 6.84 5.77 1.34 3.15 6.65 +// +H NAKH900102 +D SD of AA composition of total proteins (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C CEDJ970105 0.903 DAYM780101 0.883 NAKH920106 0.872 + CEDJ970104 0.860 NAKH900101 0.858 NAKH920101 0.854 + JUNJ780101 0.853 JOND920101 0.846 CEDJ970102 0.841 + CEDJ970101 0.832 RACS820105 -0.839 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 3.73 3.34 2.33 2.23 2.30 2.36 3. 3.36 1.55 2.52 + 3.40 3.36 1.37 1.94 3.18 2.83 2.63 1.15 1.76 2.53 +// +H NAKH900103 +D AA composition of mt-proteins (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C NAKH900105 0.992 NAKH900112 0.966 NAKH900107 0.927 + FUKS010108 0.864 NAKH900111 0.832 NAKH920105 0.829 + NAKH920108 0.826 CEDJ970103 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5.74 1.92 5.25 2.11 1.03 2.30 2.63 5.66 2.30 9.12 + 15.36 3.20 5.30 6.51 4.79 7.55 7.51 2.51 4.08 5.12 +// +H NAKH900104 +D Normalized composition of mt-proteins (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C NAKH900106 0.986 NAKH900108 0.849 EISD860101 0.812 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.60 -1.18 0.39 -1.36 -0.34 -0.71 -1.16 -0.37 0.08 1.44 + 1.82 -0.84 2.04 1.38 -0.05 0.25 0.66 1.02 0.53 -0.60 +// +H NAKH900105 +D AA composition of mt-proteins from animal (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C NAKH900103 0.992 NAKH900112 0.974 NAKH900107 0.870 + FUKS010108 0.846 NAKH900111 0.815 NAKH920105 0.806 + NAKH920108 0.801 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5.88 1.54 4.38 1.70 1.11 2.30 2.60 5.29 2.33 8.78 + 16.52 2.58 6.00 6.58 5.29 7.68 8.38 2.89 3.51 4.66 +// +H NAKH900106 +D Normalized composition from animal (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C NAKH900104 0.986 EISD860101 0.812 ARGP820103 0.810 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.57 -1.29 0.02 -1.54 -0.30 -0.71 -1.17 -0.48 0.10 1.31 + 2.16 -1.02 2.55 1.42 0.11 0.30 0.99 1.35 0.20 -0.79 +// +H NAKH900107 +D AA composition of mt-proteins from fungi and plant (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C NAKH900103 0.927 NAKH900105 0.870 NAKH900112 0.850 + FUKS010108 0.830 CEDJ970103 0.820 NAKH920108 0.816 + NAKH920105 0.814 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5.39 2.81 7.31 3.07 0.86 2.31 2.70 6.52 2.23 9.94 + 12.64 4.67 3.68 6.34 3.62 7.24 5.44 1.64 5.42 6.18 +// +H NAKH900108 +D Normalized composition from fungi and plant (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C NAKH900104 0.849 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.70 -0.91 1.28 -0.93 -0.41 -0.71 -1.13 -0.12 0.04 1.77 + 1.02 -0.40 0.86 1.29 -0.42 0.14 -0.13 0.26 1.29 -0.19 +// +H NAKH900109 +D AA composition of membrane proteins (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C CEDJ970103 0.970 FUKS010106 0.927 FUKS010107 0.903 + FUKS010105 0.892 NAKH900111 0.890 JOND920101 0.878 + FUKS010108 0.872 NAKH900101 0.866 CEDJ970102 0.865 + CEDJ970101 0.861 FUKS010110 0.853 KUMS000102 0.837 + NAKH920105 0.823 CEDJ970104 0.821 JUKT750101 0.815 + NAKH920108 0.811 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.25 3.96 3.71 3.89 1.07 3.17 4.80 8.51 1.88 6.47 + 10.94 3.50 3.14 6.36 4.36 6.26 5.66 2.22 3.28 7.55 +// +H NAKH900110 +D Normalized composition of membrane proteins (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C ROSM880105 0.859 EISD840101 0.838 BROC820101 0.830 + BIOV880102 0.829 EISD860101 0.820 GUOD860101 0.805 + MIYS850101 0.804 BLAS910101 0.801 MEIH800102 -0.802 + KIDA850101 -0.808 PARJ860101 -0.808 ROSM880101 -0.812 + HOPT810101 -0.812 WOLS870101 -0.832 VHEG790101 -0.848 + PUNT030101 -0.886 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.34 -0.57 -0.27 -0.56 -0.32 -0.34 -0.43 0.48 -0.19 0.39 + 0.52 -0.75 0.47 1.30 -0.19 -0.20 -0.04 0.77 0.07 0.36 +// +H NAKH900111 +D Transmembrane regions of non-mt-proteins (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C NAKH920108 0.975 NAKH920105 0.958 FUKS010108 0.954 + FUKS010106 0.933 FUKS010105 0.911 NAKH900109 0.890 + NAKH900112 0.878 FUKS010107 0.867 CEDJ970103 0.865 + NAKH900103 0.832 KYTJ820101 0.817 NAKH900105 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 10.17 1.21 1.36 1.18 1.48 1.57 1.15 8.87 1.07 10.91 + 16.22 1.04 4.12 9.60 2.24 5.38 5.61 2.67 2.68 11.44 +// +H NAKH900112 +D Transmembrane regions of mt-proteins (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C NAKH900105 0.974 NAKH900103 0.966 FUKS010108 0.896 + NAKH920105 0.881 NAKH920108 0.879 NAKH900111 0.878 + NAKH900107 0.850 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.61 0.41 1.84 0.59 0.83 1.20 1.63 4.88 1.14 12.91 + 21.66 1.15 7.17 7.76 3.51 6.84 8.89 2.11 2.57 6.30 +// +H NAKH900113 +D Ratio of average and computed composition (Nakashima et al., 1990) +R LIT:2004138b PMID:2235995 +A Nakashima, H., Nishikawa, K. and Ooi, T. +T Distinct character in hydrophobicity of amino acid composition of + mitochondrial proteins +J Proteins 8, 173-178 (1990) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.61 0.40 0.73 0.75 0.37 0.61 1.50 3.12 0.46 1.61 + 1.37 0.62 1.59 1.24 0.67 0.68 0.92 1.63 0.67 1.30 +// +H NAKH920101 +D AA composition of CYT of single-spanning proteins (Nakashima-Nishikawa, 1992) +R LIT:1811095b PMID:1607012 +A Nakashima, H. and Nishikawa, K. +T The amino acid composition is different between the cytoplasmic and + extracellular sides in membrane proteins +J FEBS Lett. 303, 141-146 (1992) +C CEDJ970105 0.942 NAKH920106 0.929 NAKH920102 0.929 + CEDJ970104 0.920 NAKH900101 0.907 JOND920101 0.900 + CEDJ970102 0.898 DAYM780101 0.882 FUKS010112 0.856 + NAKH900102 0.854 CEDJ970101 0.850 JUKT750101 0.849 + FUKS010110 0.833 JUNJ780101 0.826 NAKH920104 0.822 + NAKH920103 0.811 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.63 6.75 4.18 6.24 1.03 4.76 7.82 6.80 2.70 3.48 + 8.44 6.25 2.14 2.73 6.28 8.53 4.43 0.80 2.54 5.44 +// +H NAKH920102 +D AA composition of CYT2 of single-spanning proteins (Nakashima-Nishikawa, + 1992) +R LIT:1811095b PMID:1607012 +A Nakashima, H. and Nishikawa, K. +T The amino acid composition is different between the cytoplasmic and + extracellular sides in membrane proteins +J FEBS Lett. 303, 141-146 (1992) +C NAKH920101 0.929 CEDJ970105 0.843 CEDJ970104 0.834 + NAKH920106 0.832 DAYM780101 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 10.88 6.01 5.75 6.13 0.69 4.68 9.34 7.72 2.15 1.80 + 8.03 6.11 3.79 2.93 7.21 7.25 3.51 0.47 1.01 4.57 +// +H NAKH920103 +D AA composition of EXT of single-spanning proteins (Nakashima-Nishikawa, 1992) +R LIT:1811095b PMID:1607012 +A Nakashima, H. and Nishikawa, K. +T The amino acid composition is different between the cytoplasmic and + extracellular sides in membrane proteins +J FEBS Lett. 303, 141-146 (1992) +C CEDJ970102 0.906 NAKH920104 0.904 NAKH920107 0.882 + JOND920101 0.881 CEDJ970104 0.863 NAKH900101 0.854 + DAYM780101 0.851 CEDJ970101 0.843 FUKS010112 0.842 + JUKT750101 0.837 JUNJ780101 0.820 NAKH920101 0.811 + NAKH920106 0.809 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5.15 4.38 4.81 5.75 3.24 4.45 7.05 6.38 2.69 4.40 + 8.11 5.25 1.60 3.52 5.65 8.04 7.41 1.68 3.42 7.00 +// +H NAKH920104 +D AA composition of EXT2 of single-spanning proteins (Nakashima-Nishikawa, + 1992) +R LIT:1811095b PMID:1607012 +A Nakashima, H. and Nishikawa, K. +T The amino acid composition is different between the cytoplasmic and + extracellular sides in membrane proteins +J FEBS Lett. 303, 141-146 (1992) +C CEDJ970102 0.905 NAKH920103 0.904 NAKH920107 0.889 + JOND920101 0.887 FUKS010112 0.882 CEDJ970104 0.865 + CEDJ970101 0.859 NAKH900101 0.857 NAKH920106 0.829 + JUKT750101 0.827 NAKH920101 0.822 DAYM780101 0.819 + JUNJ780101 0.807 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5.04 3.73 5.94 5.26 2.20 4.50 6.07 7.09 2.99 4.32 + 9.88 6.31 1.85 3.72 6.22 8.05 5.20 2.10 3.32 6.19 +// +H NAKH920105 +D AA composition of MEM of single-spanning proteins (Nakashima-Nishikawa, 1992) +R LIT:1811095b PMID:1607012 +A Nakashima, H. and Nishikawa, K. +T The amino acid composition is different between the cytoplasmic and + extracellular sides in membrane proteins +J FEBS Lett. 303, 141-146 (1992) +C FUKS010108 0.968 NAKH920108 0.959 NAKH900111 0.958 + FUKS010106 0.931 FUKS010105 0.929 NAKH900112 0.881 + CEDJ970103 0.836 FUKS010107 0.833 NAKH900103 0.829 + NAKH900109 0.823 NAKH900107 0.814 NAKH900105 0.806 + KYTJ820101 0.803 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.90 0.09 0.94 0.35 2.55 0.87 0.08 8.14 0.20 15.25 + 22.28 0.16 1.85 6.47 2.38 4.17 4.33 2.21 3.42 14.34 +// +H NAKH920106 +D AA composition of CYT of multi-spanning proteins (Nakashima-Nishikawa, 1992) +R LIT:1811095b PMID:1607012 +A Nakashima, H. and Nishikawa, K. +T The amino acid composition is different between the cytoplasmic and + extracellular sides in membrane proteins +J FEBS Lett. 303, 141-146 (1992) +C CEDJ970105 0.930 NAKH920101 0.929 CEDJ970104 0.923 + FUKS010112 0.921 NAKH900101 0.900 JOND920101 0.889 + CEDJ970102 0.886 NAKH900102 0.872 DAYM780101 0.856 + NAKH920102 0.832 JUKT750101 0.831 NAKH920104 0.829 + JUNJ780101 0.829 CEDJ970101 0.826 FUKS010110 0.824 + FUKS010104 0.818 FUKS010109 0.814 NAKH920103 0.809 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.69 6.65 4.49 4.97 1.70 5.39 7.76 6.32 2.11 4.51 + 8.23 8.36 2.46 3.59 5.20 7.40 5.18 1.06 2.75 5.27 +// +H NAKH920107 +D AA composition of EXT of multi-spanning proteins (Nakashima-Nishikawa, 1992) +R LIT:1811095b PMID:1607012 +A Nakashima, H. and Nishikawa, K. +T The amino acid composition is different between the cytoplasmic and + extracellular sides in membrane proteins +J FEBS Lett. 303, 141-146 (1992) +C JOND920101 0.893 CEDJ970102 0.891 NAKH920104 0.889 + NAKH920103 0.882 NAKH900101 0.863 JUKT750101 0.862 + DAYM780101 0.861 CEDJ970101 0.860 CEDJ970104 0.857 + JUNJ780101 0.856 FUKS010111 0.841 KUMS000102 0.839 + FUKS010112 0.824 FUKS010110 0.810 KUMS000101 0.800 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5.08 4.75 5.75 5.96 2.95 4.24 6.04 8.20 2.10 4.95 + 8.03 4.93 2.61 4.36 4.84 6.41 5.87 2.31 4.55 6.07 +// +H NAKH920108 +D AA composition of MEM of multi-spanning proteins (Nakashima-Nishikawa, 1992) +R LIT:1811095b PMID:1607012 +A Nakashima, H. and Nishikawa, K. +T The amino acid composition is different between the cytoplasmic and + extracellular sides in membrane proteins +J FEBS Lett. 303, 141-146 (1992) +C NAKH900111 0.975 NAKH920105 0.959 FUKS010108 0.948 + FUKS010106 0.898 FUKS010105 0.890 NAKH900112 0.879 + KYTJ820101 0.868 JURD980101 0.858 NAKH900103 0.826 + CHOC760103 0.824 FUKS010107 0.817 NAKH900107 0.816 + NAKH900109 0.811 CEDJ970103 0.811 NAKH900105 0.801 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.36 0.27 2.31 0.94 2.56 1.14 0.94 6.17 0.47 13.73 + 16.64 0.58 3.93 10.99 1.96 5.58 4.68 2.20 3.13 12.43 +// +H NISK800101 +D 8 A contact number (Nishikawa-Ooi, 1980) +R LIT:2004068b PMID:7440060 +A Nishikawa, K. and Ooi, T. +T Prediction of the surface-interior diagram of globular proteins by an + empirical method +J Int. J. Peptide Protein Res. 16, 19-32 (1980) +C PONP800108 0.976 CORJ870101 0.976 PONP800102 0.965 + PONP800101 0.960 PONP930101 0.956 NISK860101 0.943 + ROSG850102 0.942 PONP800103 0.941 MANP780101 0.940 + CASG920101 0.935 BIOV880101 0.920 NADH010104 0.909 + NADH010103 0.908 RADA880108 0.902 CIDH920104 0.900 + BASU050103 0.896 WERD780101 0.891 ZHOH040103 0.888 + CORJ870103 0.886 CORJ870107 0.884 BASU050102 0.884 + NADH010102 0.881 BAEK050101 0.881 BASU050101 0.876 + JANJ790101 0.875 BIOV880102 0.873 MEIH800103 0.871 + CORJ870104 0.868 MIYS850101 0.864 NADH010105 0.860 + CORJ870106 0.857 CIDH920103 0.855 CIDH920105 0.854 + JANJ780102 0.853 DESM900102 0.852 FAUJ830101 0.849 + DESM900101 0.837 CORJ870105 0.834 ROBB790101 0.830 + LIFS790101 0.827 QIAN880121 0.818 JURD980101 0.816 + NADH010101 0.813 KYTJ820101 0.812 KANM800102 0.809 + QIAN880122 0.808 RACS770101 -0.805 GUYH850101 -0.811 + MUNV940103 -0.813 PARS000102 -0.814 RACS770102 -0.818 + GUYH850103 -0.828 KRIW710101 -0.831 PARS000101 -0.832 + VINM940103 -0.836 MEIH800102 -0.844 OOBM770101 -0.845 + MEIH800101 -0.852 PUNT030102 -0.855 MIYS990101 -0.860 + MIYS990102 -0.863 GRAR740102 -0.879 CORJ870108 -0.880 + KARP850102 -0.885 OOBM770103 -0.894 KRIW790101 -0.896 + VINM940102 -0.900 GUYH850102 -0.914 VINM940101 -0.922 + FASG890101 -0.923 MIYS990105 -0.935 MIYS990103 -0.938 + MIYS990104 -0.938 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.23 -0.26 -0.94 -1.13 1.78 -0.57 -0.75 -0.07 0.11 1.19 + 1.03 -1.05 0.66 0.48 -0.76 -0.67 -0.36 0.90 0.59 1.24 +// +H NISK860101 +D 14 A contact number (Nishikawa-Ooi, 1986) +R LIT:1211490 PMID:3818558 +A Nishikawa, K. and Ooi, T. +T Radial locations of amino acid residues in a globular protein: Correlation + with the sequence +J J. Biochem. 100, 1043-1047 (1986) Values supplied by the author +C BIOV880101 0.972 WERD780101 0.966 ROSG850102 0.962 + PONP930101 0.961 MIYS850101 0.960 BASU050102 0.951 + RADA880108 0.950 ZHOH040103 0.946 CIDH920104 0.944 + NISK800101 0.943 BIOV880102 0.939 CIDH920105 0.938 + CASG920101 0.938 BASU050103 0.937 CORJ870101 0.935 + MANP780101 0.930 PONP800101 0.930 CORJ870107 0.928 + BASU050101 0.926 PONP800102 0.924 PONP800108 0.921 + NADH010104 0.915 CORJ870103 0.914 ROBB790101 0.912 + PONP800103 0.910 NADH010103 0.910 MEIH800103 0.909 + CIDH920103 0.909 CORJ870106 0.908 FAUJ830101 0.906 + CORJ870104 0.901 CORJ870105 0.901 CIDH920102 0.897 + PLIV810101 0.892 BAEK050101 0.886 CIDH920101 0.882 + NADH010102 0.878 ZHOH040101 0.871 SWER830101 0.865 + CORJ870102 0.864 NADH010105 0.863 LIFS790101 0.859 + MEEJ810101 0.848 PONP800107 0.847 DESM900102 0.843 + GUOD860101 0.840 QIAN880120 0.837 ROSM880105 0.836 + CHOP780202 0.832 QIAN880121 0.829 PTIO830102 0.825 + KANM800102 0.819 JANJ780102 0.813 GEIM800107 0.813 + EISD860103 0.811 NADH010101 0.810 ROBB760106 0.810 + MEEJ810102 0.810 PALJ810104 0.809 JURD980101 0.808 + BLAS910101 0.803 ROSM880104 0.801 HOPT810101 -0.822 + WOEC730101 -0.822 KARP850101 -0.828 FUKS010104 -0.832 + RACS770103 -0.837 MUNV940103 -0.840 WOLS870101 -0.848 + FUKS010103 -0.850 PUNT030101 -0.854 KRIW790102 -0.855 + GUYH850101 -0.877 PARS000101 -0.884 PUNT030102 -0.885 + GRAR740102 -0.900 KARP850102 -0.901 VINM940103 -0.903 + KRIW790101 -0.907 RACS770102 -0.913 GUYH850103 -0.914 + PARJ860101 -0.916 VINM940102 -0.919 CORJ870108 -0.920 + MEIH800102 -0.920 RACS770101 -0.923 FASG890101 -0.949 + OOBM770103 -0.949 GUYH850102 -0.950 MIYS990101 -0.957 + VINM940101 -0.959 MEIH800101 -0.960 MIYS990102 -0.960 + MIYS990105 -0.972 MIYS990103 -0.974 MIYS990104 -0.980 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.22 -0.93 -2.65 -4.12 4.66 -2.76 -3.64 -1.62 1.28 5.58 + 5.01 -4.18 3.51 5.27 -3.03 -2.84 -1.20 5.20 2.15 4.45 +// +H NOZY710101 +D Transfer energy, organic solvent/water (Nozaki-Tanford, 1971) +R PMID:5555568 +A Nozaki, Y. and Tanford, C. +T The solubility of amino acids and two glycine peptides in aqueous ethanol and + dioxane solutions +J J. Biol. Chem. 246, 2211-2217 (1971) Missing values filled with zeros +C ZHOH040101 0.932 RADA880102 0.917 MEEJ810102 0.899 + VENT840101 0.897 ZHOH040102 0.897 MEEJ800102 0.895 + CIDH920102 0.889 TAKK010101 0.884 GUOD860101 0.884 + MEEJ810101 0.882 CIDH920105 0.857 ROSM880104 0.847 + BASU050102 0.847 LEVM760107 0.845 ZHOH040103 0.842 + PLIV810101 0.839 CORJ870102 0.838 ZIMJ680105 0.837 + SWER830101 0.836 ROSG850101 0.834 BROC820101 0.829 + EISD860101 0.822 GARJ730101 0.821 WIMW960101 0.818 + MIYS850101 0.810 SIMZ760101 0.807 FAUJ830101 0.803 + ARGP820101 0.800 MIYS990102 -0.819 MIYS990101 -0.821 + OOBM770103 -0.828 PARS000101 -0.829 WOLS870101 -0.874 + WEBA780101 -0.890 BULH740101 -0.892 PARJ860101 -0.900 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.8 + 1.8 0.0 1.3 2.5 0.0 0.0 0.4 3.4 2.3 1.5 +// +H OOBM770101 +D Average non-bonded energy per atom (Oobatake-Ooi, 1977) +R LIT:2004111b PMID:904331 +A Oobatake, M. and Ooi, T. +T An analysis of non-bonded energy of proteins +J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied + by the number of heavy atoms +C GUYH850104 0.966 JANJ780103 0.965 JANJ780101 0.953 + CHOC760102 0.925 ENGD860101 0.907 PRAM900101 0.907 + MEIH800102 0.881 KUHL950101 0.876 GUYH850105 0.874 + RACS770103 0.871 FASG890101 0.868 ROSM880102 0.867 + PUNT030101 0.865 ROSM880101 0.854 GUYH850101 0.848 + PUNT030102 0.845 MIYS990105 0.844 KIDA850101 0.843 + GRAR740102 0.841 RACS770102 0.838 MIYS990103 0.827 + KRIW790102 0.822 KRIW790101 0.816 MIYS990104 0.806 + WOEC730101 0.804 MANP780101 -0.806 JACR890101 -0.812 + ROSM880105 -0.824 WOLR790101 -0.831 FAUJ830101 -0.832 + PONP800101 -0.835 CASG920101 -0.838 NISK800101 -0.845 + WOLR810101 -0.847 PONP800108 -0.851 RADA880107 -0.854 + CHOC760104 -0.857 BIOV880101 -0.858 NADH010101 -0.861 + PONP800102 -0.862 RADA880101 -0.863 RADA880108 -0.864 + NADH010104 -0.871 JANJ790101 -0.871 CORJ870101 -0.875 + BIOV880102 -0.877 OLSK800101 -0.878 EISD840101 -0.878 + EISD860103 -0.880 PONP800103 -0.880 DESM900101 -0.894 + MEIH800103 -0.896 KYTJ820101 -0.899 CHOC760103 -0.902 + NADH010103 -0.902 JURD980101 -0.903 ROSG850102 -0.903 + WARP780101 -0.937 NADH010102 -0.944 DESM900102 -0.950 + JANJ790102 -0.963 JANJ780102 -0.968 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -1.895 -1.475 -1.560 -1.518 -2.035 -1.521 -1.535 -1.898 -1.755 -1.951 + -1.966 -1.374 -1.963 -1.864 -1.699 -1.753 -1.767 -1.869 -1.686 -1.981 +// +H OOBM770102 +D Short and medium range non-bonded energy per atom (Oobatake-Ooi, 1977) +R LIT:2004111b PMID:904331 +A Oobatake, M. and Ooi, T. +T An analysis of non-bonded energy of proteins +J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied + by the number of heavy atoms +C LEVM760102 0.869 LEVM760105 0.868 CHAM830106 0.858 + CHOC760101 0.824 FASG760101 0.821 FAUJ880103 0.801 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -1.404 -0.921 -1.178 -1.162 -1.365 -1.116 -1.163 -1.364 -1.215 -1.189 + -1.315 -1.074 -1.303 -1.135 -1.236 -1.297 -1.252 -1.030 -1.030 -1.254 +// +H OOBM770103 +D Long range non-bonded energy per atom (Oobatake-Ooi, 1977) +R LIT:2004111b PMID:904331 +A Oobatake, M. and Ooi, T. +T An analysis of non-bonded energy of proteins +J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied + by the number of heavy atoms +C MIYS990105 0.936 VINM940101 0.936 MIYS990104 0.931 + MIYS990103 0.908 GUYH850103 0.906 GUYH850102 0.904 + MEIH800101 0.897 GRAR740102 0.896 PARJ860101 0.891 + VINM940102 0.891 MIYS990102 0.891 MIYS990101 0.887 + FASG890101 0.869 KRIW790101 0.865 PARS000101 0.864 + MEIH800102 0.859 WOLS870101 0.852 FUKS010104 0.849 + VINM940103 0.845 WOEC730101 0.835 RACS770101 0.835 + HOPT810101 0.833 CORJ870108 0.829 RACS770102 0.828 + PUNT030102 0.828 KRIW790102 0.824 RACS770103 0.823 + KARP850102 0.820 MUNV940103 0.805 LEVM760101 0.805 + PTIO830102 -0.801 LIFS790103 -0.807 BAEK050101 -0.810 + KANM800102 -0.812 WIMW960101 -0.814 CORJ870104 -0.814 + CIDH920101 -0.818 PONP800107 -0.819 CHOP780202 -0.820 + QIAN880120 -0.824 CORJ870106 -0.826 ROSM880105 -0.828 + NOZY710101 -0.828 MEEJ810102 -0.831 CORJ870102 -0.832 + CORJ870105 -0.833 SWER830101 -0.833 NADH010102 -0.838 + GUOD860101 -0.838 CORJ870103 -0.839 PONP800101 -0.848 + BASU050101 -0.850 CORJ870107 -0.851 PLIV810101 -0.852 + PONP800102 -0.854 LIFS790101 -0.855 MANP780101 -0.859 + MEEJ810101 -0.861 NADH010103 -0.861 ZHOH040101 -0.862 + NADH010104 -0.863 CIDH920103 -0.863 PONP800103 -0.865 + MEIH800103 -0.866 BASU050103 -0.866 CIDH920102 -0.877 + RADA880108 -0.878 BASU050102 -0.893 NISK800101 -0.894 + PONP800108 -0.896 FAUJ830101 -0.899 CIDH920105 -0.904 + WERD780101 -0.906 CORJ870101 -0.907 ZHOH040103 -0.907 + ROBB790101 -0.909 MIYS850101 -0.910 CIDH920104 -0.912 + PONP930101 -0.914 CASG920101 -0.914 ROSG850102 -0.916 + BIOV880101 -0.920 BIOV880102 -0.925 NISK860101 -0.949 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.491 -0.554 -0.382 -0.356 -0.670 -0.405 -0.371 -0.534 -0.540 -0.762 + -0.650 -0.300 -0.659 -0.729 -0.463 -0.455 -0.515 -0.839 -0.656 -0.728 +// +H OOBM770104 +D Average non-bonded energy per residue (Oobatake-Ooi, 1977) +R LIT:2004111b PMID:904331 +A Oobatake, M. and Ooi, T. +T An analysis of non-bonded energy of proteins +J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied + by the number of heavy atoms +C OOBM770105 0.980 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -9.475 -16.225 -12.480 -12.144 -12.210 -13.689 -13.815 -7.592 -17.550 -15.608 + -15.728 -12.366 -15.704 -20.504 -11.893 -10.518 -12.369 -26.166 -20.232 -13.867 +// +H OOBM770105 +D Short and medium range non-bonded energy per residue (Oobatake-Ooi, 1977) +R LIT:2004111b PMID:904331 +A Oobatake, M. and Ooi, T. +T An analysis of non-bonded energy of proteins +J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied + by the number of heavy atoms +C OOBM770104 0.980 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -7.020 -10.131 -9.424 -9.296 -8.190 -10.044 -10.467 -5.456 -12.150 -9.512 + -10.520 -9.666 -10.424 -12.485 -8.652 -7.782 -8.764 -14.420 -12.360 -8.778 +// +H OOBM850101 +D Optimized beta-structure-coil equilibrium constant (Oobatake et al., 1985) +R LIT:1207075b +A Oobatake, M., Kubota, Y. and Ooi, T. +T Optimization of amino acid parameters for correspondence of sequence to + tertiary structures of proteuins +J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) +C QIAN880119 0.825 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.01 0.84 0.03 -2.05 1.98 1.02 0.93 0.12 -0.14 3.70 + 2.73 2.55 1.75 2.68 0.41 1.47 2.39 2.49 2.23 3.50 +// +H OOBM850102 +D Optimized propensity to form reverse turn (Oobatake et al., 1985) +R LIT:1207075b +A Oobatake, M., Kubota, Y. and Ooi, T. +T Optimization of amino acid parameters for correspondence of sequence to + tertiary structures of proteuins +J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) +C ZASB820101 -0.853 GARJ730101 -0.877 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.34 0.95 2.49 3.32 1.07 1.49 2.20 2.07 1.27 0.66 + 0.54 0.61 0.70 0.80 2.12 0.94 1.09 -4.65 -0.17 1.32 +// +H OOBM850103 +D Optimized transfer energy parameter (Oobatake et al., 1985) +R LIT:1207075b +A Oobatake, M., Kubota, Y. and Ooi, T. +T Optimization of amino acid parameters for correspondence of sequence to + tertiary structures of proteuins +J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.46 -1.54 1.31 -0.33 0.20 -1.12 0.48 0.64 -1.31 3.28 + 0.43 -1.71 0.15 0.52 -0.58 -0.83 -1.52 1.25 -2.21 0.54 +// +H OOBM850104 +D Optimized average non-bonded energy per atom (Oobatake et al., 1985) +R LIT:1207075b +A Oobatake, M., Kubota, Y. and Ooi, T. +T Optimization of amino acid parameters for correspondence of sequence to + tertiary structures of proteuins +J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -2.49 2.55 2.27 8.86 -3.13 1.79 4.04 -0.56 4.22 -10.87 + -7.16 -9.97 -4.96 -6.64 5.19 -1.60 -4.75 -17.84 9.25 -3.97 +// +H OOBM850105 +D Optimized side chain interaction parameter (Oobatake et al., 1985) +R LIT:1207075b +A Oobatake, M., Kubota, Y. and Ooi, T. +T Optimization of amino acid parameters for correspondence of sequence to + tertiary structures of proteuins +J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) +C QIAN880127 -0.813 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 4.55 5.97 5.56 2.85 -0.78 4.15 5.16 9.14 4.48 2.10 + 3.24 10.68 2.18 4.37 5.14 6.78 8.60 1.97 2.40 3.81 +// +H PALJ810101 +D Normalized frequency of alpha-helix from LG (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C LEVM780104 0.988 NAGK730101 0.953 GEIM800101 0.951 + LEVM780101 0.943 PRAM900102 0.943 KANM800101 0.928 + TANS770101 0.918 ROBB760101 0.914 CRAJ730101 0.891 + PALJ810102 0.889 MAXF760101 0.889 ISOY800101 0.882 + CHOP780201 0.881 RACS820108 0.872 BURA740101 0.850 + GEIM800104 0.841 KANM800103 0.836 NAGK730103 -0.808 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.30 0.93 0.90 1.02 0.92 1.04 1.43 0.63 1.33 0.87 + 1.30 1.23 1.32 1.09 0.63 0.78 0.80 1.03 0.71 0.95 +// +H PALJ810102 +D Normalized frequency of alpha-helix from CF (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C CHOP780201 0.981 ISOY800101 0.965 KANM800101 0.962 + MAXF760101 0.959 ROBB760101 0.946 TANS770101 0.923 + KANM800103 0.916 GEIM800101 0.910 LEVM780104 0.906 + PRAM900102 0.902 LEVM780101 0.902 BURA740101 0.900 + PALJ810101 0.889 AURR980112 0.888 GEIM800104 0.886 + RACS820108 0.881 AURR980109 0.877 NAGK730101 0.876 + CRAJ730101 0.872 AURR980108 0.871 QIAN880106 0.871 + PALJ810109 0.864 QIAN880107 0.856 AURR980114 0.848 + AURR980111 0.830 AURR980115 0.827 AURR980110 0.812 + BEGF750101 0.811 CHAM830101 -0.808 CRAJ730103 -0.809 + MUNV940101 -0.815 NAGK730103 -0.818 MUNV940102 -0.824 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.32 1.04 0.74 0.97 0.70 1.25 1.48 0.59 1.06 1.01 + 1.22 1.13 1.47 1.10 0.57 0.77 0.86 1.02 0.72 1.05 +// +H PALJ810103 +D Normalized frequency of beta-sheet from LG (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C LEVM780105 0.980 GEIM800105 0.945 CHOP780202 0.937 + KANM800102 0.932 LIFS790101 0.912 PALJ810104 0.907 + GEIM800107 0.890 ROBB760106 0.886 QIAN880120 0.886 + LIFS790103 0.877 QIAN880121 0.875 ROBB760105 0.869 + PTIO830102 0.867 QIAN880119 0.861 PRAM900103 0.846 + LEVM780102 0.846 QIAN880118 0.845 PALJ810112 0.841 + TANS770103 0.824 KANM800104 0.823 ISOY800102 0.807 + MUNV940103 -0.857 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.81 1.03 0.81 0.71 1.12 1.03 0.59 0.94 0.85 1.47 + 1.03 0.77 0.96 1.13 0.75 1.02 1.19 1.24 1.35 1.44 +// +H PALJ810104 +D Normalized frequency of beta-sheet from CF (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C CHOP780202 0.970 KANM800102 0.948 PTIO830102 0.937 + LIFS790101 0.929 GEIM800107 0.928 LEVM780105 0.921 + QIAN880121 0.910 PALJ810103 0.907 ROBB760106 0.894 + QIAN880120 0.886 BASU050103 0.882 BASU050101 0.873 + LEVM780102 0.868 PRAM900103 0.868 NAGK730102 0.867 + LIFS790103 0.860 PONP930101 0.857 GEIM800105 0.856 + KANM800104 0.851 CHOP780209 0.849 PALJ810112 0.849 + ROBB760105 0.835 VENT840101 0.831 BASU050102 0.826 + QIAN880119 0.822 AVBF000101 0.818 CRAJ730102 0.817 + SWER830101 0.809 CORJ870102 0.809 NISK860101 0.809 + MANP780101 0.805 BEGF750102 0.801 VINM940101 -0.801 + MIYS990104 -0.810 MIYS990103 -0.811 MUNV940103 -0.888 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.90 0.75 0.82 0.75 1.12 0.95 0.44 0.83 0.86 1.59 + 1.24 0.75 0.94 1.41 0.46 0.70 1.20 1.28 1.45 1.73 +// +H PALJ810105 +D Normalized frequency of turn from LG (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C ISOY800103 0.928 LEVM780103 0.909 PRAM900104 0.906 + LEVM780106 0.902 PALJ810116 0.891 CHOP780216 0.881 + CHOP780203 0.878 GEIM800108 0.873 CHOP780101 0.868 + TANS770110 0.860 GEIM800111 0.855 QIAN880133 0.843 + QIAN880132 0.830 CHAM830101 0.826 PALJ810106 0.809 + NAGK730103 0.804 CHOP780210 0.803 AVBF000102 -0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.84 0.91 1.48 1.28 0.69 1. 0.78 1.76 0.53 0.55 + 0.49 0.95 0.52 0.88 1.47 1.29 1.05 0.88 1.28 0.51 +// +H PALJ810106 +D Normalized frequency of turn from CF (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C CHOP780101 0.977 CHAM830101 0.939 TANS770110 0.925 + CHOP780203 0.907 CHOP780210 0.905 CHOP780216 0.904 + ROBB760113 0.895 CRAJ730103 0.884 ROBB760108 0.882 + ROBB760110 0.864 GEIM800108 0.862 QIAN880133 0.860 + BEGF750103 0.859 QIAN880132 0.859 LEVM780106 0.850 + LEVM780103 0.848 GEIM800111 0.844 PRAM900104 0.844 + QIAN880131 0.809 PALJ810105 0.809 ISOY800103 0.807 + CHOP780212 0.801 QIAN880107 -0.821 SUEM840101 -0.832 + KANM800103 -0.840 AURR980114 -0.842 AURR980109 -0.845 + BEGF750101 -0.859 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.65 0.93 1.45 1.47 1.43 0.94 0.75 1.53 0.96 0.57 + 0.56 0.95 0.71 0.72 1.51 1.46 0.96 0.90 1.12 0.55 +// +H PALJ810107 +D Normalized frequency of alpha-helix in all-alpha class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C GEIM800102 0.919 GEIM800109 -0.909 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.08 0.93 1.05 0.86 1.22 0.95 1.09 0.85 1.02 0.98 + 1.04 1.01 1.11 0.96 0.91 0.95 1.15 1.17 0.80 1.03 +// +H PALJ810108 +D Normalized frequency of alpha-helix in alpha+beta class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.34 0.91 0.83 1.06 1.27 1.13 1.69 0.47 1.11 0.84 + 1.39 1.08 0.90 1.02 0.48 1.05 0.74 0.64 0.73 1.18 +// +H PALJ810109 +D Normalized frequency of alpha-helix in alpha/beta class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C GEIM800104 0.937 PRAM900102 0.898 LEVM780101 0.898 + MAXF760101 0.876 ISOY800101 0.874 PALJ810102 0.864 + KANM800101 0.849 LEVM780104 0.819 AURR980112 0.817 + GEIM800101 0.816 CHOP780201 0.814 CRAJ730101 0.811 + ROBB760101 0.805 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.15 1.06 0.87 1. 1.03 1.43 1.37 0.64 0.95 0.99 + 1.22 1.20 1.45 0.92 0.72 0.84 0.97 1.11 0.72 0.82 +// +H PALJ810110 +D Normalized frequency of beta-sheet in all-beta class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C GEIM800106 0.851 ROBB760106 0.836 KANM800102 0.836 + BEGF750102 0.834 GEIM800107 0.826 QIAN880120 0.824 + QIAN880119 0.824 LIFS790101 0.817 AVBF000101 0.816 + CHOP780202 0.808 ROBB760105 0.804 GEIM800110 -0.840 + MUNV940103 -0.845 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.89 1.06 0.67 0.71 1.04 1.06 0.72 0.87 1.04 1.14 + 1.02 1. 1.41 1.32 0.69 0.86 1.15 1.06 1.35 1.66 +// +H PALJ810111 +D Normalized frequency of beta-sheet in alpha+beta class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.82 0.99 1.27 0.98 0.71 1.01 0.54 0.94 1.26 1.67 + 0.94 0.73 1.30 1.56 0.69 0.65 0.98 1.25 1.26 1.22 +// +H PALJ810112 +D Normalized frequency of beta-sheet in alpha/beta class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C PRAM900103 0.913 LEVM780102 0.913 GEIM800107 0.905 + LEVM780105 0.870 KANM800102 0.869 PALJ810104 0.849 + LIFS790101 0.845 PALJ810103 0.841 GEIM800105 0.830 + CHOP780202 0.815 KANM800104 0.813 QIAN880121 0.812 + PTIO830102 0.811 MUNV940103 -0.830 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.98 1.03 0.66 0.74 1.01 0.63 0.59 0.90 1.17 1.38 + 1.05 0.83 0.82 1.23 0.73 0.98 1.20 1.26 1.23 1.62 +// +H PALJ810113 +D Normalized frequency of turn in all-alpha class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. + (Arg Cys Leu Trp missing) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.69 0. 1.52 2.42 0. 1.44 0.63 2.64 0.22 0.43 + 0. 1.18 0.88 2.20 1.34 1.43 0.28 0. 1.53 0.14 +// +H PALJ810114 +D Normalized frequency of turn in all-beta class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. + (Met missing) +C ISOY800103 0.809 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.87 1.30 1.36 1.24 0.83 1.06 0.91 1.69 0.91 0.27 + 0.67 0.66 0. 0.47 1.54 1.08 1.12 1.24 0.54 0.69 +// +H PALJ810115 +D Normalized frequency of turn in alpha+beta class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C ROBB760112 0.885 QIAN880132 0.804 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.91 0.77 1.32 0.90 0.50 1.06 0.53 1.61 1.08 0.36 + 0.77 1.27 0.76 0.37 1.62 1.34 0.87 1.10 1.24 0.52 +// +H PALJ810116 +D Normalized frequency of turn in alpha/beta class (Palau et al., 1981) +R LIT:0805095 PMID:7118409 +A Palau, J., Argos, P. and Puigdomenech, P. +T Protein secondary structure +J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples + formed by 44 proteins. CF :a set of protein samples formed by 33 proteins. +C PALJ810105 0.891 ISOY800103 0.814 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.92 0.90 1.57 1.22 0.62 0.66 0.92 1.61 0.39 0.79 + 0.50 0.86 0.50 0.96 1.30 1.40 1.11 0.57 1.78 0.50 +// +H PARJ860101 +D HPLC parameter (Parker et al., 1986) +R LIT:1211071 PMID:2430611 +A Parker, J.M.R., Guo, D. and Hodges, R.S. +T New hydrophilicity scale derived from high-performance liquid chromatography + peptide retention data: Correlation of predicted surface residues with + antigencity and x-ray-derived accessible sites +J Biochemistry 25, 5425-5432 (1986) +C WOLS870101 0.964 MIYS990101 0.944 MIYS990102 0.942 + BULH740101 0.909 MEIH800101 0.905 GUYH850103 0.897 + GRAR740102 0.891 OOBM770103 0.891 MIYS990105 0.878 + MIYS990104 0.877 RACS770101 0.871 PUNT030102 0.867 + MIYS990103 0.859 PUNT030101 0.845 VINM940101 0.837 + GUYH850102 0.836 RACS770102 0.834 VINM940102 0.833 + MEIH800102 0.831 CORJ870108 0.831 FASG890101 0.825 + WOEC730101 0.821 HOPT810101 0.819 PARS000101 0.812 + KIDA850101 0.809 LEVM760101 0.806 ROSM880101 0.803 + ROSM880102 0.801 WIMW960101 -0.804 MEEJ800101 -0.806 + CORJ870103 -0.807 MEIH800103 -0.808 NAKH900110 -0.808 + CORJ870106 -0.820 CORJ870104 -0.823 ROSG850102 -0.823 + SIMZ760101 -0.825 GOLD730101 -0.827 LEVM760106 -0.832 + JOND750101 -0.834 ARGP820101 -0.835 CORJ870105 -0.837 + CORJ870107 -0.838 MANP780101 -0.841 PONP930101 -0.846 + VENT840101 -0.846 BROC820101 -0.849 ZHOH040102 -0.854 + RADA880108 -0.865 PONP800107 -0.868 WERD780101 -0.869 + TAKK010101 -0.870 BLAS910101 -0.870 CIDH920101 -0.871 + ROSM880105 -0.871 BASU050103 -0.874 BIOV880102 -0.875 + EISD860101 -0.876 RADA880102 -0.883 ZIMJ680105 -0.886 + BIOV880101 -0.889 CORJ870102 -0.892 SWER830101 -0.893 + ROBB790101 -0.893 ROSM880104 -0.896 ZHOH040103 -0.897 + MEEJ810102 -0.897 BASU050101 -0.897 NOZY710101 -0.900 + MEEJ800102 -0.902 FAUJ830101 -0.907 BASU050102 -0.908 + ZHOH040101 -0.912 CIDH920104 -0.913 NISK860101 -0.916 + CIDH920103 -0.916 MEEJ810101 -0.920 GUOD860101 -0.925 + MIYS850101 -0.929 CIDH920102 -0.930 CIDH920105 -0.948 + PLIV810101 -0.958 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.1 4.2 7.0 10.0 1.4 6.0 7.8 5.7 2.1 -8.0 + -9.2 5.7 -4.2 -9.2 2.1 6.5 5.2 -10.0 -1.9 -3.7 +// +H PLIV810101 +D Partition coefficient (Pliska et al., 1981) +R LIT:0712223 +A Pliska, V., Schmidt, M. and Fauchere, J.L. +T Partition coefficients of amino acids and hydrophobic parameters pi of their + side-chains as measured by thin-layer chromatography +J J. Chromatogr. 216, 79-92 (1981) (Arg 0.25) +C MIYS850101 0.944 GUOD860101 0.943 FAUJ830101 0.931 + MEEJ810101 0.914 CIDH920105 0.914 RADA880108 0.906 + EISD860101 0.904 CIDH920103 0.899 BIOV880101 0.899 + MEEJ810102 0.898 CIDH920104 0.893 NISK860101 0.892 + ZHOH040103 0.889 BASU050103 0.880 BASU050101 0.879 + CIDH920102 0.877 BASU050102 0.876 SWER830101 0.875 + ZIMJ680105 0.875 ROBB790101 0.875 CORJ870102 0.873 + BLAS910101 0.871 MEEJ800102 0.867 ROSM880104 0.866 + PONP800107 0.866 ZHOH040101 0.864 ROSM880105 0.862 + BIOV880102 0.858 COWR900101 0.857 MANP780101 0.856 + EISD860103 0.852 RADA880102 0.845 CIDH920101 0.843 + WERD780101 0.841 ROSG850102 0.841 NOZY710101 0.839 + LEVM760106 0.830 CORJ870107 0.829 CORJ870105 0.827 + TAKK010101 0.822 CORJ870104 0.821 CORJ870106 0.820 + ARGP820101 0.820 PONP930101 0.819 JOND750101 0.819 + MEIH800103 0.811 ZHOH040102 0.809 PONP800101 0.806 + NADH010104 0.806 SIMZ760101 0.805 NADH010103 0.804 + PONP800103 0.802 LEVM760101 -0.801 GUYH850102 -0.802 + FUKS010103 -0.805 VINM940102 -0.808 ROSM880101 -0.834 + GUYH850101 -0.836 CORJ870108 -0.838 KIDA850101 -0.841 + MEIH800102 -0.849 OOBM770103 -0.852 FASG890101 -0.858 + PUNT030102 -0.858 RACS770102 -0.859 PUNT030101 -0.860 + MIYS990103 -0.861 ROSM880102 -0.864 RACS770101 -0.868 + MIYS990104 -0.869 MIYS990105 -0.869 GUYH850103 -0.881 + GRAR740102 -0.888 MEIH800101 -0.896 BULH740101 -0.912 + MIYS990102 -0.942 MIYS990101 -0.944 PARJ860101 -0.958 + WOLS870101 -0.963 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -2.89 -3.30 -3.41 -3.38 -2.49 -3.15 -2.94 -3.25 -2.84 -1.72 + -1.61 -3.31 -1.84 -1.63 -2.50 -3.30 -2.91 -1.75 -2.42 -2.08 +// +H PONP800101 +D Surrounding hydrophobicity in folded form (Ponnuswamy et al., 1980) +R LIT:0608056 PMID:7397216 +A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. +T Hydrophobic packing and spatial arrangement of amino acid residues in + globular proteins +J Biochim. Biophys. Acta 623, 301-316 (1980) +C PONP800102 0.990 MANP780101 0.963 NISK800101 0.960 + PONP800103 0.957 PONP930101 0.945 CORJ870101 0.939 + PONP800108 0.938 ROSG850102 0.938 RADA880108 0.934 + NISK860101 0.930 CORJ870107 0.923 BIOV880101 0.918 + CORJ870103 0.917 BASU050103 0.915 CORJ870104 0.913 + NADH010103 0.894 MIYS850101 0.892 NADH010104 0.892 + CIDH920104 0.888 CORJ870106 0.887 BASU050101 0.882 + WERD780101 0.880 CIDH920103 0.876 NADH010102 0.875 + CASG920101 0.874 PONP800106 0.871 MEIH800103 0.869 + CORJ870105 0.867 JANJ790101 0.866 BIOV880102 0.860 + DESM900102 0.858 JURD980101 0.858 CIDH920105 0.856 + NADH010105 0.853 KYTJ820101 0.851 JANJ780102 0.851 + BASU050102 0.848 DESM900101 0.847 ZHOH040103 0.847 + CHOC760103 0.830 ROBB760106 0.829 KANM800102 0.829 + NADH010101 0.826 ROBB760105 0.823 KANM800104 0.823 + LIFS790101 0.823 FAUJ830101 0.822 ROBB790101 0.822 + PTIO830102 0.819 QIAN880121 0.815 BAEK050101 0.812 + PLIV810101 0.806 CIDH920101 0.805 LIFS790102 0.804 + QIAN880122 0.801 PUNT030101 -0.800 FUKS010103 -0.801 + KRIW790102 -0.804 VINM940103 -0.813 MUNV940103 -0.819 + GUYH850103 -0.822 PUNT030102 -0.827 OOBM770101 -0.835 + VINM940102 -0.845 OOBM770103 -0.848 GRAR740102 -0.849 + KRIW710101 -0.850 RACS770101 -0.863 RACS770102 -0.870 + GUYH850102 -0.873 MEIH800102 -0.877 GUYH850101 -0.877 + VINM940101 -0.878 MIYS990101 -0.883 MIYS990102 -0.886 + KRIW790101 -0.888 MEIH800101 -0.888 KARP850102 -0.889 + MIYS990105 -0.918 MIYS990104 -0.924 CORJ870108 -0.928 + FASG890101 -0.932 MIYS990103 -0.940 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 12.28 11.49 11.00 10.97 14.93 11.28 11.19 12.01 12.84 14.77 + 14.10 10.80 14.33 13.43 11.19 11.26 11.65 12.95 13.29 15.07 +// +H PONP800102 +D Average gain in surrounding hydrophobicity (Ponnuswamy et al., 1980) +R LIT:0608056 PMID:7397216 +A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. +T Hydrophobic packing and spatial arrangement of amino acid residues in + globular proteins +J Biochim. Biophys. Acta 623, 301-316 (1980) +C PONP800101 0.990 PONP800103 0.986 NISK800101 0.965 + CORJ870101 0.954 ROSG850102 0.949 PONP800108 0.948 + MANP780101 0.945 RADA880108 0.938 PONP930101 0.934 + BIOV880101 0.926 NISK860101 0.924 NADH010103 0.919 + NADH010104 0.917 CORJ870103 0.907 CORJ870107 0.905 + BASU050103 0.902 NADH010102 0.901 CORJ870104 0.901 + JANJ790101 0.897 MIYS850101 0.891 CASG920101 0.889 + MEIH800103 0.885 PONP800106 0.883 WERD780101 0.883 + DESM900102 0.880 CIDH920104 0.880 JANJ780102 0.875 + DESM900101 0.871 NADH010105 0.869 JURD980101 0.869 + BIOV880102 0.867 CORJ870106 0.864 BASU050101 0.864 + KYTJ820101 0.861 ZHOH040103 0.858 CIDH920103 0.849 + BASU050102 0.843 CORJ870105 0.841 FAUJ830101 0.841 + CHOC760103 0.836 NADH010101 0.832 CIDH920105 0.831 + ROBB760105 0.828 JANJ790102 0.822 ROBB760106 0.822 + BAEK050101 0.818 KANM800102 0.815 EISD860103 0.814 + KANM800104 0.813 ROBB790101 0.807 MUNV940103 -0.802 + GUYH850103 -0.808 RACS770103 -0.809 VINM940103 -0.820 + GUYH850104 -0.824 PUNT030102 -0.827 RACS770101 -0.827 + KRIW790102 -0.830 VINM940102 -0.842 OOBM770103 -0.854 + OOBM770101 -0.862 RACS770102 -0.864 MEIH800101 -0.870 + GRAR740102 -0.871 MIYS990101 -0.874 GUYH850102 -0.874 + MIYS990102 -0.877 GUYH850101 -0.883 MEIH800102 -0.883 + VINM940101 -0.883 KARP850102 -0.887 KRIW710101 -0.887 + CORJ870108 -0.911 KRIW790101 -0.915 MIYS990105 -0.927 + MIYS990104 -0.930 FASG890101 -0.944 MIYS990103 -0.946 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 7.62 6.81 6.17 6.18 10.93 6.67 6.38 7.31 7.85 9.99 + 9.37 5.72 9.83 8.99 6.64 6.93 7.08 8.41 8.53 10.38 +// +H PONP800103 +D Average gain ratio in surrounding hydrophobicity (Ponnuswamy et al., 1980) +R LIT:0608056 PMID:7397216 +A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. +T Hydrophobic packing and spatial arrangement of amino acid residues in + globular proteins +J Biochim. Biophys. Acta 623, 301-316 (1980) +C PONP800102 0.986 PONP800101 0.957 ROSG850102 0.947 + CORJ870101 0.944 NISK800101 0.941 RADA880108 0.934 + NADH010103 0.932 PONP800108 0.931 BIOV880101 0.926 + NADH010104 0.926 NADH010102 0.921 MANP780101 0.913 + NISK860101 0.910 PONP930101 0.909 MIYS850101 0.898 + DESM900102 0.896 MEIH800103 0.895 CORJ870103 0.889 + DESM900101 0.887 JANJ790101 0.886 CORJ870107 0.884 + CORJ870104 0.884 PONP800106 0.883 JANJ780102 0.882 + JURD980101 0.879 BIOV880102 0.879 BASU050103 0.879 + CASG920101 0.879 WERD780101 0.876 KYTJ820101 0.870 + NADH010105 0.866 FAUJ830101 0.863 CIDH920104 0.863 + ZHOH040103 0.861 JANJ790102 0.844 BASU050101 0.842 + EISD860103 0.842 CORJ870106 0.840 CHOC760103 0.837 + NADH010101 0.833 BASU050102 0.828 ROBB760105 0.823 + CIDH920103 0.823 CORJ870105 0.821 ROBB760106 0.812 + CIDH920105 0.807 NADH010106 0.803 KANM800102 0.803 + PLIV810101 0.802 OLSK800101 0.801 PUNT030101 -0.812 + JANJ780103 -0.812 VINM940103 -0.817 RACS770103 -0.819 + VINM940102 -0.820 WOEC730101 -0.823 PUNT030102 -0.834 + GUYH850104 -0.845 KRIW790102 -0.853 GUYH850102 -0.856 + MEIH800101 -0.856 RACS770102 -0.860 OOBM770103 -0.865 + KARP850102 -0.870 MIYS990101 -0.871 MIYS990102 -0.875 + VINM940101 -0.878 OOBM770101 -0.880 GUYH850101 -0.887 + CORJ870108 -0.889 KRIW710101 -0.890 MEIH800102 -0.891 + GRAR740102 -0.897 MIYS990105 -0.928 MIYS990104 -0.929 + KRIW790101 -0.930 FASG890101 -0.936 MIYS990103 -0.943 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.63 2.45 2.27 2.29 3.36 2.45 2.31 2.55 2.57 3.08 + 2.98 2.12 3.18 3.02 2.46 2.60 2.55 2.85 2.79 3.21 +// +H PONP800104 +D Surrounding hydrophobicity in alpha-helix (Ponnuswamy et al., 1980) +R LIT:0608056 PMID:7397216 +A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. +T Hydrophobic packing and spatial arrangement of amino acid residues in + globular proteins +J Biochim. Biophys. Acta 623, 301-316 (1980) +C CHOC760104 0.844 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 13.65 11.28 12.24 10.98 14.49 11.30 12.55 15.36 11.59 14.63 + 14.01 11.96 13.40 14.08 11.51 11.26 13.00 12.06 12.64 12.88 +// +H PONP800105 +D Surrounding hydrophobicity in beta-sheet (Ponnuswamy et al., 1980) +R LIT:0608056 PMID:7397216 +A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. +T Hydrophobic packing and spatial arrangement of amino acid residues in + globular proteins +J Biochim. Biophys. Acta 623, 301-316 (1980) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 14.60 13.24 11.79 13.78 15.90 12.02 13.59 14.18 15.35 14.10 + 16.49 13.28 16.23 14.18 14.10 13.36 14.50 13.90 14.76 16.30 +// +H PONP800106 +D Surrounding hydrophobicity in turn (Ponnuswamy et al., 1980) +R LIT:0608056 PMID:7397216 +A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. +T Hydrophobic packing and spatial arrangement of amino acid residues in + globular proteins +J Biochim. Biophys. Acta 623, 301-316 (1980) +C PONP800102 0.883 PONP800103 0.883 PONP800101 0.871 + CORJ870104 0.842 RADA880108 0.835 CORJ870107 0.834 + CORJ870103 0.821 MANP780101 0.813 MIYS850101 0.812 + CORJ870106 0.807 ROSG850102 0.807 MIYS990103 -0.807 + KARP850102 -0.820 FASG890101 -0.823 GUYH850101 -0.826 + KRIW710101 -0.841 CORJ870108 -0.859 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 10.67 11.05 10.85 10.21 14.15 11.71 11.71 10.95 12.07 12.95 + 13.07 9.93 15.00 13.27 10.62 11.18 10.53 11.41 11.52 13.86 +// +H PONP800107 +D Accessibility reduction ratio (Ponnuswamy et al., 1980) +R LIT:0608056 PMID:7397216 +A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. +T Hydrophobic packing and spatial arrangement of amino acid residues in + globular proteins +J Biochim. Biophys. Acta 623, 301-316 (1980) +C MIYS850101 0.884 MANP780101 0.871 PLIV810101 0.866 + GUOD860101 0.854 PONP930101 0.851 LIFS790102 0.849 + NISK860101 0.847 PTIO830102 0.837 CIDH920103 0.833 + CIDH920104 0.832 BASU050101 0.825 CIDH920105 0.818 + BIOV880101 0.816 BIOV880102 0.814 CHOC760103 0.813 + CORJ870105 0.812 BASU050103 0.812 VENT840101 0.805 + CORJ870107 0.805 BEGF750102 0.803 ROSG850102 0.803 + LIFS790101 0.801 RADA880108 0.800 CORJ870106 0.800 + PUNT030101 -0.804 CHOP780203 -0.818 OOBM770103 -0.819 + CHOP780210 -0.820 WOLS870101 -0.852 MEIH800102 -0.858 + PARJ860101 -0.868 MIYS990101 -0.877 RACS770102 -0.878 + MIYS990102 -0.879 RACS770101 -0.905 MEIH800101 -0.909 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 3.70 2.53 2.12 2.60 3.03 2.70 3.30 3.13 3.57 7.69 + 5.88 1.79 5.21 6.60 2.12 2.43 2.60 6.25 3.03 7.14 +// +H PONP800108 +D Average number of surrounding residues (Ponnuswamy et al., 1980) +R LIT:0608056 PMID:7397216 +A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. +T Hydrophobic packing and spatial arrangement of amino acid residues in + globular proteins +J Biochim. Biophys. Acta 623, 301-316 (1980) +C NISK800101 0.976 CORJ870101 0.969 PONP800102 0.948 + PONP930101 0.944 PONP800101 0.938 MANP780101 0.935 + PONP800103 0.931 BASU050103 0.921 NISK860101 0.921 + ROSG850102 0.919 CIDH920104 0.909 BIOV880101 0.907 + NADH010103 0.907 NADH010104 0.902 CASG920101 0.901 + BASU050101 0.894 NADH010102 0.890 RADA880108 0.889 + ZHOH040103 0.887 JANJ790101 0.881 BASU050102 0.880 + FAUJ830101 0.875 CORJ870103 0.873 JANJ780102 0.863 + MEIH800103 0.862 CORJ870104 0.861 CORJ870107 0.859 + JURD980101 0.856 BIOV880102 0.854 KYTJ820101 0.850 + KANM800102 0.849 KANM800104 0.849 MIYS850101 0.847 + NADH010105 0.845 WERD780101 0.843 CIDH920105 0.843 + CIDH920103 0.841 DESM900102 0.833 BAEK050101 0.833 + ROBB790101 0.831 LIFS790101 0.828 NADH010101 0.820 + ROBB760105 0.820 GEIM800107 0.817 CORJ870106 0.813 + QIAN880122 0.811 BLAS910101 0.810 EISD860103 0.809 + CHOC760103 0.809 CHOP780202 0.809 ROSM880105 0.808 + ROBB760106 0.808 QIAN880121 0.802 JANJ790102 0.802 + CORJ870105 0.801 GUYH850104 -0.807 MEIH800101 -0.825 + GUYH850103 -0.828 WOEC730101 -0.831 MEIH800102 -0.836 + OOBM770101 -0.851 CORJ870108 -0.853 PUNT030102 -0.855 + KRIW790101 -0.860 MIYS990101 -0.866 MIYS990102 -0.869 + VINM940102 -0.871 GUYH850102 -0.873 VINM940101 -0.891 + OOBM770103 -0.896 GRAR740102 -0.907 FASG890101 -0.913 + MIYS990104 -0.918 MIYS990103 -0.920 MIYS990105 -0.927 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.05 5.70 5.04 4.95 7.86 5.45 5.10 6.16 5.80 7.51 + 7.37 4.88 6.39 6.62 5.65 5.53 5.81 6.98 6.73 7.62 +// +H PRAM820101 +D Intercept in regression analysis (Prabhakaran-Ponnuswamy, 1982) +R LIT:2004113b +A Prabhakaran, M. and Ponnuswamy, P.K. +T Shape and surface features of globular proteins +J Macromolecules 15, 314-320 (1982) Regression analysis of solvent contact area + and spatial position +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.305 0.227 0.322 0.335 0.339 0.306 0.282 0.352 0.215 0.278 + 0.262 0.391 0.280 0.195 0.346 0.326 0.251 0.291 0.293 0.291 +// +H PRAM820102 +D Slope in regression analysis x 1.0E1 (Prabhakaran-Ponnuswamy, 1982) +R LIT:2004113b +A Prabhakaran, M. and Ponnuswamy, P.K. +T Shape and surface features of globular proteins +J Macromolecules 15, 314-320 (1982) Regression analysis of solvent contact area + and spatial position +C LEVM760104 0.812 PRAM820103 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.175 0.083 0.090 0.140 0.074 0.093 0.135 0.201 0.125 0.100 + 0.104 0.058 0.054 0.104 0.136 0.155 0.152 0.092 0.081 0.096 +// +H PRAM820103 +D Correlation coefficient in regression analysis (Prabhakaran-Ponnuswamy, 1982) +R LIT:2004113b +A Prabhakaran, M. and Ponnuswamy, P.K. +T Shape and surface features of globular proteins +J Macromolecules 15, 314-320 (1982) Regression analysis of solvent contact area + and spatial position +C PRAM820102 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.687 0.590 0.489 0.632 0.263 0.527 0.669 0.670 0.594 0.564 + 0.541 0.407 0.328 0.577 0.600 0.692 0.713 0.632 0.495 0.529 +// +H PRAM900101 +D Hydrophobicity (Prabhakaran, 1990) +R LIT:1614053b PMID:2390062 +A Prabhakaran, M. +T The distribution of physical, chemical and conformational properties in + signal and nascent peptides +J Biochem. J. 269, 691-696 (1990) Original references: Engelman, D.M., Steitz, + T.A. and Terwilliger, T.C. Annu. Rev. Biophys. Chem. 15, 321-353 (1986) +C ENGD860101 1.000 ROSM880101 0.917 VHEG790101 0.909 + KUHL950101 0.908 OOBM770101 0.907 JANJ780101 0.901 + ROSM880102 0.892 PUNT030101 0.889 JANJ780103 0.884 + HOPT810101 0.881 GUYH850104 0.881 LEVM760101 0.881 + WOEC730101 0.871 PUNT030102 0.869 GUYH850105 0.867 + KIDA850101 0.866 GRAR740102 0.855 ZIMJ680103 0.854 + CHOC760102 0.826 MONM990101 0.820 GUYH850101 0.820 + FAUJ880109 0.815 RADA880104 -0.803 OLSK800101 -0.806 + CHOC760103 -0.814 NADH010103 -0.815 WARP780101 -0.827 + EISD860103 -0.831 NADH010101 -0.843 KYTJ820101 -0.850 + FAUJ830101 -0.853 JANJ780102 -0.860 EISD860101 -0.862 + JURD980101 -0.862 BLAS910101 -0.864 RADA880107 -0.865 + NADH010102 -0.870 WOLR790101 -0.877 WOLR810101 -0.887 + JANJ790102 -0.890 DESM900102 -0.890 ROSM880105 -0.912 + RADA880101 -0.932 EISD840101 -0.936 JACR890101 -0.948 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -6.70 51.50 20.10 38.50 -8.40 17.20 34.30 -4.20 12.60 -13. + -11.70 36.80 -14.20 -15.50 0.80 -2.50 -5. -7.90 2.90 -10.90 +// +H PRAM900102 +D Relative frequency in alpha-helix (Prabhakaran, 1990) +R LIT:1614053b PMID:2390062 +A Prabhakaran, M. +T The distribution of physical, chemical and conformational properties in + signal and nascent peptides +J Biochem. J. 269, 691-696 (1990) Original reference of these three data: + Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman, + W.H., ed.), San Francisco P.235 (1983) +C LEVM780101 1.000 LEVM780104 0.964 PALJ810101 0.943 + KANM800101 0.942 ISOY800101 0.929 MAXF760101 0.924 + ROBB760101 0.916 GEIM800101 0.912 GEIM800104 0.907 + RACS820108 0.904 PALJ810102 0.902 PALJ810109 0.898 + NAGK730101 0.894 CRAJ730101 0.887 CHOP780201 0.873 + TANS770101 0.854 KANM800103 0.850 QIAN880107 0.829 + QIAN880106 0.827 BURA740101 0.805 NAGK730103 -0.809 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.29 0.96 0.90 1.04 1.11 1.27 1.44 0.56 1.22 0.97 + 1.30 1.23 1.47 1.07 0.52 0.82 0.82 0.99 0.72 0.91 +// +H PRAM900103 +D Relative frequency in beta-sheet (Prabhakaran, 1990) +R LIT:1614053b PMID:2390062 +A Prabhakaran, M. +T The distribution of physical, chemical and conformational properties in + signal and nascent peptides +J Biochem. J. 269, 691-696 (1990) Original reference of these three data: + Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman, + W.H., ed.), San Francisco P.235 (1983) +C LEVM780102 1.000 PALJ810112 0.913 LEVM780105 0.899 + PALJ810104 0.868 PTIO830102 0.865 LIFS790101 0.864 + QIAN880120 0.858 KANM800102 0.856 PALJ810103 0.846 + GEIM800107 0.842 BEGF750102 0.834 QIAN880119 0.834 + CHOP780202 0.833 AVBF000101 0.815 QIAN880121 0.805 + MUNV940103 -0.848 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.90 0.99 0.76 0.72 0.74 0.80 0.75 0.92 1.08 1.45 + 1.02 0.77 0.97 1.32 0.64 0.95 1.21 1.14 1.25 1.49 +// +H PRAM900104 +D Relative frequency in reverse-turn (Prabhakaran, 1990) +R LIT:1614053b PMID:2390062 +A Prabhakaran, M. +T The distribution of physical, chemical and conformational properties in + signal and nascent peptides +J Biochem. J. 269, 691-696 (1990) Original reference of these three data: + Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman, + W.H., ed.), San Francisco P.235 (1983) +C LEVM780103 1.000 LEVM780106 0.983 GEIM800111 0.954 + CHOP780216 0.951 QIAN880133 0.947 QIAN880134 0.934 + ISOY800103 0.934 QIAN880132 0.932 GEIM800108 0.931 + CHOP780203 0.928 CHAM830101 0.909 PALJ810105 0.906 + QIAN880135 0.903 CHOP780101 0.891 TANS770110 0.873 + CHOP780210 0.850 PALJ810106 0.844 RACS770101 0.809 + KANM800103 -0.814 AURR980109 -0.815 QIAN880108 -0.819 + QIAN880107 -0.829 AVBF000102 -0.834 ROBB760103 -0.840 + FAUJ880102 -0.844 QIAN880109 -0.846 PTIO830101 -0.858 + SUEM840101 -0.865 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.78 0.88 1.28 1.41 0.80 0.97 1. 1.64 0.69 0.51 + 0.59 0.96 0.39 0.58 1.91 1.33 1.03 0.75 1.05 0.47 +// +H PTIO830101 +D Helix-coil equilibrium constant (Ptitsyn-Finkelstein, 1983) +R LIT:0904057 PMID:6673754 +A Ptitsyn, O.B. and Finkelstein, A.V. +T Theory of protein secondary structure and algorithm of its prediction +J Biopolymers 22, 15-25 (1983) Charged state for Arg, His, Lys, Asp, and Glu +C ROBB760103 0.903 QIAN880109 0.886 QIAN880108 0.884 + SUEM840101 0.877 BLAM930101 0.868 QIAN880111 0.857 + ONEK900101 0.847 QIAN880107 0.846 QIAN880110 0.835 + AURR980113 0.833 FAUJ880102 0.832 FINA770101 0.826 + AURR980109 0.820 ROBB760104 0.817 AURR980114 0.809 + MUNV940104 -0.807 QIAN880131 -0.826 ONEK900102 -0.830 + ISOY800104 -0.832 MUNV940105 -0.833 QIAN880132 -0.833 + CHOP780213 -0.835 GEIM800108 -0.840 CHAM830101 -0.841 + MUNV940102 -0.844 LEVM780106 -0.854 CHOP780216 -0.855 + PRAM900104 -0.858 LEVM780103 -0.860 QIAN880133 -0.864 + GEIM800111 -0.876 MUNV940101 -0.880 QIAN880135 -0.899 + QIAN880134 -0.920 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.10 0.95 0.80 0.65 0.95 1.00 1.00 0.60 0.85 1.10 + 1.25 1.00 1.15 1.10 0.10 0.75 0.75 1.10 1.10 0.95 +// +H PTIO830102 +D Beta-coil equilibrium constant (Ptitsyn-Finkelstein, 1983) +R LIT:0904057 PMID:6673754 +A Ptitsyn, O.B. and Finkelstein, A.V. +T Theory of protein secondary structure and algorithm of its prediction +J Biopolymers 22, 15-25 (1983) Charged state for Arg, His, Lys, Asp, and Glu +C LIFS790101 0.941 PALJ810104 0.937 KANM800102 0.917 + CHOP780202 0.913 QIAN880120 0.908 BASU050101 0.903 + LEVM780105 0.894 BASU050103 0.888 ROBB760106 0.882 + QIAN880121 0.880 PONP930101 0.879 ROBB760105 0.878 + LIFS790102 0.874 PALJ810103 0.867 QIAN880119 0.865 + LEVM780102 0.865 PRAM900103 0.865 AVBF000101 0.861 + MANP780101 0.861 KANM800104 0.858 SWER830101 0.856 + CORJ870102 0.854 GEIM800107 0.850 BASU050102 0.848 + VENT840101 0.842 CIDH920104 0.842 PONP800107 0.837 + NISK860101 0.825 LIFS790103 0.822 CRAJ730102 0.820 + PONP800101 0.819 CHOP780209 0.814 ZHOH040103 0.813 + CIDH920105 0.813 NAGK730102 0.811 PALJ810112 0.811 + GEIM800105 0.810 CORJ870107 0.810 CORJ870106 0.809 + CIDH920103 0.807 BEGF750102 0.807 MIYS850101 0.807 + OOBM770103 -0.801 KRIW790101 -0.801 CORJ870108 -0.812 + MIYS990104 -0.818 MIYS990103 -0.820 MEIH800101 -0.828 + MIYS990101 -0.833 MIYS990102 -0.834 MUNV940103 -0.903 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.00 0.70 0.60 0.50 1.90 1.00 0.70 0.30 0.80 4.00 + 2.00 0.70 1.90 3.10 0.20 0.90 1.70 2.20 2.80 4.00 +// +H QIAN880101 +D Weights for alpha-helix at the window position of -6 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.12 0.04 -0.10 0.01 -0.25 -0.03 -0.02 -0.02 -0.06 -0.07 + 0.05 0.26 0.00 0.05 -0.19 -0.19 -0.04 -0.06 -0.14 -0.03 +// +H QIAN880102 +D Weights for alpha-helix at the window position of -5 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.26 -0.14 -0.03 0.15 -0.15 -0.13 0.21 -0.37 0.10 -0.03 + -0.02 0.12 0.00 0.12 -0.08 0.01 -0.34 -0.01 -0.29 0.02 +// +H QIAN880103 +D Weights for alpha-helix at the window position of -4 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.64 -0.10 0.09 0.33 0.03 -0.23 0.51 -0.09 -0.23 -0.22 + 0.41 -0.17 0.13 -0.03 -0.43 -0.10 -0.07 -0.02 -0.38 -0.01 +// +H QIAN880104 +D Weights for alpha-helix at the window position of -3 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880106 0.851 QIAN880105 0.824 AURR980108 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.29 -0.03 -0.04 0.11 -0.05 0.26 0.28 -0.67 -0.26 0.00 + 0.47 -0.19 0.27 0.24 -0.34 -0.17 -0.20 0.25 -0.30 -0.01 +// +H QIAN880105 +D Weights for alpha-helix at the window position of -2 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C ROBB760101 0.874 QIAN880106 0.846 CHOP780201 0.835 + AURR980113 0.833 BEGF750101 0.833 QIAN880107 0.829 + ISOY800101 0.828 KANM800101 0.827 QIAN880104 0.824 + RACS820108 0.820 KANM800103 0.820 ROBB760103 0.811 + MAXF760101 0.811 CHAM830101 -0.803 MUNV940102 -0.816 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.68 -0.22 -0.09 -0.02 -0.15 -0.15 0.44 -0.73 -0.14 -0.08 + 0.61 0.03 0.39 0.06 -0.76 -0.26 -0.10 0.20 -0.04 0.12 +// +H QIAN880106 +D Weights for alpha-helix at the window position of -1 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C ROBB760101 0.904 ISOY800101 0.903 QIAN880107 0.896 + KANM800103 0.889 MAXF760101 0.881 CHOP780201 0.874 + PALJ810102 0.871 RACS820108 0.866 AURR980109 0.862 + ROBB760103 0.854 KANM800101 0.854 QIAN880104 0.851 + QIAN880105 0.846 AURR980112 0.839 AURR980108 0.838 + AURR980113 0.835 RICJ880109 0.834 PRAM900102 0.827 + LEVM780101 0.827 TANS770101 0.819 FINA770101 0.810 + LEVM780104 0.804 AURR980110 0.804 AURR980114 0.803 + QIAN880132 -0.813 MUNV940101 -0.835 CHAM830101 -0.856 + MUNV940102 -0.867 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.34 0.22 -0.33 0.06 -0.18 0.01 0.20 -0.88 -0.09 -0.03 + 0.20 -0.11 0.43 0.15 -0.81 -0.35 -0.37 0.07 -0.31 0.13 +// +H QIAN880107 +D Weights for alpha-helix at the window position of 0 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C KANM800103 0.908 QIAN880106 0.896 AURR980109 0.893 + ROBB760103 0.889 ISOY800101 0.887 MAXF760101 0.885 + AURR980114 0.876 QIAN880108 0.872 ROBB760101 0.867 + QIAN880109 0.865 PALJ810102 0.856 KANM800101 0.854 + QIAN880110 0.853 PTIO830101 0.846 CHOP780201 0.843 + AURR980113 0.832 RACS820108 0.831 LEVM780101 0.829 + PRAM900102 0.829 QIAN880105 0.829 LEVM780104 0.822 + BEGF750101 0.815 AURR980110 0.815 FINA770101 0.814 + TANS770101 0.804 AURR980108 0.803 SUEM840101 0.803 + AURR980112 0.802 CHOP780216 -0.808 QIAN880133 -0.809 + CHOP780101 -0.809 LEVM780106 -0.813 PALJ810106 -0.821 + PRAM900104 -0.829 LEVM780103 -0.834 CRAJ730103 -0.840 + CHAM830101 -0.858 MUNV940101 -0.880 MUNV940102 -0.882 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.57 0.23 -0.36 -0.46 -0.15 0.15 0.26 -0.71 -0.05 0.00 + 0.48 0.16 0.41 0.03 -1.12 -0.47 -0.54 -0.10 -0.35 0.31 +// +H QIAN880108 +D Weights for alpha-helix at the window position of 1 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880109 0.951 ROBB760103 0.914 QIAN880110 0.901 + PTIO830101 0.884 ROBB760104 0.879 QIAN880107 0.872 + ONEK900101 0.866 BLAM930101 0.860 KANM800103 0.829 + RACS820108 0.820 QIAN880111 0.819 PRAM900104 -0.819 + LEVM780103 -0.820 QIAN880135 -0.836 MUNV940102 -0.839 + QIAN880136 -0.843 QIAN880134 -0.845 ISOY800104 -0.847 + ONEK900102 -0.860 MUNV940101 -0.864 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.33 0.10 -0.19 -0.44 -0.03 0.19 0.21 -0.46 0.27 -0.33 + 0.57 0.23 0.79 0.48 -1.86 -0.23 -0.33 0.15 -0.19 0.24 +// +H QIAN880109 +D Weights for alpha-helix at the window position of 2 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880110 0.953 QIAN880108 0.951 QIAN880111 0.912 + PTIO830101 0.886 ROBB760104 0.871 ROBB760103 0.868 + QIAN880107 0.865 BLAM930101 0.828 KANM800103 0.824 + QIAN880112 0.824 ONEK900101 0.824 AURR980114 0.810 + AURR980109 0.807 CHOP780205 0.806 ONEK900102 -0.800 + LEVM780106 -0.815 MUNV940101 -0.841 QIAN880134 -0.841 + PRAM900104 -0.846 LEVM780103 -0.848 QIAN880135 -0.884 + QIAN880136 -0.927 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.13 0.08 -0.07 -0.71 -0.09 0.12 0.13 -0.39 0.32 0.00 + 0.50 0.37 0.63 0.15 -1.40 -0.28 -0.21 0.02 -0.10 0.17 +// +H QIAN880110 +D Weights for alpha-helix at the window position of 3 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. 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Biol. 202, 865-884 (1988) +C QIAN880115 0.832 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.18 -0.13 0.28 0.05 -0.26 0.21 -0.06 0.23 0.24 -0.42 + -0.23 0.03 -0.42 -0.18 -0.13 0.41 0.33 -0.10 -0.10 -0.07 +// +H QIAN880115 +D Weights for beta-sheet at the window position of -5 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880114 0.832 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.01 0.02 0.41 -0.09 -0.27 0.01 0.09 0.13 0.22 -0.27 + -0.25 0.08 -0.57 -0.12 0.26 0.44 0.35 -0.15 0.15 -0.09 +// +H QIAN880116 +D Weights for beta-sheet at the window position of -4 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880126 0.823 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.19 0.03 0.02 -0.06 -0.29 0.02 -0.10 0.19 -0.16 -0.08 + -0.42 -0.09 -0.38 -0.32 0.05 0.25 0.22 -0.19 0.05 -0.15 +// +H QIAN880117 +D Weights for beta-sheet at the window position of -3 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.14 0.14 -0.27 -0.10 -0.64 -0.11 -0.39 0.46 -0.04 0.16 + -0.57 0.04 0.24 0.08 0.02 -0.12 0.00 -0.10 0.18 0.29 +// +H QIAN880118 +D Weights for beta-sheet at the window position of -2 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C PALJ810103 0.845 LEVM780105 0.819 QIAN880119 0.812 + GEIM800105 0.810 KANM800102 0.801 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.31 0.25 -0.53 -0.54 -0.06 0.07 -0.52 0.37 -0.32 0.57 + 0.09 -0.29 0.29 0.24 -0.31 0.11 0.03 0.15 0.29 0.48 +// +H QIAN880119 +D Weights for beta-sheet at the window position of -1 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880120 0.959 LIFS790101 0.929 LEVM780105 0.903 + ROBB760106 0.897 KANM800102 0.888 LIFS790103 0.877 + PTIO830102 0.865 QIAN880121 0.862 PALJ810103 0.861 + ROBB760105 0.859 AVBF000101 0.859 CHOP780202 0.855 + KANM800104 0.841 PONP930101 0.836 PRAM900103 0.834 + LEVM780102 0.834 GEIM800105 0.829 OOBM850101 0.825 + PALJ810110 0.824 PALJ810104 0.822 QIAN880118 0.812 + BEGF750102 0.811 CORJ870105 0.810 GEIM800107 0.807 + CHOP780208 0.807 BASU050101 0.805 CORJ870106 0.803 + LEVM780106 -0.810 GEIM800108 -0.810 CHOP780203 -0.814 + QIAN880131 -0.830 QIAN880133 -0.849 GEIM800110 -0.853 + QIAN880132 -0.858 MUNV940103 -0.927 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.10 0.19 -0.89 -0.89 0.13 -0.04 -0.34 -0.45 -0.34 0.95 + 0.32 -0.46 0.43 0.36 -0.91 -0.12 0.49 0.34 0.42 0.76 +// +H QIAN880120 +D Weights for beta-sheet at the window position of 0 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C LIFS790101 0.969 QIAN880119 0.959 LIFS790103 0.939 + QIAN880121 0.935 CHOP780202 0.915 LEVM780105 0.913 + PTIO830102 0.908 ROBB760106 0.908 KANM800102 0.896 + PALJ810103 0.886 PALJ810104 0.886 PONP930101 0.879 + AVBF000101 0.876 CORJ870106 0.866 ROBB760105 0.860 + PRAM900103 0.858 LEVM780102 0.858 CORJ870105 0.858 + BASU050101 0.856 GEIM800107 0.843 CORJ870107 0.840 + BASU050102 0.837 NISK860101 0.837 BEGF750102 0.829 + CORJ870102 0.825 SWER830101 0.825 GEIM800106 0.825 + PALJ810110 0.824 GEIM800105 0.822 BASU050103 0.811 + MANP780101 0.806 KANM800104 0.803 CORJ870101 0.802 + CHOP780208 0.800 CHOP780216 -0.800 QIAN880131 -0.801 + GEIM800108 -0.804 VINM940102 -0.813 GEIM800111 -0.816 + VINM940101 -0.823 OOBM770103 -0.824 MIYS990103 -0.829 + LEVM780106 -0.831 MIYS990104 -0.833 CORJ870108 -0.834 + QIAN880132 -0.839 QIAN880134 -0.842 PARS000101 -0.863 + QIAN880133 -0.863 GEIM800110 -0.898 MUNV940103 -0.959 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.25 -0.02 -0.77 -1.01 0.13 -0.12 -0.62 -0.72 -0.16 1.10 + 0.23 -0.59 0.32 0.48 -1.24 -0.31 0.17 0.45 0.77 0.69 +// +H QIAN880121 +D Weights for beta-sheet at the window position of 1 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880120 0.935 LIFS790101 0.930 CHOP780202 0.911 + PALJ810104 0.910 ROBB760106 0.907 KANM800102 0.900 + PONP930101 0.893 LIFS790103 0.882 PTIO830102 0.880 + LEVM780105 0.876 PALJ810103 0.875 GEIM800107 0.875 + QIAN880119 0.862 AVBF000101 0.855 CORJ870101 0.842 + QIAN880122 0.838 BAEK050101 0.836 ROBB760105 0.834 + NISK860101 0.829 KANM800104 0.829 BASU050103 0.828 + BASU050101 0.828 BASU050102 0.825 NISK800101 0.818 + PONP800101 0.815 PALJ810112 0.812 GEIM800105 0.811 + CHOP780209 0.809 CORJ870107 0.806 CORJ870106 0.806 + PRAM900103 0.805 LEVM780102 0.805 PONP800108 0.802 + MANP780101 0.802 QIAN880133 -0.802 KRIW790101 -0.803 + GEIM800110 -0.806 PARS000101 -0.809 VINM940101 -0.828 + MIYS990104 -0.832 QIAN880134 -0.838 MIYS990103 -0.838 + MUNV940103 -0.938 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.26 -0.09 -0.34 -0.55 0.47 -0.33 -0.75 -0.56 -0.04 0.94 + 0.25 -0.55 -0.05 0.20 -1.28 -0.28 0.08 0.22 0.53 0.67 +// +H QIAN880122 +D Weights for beta-sheet at the window position of 2 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880121 0.838 PONP930101 0.837 CORJ870101 0.826 + PONP800108 0.811 NADH010103 0.809 CORJ870103 0.808 + NISK800101 0.808 NADH010104 0.804 PONP800101 0.801 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.05 -0.11 -0.40 -0.11 0.36 -0.67 -0.35 0.14 0.02 0.47 + 0.32 -0.51 -0.10 0.20 -0.79 0.03 -0.15 0.09 0.34 0.58 +// +H QIAN880123 +D Weights for beta-sheet at the window position of 3 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.44 -0.13 0.05 -0.20 0.13 -0.58 -0.28 0.08 0.09 -0.04 + -0.12 -0.33 -0.21 -0.13 -0.48 0.27 0.47 -0.22 -0.11 0.06 +// +H QIAN880124 +D Weights for beta-sheet at the window position of 4 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.31 -0.10 0.06 0.13 -0.11 -0.47 -0.05 0.45 -0.06 -0.25 + -0.44 -0.44 -0.28 -0.04 -0.29 0.34 0.27 -0.08 0.06 0.11 +// +H QIAN880125 +D Weights for beta-sheet at the window position of 5 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.02 0.04 0.03 0.11 -0.02 -0.17 0.10 0.38 -0.09 -0.48 + -0.26 -0.39 -0.14 -0.03 -0.04 0.41 0.36 -0.01 -0.08 -0.18 +// +H QIAN880126 +D Weights for beta-sheet at the window position of 6 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880116 0.823 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.06 0.02 0.10 0.24 -0.19 -0.04 -0.04 0.17 0.19 -0.20 + -0.46 -0.43 -0.52 -0.33 0.37 0.43 0.50 -0.32 0.35 0.00 +// +H QIAN880127 +D Weights for coil at the window position of -6 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C OOBM850105 -0.813 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.05 0.06 0.00 0.15 0.30 -0.08 -0.02 -0.14 -0.07 0.26 + 0.04 -0.42 0.25 0.09 0.31 -0.11 -0.06 0.19 0.33 0.04 +// +H QIAN880128 +D Weights for coil at the window position of -5 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.19 0.17 -0.38 0.09 0.41 0.04 -0.20 0.28 -0.19 -0.06 + 0.34 -0.20 0.45 0.07 0.04 -0.23 -0.02 0.16 0.22 0.05 +// +H QIAN880129 +D Weights for coil at the window position of -4 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.43 0.06 0.00 -0.31 0.19 0.14 -0.41 -0.21 0.21 0.29 + -0.10 0.33 -0.01 0.25 0.28 -0.23 -0.26 0.15 0.09 -0.10 +// +H QIAN880130 +D Weights for coil at the window position of -3 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.19 -0.07 0.17 -0.27 0.42 -0.29 -0.22 0.17 0.17 -0.34 + -0.22 0.00 -0.53 -0.31 0.14 0.22 0.10 -0.15 -0.02 -0.33 +// +H QIAN880131 +D Weights for coil at the window position of -2 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C CHOP780216 0.873 TANS770110 0.873 QIAN880133 0.871 + CHOP780203 0.861 CHAM830101 0.860 GEIM800108 0.860 + GEIM800111 0.857 QIAN880132 0.847 QIAN880135 0.844 + QIAN880134 0.832 CHOP780210 0.826 CHOP780101 0.824 + PALJ810106 0.809 QIAN880120 -0.801 SUEM840101 -0.823 + PTIO830101 -0.826 QIAN880119 -0.830 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.25 0.12 0.61 0.60 0.18 0.09 -0.12 0.09 0.42 -0.54 + -0.55 0.14 -0.47 -0.29 0.89 0.24 0.16 -0.44 -0.19 -0.45 +// +H QIAN880132 +D Weights for coil at the window position of -1 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880133 0.957 LEVM780106 0.943 PRAM900104 0.932 + LEVM780103 0.931 CHOP780216 0.931 GEIM800111 0.929 + CHOP780203 0.928 CHAM830101 0.925 QIAN880134 0.909 + GEIM800108 0.906 TANS770110 0.903 CHOP780101 0.896 + ISOY800103 0.892 PALJ810106 0.859 CHOP780210 0.852 + QIAN880131 0.847 PALJ810105 0.830 QIAN880135 0.824 + PALJ810115 0.804 ROBB760112 0.800 AURR980109 -0.806 + LIFS790101 -0.806 AVBF000101 -0.809 QIAN880106 -0.813 + ROBB760103 -0.827 PTIO830101 -0.833 QIAN880120 -0.839 + AVBF000102 -0.849 FAUJ880102 -0.849 QIAN880119 -0.858 + SUEM840101 -0.880 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.27 -0.40 0.71 0.54 0.00 -0.08 -0.12 1.14 0.18 -0.74 + -0.54 0.45 -0.76 -0.47 1.40 0.40 -0.10 -0.46 -0.05 -0.86 +// +H QIAN880133 +D Weights for coil at the window position of 0 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C LEVM780106 0.971 QIAN880132 0.957 LEVM780103 0.948 + PRAM900104 0.947 GEIM800111 0.943 CHOP780216 0.939 + QIAN880134 0.938 GEIM800108 0.930 TANS770110 0.920 + CHOP780203 0.915 CHAM830101 0.913 ISOY800103 0.908 + QIAN880135 0.907 CHOP780101 0.897 QIAN880131 0.871 + PALJ810106 0.860 PALJ810105 0.843 MUNV940103 0.836 + GEIM800110 0.822 CHOP780210 0.820 ROBB760112 0.814 + QIAN880121 -0.802 ROBB760103 -0.807 AVBF000101 -0.807 + QIAN880107 -0.809 AVBF000102 -0.823 LIFS790101 -0.848 + QIAN880119 -0.849 FAUJ880102 -0.851 QIAN880120 -0.863 + PTIO830101 -0.864 SUEM840101 -0.879 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.42 -0.23 0.81 0.95 -0.18 -0.01 -0.09 1.24 0.05 -1.17 + -0.69 0.09 -0.86 -0.39 1.77 0.63 0.29 -0.37 -0.41 -1.32 +// +H QIAN880134 +D Weights for coil at the window position of 1 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880135 0.961 QIAN880133 0.938 LEVM780103 0.935 + PRAM900104 0.934 LEVM780106 0.932 GEIM800111 0.919 + QIAN880132 0.909 CHOP780216 0.900 MUNV940105 0.899 + MUNV940104 0.897 ISOY800104 0.893 GEIM800108 0.884 + CHOP780213 0.870 MUNV940103 0.858 GEIM800110 0.853 + CHAM830101 0.841 CHOP780203 0.838 TANS770104 0.837 + QIAN880131 0.832 ISOY800103 0.828 ROBB760104 -0.802 + LIFS790101 -0.804 AVBF000101 -0.822 BLAM930101 -0.836 + QIAN880121 -0.838 QIAN880109 -0.841 QIAN880120 -0.842 + QIAN880108 -0.845 FAUJ880102 -0.852 ROBB760103 -0.855 + PTIO830101 -0.920 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.24 -0.04 0.45 0.65 -0.38 0.01 0.07 0.85 -0.21 -0.65 + -0.80 0.17 -0.71 -0.61 2.27 0.33 0.13 -0.44 -0.49 -0.99 +// +H QIAN880135 +D Weights for coil at the window position of 2 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) (Gin !) +C QIAN880134 0.961 QIAN880133 0.907 LEVM780103 0.906 + PRAM900104 0.903 LEVM780106 0.902 GEIM800111 0.895 + CHOP780216 0.884 GEIM800108 0.877 CHOP780213 0.851 + QIAN880131 0.844 GEIM800110 0.842 QIAN880136 0.838 + ISOY800104 0.837 MUNV940105 0.829 QIAN880132 0.824 + MUNV940103 0.820 MUNV940104 0.819 CHAM830101 0.814 + CHOP780203 0.811 ROBB760103 -0.834 QIAN880108 -0.836 + QIAN880111 -0.878 QIAN880109 -0.884 PTIO830101 -0.899 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.14 0.21 0.35 0.66 -0.09 0.11 0.06 0.36 -0.31 -0.51 + -0.80 -0.14 -0.56 -0.25 1.59 0.32 0.21 -0.17 -0.35 -0.70 +// +H QIAN880136 +D Weights for coil at the window position of 3 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C QIAN880135 0.838 QIAN880112 -0.812 QIAN880108 -0.843 + QIAN880110 -0.890 QIAN880111 -0.900 QIAN880109 -0.927 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.01 -0.13 -0.11 0.78 -0.31 -0.13 0.09 0.14 -0.56 -0.09 + -0.81 -0.43 -0.49 -0.20 1.14 0.13 -0.02 -0.20 0.10 -0.11 +// +H QIAN880137 +D Weights for coil at the window position of 4 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.30 -0.09 -0.12 0.44 0.03 0.24 0.18 -0.12 -0.20 -0.07 + -0.18 0.06 -0.44 0.11 0.77 -0.09 -0.27 -0.09 -0.25 -0.06 +// +H QIAN880138 +D Weights for coil at the window position of 5 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.23 -0.20 0.06 0.34 0.19 0.47 0.28 0.14 -0.22 0.42 + -0.36 -0.15 -0.19 -0.02 0.78 -0.29 -0.30 -0.18 0.07 0.29 +// +H QIAN880139 +D Weights for coil at the window position of 6 (Qian-Sejnowski, 1988) +R LIT:1411084 PMID:3172241 +A Qian, N. and Sejnowski, T.J. +T Predicting the secondary structure of globular proteins using neural network + models +J J. Mol. Biol. 202, 865-884 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.08 -0.01 -0.06 0.04 0.37 0.48 0.36 -0.02 -0.45 0.09 + 0.24 -0.27 0.16 0.34 0.16 -0.35 -0.04 -0.06 -0.20 0.18 +// +H RACS770101 +D Average reduced distance for C-alpha (Rackovsky-Scheraga, 1977) +R LIT:2004126b PMID:271950 +A Rackovsky, S. and Scheraga, H.A. +T Hydrophobicity, hydrophilicity, and the radial and orientational + distributions of residues in native proteins +J Proc. Natl. Acad. Sci. USA 74, 5248-5251 (1977) +C MEIH800101 0.973 RACS770102 0.946 MIYS990102 0.921 + MIYS990101 0.920 MEIH800102 0.905 CORJ870108 0.891 + MIYS990103 0.887 MIYS990104 0.884 FASG890101 0.872 + PARJ860101 0.871 KARP850102 0.869 MIYS990105 0.866 + GUYH850102 0.859 GUYH850101 0.853 GUYH850103 0.844 + KARP850101 0.837 VINM940101 0.835 OOBM770103 0.835 + VINM940103 0.829 KRIW790101 0.828 CHOP780203 0.827 + PUNT030101 0.821 FUKS010103 0.819 KRIW790102 0.814 + PRAM900104 0.809 LEVM780103 0.808 PARS000101 0.804 + RACS770103 0.801 CORJ870102 -0.802 SWER830101 -0.803 + GUOD860101 -0.805 NISK800101 -0.805 NADH010103 -0.807 + CASG920101 -0.807 NADH010104 -0.813 CIDH920102 -0.825 + PONP800102 -0.827 ZHOH040103 -0.835 CIDH920101 -0.837 + ROBB790101 -0.839 BEGF750102 -0.840 MEIH800103 -0.845 + RICJ880111 -0.846 BASU050103 -0.848 BASU050101 -0.850 + BASU050102 -0.854 CORJ870104 -0.860 PONP800101 -0.863 + CIDH920104 -0.864 PLIV810101 -0.868 CORJ870103 -0.870 + BIOV880102 -0.875 CORJ870105 -0.876 MANP780101 -0.878 + CORJ870106 -0.879 ROSG850102 -0.880 CIDH920103 -0.881 + PONP930101 -0.886 RADA880108 -0.887 CIDH920105 -0.887 + BIOV880101 -0.893 CORJ870107 -0.898 PONP800107 -0.905 + WERD780101 -0.912 NISK860101 -0.923 MIYS850101 -0.940 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.934 0.962 0.986 0.994 0.900 1.047 0.986 1.015 0.882 0.766 + 0.825 1.040 0.804 0.773 1.047 1.056 1.008 0.848 0.931 0.825 +// +H RACS770102 +D Average reduced distance for side chain (Rackovsky-Scheraga, 1977) +R LIT:2004126b PMID:271950 +A Rackovsky, S. and Scheraga, H.A. +T Hydrophobicity, hydrophilicity, and the radial and orientational + distributions of residues in native proteins +J Proc. Natl. Acad. Sci. USA 74, 5248-5251 (1977) (Gly 0.080) +C MEIH800102 0.987 MEIH800101 0.963 RACS770101 0.946 + FASG890101 0.935 GUYH850101 0.934 MIYS990102 0.919 + MIYS990101 0.917 MIYS990103 0.908 KRIW790102 0.895 + PUNT030101 0.894 MIYS990105 0.893 MIYS990104 0.892 + RACS770103 0.889 KRIW790101 0.871 CORJ870108 0.863 + GUYH850102 0.853 KARP850102 0.852 GUYH850104 0.849 + VINM940101 0.844 VINM940103 0.839 OOBM770101 0.838 + PARJ860101 0.834 PUNT030102 0.828 OOBM770103 0.828 + ROSM880102 0.824 JANJ780103 0.823 CHOC760102 0.809 + WOLS870101 0.802 NADH010105 -0.800 DESM900101 -0.801 + BASU050102 -0.807 NADH010101 -0.808 BASU050101 -0.813 + NISK800101 -0.818 CIDH920105 -0.830 ZHOH040103 -0.832 + CIDH920103 -0.834 CORJ870101 -0.837 CORJ870104 -0.838 + CORJ870106 -0.839 CORJ870105 -0.839 FAUJ830101 -0.843 + KYTJ820101 -0.844 OLSK800101 -0.845 CASG920101 -0.849 + JANJ790102 -0.851 CORJ870103 -0.852 CIDH920104 -0.854 + JURD980101 -0.855 EISD860103 -0.858 PLIV810101 -0.859 + PONP800103 -0.860 BASU050103 -0.861 PONP800102 -0.864 + MANP780101 -0.865 DESM900102 -0.867 JANJ780102 -0.869 + PONP800101 -0.870 PONP930101 -0.871 CORJ870107 -0.871 + CHOC760103 -0.875 PONP800107 -0.878 NADH010104 -0.883 + NADH010103 -0.893 NADH010102 -0.899 WERD780101 -0.906 + NISK860101 -0.913 MEIH800103 -0.918 BIOV880102 -0.932 + BIOV880101 -0.937 ROSG850102 -0.940 RADA880108 -0.942 + MIYS850101 -0.943 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.941 1.112 1.038 1.071 0.866 1.150 1.100 1.055 0.911 0.742 + 0.798 1.232 0.781 0.723 1.093 1.082 1.043 0.867 1.050 0.817 +// +H RACS770103 +D Side chain orientational preference (Rackovsky-Scheraga, 1977) +R LIT:2004126b PMID:271950 +A Rackovsky, S. and Scheraga, H.A. +T Hydrophobicity, hydrophilicity, and the radial and orientational + distributions of residues in native proteins +J Proc. Natl. Acad. Sci. USA 74, 5248-5251 (1977) (Gly !) (Ratio of the numbers + of occurrences in two orientations) +C MEIH800102 0.903 RACS770102 0.889 KRIW790102 0.889 + OOBM770101 0.871 MIYS990105 0.852 JANJ780103 0.847 + FASG890101 0.842 MIYS990103 0.840 GUYH850104 0.839 + MEIH800101 0.837 MIYS990104 0.833 VINM940101 0.830 + PUNT030101 0.830 OOBM770103 0.823 GUYH850102 0.821 + GUYH850101 0.816 VINM940104 0.804 RACS770101 0.801 + CORJ870107 -0.808 PONP800102 -0.809 MIYS850101 -0.818 + PONP800103 -0.819 CORJ870103 -0.827 JANJ780102 -0.828 + NADH010104 -0.832 CORJ870101 -0.832 JANJ790102 -0.834 + DESM900101 -0.837 NISK860101 -0.837 WERD780101 -0.846 + CASG920101 -0.846 WARP780101 -0.848 NADH010103 -0.851 + BIOV880101 -0.856 RADA880108 -0.863 DESM900102 -0.868 + NADH010102 -0.876 ROSG850102 -0.901 BIOV880102 -0.906 + MEIH800103 -0.919 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.16 1.72 1.97 2.66 0.50 3.87 2.40 1.63 0.86 0.57 + 0.51 3.90 0.40 0.43 2.04 1.61 1.48 0.75 1.72 0.59 +// +H RACS820101 +D Average relative fractional occurrence in A0(i) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.85 2.02 0.88 1.50 0.90 1.71 1.79 1.54 1.59 0.67 + 1.03 0.88 1.17 0.85 1.47 1.50 1.96 0.83 1.34 0.89 +// +H RACS820102 +D Average relative fractional occurrence in AR(i) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.58 1.14 0.77 0.98 1.04 1.24 1.49 0.66 0.99 1.09 + 1.21 1.27 1.41 1.00 1.46 1.05 0.87 1.23 0.68 0.88 +// +H RACS820103 +D Average relative fractional occurrence in AL(i) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.82 2.60 2.07 2.64 0.00 0.00 2.62 1.63 0.00 2.32 + 0.00 2.86 0.00 0.00 0.00 1.23 2.48 0.00 1.90 1.62 +// +H RACS820104 +D Average relative fractional occurrence in EL(i) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.78 1.75 1.32 1.25 3.14 0.93 0.94 1.13 1.03 1.26 + 0.91 0.85 0.41 1.07 1.73 1.31 1.57 0.98 1.31 1.11 +// +H RACS820105 +D Average relative fractional occurrence in E0(i) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C NAKH900102 -0.839 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.88 0.99 1.02 1.16 1.14 0.93 1.01 0.70 1.87 1.61 + 1.09 0.83 1.71 1.52 0.87 1.14 0.96 1.96 1.68 1.56 +// +H RACS820106 +D Average relative fractional occurrence in ER(i) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C ISOY800108 0.831 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.30 0.90 2.73 1.26 0.72 0.97 1.33 3.09 1.33 0.45 + 0.96 0.71 1.89 1.20 0.83 1.16 0.97 1.58 0.86 0.64 +// +H RACS820107 +D Average relative fractional occurrence in A0(i-1) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.40 1.20 1.24 1.59 2.98 0.50 1.26 1.89 2.71 1.31 + 0.57 0.87 0.00 1.27 0.38 0.92 1.38 1.53 1.79 0.95 +// +H RACS820108 +D Average relative fractional occurrence in AR(i-1) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C KANM800101 0.914 LEVM780101 0.904 PRAM900102 0.904 + ISOY800101 0.904 ROBB760101 0.889 LEVM780104 0.889 + PALJ810102 0.881 GEIM800101 0.880 PALJ810101 0.872 + CHOP780201 0.868 QIAN880106 0.866 MAXF760101 0.860 + KANM800103 0.858 ROBB760103 0.851 GEIM800104 0.851 + TANS770101 0.845 AURR980112 0.840 CRAJ730101 0.839 + QIAN880107 0.831 QIAN880108 0.820 NAGK730101 0.820 + QIAN880105 0.820 AURR980114 0.818 BURA740101 0.809 + AURR980109 0.804 AURR980115 0.802 MUNV940101 -0.859 + MUNV940102 -0.894 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.48 1.02 0.99 1.19 0.86 1.42 1.43 0.46 1.27 1.12 + 1.33 1.36 1.41 1.30 0.25 0.89 0.81 1.27 0.91 0.93 +// +H RACS820109 +D Average relative fractional occurrence in AL(i-1) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C ISOY800108 0.848 MAXF760104 0.844 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.00 0.00 4.14 2.15 0.00 0.00 0.00 6.49 0.00 0.00 + 0.00 0.00 0.00 2.11 1.99 0.00 1.24 0.00 1.90 0.00 +// +H RACS820110 +D Average relative fractional occurrence in EL(i-1) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C MUNV940105 0.833 MUNV940104 0.831 AVBF000102 -0.801 + ROBB760104 -0.818 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.02 1.00 1.31 1.76 1.05 1.05 0.83 2.39 0.40 0.83 + 1.06 0.94 1.33 0.41 2.73 1.18 0.77 1.22 1.09 0.88 +// +H RACS820111 +D Average relative fractional occurrence in E0(i-1) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C TANS770103 0.841 MAXF760102 0.815 ROBB760105 0.803 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.93 1.52 0.92 0.60 1.08 0.94 0.73 0.78 1.08 1.74 + 1.03 1.00 1.31 1.51 1.37 0.97 1.38 1.12 1.65 1.70 +// +H RACS820112 +D Average relative fractional occurrence in ER(i-1) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.99 1.19 1.15 1.18 2.32 1.52 1.36 1.40 1.06 0.81 + 1.26 0.91 1.00 1.25 0.00 1.50 1.18 1.33 1.09 1.01 +// +H RACS820113 +D Value of theta(i) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 17.05 21.25 34.81 19.27 28.84 15.42 20.12 38.14 23.07 16.66 + 10.89 16.46 20.61 16.26 23.94 19.95 18.92 23.36 26.49 17.06 +// +H RACS820114 +D Value of theta(i-1) (Rackovsky-Scheraga, 1982) +R LIT:0903736 +A Rackovsky, S. and Scheraga, H.A. +T Differential geometry and polymer conformation. 4. Conformational and + nucleation properties of individual amino acids +J Macromolecules 15, 1340-1346 (1982) +C MUNV940102 0.877 ONEK900102 0.855 MUNV940101 0.828 + ROBB760103 -0.806 BLAM930101 -0.862 ONEK900101 -0.880 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 14.53 17.82 13.59 19.78 30.57 22.18 18.19 37.16 22.63 20.28 + 14.30 14.07 20.61 19.61 52.63 18.56 21.09 19.78 26.36 21.87 +// +H RADA880101 +D Transfer free energy from chx to wat (Radzicka-Wolfenden, 1988) +R LIT:1405051b +A Radzicka, A. and Wolfenden, R. +T Comparing the polarities of the amino acids: Side-chain distribution + coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral + aqueous solution +J Biochemistry 27, 1664-1670 (1988) (Pro missing) +C EISD840101 0.968 WOLR810101 0.939 JACR890101 0.936 + ROSM880105 0.933 WOLR790101 0.933 BLAS910101 0.922 + NADH010101 0.902 RADA880104 0.901 JURD980101 0.893 + EISD860101 0.891 KYTJ820101 0.884 RADA880107 0.881 + FAUJ830101 0.873 JANJ780102 0.855 CHOC760103 0.853 + EISD860103 0.850 NADH010102 0.845 COWR900101 0.840 + OLSK800101 0.840 JANJ790102 0.839 DESM900102 0.828 + BASU050103 0.809 NADH010103 0.809 RADA880108 0.807 + YUTK870101 0.803 WOEC730101 -0.812 CHOC760102 -0.814 + GUYH850101 -0.815 JANJ780103 -0.817 WOLS870101 -0.823 + HOPT810101 -0.829 GUYH850104 -0.831 FAUJ880110 -0.838 + LEVM760101 -0.838 JANJ780101 -0.844 GRAR740102 -0.861 + OOBM770101 -0.863 FAUJ880109 -0.873 PUNT030102 -0.881 + KIDA850101 -0.883 PUNT030101 -0.886 GUYH850105 -0.899 + ROSM880102 -0.917 VHEG790101 -0.925 ENGD860101 -0.932 + PRAM900101 -0.932 KUHL950101 -0.950 ROSM880101 -0.978 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.81 -14.92 -6.64 -8.72 1.28 -5.54 -6.81 0.94 -4.66 4.92 + 4.92 -5.55 2.35 2.98 0. -3.40 -2.57 2.33 -0.14 4.04 +// +H RADA880102 +D Transfer free energy from oct to wat (Radzicka-Wolfenden, 1988) +R LIT:1405051b +A Radzicka, A. and Wolfenden, R. +T Comparing the polarities of the amino acids: Side-chain distribution + coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral + aqueous solution +J Biochemistry 27, 1664-1670 (1988) (Pro Cys Asp missing) +C NOZY710101 0.917 EISD860101 0.912 MEEJ800102 0.900 + ROSM880105 0.870 CIDH920102 0.862 CIDH920105 0.861 + ZIMJ680105 0.851 FAUJ830101 0.846 PLIV810101 0.845 + TAKK010101 0.830 GUOD860101 0.829 ZHOH040101 0.828 + VENT840101 0.826 BLAS910101 0.826 MIYS850101 0.824 + CORJ870102 0.821 SWER830101 0.820 CIDH920103 0.819 + CIDH920104 0.817 BASU050103 0.815 MEEJ810102 0.813 + ZHOH040103 0.813 BROC820101 0.811 BASU050102 0.809 + PUNT030102 -0.811 MEIH800101 -0.816 VHEG790101 -0.818 + PUNT030101 -0.821 MIYS990102 -0.834 MIYS990101 -0.837 + LEVM760101 -0.838 BULH740101 -0.856 HOPT810101 -0.859 + WOLS870101 -0.873 PARJ860101 -0.883 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.52 -1.32 -0.01 0. 0. -0.07 -0.79 0. 0.95 2.04 + 1.76 0.08 1.32 2.09 0. 0.04 0.27 2.51 1.63 1.18 +// +H RADA880103 +D Transfer free energy from vap to chx (Radzicka-Wolfenden, 1988) +R LIT:1405051b +A Radzicka, A. and Wolfenden, R. +T Comparing the polarities of the amino acids: Side-chain distribution + coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral + aqueous solution +J Biochemistry 27, 1664-1670 (1988) (Pro missing) +C FAUJ880104 -0.806 CHAM830105 -0.808 HUTJ700102 -0.812 + ROSG850101 -0.814 FAUJ880106 -0.823 MCMT640101 -0.833 + HARY940101 -0.840 GOLD730102 -0.864 BIGC670101 -0.865 + KRIW790103 -0.871 PONJ960101 -0.873 TSAJ990101 -0.875 + TSAJ990102 -0.879 GRAR740103 -0.881 CHOC750101 -0.892 + LEVM760105 -0.893 RADA880106 -0.895 CHAM830106 -0.901 + CHAM820101 -0.912 LEVM760102 -0.913 FAUJ880103 -0.923 + CHOC760101 -0.924 FASG760101 -0.954 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.13 -5. -3.04 -2.23 -2.52 -3.84 -3.43 1.45 -5.61 -2.77 + -2.64 -3.97 -3.83 -3.74 0. -1.66 -2.31 -8.21 -5.97 -2.05 +// +H RADA880104 +D Transfer free energy from chx to oct (Radzicka-Wolfenden, 1988) +R LIT:1405051b +A Radzicka, A. and Wolfenden, R. +T Comparing the polarities of the amino acids: Side-chain distribution + coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral + aqueous solution +J Biochemistry 27, 1664-1670 (1988) (Pro Cys Asp missing) +C WOLR790101 0.926 RADA880105 0.918 WOLR810101 0.910 + EISD840101 0.908 RADA880101 0.901 RADA880107 0.897 + JACR890101 0.868 JURD980101 0.824 CHOC760103 0.821 + KYTJ820101 0.819 NADH010101 0.819 COWR900101 0.818 + OLSK800101 0.814 ENGD860101 -0.803 PRAM900101 -0.803 + KIDA850101 -0.805 JANJ780101 -0.825 CHOC760102 -0.830 + KUHL950101 -0.847 ROSM880102 -0.855 ROSM880101 -0.863 + GUYH850105 -0.899 FAUJ880109 -0.926 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.29 -13.60 -6.63 0. 0. -5.47 -6.02 0.94 -5.61 2.88 + 3.16 -5.63 1.03 0.89 0. -3.44 -2.84 -0.18 -1.77 2.86 +// +H RADA880105 +D Transfer free energy from vap to oct (Radzicka-Wolfenden, 1988) +R LIT:1405051b +A Radzicka, A. and Wolfenden, R. +T Comparing the polarities of the amino acids: Side-chain distribution + coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral + aqueous solution +J Biochemistry 27, 1664-1670 (1988) (Pro Cys Asp missing) +C RADA880104 0.918 WOLR790101 0.903 WOLR810101 0.875 + RADA880107 0.846 GUYH850105 -0.809 FAUJ880109 -0.889 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.42 -18.60 -9.67 0. 0. -9.31 -9.45 2.39 -11.22 0.11 + 0.52 -9.60 -2.80 -2.85 0. -5.10 -5.15 -8.39 -7.74 0.81 +// +H RADA880106 +D Accessible surface area (Radzicka-Wolfenden, 1988) +R LIT:1405051b +A Radzicka, A. and Wolfenden, R. +T Comparing the polarities of the amino acids: Side-chain distribution + coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral + aqueous solution +J Biochemistry 27, 1664-1670 (1988) (Pro missing) +C CHAM830106 0.922 GRAR740103 0.920 KRIW790103 0.883 + CHOC760101 0.875 LEVM760102 0.871 LEVM760105 0.871 + FASG760101 0.870 FAUJ880103 0.869 CHOC750101 0.867 + TSAJ990102 0.864 TSAJ990101 0.861 PONJ960101 0.860 + BIGC670101 0.856 GOLD730102 0.854 CHAM820101 0.847 + HARY940101 0.846 ROSG850101 0.814 RADA880103 -0.895 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 93.7 250.4 146.3 142.6 135.2 177.7 182.9 52.6 188.1 182.2 + 173.7 215.2 197.6 228.6 0. 109.5 142.1 271.6 239.9 157.2 +// +H RADA880107 +D Energy transfer from out to in(95%buried) (Radzicka-Wolfenden, 1988) +R LIT:1405051b +A Radzicka, A. and Wolfenden, R. +T Comparing the polarities of the amino acids: Side-chain distribution + coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral + aqueous solution +J Biochemistry 27, 1664-1670 (1988) (Pro missing) +C EISD840101 0.927 JANJ790102 0.906 WOLR790101 0.905 + RADA880104 0.897 JACR890101 0.895 WOLR810101 0.890 + RADA880101 0.881 OLSK800101 0.874 CHOC760103 0.870 + JANJ780102 0.856 RADA880105 0.846 JURD980101 0.842 + KYTJ820101 0.828 NADH010102 0.823 EISD860103 0.812 + COWR900101 0.810 EISD860102 -0.837 KIDA850101 -0.837 + OOBM770101 -0.854 JANJ780103 -0.856 KUHL950101 -0.857 + ENGD860101 -0.865 PRAM900101 -0.865 ROSM880101 -0.867 + ROSM880102 -0.894 GUYH850104 -0.896 JANJ780101 -0.917 + CHOC760102 -0.925 GUYH850105 -0.953 FAUJ880109 -0.957 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.29 -2.71 -1.18 -1.02 0. -1.53 -0.90 -0.34 -0.94 0.24 + -0.12 -2.05 -0.24 0. 0. -0.75 -0.71 -0.59 -1.02 0.09 +// +H RADA880108 +D Mean polarity (Radzicka-Wolfenden, 1988) +R LIT:1405051b +A Radzicka, A. and Wolfenden, R. +T Comparing the polarities of the amino acids: Side-chain distribution + coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral + aqueous solution +J Biochemistry 27, 1664-1670 (1988) (Pro missing) +C BIOV880101 0.981 ROSG850102 0.967 MIYS850101 0.950 + NISK860101 0.950 BIOV880102 0.942 PONP800102 0.938 + PONP800103 0.934 PONP800101 0.934 FAUJ830101 0.932 + WERD780101 0.930 BASU050103 0.926 NADH010103 0.919 + MEIH800103 0.916 NADH010104 0.915 CIDH920104 0.914 + NADH010102 0.911 PLIV810101 0.906 ZHOH040103 0.904 + CASG920101 0.903 NISK800101 0.902 MANP780101 0.900 + CIDH920105 0.898 CORJ870101 0.895 PONP930101 0.891 + CIDH920103 0.891 CORJ870107 0.889 PONP800108 0.889 + DESM900102 0.881 CORJ870104 0.880 CORJ870103 0.876 + EISD860103 0.873 BASU050102 0.870 JANJ780102 0.869 + BASU050101 0.867 ROBB790101 0.867 CORJ870106 0.863 + ROSM880105 0.861 CIDH920101 0.858 JURD980101 0.857 + CORJ870105 0.854 JANJ790102 0.853 NADH010105 0.845 + EISD860101 0.844 KYTJ820101 0.842 NADH010101 0.838 + PONP800106 0.835 CIDH920102 0.833 CHOC760103 0.830 + BLAS910101 0.826 SWER830101 0.826 JANJ790101 0.824 + CORJ870102 0.823 EISD840101 0.817 GUOD860101 0.812 + DESM900101 0.812 RADA880101 0.807 MEEJ810101 0.804 + PONP800107 0.800 KARP850101 -0.804 JANJ780103 -0.805 + FUKS010102 -0.815 LEVM760101 -0.824 WOEC730101 -0.825 + ROSM880101 -0.831 HOPT810101 -0.831 KUHL950101 -0.839 + FUKS010103 -0.840 WOLS870101 -0.840 VINM940102 -0.846 + GUYH850104 -0.847 KRIW710101 -0.847 FUKS010104 -0.851 + KRIW790102 -0.856 ROSM880102 -0.861 VINM940103 -0.862 + RACS770103 -0.863 OOBM770101 -0.864 PARJ860101 -0.865 + PUNT030102 -0.869 GUYH850103 -0.870 KIDA850101 -0.875 + OOBM770103 -0.878 KARP850102 -0.879 PUNT030101 -0.884 + RACS770101 -0.887 CORJ870108 -0.893 KRIW790101 -0.897 + GRAR740102 -0.899 GUYH850102 -0.902 VINM940101 -0.906 + MIYS990101 -0.932 MIYS990102 -0.934 MEIH800101 -0.940 + RACS770102 -0.942 MIYS990104 -0.943 GUYH850101 -0.948 + MIYS990105 -0.950 MIYS990103 -0.950 MEIH800102 -0.953 + FASG890101 -0.977 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.06 -0.84 -0.48 -0.80 1.36 -0.73 -0.77 -0.41 0.49 1.31 + 1.21 -1.18 1.27 1.27 0. -0.50 -0.27 0.88 0.33 1.09 +// +H RICJ880101 +D Relative preference value at N" (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C RICJ880102 1.000 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.7 0.4 1.2 1.4 0.6 1. 1. 1.6 1.2 0.9 + 0.9 1. 0.3 1.2 0.7 1.6 0.3 1.1 1.9 0.7 +// +H RICJ880102 +D Relative preference value at N' (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C RICJ880101 1.000 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.7 0.4 1.2 1.4 0.6 1. 1. 1.6 1.2 0.9 + 0.9 1. 0.3 1.2 0.7 1.6 0.3 1.1 1.9 0.7 +// +H RICJ880103 +D Relative preference value at N-cap (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.5 0.4 3.5 2.1 0.6 0.4 0.4 1.8 1.1 0.2 + 0.2 0.7 0.8 0.2 0.8 2.3 1.6 0.3 0.8 0.1 +// +H RICJ880104 +D Relative preference value at N1 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.2 0.7 0.7 0.8 0.8 0.7 2.2 0.3 0.7 0.9 + 0.9 0.6 0.3 0.5 2.6 0.7 0.8 2.1 1.8 1.1 +// +H RICJ880105 +D Relative preference value at N2 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.6 0.9 0.7 2.6 1.2 0.8 2. 0.9 0.7 0.7 + 0.3 1. 1. 0.9 0.5 0.8 0.7 1.7 0.4 0.6 +// +H RICJ880106 +D Relative preference value at N3 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C FAUJ880112 0.849 AURR980107 0.800 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1. 0.4 0.7 2.2 0.6 1.5 3.3 0.6 0.7 0.4 + 0.6 0.8 1. 0.6 0.4 0.4 1. 1.4 1.2 1.1 +// +H RICJ880107 +D Relative preference value at N4 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C CHOP780210 -0.818 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.1 1.5 0. 0.3 1.1 1.3 0.5 0.4 1.5 1.1 + 2.6 0.8 1.7 1.9 0.1 0.4 0.5 3.1 0.6 1.5 +// +H RICJ880108 +D Relative preference value at N5 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.4 1.2 1.2 0.6 1.6 1.4 0.9 0.6 0.9 0.9 + 1.1 1.9 1.7 1. 0.3 1.1 0.6 1.4 0.2 0.8 +// +H RICJ880109 +D Relative preference value at Mid (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C QIAN880106 0.834 ROBB760103 0.831 KANM800103 0.829 + AURR980109 0.828 AURR980113 0.808 CHAM830101 -0.826 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.8 1.3 0.9 1. 0.7 1.3 0.8 0.5 1. 1.2 + 1.2 1.1 1.5 1.3 0.3 0.6 1. 1.5 0.8 1.2 +// +H RICJ880110 +D Relative preference value at C5 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.8 1. 0.6 0.7 0. 1. 1.1 0.5 2.4 1.3 + 1.2 1.4 2.7 1.9 0.3 0.5 0.5 1.1 1.3 0.4 +// +H RICJ880111 +D Relative preference value at C4 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C MEIH800101 -0.802 CHOP780210 -0.804 BHAR880101 -0.813 + RACS770101 -0.846 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.3 0.8 0.6 0.5 0.7 0.2 0.7 0.5 1.9 1.6 + 1.4 1. 2.8 2.9 0. 0.5 0.6 2.1 0.8 1.4 +// +H RICJ880112 +D Relative preference value at C3 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.7 0.8 0.8 0.6 0.2 1.3 1.6 0.1 1.1 1.4 + 1.9 2.2 1. 1.8 0. 0.6 0.7 0.4 1.1 1.3 +// +H RICJ880113 +D Relative preference value at C2 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.4 2.1 0.9 0.7 1.2 1.6 1.7 0.2 1.8 0.4 + 0.8 1.9 1.3 0.3 0.2 1.6 0.9 0.4 0.3 0.7 +// +H RICJ880114 +D Relative preference value at C1 (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.1 1. 1.2 0.4 1.6 2.1 0.8 0.2 3.4 0.7 + 0.7 2. 1. 0.7 0. 1.7 1. 0. 1.2 0.7 +// +H RICJ880115 +D Relative preference value at C-cap (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C AURR980117 0.921 MAXF760104 0.919 ISOY800108 0.889 + TANS770107 0.807 MAXF760105 0.802 LEVM760103 -0.829 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.8 0.9 1.6 0.7 0.4 0.9 0.3 3.9 1.3 0.7 + 0.7 1.3 0.8 0.5 0.7 0.8 0.3 0. 0.8 0.2 +// +H RICJ880116 +D Relative preference value at C' (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1. 1.4 0.9 1.4 0.8 1.4 0.8 1.2 1.2 1.1 + 0.9 1.2 0.8 0.1 1.9 0.7 0.8 0.4 0.9 0.6 +// +H RICJ880117 +D Relative preference value at C" (Richardson-Richardson, 1988) +R LIT:1408116 PMID:3381086 +A Richardson, J.S. and Richardson, D.C. +T Amino acid preferences for specific locations at the ends of alpha helices +J Science 240, 1648-1652 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.7 1.1 1.5 1.4 0.4 1.1 0.7 0.6 1. 0.7 + 0.5 1.3 0. 1.2 1.5 0.9 2.1 2.7 0.5 1. +// +H ROBB760101 +D Information measure for alpha-helix (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C CHOP780201 0.969 ISOY800101 0.957 MAXF760101 0.956 + TANS770101 0.948 PALJ810102 0.946 KANM800101 0.945 + PRAM900102 0.916 LEVM780101 0.916 PALJ810101 0.914 + BURA740101 0.912 LEVM780104 0.911 NAGK730101 0.910 + QIAN880106 0.904 GEIM800101 0.897 RACS820108 0.889 + KANM800103 0.886 CRAJ730101 0.875 QIAN880105 0.874 + QIAN880107 0.867 GEIM800104 0.855 AURR980108 0.814 + AURR980109 0.810 ROBB760103 0.807 AURR980112 0.806 + PALJ810109 0.805 MUNV940101 -0.822 MUNV940102 -0.827 + CHAM830101 -0.828 NAGK730103 -0.861 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.5 -0.9 -5.1 0.5 -1.3 1.0 7.8 -8.6 1.2 0.6 + 3.2 2.3 5.3 1.6 -7.7 -3.9 -2.6 1.2 -4.5 1.4 +// +H ROBB760102 +D Information measure for N-terminal helix (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C CHOP780204 0.911 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.3 -5.2 0.3 7.4 0.8 -0.7 10.3 -5.2 -2.8 -4.0 + -2.1 -4.1 -3.5 -1.1 8.1 -3.5 2.3 -0.9 -3.7 -4.4 +// +H ROBB760103 +D Information measure for middle helix (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C QIAN880108 0.914 PTIO830101 0.903 QIAN880107 0.889 + KANM800103 0.887 BLAM930101 0.883 ONEK900101 0.878 + QIAN880109 0.868 AURR980109 0.857 QIAN880106 0.854 + BEGF750101 0.852 RACS820108 0.851 ISOY800101 0.841 + AURR980113 0.838 AURR980108 0.835 RICJ880109 0.831 + QIAN880105 0.811 ROBB760101 0.807 QIAN880110 0.807 + CHOP780201 0.806 FAUJ880113 0.802 AURR980114 0.801 + GEIM800108 -0.802 RACS820114 -0.806 QIAN880133 -0.807 + QIAN880132 -0.827 ISOY800104 -0.830 QIAN880135 -0.834 + PRAM900104 -0.840 CHOP780216 -0.841 LEVM780103 -0.843 + GEIM800111 -0.843 QIAN880134 -0.855 ONEK900102 -0.867 + CHAM830101 -0.878 MUNV940102 -0.913 MUNV940101 -0.918 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.7 0.3 -6.1 -3.1 -4.9 0.6 2.2 -6.8 -1.0 3.2 + 5.5 0.5 7.2 2.8 -22.8 -3.0 -4.0 4.0 -4.6 2.5 +// +H ROBB760104 +D Information measure for C-terminal helix (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C QIAN880108 0.879 BLAM930101 0.878 QIAN880109 0.871 + ONEK900101 0.844 CHOP780205 0.841 BUNA790101 0.823 + PTIO830101 0.817 QIAN880110 0.806 QIAN880134 -0.802 + MUNV940102 -0.803 ISOY800104 -0.817 RACS820110 -0.818 + MUNV940101 -0.831 MUNV940104 -0.840 FINA910102 -0.844 + MUNV940105 -0.859 ONEK900102 -0.861 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.3 1.4 -3.3 -4.4 6.1 2.7 2.5 -8.3 5.9 -0.5 + 0.1 7.3 3.5 1.6 -24.4 -1.9 -3.7 -0.9 -0.6 2.3 +// +H ROBB760105 +D Information measure for extended (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C ROBB760106 0.949 KANM800102 0.898 KANM800104 0.885 + CHOP780202 0.885 PTIO830102 0.878 GEIM800105 0.877 + TANS770103 0.871 PALJ810103 0.869 LIFS790101 0.867 + QIAN880120 0.860 QIAN880119 0.859 BASU050101 0.853 + ISOY800102 0.847 LEVM780105 0.842 BASU050103 0.839 + GEIM800107 0.836 PALJ810104 0.835 QIAN880121 0.834 + PONP930101 0.829 PONP800102 0.828 PONP800101 0.823 + PONP800103 0.823 BURA740102 0.821 PONP800108 0.820 + NAGK730102 0.815 CORJ870101 0.809 MANP780101 0.805 + PALJ810110 0.804 CORJ870104 0.803 RACS820111 0.803 + CORJ870107 0.800 CORJ870108 -0.811 MUNV940103 -0.832 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -2.3 0.4 -4.1 -4.4 4.4 1.2 -5.0 -4.2 -2.5 6.7 + 2.3 -3.3 2.3 2.6 -1.8 -1.7 1.3 -1.0 4.0 6.8 +// +H ROBB760106 +D Information measure for pleated-sheet (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C ROBB760105 0.949 KANM800102 0.938 CHOP780202 0.931 + QIAN880120 0.908 QIAN880121 0.907 LIFS790101 0.906 + GEIM800107 0.899 QIAN880119 0.897 PALJ810104 0.894 + NAGK730102 0.887 PALJ810103 0.886 PTIO830102 0.882 + KANM800104 0.877 LEVM780105 0.869 PONP930101 0.866 + CRAJ730102 0.865 GEIM800105 0.856 BASU050101 0.851 + CHOP780208 0.846 BASU050103 0.840 GEIM800106 0.838 + PALJ810110 0.836 AVBF000101 0.834 CORJ870101 0.829 + PONP800101 0.829 LIFS790103 0.827 MANP780101 0.824 + PONP800102 0.822 CORJ870107 0.819 PONP800103 0.812 + NISK860101 0.810 BEGF750102 0.809 PONP800108 0.808 + CORJ870104 0.808 MIYS990104 -0.815 GEIM800110 -0.819 + CORJ870108 -0.820 MIYS990103 -0.836 MUNV940103 -0.888 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -2.7 0.4 -4.2 -4.4 3.7 0.8 -8.1 -3.9 -3.0 7.7 + 3.7 -2.9 3.7 3.0 -6.6 -2.4 1.7 0.3 3.3 7.1 +// +H ROBB760107 +D Information measure for extended without H-bond (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.0 1.1 -2.0 -2.6 5.4 2.4 3.1 -3.4 0.8 -0.1 + -3.7 -3.1 -2.1 0.7 7.4 1.3 0.0 -3.4 4.8 2.7 +// +H ROBB760108 +D Information measure for turn (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C ROBB760113 0.994 ROBB760110 0.960 BEGF750103 0.922 + CRAJ730103 0.912 CHOP780101 0.887 PALJ810106 0.882 + TANS770110 0.839 CHAM830101 0.812 BEGF750101 -0.819 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -5.0 2.1 4.2 3.1 4.4 0.4 -4.7 5.7 -0.3 -4.6 + -5.6 1.0 -4.8 -1.8 2.6 2.6 0.3 3.4 2.9 -6.0 +// +H ROBB760109 +D Information measure for N-terminal turn (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -3.3 0.0 5.4 3.9 -0.3 -0.4 -1.8 -1.2 3.0 -0.5 + -2.3 -1.2 -4.3 0.8 6.5 1.8 -0.7 -0.8 3.1 -3.5 +// +H ROBB760110 +D Information measure for middle turn (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C ROBB760108 0.960 ROBB760113 0.957 BEGF750103 0.903 + CRAJ730103 0.887 PALJ810106 0.864 CHOP780101 0.863 + TANS770110 0.805 CHAM830101 0.804 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -4.7 2.0 3.9 1.9 6.2 -2.0 -4.2 5.7 -2.6 -7.0 + -6.2 2.8 -4.8 -3.7 3.6 2.1 0.6 3.3 3.8 -6.2 +// +H ROBB760111 +D Information measure for C-terminal turn (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C CHOP780215 0.825 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -3.7 1.0 -0.6 -0.6 4.0 3.4 -4.3 5.9 -0.8 -0.5 + -2.8 1.3 -1.6 1.6 -6.0 1.5 1.2 6.5 1.3 -4.6 +// +H ROBB760112 +D Information measure for coil (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C PALJ810115 0.885 CHOP780211 0.841 QIAN880133 0.814 + ISOY800103 0.807 QIAN880132 0.800 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -2.5 -1.2 4.6 0.0 -4.7 -0.5 -4.4 4.9 1.6 -3.3 + -2.0 -0.8 -4.1 -4.1 5.8 2.5 1.7 1.2 -0.6 -3.5 +// +H ROBB760113 +D Information measure for loop (Robson-Suzuki, 1976) +R PMID:1003471 +A Robson, B. and Suzuki, E. +T Conformational properties of amino acid residues in globular proteins +J J. Mol. Biol. 107, 327-356 (1976) +C ROBB760108 0.994 ROBB760110 0.957 BEGF750103 0.924 + CRAJ730103 0.916 CHOP780101 0.907 PALJ810106 0.895 + TANS770110 0.853 CHAM830101 0.841 NAGK730103 0.811 + CHOP780201 -0.811 BEGF750101 -0.826 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -5.1 2.6 4.7 3.1 3.8 0.2 -5.2 5.6 -0.9 -4.5 + -5.4 1.0 -5.3 -2.4 3.5 3.2 0.0 2.9 3.2 -6.3 +// +H ROBB790101 +D Hydration free energy (Robson-Osguthorpe, 1979) +R LIT:0511124 PMID:513136 +A Robson, B. and Osguthorpe, D.J. +T Refined models for computer simulation of protein folding: Applications to + the study of conserved secondary structure and flexible hinge points during + the folding of pancreatic trypsin inhibitor +J J. Mol. Biol. 132, 19-51 (1979) (Gly 0.67) +C CIDH920105 0.921 NISK860101 0.912 CIDH920104 0.903 + BASU050102 0.897 CIDH920102 0.896 MIYS850101 0.895 + BIOV880101 0.890 CIDH920103 0.884 PLIV810101 0.875 + ZHOH040101 0.872 WERD780101 0.872 ZHOH040103 0.872 + FAUJ830101 0.868 RADA880108 0.867 MEEJ810101 0.861 + PONP930101 0.858 CASG920101 0.850 BASU050103 0.849 + ROSG850102 0.846 CIDH920101 0.846 BASU050101 0.845 + CORJ870102 0.835 SWER830101 0.835 MANP780101 0.834 + CORJ870106 0.834 CORJ870107 0.832 PONP800108 0.831 + NISK800101 0.830 CORJ870105 0.827 PONP800101 0.822 + MEEJ810102 0.821 BIOV880102 0.821 CORJ870101 0.819 + GUOD860101 0.815 ROSM880104 0.807 MEEJ800102 0.807 + PONP800102 0.807 CORJ870104 0.807 CORJ870103 0.804 + LEVM760106 0.804 MEIH800103 0.801 BULH740101 -0.813 + PARS000101 -0.819 CORJ870108 -0.829 WOLS870101 -0.831 + GRAR740102 -0.832 RACS770101 -0.839 MIYS990103 -0.854 + VINM940101 -0.858 FASG890101 -0.860 GUYH850102 -0.862 + FUKS010103 -0.865 VINM940102 -0.866 MEIH800101 -0.868 + MIYS990104 -0.877 MIYS990101 -0.883 MIYS990102 -0.885 + MIYS990105 -0.885 PARJ860101 -0.893 OOBM770103 -0.909 + GUYH850103 -0.999 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -1.0 0.3 -0.7 -1.2 2.1 -0.1 -0.7 0.3 1.1 4.0 + 2.0 -0.9 1.8 2.8 0.4 -1.2 -0.5 3.0 2.1 1.4 +// +H ROSG850101 +D Mean area buried on transfer (Rose et al., 1985) +R LIT:1109092 PMID:4023714 +A Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H. and Zehfus, M.H. +T Hydrophobicity of amino acid residues in globular proteins +J Science 229, 834-838 (1985) +C ZHOH040102 0.930 GRAR740103 0.922 KRIW790103 0.920 + CHAM820101 0.917 TSAJ990101 0.914 BIGC670101 0.910 + GOLD730102 0.909 TSAJ990102 0.909 CHOC750101 0.908 + ZHOH040101 0.904 LEVM760106 0.896 FAUJ880103 0.892 + HARY940101 0.869 CIDH920102 0.866 PONJ960101 0.862 + MCMT640101 0.857 LEVM760107 0.852 CHOC760101 0.842 + FASG760101 0.838 NOZY710101 0.834 CIDH920101 0.831 + RADA880106 0.814 PARS000101 -0.805 KARP850101 -0.807 + VINM940102 -0.810 RADA880103 -0.814 WEBA780101 -0.817 + FUKS010103 -0.819 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 86.6 162.2 103.3 97.8 132.3 119.2 113.9 62.9 155.8 158.0 + 164.1 115.5 172.9 194.1 92.9 85.6 106.5 224.6 177.7 141.0 +// +H ROSG850102 +D Mean fractional area loss (Rose et al., 1985) +R LIT:1109092 PMID:4023714 +A Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H. and Zehfus, M.H. +T Hydrophobicity of amino acid residues in globular proteins +J Science 229, 834-838 (1985) +C BIOV880101 0.981 RADA880108 0.967 NISK860101 0.962 + BIOV880102 0.960 NADH010103 0.958 NADH010104 0.953 + CASG920101 0.952 PONP800102 0.949 MEIH800103 0.948 + NADH010102 0.948 CORJ870101 0.948 PONP800103 0.947 + WERD780101 0.943 NISK800101 0.942 PONP800101 0.938 + MIYS850101 0.937 PONP930101 0.928 PONP800108 0.919 + DESM900102 0.914 JANJ780102 0.909 FAUJ830101 0.904 + MANP780101 0.903 BASU050103 0.903 ZHOH040103 0.903 + CORJ870107 0.898 CIDH920104 0.896 JANJ790102 0.892 + CORJ870103 0.883 CORJ870106 0.878 BASU050102 0.870 + BAEK050101 0.868 DESM900101 0.866 NADH010105 0.865 + CORJ870105 0.864 CORJ870104 0.860 CIDH920105 0.858 + JANJ790101 0.857 JURD980101 0.854 CHOC760103 0.851 + BASU050101 0.849 CIDH920103 0.846 EISD860103 0.846 + ROBB790101 0.846 PLIV810101 0.841 KYTJ820101 0.841 + ROSM880105 0.838 NADH010101 0.833 WARP780101 0.823 + PONP800106 0.807 EISD840101 0.806 PONP800107 0.803 + WOEC730101 -0.804 FUKS010103 -0.808 VINM940104 -0.809 + CHOC760102 -0.819 PARS000101 -0.820 ROSM880102 -0.822 + PARJ860101 -0.823 HOPT810101 -0.825 JANJ780101 -0.836 + GUYH850103 -0.844 KIDA850101 -0.849 VINM940102 -0.849 + KRIW710101 -0.852 PUNT030102 -0.869 FUKS010104 -0.877 + JANJ780103 -0.879 GRAR740102 -0.880 RACS770101 -0.880 + PUNT030101 -0.883 CORJ870108 -0.890 GUYH850104 -0.891 + KARP850102 -0.897 VINM940103 -0.901 RACS770103 -0.901 + OOBM770101 -0.903 MIYS990101 -0.913 MIYS990102 -0.916 + OOBM770103 -0.916 KRIW790102 -0.922 GUYH850102 -0.925 + GUYH850101 -0.929 MEIH800101 -0.930 KRIW790101 -0.935 + RACS770102 -0.940 VINM940101 -0.943 MEIH800102 -0.959 + MIYS990104 -0.962 MIYS990103 -0.966 MIYS990105 -0.968 + FASG890101 -0.976 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.74 0.64 0.63 0.62 0.91 0.62 0.62 0.72 0.78 0.88 + 0.85 0.52 0.85 0.88 0.64 0.66 0.70 0.85 0.76 0.86 +// +H ROSM880101 +D Side chain hydropathy, uncorrected for solvation (Roseman, 1988) +R LIT:1405111b PMID:3398047 +A Roseman, M.A. +T Hydrophilicity of polar amino acid side-chains is markedly reduced by + flanking peptide bonds +J J. Mol. Biol. 200, 513-522 (1988) +C KUHL950101 0.962 ROSM880102 0.938 KIDA850101 0.933 + PRAM900101 0.917 ENGD860101 0.917 FAUJ880110 0.888 + GRAR740102 0.887 PUNT030101 0.884 VHEG790101 0.883 + LEVM760101 0.876 WOLS870101 0.866 PUNT030102 0.864 + OOBM770101 0.854 GUYH850105 0.849 HOPT810101 0.848 + FAUJ880109 0.846 WOEC730101 0.844 JANJ780101 0.822 + GUYH850104 0.814 JANJ780103 0.810 GUYH850101 0.803 + PARJ860101 0.803 BASU050103 -0.804 OLSK800101 -0.806 + NAKH900110 -0.812 DESM900102 -0.812 WARP780101 -0.816 + CHOC760103 -0.819 BIOV880102 -0.824 JANJ790102 -0.824 + CIDH920104 -0.828 BIOV880101 -0.830 NADH010102 -0.830 + RADA880108 -0.831 PLIV810101 -0.834 JANJ780102 -0.835 + KYTJ820101 -0.845 COWR900101 -0.849 JURD980101 -0.851 + RADA880104 -0.863 NADH010101 -0.866 RADA880107 -0.867 + EISD860103 -0.871 WOLR810101 -0.884 WOLR790101 -0.887 + JACR890101 -0.892 FAUJ830101 -0.907 EISD860101 -0.917 + BLAS910101 -0.940 EISD840101 -0.947 ROSM880105 -0.951 + RADA880101 -0.978 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.67 12.1 7.23 8.72 -0.34 6.39 7.35 0.00 3.82 -3.02 + -3.02 6.13 -1.30 -3.24 -1.75 4.35 3.86 -2.86 0.98 -2.18 +// +H ROSM880102 +D Side chain hydropathy, corrected for solvation (Roseman, 1988) +R LIT:1405111b PMID:3398047 +A Roseman, M.A. +T Hydrophilicity of polar amino acid side-chains is markedly reduced by + flanking peptide bonds +J J. Mol. Biol. 200, 513-522 (1988) +C ROSM880101 0.938 KUHL950101 0.922 KIDA850101 0.920 + PRAM900101 0.892 ENGD860101 0.891 WOLS870101 0.877 + GUYH850105 0.874 GRAR740102 0.870 OOBM770101 0.867 + PUNT030101 0.861 MEIH800102 0.859 GUYH850104 0.856 + JANJ780101 0.853 PUNT030102 0.851 CHOC760102 0.845 + FASG890101 0.839 JANJ780103 0.838 GUYH850101 0.837 + VHEG790101 0.828 FAUJ880109 0.824 RACS770102 0.824 + LEVM760101 0.823 MIYS990101 0.819 MIYS990102 0.818 + WOEC730101 0.801 PARJ860101 0.801 WARP780101 -0.801 + BASU050103 -0.814 DESM900102 -0.816 ROSG850102 -0.822 + MIYS850101 -0.825 GUOD860101 -0.829 WOLR810101 -0.829 + MEIH800103 -0.829 CIDH920104 -0.831 WOLR790101 -0.836 + JACR890101 -0.837 BIOV880102 -0.837 NADH010104 -0.839 + OLSK800101 -0.847 BIOV880101 -0.854 RADA880104 -0.855 + NADH010103 -0.857 RADA880108 -0.861 PLIV810101 -0.864 + JANJ790102 -0.866 EISD860101 -0.868 CHOC760103 -0.869 + NADH010101 -0.870 JANJ780102 -0.870 ROSM880105 -0.871 + KYTJ820101 -0.878 NADH010102 -0.881 BLAS910101 -0.884 + JURD980101 -0.894 RADA880107 -0.894 COWR900101 -0.897 + RADA880101 -0.917 EISD840101 -0.925 FAUJ830101 -0.927 + EISD860103 -0.943 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.67 3.89 2.27 1.57 -2.00 2.12 1.78 0.00 1.09 -3.02 + -3.02 2.46 -1.67 -3.24 -1.75 0.10 -0.42 -2.86 0.98 -2.18 +// +H ROSM880103 +D Loss of Side chain hydropathy by helix formation (Roseman, 1988) +R LIT:1405111b PMID:3398047 +A Roseman, M.A. +T Hydrophilicity of polar amino acid side-chains is markedly reduced by + flanking peptide bonds +J J. Mol. Biol. 200, 513-522 (1988) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.4 0.3 0.9 0.8 0.5 0.7 1.3 0.0 1.0 0.4 + 0.6 0.4 0.3 0.7 0.9 0.4 0.4 0.6 1.2 0.4 +// +H SIMZ760101 +D Transfer free energy (Simon, 1976), Cited by Charton-Charton (1982) +R +A Simon, Z. +T +J Quantum Biochemistry and Specific Interactions, Abacus Press, Tunbridge + Wells, Kent, England (1976) Cited by Charton-Charton (1982) +C ARGP820101 0.967 JOND750101 0.966 GOLD730101 0.939 + TAKK010101 0.936 MEEJ800102 0.861 ROSM880104 0.855 + LEVM760106 0.848 CIDH920105 0.837 MEEJ810101 0.836 + CIDH920102 0.832 ZIMJ680101 0.821 BULH740102 0.815 + LAWE840101 0.815 ZHOH040102 0.814 ZIMJ680102 0.810 + ZHOH040101 0.808 MEEJ810102 0.808 NOZY710101 0.807 + VENT840101 0.806 ZIMJ680105 0.805 PLIV810101 0.805 + PARJ860101 -0.825 WOLS870101 -0.830 BULH740101 -0.894 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.73 0.73 -0.01 0.54 0.70 -0.10 0.55 0.00 1.10 2.97 + 2.49 1.50 1.30 2.65 2.60 0.04 0.44 3.00 2.97 1.69 +// +H SNEP660101 +D Principal component I (Sneath, 1966) +R PMID:4291386 +A Sneath, P.H.A. +T Relations between chemical structure and biological activity in peptides +J J. Theor. Biol. 12, 157-195 (1966) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.239 0.211 0.249 0.171 0.220 0.260 0.187 0.160 0.205 0.273 + 0.281 0.228 0.253 0.234 0.165 0.236 0.213 0.183 0.193 0.255 +// +H SNEP660102 +D Principal component II (Sneath, 1966) +R PMID:4291386 +A Sneath, P.H.A. +T Relations between chemical structure and biological activity in peptides +J J. Theor. Biol. 12, 157-195 (1966) +C FAUJ880110 -0.804 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.330 -0.176 -0.233 -0.371 0.074 -0.254 -0.409 0.370 -0.078 0.149 + 0.129 -0.075 -0.092 -0.011 0.370 0.022 0.136 -0.011 -0.138 0.245 +// +H SNEP660103 +D Principal component III (Sneath, 1966) +R PMID:4291386 +A Sneath, P.H.A. +T Relations between chemical structure and biological activity in peptides +J J. Theor. Biol. 12, 157-195 (1966) +C LEVM760107 0.818 CHAM820101 0.808 ZASB820101 0.804 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.110 0.079 -0.136 -0.285 -0.184 -0.067 -0.246 -0.073 0.320 0.001 + -0.008 0.049 -0.041 0.438 -0.016 -0.153 -0.208 0.493 0.381 -0.155 +// +H SNEP660104 +D Principal component IV (Sneath, 1966) +R PMID:4291386 +A Sneath, P.H.A. +T Relations between chemical structure and biological activity in peptides +J J. Theor. Biol. 12, 157-195 (1966) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.062 -0.167 0.166 -0.079 0.380 -0.025 -0.184 -0.017 0.056 -0.309 + -0.264 -0.371 0.077 0.074 -0.036 0.470 0.348 0.050 0.220 -0.212 +// +H SUEM840101 +D Zimm-Bragg parameter s at 20 C (Sueki et al., 1984) +R LIT:1004141 +A Sueki, M., Lee, S., Powers, S.P., Denton, J.B., Konishi, Y. and Scheraga, + H.A. +T Helix-coil stability constants for the naturally occurring amino acids in + water. 22. Histidine parameters from random + poly{(hydroxybutyl)glutamine-co-L-histidine} +J Macromolecules 17, 148-155 (1984) Charged state for Arg, His, Asp, and Glu + (Cys Pro 0.100) +C AURR980113 0.887 FINA770101 0.883 AURR980109 0.882 + PTIO830101 0.877 AURR980114 0.845 KANM800103 0.820 + QIAN880107 0.803 QIAN880131 -0.823 PALJ810106 -0.832 + CHOP780101 -0.845 ISOY800103 -0.850 LEVM780103 -0.864 + TANS770110 -0.864 PRAM900104 -0.865 CHOP780216 -0.874 + GEIM800108 -0.875 LEVM780106 -0.878 QIAN880133 -0.879 + QIAN880132 -0.880 GEIM800111 -0.885 CHAM830101 -0.891 + CHOP780203 -0.892 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.071 1.033 0.784 0.680 0.922 0.977 0.970 0.591 0.850 1.140 + 1.140 0.939 1.200 1.086 0.659 0.760 0.817 1.107 1.020 0.950 +// +H SUEM840102 +D Zimm-Bragg parameter sigma x 1.0E4 (Sueki et al., 1984) +R LIT:1004141 +A Sueki, M., Lee, S., Powers, S.P., Denton, J.B., Konishi, Y. and Scheraga, + H.A. +T Helix-coil stability constants for the naturally occurring amino acids in + water. 22. Histidine parameters from random + poly{(hydroxybutyl)glutamine-co-L-histidine} +J Macromolecules 17, 148-155 (1984) Charged state for Arg, His, Asp, and Glu + (Cys Pro !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.0 0.1 0.1 70.0 26.0 33.0 6.0 0.1 0.1 55.0 + 33.0 1.0 54.0 18.0 42.0 0.1 0.1 77.0 66.0 0.1 +// +H SWER830101 +D Optimal matching hydrophobicity (Sweet-Eisenberg, 1983) +R LIT:2004095b PMID:6663622 +A Sweet, R.M. and Eisenberg, D. +T Correlation of sequence hydrophobicities measures similarity in + three-dimensional protein structure +J J. Mol. Biol. 171, 479-488 (1983) +C CORJ870102 1.000 BASU050101 0.922 BASU050103 0.892 + CIDH920105 0.890 MIYS850101 0.889 BLAS910101 0.887 + CORJ870104 0.883 CORJ870107 0.883 BASU050102 0.880 + PLIV810101 0.875 CIDH920102 0.870 CIDH920103 0.865 + NISK860101 0.865 ZHOH040103 0.863 CIDH920104 0.862 + CORJ870103 0.862 ZHOH040101 0.860 PTIO830102 0.856 + GUOD860101 0.853 CIDH920101 0.853 CORJ870105 0.848 + CORJ870106 0.845 ROSM880104 0.844 ROSM880105 0.843 + BIOV880101 0.839 VENT840101 0.836 NOZY710101 0.836 + ROBB790101 0.835 PONP930101 0.835 FAUJ830101 0.833 + ZIMJ680105 0.829 RADA880108 0.826 QIAN880120 0.825 + EISD860101 0.824 CHOP780202 0.823 MANP780101 0.821 + RADA880102 0.820 LIFS790101 0.815 PALJ810104 0.809 + MEEJ810101 0.806 WERD780101 0.804 MUNV940103 -0.802 + RACS770101 -0.803 VINM940102 -0.811 VINM940101 -0.817 + MEIH800101 -0.830 WOEC730101 -0.832 OOBM770103 -0.833 + PUNT030101 -0.838 GUYH850103 -0.839 PARS000101 -0.846 + MIYS990103 -0.878 MIYS990105 -0.883 CORJ870108 -0.884 + MIYS990104 -0.887 WOLS870101 -0.887 PARJ860101 -0.893 + GRAR740102 -0.896 MIYS990102 -0.921 BULH740101 -0.923 + MIYS990101 -0.923 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.40 -0.59 -0.92 -1.31 0.17 -0.91 -1.22 -0.67 -0.64 1.25 + 1.22 -0.67 1.02 1.92 -0.49 -0.55 -0.28 0.50 1.67 0.91 +// +H TANS770101 +D Normalized frequency of alpha-helix (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C ROBB760101 0.948 CHOP780201 0.947 MAXF760101 0.930 + KANM800101 0.927 NAGK730101 0.925 PALJ810102 0.923 + GEIM800101 0.918 PALJ810101 0.918 BURA740101 0.917 + LEVM780104 0.908 ISOY800101 0.906 PRAM900102 0.854 + LEVM780101 0.854 RACS820108 0.845 KANM800103 0.843 + CRAJ730101 0.843 GEIM800104 0.841 AURR980115 0.834 + QIAN880106 0.819 AURR980111 0.817 QIAN880107 0.804 + AURR980114 0.800 NAGK730103 -0.800 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.42 1.06 0.71 1.01 0.73 1.02 1.63 0.50 1.20 1.12 + 1.29 1.24 1.21 1.16 0.65 0.71 0.78 1.05 0.67 0.99 +// +H TANS770102 +D Normalized frequency of isolated helix (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.946 1.128 0.432 1.311 0.481 1.615 0.698 0.360 2.168 1.283 + 1.192 1.203 0.000 0.963 2.093 0.523 1.961 1.925 0.802 0.409 +// +H TANS770103 +D Normalized frequency of extended structure (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C ISOY800102 0.929 MAXF760102 0.891 ROBB760105 0.871 + GEIM800105 0.850 RACS820111 0.841 PALJ810103 0.824 + WOEC730101 -0.806 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.790 1.087 0.832 0.530 1.268 1.038 0.643 0.725 0.864 1.361 + 1.111 0.735 1.092 1.052 1.249 1.093 1.214 1.114 1.340 1.428 +// +H TANS770104 +D Normalized frequency of chain reversal R (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C CHOP780213 0.954 ISOY800104 0.918 FINA910102 0.876 + MUNV940104 0.870 MUNV940105 0.846 QIAN880134 0.837 + ONEK900102 0.826 FODM020101 -0.802 BLAM930101 -0.837 + BUNA790101 -0.867 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.194 0.795 0.659 1.056 0.678 1.290 0.928 1.015 0.611 0.603 + 0.595 1.060 0.831 0.377 3.159 1.444 1.172 0.452 0.816 0.640 +// +H TANS770105 +D Normalized frequency of chain reversal S (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C CHOP780214 0.862 ISOY800105 0.836 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.497 0.677 2.072 1.498 1.348 0.711 0.651 1.848 1.474 0.471 + 0.656 0.932 0.425 1.348 0.179 1.151 0.749 1.283 1.283 0.654 +// +H TANS770106 +D Normalized frequency of chain reversal D (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.937 1.725 1.080 1.640 1.004 1.078 0.679 0.901 1.085 0.178 + 0.808 1.254 0.886 0.803 0.748 1.145 1.487 0.803 1.227 0.625 +// +H TANS770107 +D Normalized frequency of left-handed helix (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C MAXF760104 0.913 ISOY800108 0.827 RICJ880115 0.807 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.289 1.380 3.169 0.917 1.767 2.372 0.285 4.259 1.061 0.262 + 0.000 1.288 0.000 0.393 0.000 0.160 0.218 0.000 0.654 0.167 +// +H TANS770108 +D Normalized frequency of zeta R (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.328 2.088 1.498 3.379 0.000 0.000 0.000 0.500 1.204 2.078 + 0.414 0.835 0.982 1.336 0.415 1.089 1.732 1.781 0.000 0.946 +// +H TANS770109 +D Normalized frequency of coil (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C MAXF760105 0.878 MAXF760104 0.821 ISOY800108 0.816 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.945 0.364 1.202 1.315 0.932 0.704 1.014 2.355 0.525 0.673 + 0.758 0.947 1.028 0.622 0.579 1.140 0.863 0.777 0.907 0.561 +// +H TANS770110 +D Normalized frequency of chain reversal (Tanaka-Scheraga, 1977) +R PMID:557155 +A Tanaka, S. and Scheraga, H.A. +T Statistical mechanical treatment of protein conformation. 5. A multiphasic + model for specific-sequence copolymers of amino acids +J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized + frequencies +C CHOP780101 0.956 CHOP780203 0.940 CHOP780216 0.930 + PALJ810106 0.925 QIAN880133 0.920 CHAM830101 0.917 + QIAN880132 0.903 ISOY800103 0.897 LEVM780106 0.892 + GEIM800108 0.886 GEIM800111 0.883 LEVM780103 0.875 + PRAM900104 0.873 QIAN880131 0.873 PALJ810105 0.860 + CRAJ730103 0.859 CHOP780210 0.858 ROBB760113 0.853 + ROBB760108 0.839 BEGF750103 0.834 ROBB760110 0.805 + AURR980109 -0.816 SUEM840101 -0.864 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.842 0.936 1.352 1.366 1.032 0.998 0.758 1.349 1.079 0.459 + 0.665 1.045 0.668 0.881 1.385 1.257 1.055 0.881 1.101 0.643 +// +H VASM830101 +D Relative population of conformational state A (Vasquez et al., 1983) +R LIT:0908110 +A Vasquez, M., Nemethy, G. and Scheraga, H.A. +T Computed conformational states of the 20 naturally occurring amino acid + residues and of the prototype residue alpha-aminobutyric acid +J Macromolecules 16, 1043-1049 (1983) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.135 0.296 0.196 0.289 0.159 0.236 0.184 0.051 0.223 0.173 + 0.215 0.170 0.239 0.087 0.151 0.010 0.100 0.166 0.066 0.285 +// +H VASM830102 +D Relative population of conformational state C (Vasquez et al., 1983) +R LIT:0908110 +A Vasquez, M., Nemethy, G. and Scheraga, H.A. +T Computed conformational states of the 20 naturally occurring amino acid + residues and of the prototype residue alpha-aminobutyric acid +J Macromolecules 16, 1043-1049 (1983) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.507 0.459 0.287 0.223 0.592 0.383 0.445 0.390 0.310 0.111 + 0.619 0.559 0.431 0.077 0.739 0.689 0.785 0.160 0.060 0.356 +// +H VASM830103 +D Relative population of conformational state E (Vasquez et al., 1983) +R LIT:0908110 +A Vasquez, M., Nemethy, G. and Scheraga, H.A. +T Computed conformational states of the 20 naturally occurring amino acid + residues and of the prototype residue alpha-aminobutyric acid +J Macromolecules 16, 1043-1049 (1983) (Pro !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.159 0.194 0.385 0.283 0.187 0.236 0.206 0.049 0.233 0.581 + 0.083 0.159 0.198 0.682 0.366 0.150 0.074 0.463 0.737 0.301 +// +H VELV850101 +D Electron-ion interaction potential (Veljkovic et al., 1985) +R LIT:2004067b +A Veljkovic, V., Cosic, I., Dimitrijevic, B. and Lalovic, D. +T Is it possible to analyze DNA and protein sequences by the method of digital + signal processing? +J IEEE Trans. Biomed. Eng. 32, 337-341 (1985) +C COSI940101 1.000 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + .03731 .09593 .00359 .12630 .08292 .07606 .00580 .00499 .02415 .00000 + .00000 .03710 .08226 .09460 .01979 .08292 .09408 .05481 .05159 .00569 +// +H VENT840101 +D Bitterness (Venanzi, 1984) +R LIT:1103107b PMID:6521488 +A Venanzi, T.J. +T Hydrophobicity parameters and the bitter taste of L-amino acids +J J. Theor. Biol. 111, 447-450 (1984) +C NOZY710101 0.897 BASU050101 0.858 ZHOH040101 0.858 + BASU050102 0.851 GUOD860101 0.848 PTIO830102 0.842 + WILM950101 0.840 CORJ870102 0.837 SWER830101 0.836 + ZHOH040102 0.831 MEEJ810102 0.831 PALJ810104 0.831 + ROSM880104 0.829 RADA880102 0.826 CHOP780209 0.817 + BASU050103 0.814 LIFS790101 0.814 MEEJ810101 0.813 + CIDH920105 0.813 TAKK010101 0.812 ZHOH040103 0.807 + SIMZ760101 0.806 PONP800107 0.805 CHOP780202 0.805 + GOLD730101 0.802 MIYS990102 -0.820 MIYS990101 -0.821 + WOLS870101 -0.835 PARJ860101 -0.846 BULH740101 -0.907 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. + 1. 0. 0. 1. 0. 0. 0. 1. 1. 1. +// +H VHEG790101 +D Transfer free energy to lipophilic phase (von Heijne-Blomberg, 1979) +R LIT:0509382 PMID:477664 +A von Heijne, G. and Blomberg, C. +T Trans-membrane translocation of proteins: The direct transfer model +J Eur. J. Biochem. 97, 175-181 (1979) +C ENGD860101 0.909 PRAM900101 0.909 ROSM880101 0.883 + PUNT030101 0.876 PUNT030102 0.873 KUHL950101 0.858 + HOPT810101 0.849 GUYH850105 0.845 ROSM880102 0.828 + LEVM760101 0.825 JURD980101 -0.814 RADA880102 -0.818 + NADH010101 -0.827 WOLR790101 -0.844 BLAS910101 -0.847 + NAKH900110 -0.848 EISD860101 -0.862 WOLR810101 -0.867 + ROSM880105 -0.901 JACR890101 -0.903 EISD840101 -0.924 + RADA880101 -0.925 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -12.04 39.23 4.25 23.22 3.95 2.16 16.81 -7.85 6.28 -18.32 + -17.79 9.71 -8.86 -21.98 5.82 -1.54 -4.15 -16.19 -1.51 -16.22 +// +H WARP780101 +D Average interactions per side chain atom (Warme-Morgan, 1978) +R LIT:0405099 PMID:633361 +A Warme, P.K. and Morgan, R.S. +T A survey of amino acid side-chain interactions in 21 proteins +J J. Mol. Biol. 118, 289-304 (1978) (Gly 0.81) +C DESM900102 0.882 JANJ780102 0.878 JANJ790102 0.877 + NADH010102 0.870 DESM900101 0.864 BIOV880102 0.853 + KYTJ820101 0.845 MEIH800103 0.835 JURD980101 0.827 + CHOC760103 0.824 ROSG850102 0.823 EISD860103 0.820 + OLSK800101 0.818 CHOC760104 0.815 NADH010103 0.811 + CORJ870101 0.800 ROSM880102 -0.801 KUHL950101 -0.811 + PUNT030101 -0.814 ROSM880101 -0.816 MEIH800102 -0.826 + PRAM900101 -0.827 ENGD860101 -0.827 RACS770103 -0.848 + CHOC760102 -0.849 JANJ780101 -0.869 GUYH850104 -0.882 + JANJ780103 -0.890 OOBM770101 -0.937 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 10.04 6.18 5.63 5.76 8.89 5.41 5.37 7.99 7.49 8.72 + 8.79 4.40 9.15 7.98 7.79 7.08 7.00 8.07 6.90 8.88 +// +H WEBA780101 +D RF value in high salt chromatography (Weber-Lacey, 1978) +R LIT:2004106b PMID:691071 +A Weber, A.L. and Lacey, J.C.,Jr. +T Genetic code correlations: Amino acids and their anticodon nucleotides +J J. Mol. Evol. 11, 199-210 (1978) +C ZHOH040102 -0.807 MEEJ800102 -0.808 ROSG850101 -0.817 + MEEJ810101 -0.831 MEEJ810102 -0.854 ZHOH040101 -0.865 + NOZY710101 -0.890 LEVM760107 -0.923 GARJ730101 -0.924 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.89 0.88 0.89 0.87 0.85 0.82 0.84 0.92 0.83 0.76 + 0.73 0.97 0.74 0.52 0.82 0.96 0.92 0.20 0.49 0.85 +// +H WERD780101 +D Propensity to be buried inside (Wertz-Scheraga, 1978) +R LIT:0405105 PMID:621952 +A Wertz, D.H. and Scheraga, H.A. +T Influence of water on protein structure. An analysis of the preferences of + amino acid residues for the inside or outside and for specific conformations + in a protein molecule +J Macromolecules 11, 9-15 (1978) Adjusted values +C NISK860101 0.966 BIOV880101 0.951 ROSG850102 0.943 + MIYS850101 0.934 RADA880108 0.930 BIOV880102 0.929 + CASG920101 0.927 ZHOH040103 0.923 BASU050102 0.920 + CIDH920105 0.905 CIDH920104 0.896 PONP930101 0.895 + MEIH800103 0.895 BAEK050101 0.895 NISK800101 0.891 + NADH010104 0.890 CORJ870107 0.887 PONP800102 0.883 + CORJ870103 0.882 CIDH920103 0.881 NADH010103 0.880 + PONP800101 0.880 CIDH920101 0.878 CORJ870106 0.878 + PONP800103 0.876 CORJ870101 0.873 ROBB790101 0.872 + CIDH920102 0.871 FAUJ830101 0.862 ZHOH040101 0.859 + CORJ870105 0.858 BASU050103 0.857 MANP780101 0.853 + CORJ870104 0.850 PONP800108 0.843 BASU050101 0.843 + PLIV810101 0.841 NADH010102 0.841 NADH010105 0.837 + MEEJ810101 0.825 DESM900102 0.814 CORJ870102 0.804 + SWER830101 0.804 FUKS010102 -0.801 BHAR880101 -0.803 + KRIW710101 -0.819 PUNT030101 -0.821 GRAR740102 -0.826 + FUKS010104 -0.832 KARP850101 -0.842 RACS770103 -0.846 + PARS000101 -0.853 PARJ860101 -0.869 FUKS010103 -0.869 + GUYH850101 -0.871 KRIW790102 -0.875 GUYH850103 -0.876 + CORJ870108 -0.878 VINM940102 -0.886 KRIW790101 -0.899 + MEIH800102 -0.903 RACS770102 -0.906 OOBM770103 -0.906 + KARP850102 -0.909 MIYS990101 -0.912 RACS770101 -0.912 + MIYS990102 -0.914 FASG890101 -0.926 VINM940103 -0.926 + VINM940101 -0.931 MIYS990105 -0.936 MIYS990103 -0.938 + MEIH800101 -0.943 MIYS990104 -0.949 GUYH850102 -0.976 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.52 0.49 0.42 0.37 0.83 0.35 0.38 0.41 0.70 0.79 + 0.77 0.31 0.76 0.87 0.35 0.49 0.38 0.86 0.64 0.72 +// +H WERD780102 +D Free energy change of epsilon(i) to epsilon(ex) (Wertz-Scheraga, 1978) +R LIT:0405105 PMID:621952 +A Wertz, D.H. and Scheraga, H.A. +T Influence of water on protein structure. An analysis of the preferences of + amino acid residues for the inside or outside and for specific conformations + in a protein molecule +J Macromolecules 11, 9-15 (1978) Adjusted values +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.16 -0.20 1.03 -0.24 -0.12 -0.55 -0.45 -0.16 -0.18 -0.19 + -0.44 -0.12 -0.79 -0.25 -0.59 -0.01 0.05 -0.33 -0.42 -0.46 +// +H WERD780103 +D Free energy change of alpha(Ri) to alpha(Rh) (Wertz-Scheraga, 1978) +R LIT:0405105 PMID:621952 +A Wertz, D.H. and Scheraga, H.A. +T Influence of water on protein structure. An analysis of the preferences of + amino acid residues for the inside or outside and for specific conformations + in a protein molecule +J Macromolecules 11, 9-15 (1978) Adjusted values (Met !) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.15 -0.37 0.69 -0.22 -0.19 -0.06 0.14 0.36 -0.25 0.02 + 0.06 -0.16 0.11 1.18 0.11 0.13 0.28 -0.12 0.19 -0.08 +// +H WERD780104 +D Free energy change of epsilon(i) to alpha(Rh) (Wertz-Scheraga, 1978) +R LIT:0405105 PMID:621952 +A Wertz, D.H. and Scheraga, H.A. +T Influence of water on protein structure. An analysis of the preferences of + amino acid residues for the inside or outside and for specific conformations + in a protein molecule +J Macromolecules 11, 9-15 (1978) Adjusted values +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.07 -0.40 -0.57 -0.80 0.17 -0.26 -0.63 0.27 -0.49 0.06 + -0.17 -0.45 0.03 0.40 -0.47 -0.11 0.09 -0.61 -0.61 -0.11 +// +H WOEC730101 +D Polar requirement (Woese, 1973) +R PMID:4588588 +A Woese, C.R. +T Evolution of genetic code +J Naturwiss. 60, 447-459 (1973) +C GRAR740102 0.960 PUNT030102 0.894 HOPT810101 0.886 + HOPA770101 0.876 LEVM760101 0.872 ENGD860101 0.871 + PRAM900101 0.871 MIYS990105 0.849 ROSM880101 0.844 + WOLS870101 0.841 KUHL950101 0.837 OOBM770103 0.835 + VINM940101 0.834 MIYS990104 0.827 PUNT030101 0.825 + MIYS990103 0.824 PARJ860101 0.821 FUKS010102 0.820 + FAUJ880110 0.812 KIDA850101 0.807 MIYS990102 0.805 + MIYS990101 0.805 OOBM770101 0.804 ROSM880102 0.801 + NADH010102 -0.800 CIDH920105 -0.800 MEIH800103 -0.802 + ISOY800102 -0.803 EISD860103 -0.803 ROSG850102 -0.804 + TANS770103 -0.806 BASU050101 -0.811 RADA880101 -0.812 + BIOV880102 -0.819 WIMW960101 -0.821 NISK860101 -0.822 + PONP800103 -0.823 CIDH920104 -0.823 RADA880108 -0.825 + CORJ870102 -0.828 BIOV880101 -0.829 PONP800108 -0.831 + SWER830101 -0.832 BASU050103 -0.836 EISD860101 -0.838 + CORJ870101 -0.841 MAXF760102 -0.842 DESM900102 -0.847 + FAUJ830101 -0.880 ROSM880105 -0.902 BLAS910101 -0.902 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 7.0 9.1 10.0 13.0 5.5 8.6 12.5 7.9 8.4 4.9 + 4.9 10.1 5.3 5.0 6.6 7.5 6.6 5.3 5.7 5.6 +// +H WOLR810101 +D Hydration potential (Wolfenden et al., 1981) +R LIT:0704095 PMID:7213619 +A Wolfenden, R. andersson, L., Cullis, P.M. and Southgate, C.C.B. +T Affinties of amino acid side chains for solvent water +J Biochemistry 20, 849-855 (1981) (Pro 2.9) +C WOLR790101 0.996 RADA880101 0.939 EISD840101 0.914 + RADA880104 0.910 JACR890101 0.908 RADA880107 0.890 + KYTJ820101 0.885 JURD980101 0.881 RADA880105 0.875 + CHOC760103 0.873 OLSK800101 0.869 CHOC760104 0.868 + JANJ780102 0.851 NADH010101 0.848 JANJ790102 0.828 + JANJ780103 -0.822 GUYH850104 -0.826 ROSM880102 -0.829 + CHOC760102 -0.840 OOBM770101 -0.847 JANJ780101 -0.864 + VHEG790101 -0.867 ROSM880101 -0.884 ENGD860101 -0.887 + PRAM900101 -0.887 KUHL950101 -0.898 FAUJ880109 -0.904 + GUYH850105 -0.916 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.94 -19.92 -9.68 -10.95 -1.24 -9.38 -10.20 2.39 -10.27 2.15 + 2.28 -9.52 -1.48 -0.76 -3.68 -5.06 -4.88 -5.88 -6.11 1.99 +// +H WOLS870101 +D Principal property value z1 (Wold et al., 1987) +R LIT:1312098b +A Wold, S., Eriksson, L., Hellberg, S., Jonsson, J., Sjostrom, M., Skagerberg, + B. and Wikstrom, C. +T Principal property values for six non-natural amino acids and their + application to a structure-activity relationship for oxytocin peptide + analogues +J Can. J. Chem. 65, 1814-1820 (1987) +C PARJ860101 0.964 BULH740101 0.929 MIYS990101 0.912 + MIYS990102 0.910 GRAR740102 0.910 ROSM880102 0.877 + PUNT030102 0.868 ROSM880101 0.866 PUNT030101 0.853 + MEIH800101 0.852 OOBM770103 0.852 KIDA850101 0.852 + LEVM760101 0.845 WOEC730101 0.841 MIYS990105 0.838 + GUYH850103 0.836 HOPT810101 0.830 MIYS990104 0.830 + MIYS990103 0.815 MEIH800102 0.813 RACS770102 0.802 + MANP780101 -0.809 EISD840101 -0.820 RADA880101 -0.823 + MEEJ800101 -0.823 SIMZ760101 -0.830 ROBB790101 -0.831 + NAKH900110 -0.832 VENT840101 -0.835 JOND750101 -0.837 + ARGP820101 -0.838 RADA880108 -0.840 EISD860103 -0.841 + BIOV880102 -0.842 NISK860101 -0.848 BASU050102 -0.849 + WILM950101 -0.851 PONP800107 -0.852 BIOV880101 -0.854 + GOLD730101 -0.854 ZHOH040101 -0.858 TAKK010101 -0.858 + BASU050103 -0.866 BASU050101 -0.869 CIDH920102 -0.869 + ZHOH040103 -0.870 ROSM880104 -0.870 BROC820101 -0.871 + RADA880102 -0.873 NOZY710101 -0.874 CIDH920103 -0.879 + COWR900101 -0.883 CORJ870102 -0.885 SWER830101 -0.887 + CIDH920104 -0.891 CIDH920105 -0.899 ROSM880105 -0.899 + MIYS850101 -0.899 MEEJ810102 -0.905 MEEJ810101 -0.906 + EISD860101 -0.918 MEEJ800102 -0.925 FAUJ830101 -0.928 + BLAS910101 -0.930 ZIMJ680105 -0.937 GUOD860101 -0.955 + PLIV810101 -0.963 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.07 2.88 3.22 3.64 0.71 2.18 3.08 2.23 2.41 -4.44 + -4.19 2.84 -2.49 -4.92 -1.22 1.96 0.92 -4.75 -1.39 -2.69 +// +H WOLS870102 +D Principal property value z2 (Wold et al., 1987) +R LIT:1312098b +A Wold, S., Eriksson, L., Hellberg, S., Jonsson, J., Sjostrom, M., Skagerberg, + B. and Wikstrom, C. +T Principal property values for six non-natural amino acids and their + application to a structure-activity relationship for oxytocin peptide + analogues +J Can. J. Chem. 65, 1814-1820 (1987) +C LEVM760102 0.881 FASG760101 0.866 FAUJ880106 0.866 + CHOC760101 0.845 LEVM760105 0.836 FAUJ880103 0.814 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -1.73 2.52 1.45 1.13 -0.97 0.53 0.39 -5.36 1.74 -1.68 + -1.03 1.41 -0.27 1.30 0.88 -1.63 -2.09 3.65 2.32 -2.53 +// +H WOLS870103 +D Principal property value z3 (Wold et al., 1987) +R LIT:1312098b +A Wold, S., Eriksson, L., Hellberg, S., Jonsson, J., Sjostrom, M., Skagerberg, + B. and Wikstrom, C. +T Principal property values for six non-natural amino acids and their + application to a structure-activity relationship for oxytocin peptide + analogues +J Can. J. Chem. 65, 1814-1820 (1987) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.09 -3.44 0.84 2.36 4.13 -1.14 -0.07 0.30 1.11 -1.03 + -0.98 -3.14 -0.41 0.45 2.23 0.57 -1.40 0.85 0.01 -1.29 +// +H YUTK870101 +D Unfolding Gibbs energy in water, pH7.0 (Yutani et al., 1987) +R LIT:2004127b PMID:3299367 +A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. +T Dependence of conformational stability on hydrophobicity of the amino acid + residue in a series of variant proteins substituted at a unique position of + tryptophan synthase alpha subunit +J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) (Arg missing) +C YUTK870102 0.827 EISD840101 0.809 RADA880101 0.803 + GUYH850101 -0.813 GUYH850105 -0.841 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.5 0. 8.2 8.5 11.0 6.3 8.8 7.1 10.1 16.8 + 15.0 7.9 13.3 11.2 8.2 7.4 8.8 9.9 8.8 12.0 +// +H YUTK870102 +D Unfolding Gibbs energy in water, pH9.0 (Yutani et al., 1987) +R LIT:2004127b PMID:3299367 +A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. +T Dependence of conformational stability on hydrophobicity of the amino acid + residue in a series of variant proteins substituted at a unique position of + tryptophan synthase alpha subunit +J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) (Arg missing) +C YUTK870101 0.827 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.8 0. 6.2 7.0 8.3 8.5 4.9 6.4 9.2 10.0 + 12.2 7.5 8.4 8.3 6.9 8.0 7.0 5.7 6.8 9.4 +// +H YUTK870103 +D Activation Gibbs energy of unfolding, pH7.0 (Yutani et al., 1987) +R LIT:2004127b PMID:3299367 +A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. +T Dependence of conformational stability on hydrophobicity of the amino acid + residue in a series of variant proteins substituted at a unique position of + tryptophan synthase alpha subunit +J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) (Arg missing) +C YUTK870104 0.997 EISD860102 -0.839 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 18.08 0. 17.47 17.36 18.17 17.93 18.16 18.24 18.49 18.62 + 18.60 17.96 18.11 17.30 18.16 17.57 17.54 17.19 17.99 18.30 +// +H YUTK870104 +D Activation Gibbs energy of unfolding, pH9.0 (Yutani et al., 1987) +R LIT:2004127b PMID:3299367 +A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. +T Dependence of conformational stability on hydrophobicity of the amino acid + residue in a series of variant proteins substituted at a unique position of + tryptophan synthase alpha subunit +J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) (Arg missing) +C YUTK870103 0.997 EISD860102 -0.840 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 18.56 0. 18.24 17.94 17.84 18.51 17.97 18.57 18.64 19.21 + 19.01 18.36 18.49 17.95 18.77 18.06 17.71 16.87 18.23 18.98 +// +H ZASB820101 +D Dependence of partition coefficient on ionic strength (Zaslavsky et al., + 1982) +R LIT:0806206 +A Zaslavsky, B.Yu, Mestechkina, N.M., Miheeva, L.M. and Rogozhin, S.V. +T Measurement of relative hydrophobicity of amino acid side-chains by partition + in an aqueous two-phase polymeric system: Hydrophobicity scale for non-polar + and ionogenic side-chains +J J. Chromatogr. 240, 21-28 (1982) (C H Y missing?) +C WIMW960101 0.885 CIDH920102 0.809 SNEP660103 0.804 + OOBM850102 -0.853 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.152 -0.089 -0.203 -0.355 0. -0.181 -0.411 -0.190 0. -0.086 + -0.102 -0.062 -0.107 0.001 -0.181 -0.203 -0.170 0.275 0. -0.125 +// +H ZIMJ680101 +D Hydrophobicity (Zimmerman et al., 1968) +R LIT:2004109b PMID:5700434 +A Zimmerman, J.M., Eliezer, N. and Simha, R. +T The characterization of amino acid sequences in proteins by statistical + methods +J J. Theor. Biol. 21, 170-201 (1968) +C SIMZ760101 0.821 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.83 0.83 0.09 0.64 1.48 0.00 0.65 0.10 1.10 3.07 + 2.52 1.60 1.40 2.75 2.70 0.14 0.54 0.31 2.97 1.79 +// +H ZIMJ680102 +D Bulkiness (Zimmerman et al., 1968) +R LIT:2004109b PMID:5700434 +A Zimmerman, J.M., Eliezer, N. and Simha, R. +T The characterization of amino acid sequences in proteins by statistical + methods +J J. Theor. Biol. 21, 170-201 (1968) +C FAUJ880101 0.888 ZHOH040102 0.878 LEVM760106 0.873 + TAKK010101 0.840 BULH740102 0.825 GOLD730101 0.818 + SIMZ760101 0.810 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 11.50 14.28 12.82 11.68 13.46 14.45 13.57 3.40 13.69 21.40 + 21.40 15.71 16.25 19.80 17.43 9.47 15.77 21.67 18.03 21.57 +// +H ZIMJ680103 +D Polarity (Zimmerman et al., 1968) +R LIT:2004109b PMID:5700434 +A Zimmerman, J.M., Eliezer, N. and Simha, R. +T The characterization of amino acid sequences in proteins by statistical + methods +J J. Theor. Biol. 21, 170-201 (1968) +C PRAM900101 0.854 ENGD860101 0.854 HOPA770101 0.815 + JACR890101 -0.835 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.00 52.00 3.38 49.70 1.48 3.53 49.90 0.00 51.60 0.13 + 0.13 49.50 1.43 0.35 1.58 1.67 1.66 2.10 1.61 0.13 +// +H ZIMJ680104 +D Isoelectric point (Zimmerman et al., 1968) +R LIT:2004109b PMID:5700434 +A Zimmerman, J.M., Eliezer, N. and Simha, R. +T The characterization of amino acid sequences in proteins by statistical + methods +J J. Theor. Biol. 21, 170-201 (1968) +C KLEP840101 0.941 FAUJ880111 0.813 FINA910103 0.805 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.00 10.76 5.41 2.77 5.05 5.65 3.22 5.97 7.59 6.02 + 5.98 9.74 5.74 5.48 6.30 5.68 5.66 5.89 5.66 5.96 +// +H ZIMJ680105 +D RF rank (Zimmerman et al., 1968) +R LIT:2004109b PMID:5700434 +A Zimmerman, J.M., Eliezer, N. and Simha, R. +T The characterization of amino acid sequences in proteins by statistical + methods +J J. Theor. Biol. 21, 170-201 (1968) +C MEEJ800102 0.921 EISD860101 0.900 BROC820101 0.896 + PLIV810101 0.875 BROC820102 0.865 ROSM880105 0.857 + TAKK010101 0.856 BLAS910101 0.855 RADA880102 0.851 + GUOD860101 0.850 MEEJ800101 0.842 NOZY710101 0.837 + SWER830101 0.829 CORJ870102 0.828 GOLD730101 0.820 + FAUJ830101 0.816 LAWE840101 0.809 SIMZ760101 0.805 + MIYS990101 -0.801 HOPT810101 -0.816 LEVM760101 -0.844 + BULH740101 -0.879 PARJ860101 -0.886 WOLS870101 -0.937 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.9 4.6 5.4 2.8 2.8 9.0 3.2 5.6 8.2 17.1 + 17.6 3.5 14.9 18.8 14.8 6.9 9.5 17.1 15.0 14.3 +// +H AURR980101 +D Normalized positional residue frequency at helix termini N4'(Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.94 1.15 0.79 1.19 0.60 0.94 1.41 1.18 1.15 1.07 + 0.95 1.03 0.88 1.06 1.18 0.69 0.87 0.91 1.04 0.90 +// +H AURR980102 +D Normalized positional residue frequency at helix termini N"' (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.98 1.14 1.05 1.05 0.41 0.90 1.04 1.25 1.01 0.88 + 0.80 1.06 1.12 1.12 1.31 1.02 0.80 0.90 1.12 0.87 +// +H AURR980103 +D Normalized positional residue frequency at helix termini N" (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.05 0.81 0.91 1.39 0.60 0.87 1.11 1.26 1.43 0.95 + 0.96 0.97 0.99 0.95 1.05 0.96 1.03 1.06 0.94 0.62 +// +H AURR980104 +D Normalized positional residue frequency at helix termini N'(Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C AURR980105 0.839 FINA910101 0.804 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.75 0.90 1.24 1.72 0.66 1.08 1.10 1.14 0.96 0.80 + 1.01 0.66 1.02 0.88 1.33 1.20 1.13 0.68 0.80 0.58 +// +H AURR980105 +D Normalized positional residue frequency at helix termini Nc (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C AURR980104 0.839 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.67 0.76 1.28 1.58 0.37 1.05 0.94 0.98 0.83 0.78 + 0.79 0.84 0.98 0.96 1.12 1.25 1.41 0.94 0.82 0.67 +// +H AURR980106 +D Normalized positional residue frequency at helix termini N1 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.10 1.05 0.72 1.14 0.26 1.31 2.30 0.55 0.83 1.06 + 0.84 1.08 0.90 0.90 1.67 0.81 0.77 1.26 0.99 0.76 +// +H AURR980107 +D Normalized positional residue frequency at helix termini N2 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C RICJ880106 0.800 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.39 0.95 0.67 1.64 0.52 1.60 2.07 0.65 1.36 0.64 + 0.91 0.80 1.10 1.00 0.94 0.69 0.92 1.10 0.73 0.70 +// +H AURR980108 +D Normalized positional residue frequency at helix termini N3 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C AURR980112 0.910 PALJ810102 0.871 CHOP780201 0.867 + KANM800103 0.857 ISOY800101 0.856 AURR980109 0.848 + MAXF760101 0.841 QIAN880106 0.838 ROBB760103 0.835 + AURR980113 0.821 QIAN880104 0.815 ROBB760101 0.814 + BEGF750101 0.810 BURA740101 0.808 QIAN880107 0.803 + MUNV940102 -0.803 MUNV940101 -0.814 CHAM830101 -0.834 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.43 1.33 0.55 0.90 0.52 1.43 1.70 0.56 0.66 1.18 + 1.52 0.82 1.68 1.10 0.15 0.61 0.75 1.68 0.65 1.14 +// +H AURR980109 +D Normalized positional residue frequency at helix termini N4 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C KANM800103 0.944 AURR980114 0.939 ISOY800101 0.894 + QIAN880107 0.893 AURR980113 0.892 SUEM840101 0.882 + PALJ810102 0.877 AURR980112 0.875 MAXF760101 0.865 + QIAN880106 0.862 CHOP780201 0.859 ROBB760103 0.857 + KANM800101 0.852 AURR980108 0.848 RICJ880109 0.828 + BEGF750101 0.821 PTIO830101 0.820 AURR980110 0.817 + ROBB760101 0.810 QIAN880109 0.807 RACS820108 0.804 + QIAN880110 0.802 FINA770101 0.802 QIAN880132 -0.806 + LEVM780103 -0.814 GEIM800111 -0.814 PRAM900104 -0.815 + TANS770110 -0.816 MUNV940102 -0.818 MUNV940101 -0.828 + CHOP780101 -0.837 PALJ810106 -0.845 CHAM830101 -0.896 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.55 1.39 0.60 0.61 0.59 1.43 1.34 0.37 0.89 1.47 + 1.36 1.27 2.13 1.39 0.03 0.44 0.65 1.10 0.93 1.18 +// +H AURR980110 +D Normalized positional residue frequency at helix termini N5 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C AURR980115 0.907 AURR980111 0.867 MAXF760101 0.860 + ISOY800101 0.855 KANM800101 0.830 AURR980109 0.817 + AURR980112 0.816 QIAN880107 0.815 CHOP780201 0.814 + PALJ810102 0.812 AURR980114 0.811 GEOR030108 0.804 + QIAN880106 0.804 MUNV940101 -0.822 MUNV940102 -0.846 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.80 1.73 0.73 0.90 0.55 0.97 1.73 0.32 0.46 1.09 + 1.47 1.24 1.64 0.96 0.15 0.67 0.70 0.68 0.91 0.81 +// +H AURR980111 +D Normalized positional residue frequency at helix termini C5 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C AURR980110 0.867 GEOR030108 0.846 AURR980115 0.835 + PALJ810102 0.830 TANS770101 0.817 CHOP780201 0.813 + AURR980114 0.811 MAXF760101 0.811 ISOY800101 0.801 + AURR980112 0.800 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.52 1.49 0.58 1.04 0.26 1.41 1.76 0.30 0.83 1.25 + 1.26 1.10 1.14 1.14 0.44 0.66 0.73 0.68 1.04 1.03 +// +H AURR980112 +D Normalized positional residue frequency at helix termini C4 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C AURR980108 0.910 PALJ810102 0.888 AURR980109 0.875 + KANM800103 0.871 ISOY800101 0.870 CHOP780201 0.856 + AURR980114 0.853 AURR980115 0.850 AURR980113 0.848 + KANM800101 0.847 GEOR030108 0.846 RACS820108 0.840 + QIAN880106 0.839 MAXF760101 0.838 PALJ810109 0.817 + AURR980110 0.816 GEIM800104 0.815 ROBB760101 0.806 + QIAN880107 0.802 GEIM800101 0.802 AURR980111 0.800 + MUNV940101 -0.819 MUNV940102 -0.853 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.49 1.41 0.67 0.94 0.37 1.52 1.55 0.29 0.96 1.04 + 1.40 1.17 1.84 0.86 0.20 0.68 0.79 1.52 1.06 0.94 +// +H AURR980113 +D Normalized positional residue frequency at helix termini C3 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C KANM800103 0.905 AURR980109 0.892 SUEM840101 0.887 + BEGF750101 0.857 FINA770101 0.849 AURR980112 0.848 + ROBB760103 0.838 AURR980114 0.836 QIAN880106 0.835 + QIAN880105 0.833 PTIO830101 0.833 QIAN880107 0.832 + AURR980108 0.821 ISOY800101 0.815 RICJ880109 0.808 + CHAM830101 -0.828 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.73 1.24 0.70 0.68 0.63 0.88 1.16 0.32 0.76 1.15 + 1.80 1.22 2.21 1.35 0.07 0.65 0.46 1.57 1.10 0.94 +// +H AURR980114 +D Normalized positional residue frequency at helix termini C2 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C AURR980109 0.939 KANM800103 0.916 QIAN880107 0.876 + FINA770101 0.875 ISOY800101 0.857 MAXF760101 0.853 + AURR980112 0.853 KANM800101 0.852 PALJ810102 0.848 + SUEM840101 0.845 AURR980113 0.836 CHOP780201 0.828 + QIAN880110 0.819 RACS820108 0.818 AURR980111 0.811 + AURR980110 0.811 QIAN880109 0.810 PTIO830101 0.809 + AURR980115 0.804 GEOR030108 0.804 QIAN880106 0.803 + ROBB760103 0.801 TANS770101 0.800 CHOP780101 -0.803 + MUNV940102 -0.820 MUNV940101 -0.821 CHAM830101 -0.842 + PALJ810106 -0.842 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.33 1.39 0.64 0.60 0.44 1.37 1.43 0.20 1.02 1.58 + 1.63 1.71 1.76 1.22 0.07 0.42 0.57 1.00 1.02 1.08 +// +H AURR980115 +D Normalized positional residue frequency at helix termini C1 (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C AURR980110 0.907 KANM800101 0.858 MAXF760101 0.852 + AURR980112 0.850 ISOY800101 0.844 AURR980111 0.835 + TANS770101 0.834 PALJ810102 0.827 GEOR030108 0.821 + LEVM780104 0.818 CHOP780201 0.816 GEIM800101 0.804 + AURR980114 0.804 RACS820108 0.802 MUNV940101 -0.807 + MUNV940102 -0.852 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.87 1.66 0.70 0.91 0.33 1.24 1.88 0.33 0.89 0.90 + 1.65 1.63 1.35 0.67 0.03 0.71 0.50 1.00 0.73 0.51 +// +H AURR980116 +D Normalized positional residue frequency at helix termini Cc (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.19 1.45 1.33 0.72 0.44 1.43 1.27 0.74 1.55 0.61 + 1.36 1.45 1.35 1.20 0.10 1.02 0.82 0.58 1.06 0.46 +// +H AURR980117 +D Normalized positional residue frequency at helix termini C' (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C RICJ880115 0.921 MAXF760104 0.849 ISOY800108 0.822 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.77 1.11 1.39 0.79 0.44 0.95 0.92 2.74 1.65 0.64 + 0.66 1.19 0.74 1.04 0.66 0.64 0.82 0.58 0.93 0.53 +// +H AURR980118 +D Normalized positional residue frequency at helix termini C" (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.93 0.96 0.82 1.15 0.67 1.02 1.07 1.08 1.40 1.14 + 1.16 1.27 1.11 1.05 1.01 0.71 0.84 1.06 1.15 0.74 +// +H AURR980119 +D Normalized positional residue frequency at helix termini C"' (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C MUNV940104 0.804 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.09 1.29 1.03 1.17 0.26 1.08 1.31 0.97 0.88 0.97 + 0.87 1.13 0.96 0.84 2.01 0.76 0.79 0.91 0.64 0.77 +// +H AURR980120 +D Normalized positional residue frequency at helix termini C4' (Aurora-Rose, + 1998) +R LIT:2409041 PMID:9514257 +A Aurora, R. and Rose, G. +T Helix capping +J Protein Science 7, 21-38 (1998) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.71 1.09 0.95 1.43 0.65 0.87 1.19 1.07 1.13 1.05 + 0.84 1.10 0.80 0.95 1.70 0.65 .086 1.25 0.85 1.12 +// +H ONEK900101 +D Delta G values for the peptides extrapolated to 0 M urea (O'Neil-DeGrado, + 1990) +R LIT:1701155 PMID:2237415 +A O'Neil, K.T. and DeGrado, W.F. +T A thermodynamic scale for the helix-forming tendencies of the commonly + occurring amino acids +J Science 250, 646-651 (1990) +C BLAM930101 0.965 BUNA790101 0.902 ROBB760103 0.878 + QIAN880108 0.866 PTIO830101 0.847 ROBB760104 0.844 + QIAN880109 0.824 FAUJ880113 0.820 MUNV940105 -0.839 + RACS820114 -0.880 GEOR030109 -0.884 MUNV940101 -0.890 + AVBF000104 -0.899 MUNV940102 -0.910 FINA910102 -0.920 + ONEK900102 -0.982 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 13.4 13.3 12.0 11.7 11.6 12.8 12.2 11.3 11.6 12.0 + 13.0 13.0 12.8 12.1 6.5 12.2 11.7 12.4 12.1 11.9 +// +H ONEK900102 +D Helix formation parameters (delta delta G) (O'Neil-DeGrado, 1990) +R LIT:1701155 PMID:2237415 +A O'Neil, K.T. and DeGrado, W.F. +T A thermodynamic scale for the helix-forming tendencies of the commonly + occurring amino acids +J Science 250, 646-651 (1990) +C FINA910102 0.964 AVBF000104 0.919 GEOR030109 0.908 + MUNV940105 0.876 MUNV940101 0.861 MUNV940102 0.860 + RACS820114 0.855 MUNV940104 0.845 ISOY800104 0.828 + TANS770104 0.826 QIAN880109 -0.800 PTIO830101 -0.830 + FAUJ880113 -0.839 QIAN880108 -0.860 ROBB760104 -0.861 + ROBB760103 -0.867 BUNA790101 -0.949 BLAM930101 -0.974 + ONEK900101 -0.982 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.77 -0.68 -0.07 -0.15 -0.23 -0.33 -0.27 0.00 -0.06 -0.23 + -0.62 -0.65 -0.50 -0.41 3 -0.35 -0.11 -0.45 -0.17 -0.14 +// +H VINM940101 +D Normalized flexibility parameters (B-values), average (Vihinen et al., 1994) +R LIT:2014123 PMID:8090708 +A Vihinen, M., Torkkila, E. and Riikonen, P. +T Accuracy of protein flexibility predictions +J Proteins 19, 141-149 (1994) +C MIYS990104 0.965 MIYS990105 0.952 MIYS990103 0.951 + VINM940102 0.940 OOBM770103 0.936 GUYH850102 0.924 + VINM940103 0.921 FUKS010104 0.919 PARS000101 0.919 + FASG890101 0.904 MEIH800101 0.900 KRIW790101 0.890 + KARP850102 0.885 MIYS990102 0.883 MIYS990101 0.880 + PARS000102 0.877 FUKS010102 0.876 MEIH800102 0.872 + GRAR740102 0.869 CORJ870108 0.862 GUYH850103 0.860 + HOPT810101 0.859 KRIW790102 0.853 PUNT030102 0.850 + RACS770102 0.844 PARJ860101 0.837 RACS770101 0.835 + WOEC730101 0.834 RACS770103 0.830 GUYH850101 0.829 + FUKS010103 0.827 KARP850101 0.821 VINM940104 0.815 + LEVM760101 0.815 MUNV940103 0.811 PUNT030101 0.805 + PALJ810104 -0.801 WIMW960101 -0.804 DESM900101 -0.806 + NADH010105 -0.808 CORJ870102 -0.817 SWER830101 -0.817 + ROSM880105 -0.818 GEIM800107 -0.819 QIAN880120 -0.823 + CORJ870104 -0.826 QIAN880121 -0.828 LIFS790103 -0.829 + DESM900102 -0.829 CHOP780202 -0.831 ZHOH040101 -0.833 + LIFS790101 -0.834 MANP780101 -0.836 CIDH920103 -0.837 + CORJ870103 -0.848 CIDH920101 -0.854 ROBB790101 -0.858 + NADH010102 -0.859 MEIH800103 -0.861 BASU050101 -0.867 + FAUJ830101 -0.871 CIDH920102 -0.872 CORJ870105 -0.873 + CORJ870107 -0.877 PONP800103 -0.878 PONP800101 -0.878 + CORJ870106 -0.881 CIDH920104 -0.883 MIYS850101 -0.883 + PONP800102 -0.883 CIDH920105 -0.885 NADH010103 -0.889 + PONP800108 -0.891 NADH010104 -0.891 BAEK050101 -0.896 + BASU050103 -0.902 BASU050102 -0.904 RADA880108 -0.906 + PONP930101 -0.913 NISK800101 -0.922 ZHOH040103 -0.922 + CORJ870101 -0.924 BIOV880102 -0.929 WERD780101 -0.931 + BIOV880101 -0.941 ROSG850102 -0.943 CASG920101 -0.947 + NISK860101 -0.959 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.984 1.008 1.048 1.068 0.906 1.037 1.094 1.031 0.950 0.927 + 0.935 1.102 0.952 0.915 1.049 1.046 0.997 0.904 0.929 0.931 +// +H VINM940102 +D Normalized flexibility parameters (B-values) for each residue surrounded by + none rigid neighbours (Vihinen et al., 1994) +R LIT:2014123 PMID:8090708 +A Vihinen, M., Torkkila, E. and Riikonen, P. +T Accuracy of protein flexibility predictions +J Proteins 19, 141-149 (1994) +C VINM940101 0.940 MIYS990104 0.922 PARS000101 0.917 + GUYH850102 0.905 MIYS990103 0.895 MIYS990105 0.891 + OOBM770103 0.891 GUYH850103 0.875 KARP850101 0.874 + FUKS010103 0.864 VINM940103 0.855 MIYS990102 0.842 + MIYS990101 0.841 GRAR740102 0.837 FASG890101 0.836 + KARP850102 0.834 KRIW790101 0.834 PARJ860101 0.833 + MEIH800101 0.833 CORJ870108 0.810 FUKS010102 0.808 + FUKS010104 0.807 MUNV940103 0.803 PARS000102 0.803 + CORJ870105 -0.807 PLIV810101 -0.808 NADH010105 -0.809 + ROSG850101 -0.810 CHOP780202 -0.810 SWER830101 -0.811 + CORJ870107 -0.811 NADH010103 -0.812 CORJ870102 -0.812 + QIAN880120 -0.813 PONP800103 -0.820 MANP780101 -0.821 + BIOV880102 -0.826 CORJ870106 -0.830 MIYS850101 -0.832 + NADH010104 -0.834 MEEJ810101 -0.839 PONP800102 -0.842 + LIFS790101 -0.843 FAUJ830101 -0.844 PONP800101 -0.845 + RADA880108 -0.846 CORJ870101 -0.847 ROSG850102 -0.849 + CIDH920103 -0.855 LIFS790103 -0.862 ROBB790101 -0.866 + PONP930101 -0.869 PONP800108 -0.871 BAEK050101 -0.873 + CASG920101 -0.874 BASU050101 -0.874 BIOV880101 -0.876 + BASU050103 -0.880 CIDH920104 -0.884 CIDH920101 -0.885 + WERD780101 -0.886 ZHOH040101 -0.899 NISK800101 -0.900 + CIDH920105 -0.910 NISK860101 -0.919 CIDH920102 -0.925 + BASU050102 -0.937 ZHOH040103 -0.939 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.315 1.310 1.380 1.372 1.196 1.342 1.376 1.382 1.279 1.241 + 1.234 1.367 1.269 1.247 1.342 1.381 1.324 1.186 1.199 1.235 +// +H VINM940103 +D Normalized flexibility parameters (B-values) for each residue surrounded by + one rigid neighbours (Vihinen et al., 1994) +R LIT:2014123 PMID:8090708 +A Vihinen, M., Torkkila, E. and Riikonen, P. +T Accuracy of protein flexibility predictions +J Proteins 19, 141-149 (1994) +C VINM940101 0.921 MIYS990104 0.898 GUYH850102 0.895 + MIYS990103 0.886 MIYS990105 0.880 MEIH800101 0.875 + KRIW790101 0.875 BHAR880101 0.869 FASG890101 0.868 + GUYH850101 0.865 KARP850102 0.863 VINM940102 0.855 + OOBM770103 0.845 MEIH800102 0.841 RACS770102 0.839 + FUKS010104 0.838 KARP850101 0.837 KRIW790102 0.836 + RACS770101 0.829 PARS000101 0.823 MIYS990102 0.818 + MIYS990101 0.817 FUKS010102 0.809 PARS000102 0.808 + FAUJ830101 -0.804 NADH010106 -0.813 PONP800101 -0.813 + CIDH920101 -0.814 BASU050103 -0.814 PONP800103 -0.817 + PONP930101 -0.818 PONP800102 -0.820 NADH010102 -0.824 + DESM900102 -0.824 CIDH920102 -0.826 MEIH800103 -0.830 + CIDH920105 -0.832 CIDH920104 -0.835 NISK800101 -0.836 + CORJ870101 -0.837 MIYS850101 -0.849 BASU050102 -0.856 + RADA880108 -0.862 ZHOH040103 -0.882 NADH010103 -0.882 + NADH010105 -0.884 BIOV880102 -0.889 NADH010104 -0.899 + ROSG850102 -0.901 BIOV880101 -0.901 NISK860101 -0.903 + BAEK050101 -0.906 CASG920101 -0.915 WERD780101 -0.926 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.994 1.026 1.022 1.022 0.939 1.041 1.052 1.018 0.967 0.977 + 0.982 1.029 0.963 0.934 1.050 1.025 0.998 0.938 0.981 0.968 +// +H VINM940104 +D Normalized flexibility parameters (B-values) for each residue surrounded by + two rigid neighbours (Vihinen et al., 1994) +R LIT:2014123 PMID:8090708 +A Vihinen, M., Torkkila, E. and Riikonen, P. +T Accuracy of protein flexibility predictions +J Proteins 19, 141-149 (1994) +C VINM940101 0.815 JANJ780103 0.811 MEIH800102 0.808 + RACS770103 0.804 DESM900102 -0.803 CORJ870101 -0.805 + ROSG850102 -0.809 CASG920101 -0.810 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.783 0.807 0.799 0.822 0.785 0.817 0.826 0.784 0.777 0.776 + 0.783 0.834 0.806 0.774 0.809 0.811 0.795 0.796 0.788 0.781 +// +H MUNV940101 +D Free energy in alpha-helical conformation (Munoz-Serrano, 1994) +R LIT:2105109 PMID:7731949 +A Munoz, V. and Serrano, L. +T Intrinsic secondary structure propensities of the amino acids, using + statistical phi-psi matrices: comparison with experimental scales +J Proteins 20, 301-311 (1994) +C MUNV940102 0.964 ONEK900102 0.861 RACS820114 0.828 + GEOR030109 0.801 CHOP780201 -0.802 AURR980115 -0.807 + AURR980108 -0.814 PALJ810102 -0.815 AURR980112 -0.819 + AURR980114 -0.821 ROBB760101 -0.822 AURR980110 -0.822 + KANM800103 -0.826 AURR980109 -0.828 ROBB760104 -0.831 + MAXF760101 -0.833 QIAN880106 -0.835 FAUJ880113 -0.836 + QIAN880109 -0.841 KANM800101 -0.846 RACS820108 -0.859 + QIAN880108 -0.864 ISOY800101 -0.875 QIAN880107 -0.880 + PTIO830101 -0.880 BLAM930101 -0.882 ONEK900101 -0.890 + ROBB760103 -0.918 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.423 0.503 0.906 0.870 0.877 0.594 0.167 1.162 0.802 0.566 + 0.494 0.615 0.444 0.706 1.945 0.928 0.884 0.690 0.778 0.706 +// +H MUNV940102 +D Free energy in alpha-helical region (Munoz-Serrano, 1994) +R LIT:2105109 PMID:7731949 +A Munoz, V. and Serrano, L. +T Intrinsic secondary structure propensities of the amino acids, using + statistical phi-psi matrices: comparison with experimental scales +J Proteins 20, 301-311 (1994) +C MUNV940101 0.964 RACS820114 0.877 ONEK900102 0.860 + AURR980108 -0.803 ROBB760104 -0.803 CHOP780201 -0.812 + QIAN880105 -0.816 AURR980109 -0.818 AURR980114 -0.820 + KANM800103 -0.823 PALJ810102 -0.824 FAUJ880113 -0.826 + ROBB760101 -0.827 MAXF760101 -0.829 QIAN880108 -0.839 + KANM800101 -0.843 PTIO830101 -0.844 AURR980110 -0.846 + AURR980115 -0.852 AURR980112 -0.853 QIAN880106 -0.867 + BLAM930101 -0.876 ISOY800101 -0.877 QIAN880107 -0.882 + RACS820108 -0.894 ONEK900101 -0.910 ROBB760103 -0.913 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.619 0.753 1.089 0.932 1.107 0.770 0.675 1.361 1.034 0.876 + 0.740 0.784 0.736 0.968 1.780 0.969 1.053 0.910 1.009 0.939 +// +H MUNV940103 +D Free energy in beta-strand conformation (Munoz-Serrano, 1994) +R LIT:2105109 PMID:7731949 +A Munoz, V. and Serrano, L. +T Intrinsic secondary structure propensities of the amino acids, using + statistical phi-psi matrices: comparison with experimental scales +J Proteins 20, 301-311 (1994) +C GEIM800110 0.880 QIAN880134 0.858 QIAN880133 0.836 + MIYS990103 0.831 CORJ870108 0.830 MIYS990104 0.827 + PARS000101 0.826 QIAN880135 0.820 LEVM780106 0.815 + VINM940101 0.811 GEIM800108 0.806 OOBM770103 0.805 + VINM940102 0.803 GEIM800106 -0.800 PONP800102 -0.802 + CORJ870102 -0.802 SWER830101 -0.802 NISK800101 -0.813 + BASU050103 -0.814 MANP780101 -0.815 CORJ870101 -0.817 + PONP800101 -0.819 CORJ870105 -0.829 PALJ810112 -0.830 + ROBB760105 -0.832 CORJ870107 -0.832 BASU050102 -0.839 + NISK860101 -0.840 GEIM800105 -0.841 PALJ810110 -0.845 + BASU050101 -0.846 CORJ870106 -0.848 LEVM780102 -0.848 + PRAM900103 -0.848 PALJ810103 -0.857 KANM800104 -0.857 + PONP930101 -0.864 GEIM800107 -0.869 PALJ810104 -0.888 + ROBB760106 -0.888 LEVM780105 -0.891 CHOP780202 -0.892 + LIFS790103 -0.902 PTIO830102 -0.903 KANM800102 -0.916 + AVBF000101 -0.917 QIAN880119 -0.927 QIAN880121 -0.938 + LIFS790101 -0.941 QIAN880120 -0.959 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.080 0.976 1.197 1.266 0.733 1.050 1.085 1.104 0.906 0.583 + 0.789 1.026 0.812 0.685 1.412 0.987 0.784 0.755 0.665 0.546 +// +H MUNV940104 +D Free energy in beta-strand region (Munoz-Serrano, 1994) +R LIT:2105109 PMID:7731949 +A Munoz, V. and Serrano, L. +T Intrinsic secondary structure propensities of the amino acids, using + statistical phi-psi matrices: comparison with experimental scales +J Proteins 20, 301-311 (1994) +C MUNV940105 0.987 QIAN880134 0.897 FINA910102 0.896 + TANS770104 0.870 ISOY800104 0.866 ONEK900102 0.845 + CHOP780213 0.836 RACS820110 0.831 QIAN880135 0.819 + AURR980119 0.804 PTIO830101 -0.807 AVBF000101 -0.821 + FAUJ880102 -0.824 ROBB760104 -0.840 BUNA790101 -0.865 + BLAM930101 -0.904 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.978 0.784 0.915 1.038 0.573 0.863 0.962 1.405 0.724 0.502 + 0.766 0.841 0.729 0.585 2.613 0.784 0.569 0.671 0.560 0.444 +// +H MUNV940105 +D Free energy in beta-strand region (Munoz-Serrano, 1994) +R LIT:2105109 PMID:7731949 +A Munoz, V. and Serrano, L. +T Intrinsic secondary structure propensities of the amino acids, using + statistical phi-psi matrices: comparison with experimental scales +J Proteins 20, 301-311 (1994) +C MUNV940104 0.987 FINA910102 0.911 QIAN880134 0.899 + ONEK900102 0.876 TANS770104 0.846 ISOY800104 0.844 + RACS820110 0.833 QIAN880135 0.829 CHOP780213 0.826 + PTIO830101 -0.833 ONEK900101 -0.839 ROBB760104 -0.859 + BUNA790101 -0.874 BLAM930101 -0.925 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.40 1.23 1.61 1.89 1.14 1.33 1.42 2.06 1.25 1.02 + 1.33 1.34 1.12 1.07 3.90 1.20 0.99 1.10 0.98 0.87 +// +H WIMW960101 +D Free energies of transfer of AcWl-X-LL peptides from bilayer interface to + water (Wimley-White, 1996) +R LIT:2223095 PMID:8836100 +A Wimley, W.C. and White, S. +T Experimentally determined hydrophobicity scale for proteins at membrane + interfaces +J Nature Structual biol. 3, 842-848 (1996) +C ZASB820101 0.885 MEEJ800101 0.838 CIDH920102 0.837 + MEEJ800102 0.821 ZHOH040101 0.821 NOZY710101 0.818 + PARJ860101 -0.804 VINM940101 -0.804 GRAR740102 -0.804 + FUKS010102 -0.808 LEVM760101 -0.812 OOBM770103 -0.814 + WOEC730101 -0.821 HOPT810101 -0.855 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 4.08 3.91 3.83 3.02 4.49 3.67 2.23 4.24 4.08 4.52 + 4.81 3.77 4.48 5.38 3.80 4.12 4.11 6.10 5.19 4.18 +// +H KIMC930101 +D Thermodynamic beta sheet propensity (Kim-Berg, 1993) +R LIT:1909070 PMID:8459852 +A Kim, C.A. and Berg, J.M. +T Thermodynamic beta-sheet propensities measured using a zinc-finger host + peptide +J Nature 362, 267-270 (1993) +C LEVM760104 0.842 AVBF000101 -0.814 CHAM810101 -0.848 + LEVM760103 -0.861 FAUJ880102 -0.886 AVBF000102 -0.900 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.35 -0.44 -0.38 -0.41 -0.47 -0.40 -0.41 0.0 -0.46 -0.56 + -0.48 -0.41 -0.46 -0.55 -0.23 -0.39 -0.48 -0.48 -0.50 -0.53 +// +H MONM990101 +D Turn propensity scale for transmembrane helices (Monne et al., 1999) +R PMID:10329132 +A Monne, M., Hermansson, M. and von Heijne, G. +T A turn propensity scale for transmembrane helices +J J. Mol. Biol. 288, 141-145 (1999) +C PUNT030102 0.839 PUNT030101 0.839 GRAR740102 0.831 + KRIW790101 0.830 ENGD860101 0.820 PRAM900101 0.820 + MIYS990103 0.809 NADH010105 -0.815 KYTJ820101 -0.842 + DESM900101 -0.848 NADH010104 -0.848 DESM900102 -0.850 + JURD980101 -0.853 NADH010101 -0.860 NADH010103 -0.862 + NADH010102 -0.871 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.5 1.7 1.7 1.6 0.6 1.6 1.6 1.3 1.6 0.6 + 0.4 1.6 0.5 0.4 1.7 0.7 0.4 0.7 0.6 0.5 +// +H BLAM930101 +D Alpha helix propensity of position 44 in T4 lysozyme (Blaber et al., 1993) +R LIT:1915114 PMID:8503008 +A Blaber, M., Zhang, X.J. and Matthews, B.W. +T Structural basis of amino acid alpha helix propensity +J Science 260, 1637-1640 (1993) +C ONEK900101 0.965 BUNA790101 0.945 ROBB760103 0.883 + ROBB760104 0.878 PTIO830101 0.868 QIAN880108 0.860 + FAUJ880113 0.839 QIAN880109 0.828 CHOP780213 -0.824 + QIAN880134 -0.836 TANS770104 -0.837 ISOY800104 -0.860 + RACS820114 -0.862 AVBF000104 -0.872 MUNV940102 -0.876 + MUNV940101 -0.882 GEOR030109 -0.889 MUNV940104 -0.904 + MUNV940105 -0.925 FINA910102 -0.961 ONEK900102 -0.974 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.96 0.77 0.39 0.42 0.42 0.80 0.53 0.00 0.57 0.84 + 0.92 0.73 0.86 0.59 -2.50 0.53 0.54 0.58 0.72 0.63 +// +H PARS000101 +D p-Values of mesophilic proteins based on the distributions of B values + (Parthasarathy-Murthy, 2000) +R PMID:10679524 +A Parthasarathy, S. and Murthy, M.R. +T Protein thermal stability: insights from atomic displacement parameters (B + values) +J Protein Eng. 13, 9-13 (2000) +C VINM940101 0.919 VINM940102 0.917 MIYS990104 0.903 + MIYS990103 0.879 MIYS990105 0.877 OOBM770103 0.864 + CORJ870108 0.854 KARP850102 0.852 GUYH850102 0.839 + GEIM800110 0.831 MIYS990102 0.830 MIYS990101 0.830 + MUNV940103 0.826 VINM940103 0.823 GUYH850103 0.822 + KARP850101 0.816 MEIH800101 0.813 PARJ860101 0.812 + RACS770101 0.804 KRIW790101 0.804 CORJ870104 -0.800 + ROSG850101 -0.805 QIAN880121 -0.809 BIOV880102 -0.813 + CORJ870103 -0.815 BIOV880101 -0.819 ROBB790101 -0.819 + ROSG850102 -0.820 BASU050103 -0.820 BAEK050101 -0.821 + CIDH920103 -0.821 MIYS850101 -0.821 CASG920101 -0.826 + NOZY710101 -0.829 NISK800101 -0.832 BASU050101 -0.835 + LIFS790101 -0.844 ZHOH040101 -0.845 SWER830101 -0.846 + ZHOH040103 -0.846 CORJ870102 -0.848 PONP930101 -0.849 + WERD780101 -0.853 CIDH920105 -0.860 LIFS790103 -0.861 + QIAN880120 -0.863 BASU050102 -0.864 CORJ870107 -0.865 + CIDH920102 -0.871 CIDH920101 -0.877 CORJ870105 -0.878 + NISK860101 -0.884 CORJ870106 -0.891 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.343 0.353 0.409 0.429 0.319 0.395 0.405 0.389 0.307 0.296 + 0.287 0.429 0.293 0.292 0.432 0.416 0.362 0.268 0.22 0.307 +// +H PARS000102 +D p-Values of thermophilic proteins based on the distributions of B values + (Parthasarathy-Murthy, 2000) +R PMID:10679524 +A Parthasarathy, S. and Murthy, M.R. +T Protein thermal stability: insights from atomic displacement parameters (B + values) +J Protein Eng. 13, 9-13 (2000) +C VINM940101 0.877 FUKS010102 0.868 FUKS010104 0.850 + VINM940103 0.808 VINM940102 0.803 NISK800101 -0.814 + CORJ870101 -0.850 CASG920101 -0.859 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.320 0.327 0.384 0.424 0.198 0.436 0.514 0.374 0.299 0.306 + 0.340 0.446 0.313 0.314 0.354 0.376 0.339 0.291 0.287 0.294 +// +H KUMS000101 +D Distribution of amino acid residues in the 18 non-redundant families of + thermophilic proteins (Kumar et al., 2000) +R PMID:10775659 +A Kumar, S., Tsai, C.J. and Nussinov, R. +T Factors enhancing protein thermostability +J Protein Eng. 13, 179-191 (2000) +C KUMS000102 0.971 FUKS010110 0.947 FUKS010109 0.894 + JUKT750101 0.879 CEDJ970104 0.871 DAYM780101 0.866 + JOND920101 0.863 NAKH900101 0.856 JUNJ780101 0.854 + CEDJ970101 0.830 CEDJ970102 0.826 FUKS010111 0.826 + NAKH920107 0.800 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.9 4.6 4.4 6.3 0.6 2.8 6.9 9.4 2.2 7.0 + 7.4 6.1 2.3 3.3 4.2 4.0 5.7 1.3 4.5 8.2 +// +H KUMS000102 +D Distribution of amino acid residues in the 18 non-redundant families of + mesophilic proteins (Kumar et al., 2000) +R PMID:10775659 +A Kumar, S., Tsai, C.J. and Nussinov, R. +T Factors enhancing protein thermostability +J Protein Eng. 13, 179-191 (2000) +C KUMS000101 0.971 JUKT750101 0.948 FUKS010110 0.943 + JUNJ780101 0.927 DAYM780101 0.925 CEDJ970101 0.914 + JOND920101 0.909 CEDJ970104 0.908 FUKS010111 0.898 + NAKH900101 0.894 CEDJ970102 0.881 FUKS010109 0.850 + NAKH920107 0.839 NAKH900109 0.837 FUKS010112 0.819 + CEDJ970103 0.812 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.2 3.6 5.1 6.0 1.0 2.9 6.0 9.4 2.1 6.0 + 7.7 6.5 2.4 3.4 4.2 5.5 5.7 1.2 3.7 8.2 +// +H KUMS000103 +D Distribution of amino acid residues in the alpha-helices in thermophilic + proteins (Kumar et al., 2000) +R PMID:10775659 +A Kumar, S., Tsai, C.J. and Nussinov, R. +T Factors enhancing protein thermostability +J Protein Eng. 13, 179-191 (2000) +C KUMS000104 0.961 FUKS010110 0.827 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 14.1 5.5 3.2 5.7 0.1 3.7 8.8 4.1 2.0 7.1 + 9.1 7.7 3.3 5.0 0.7 3.9 4.4 1.2 4.5 5.9 +// +H KUMS000104 +D Distribution of amino acid residues in the alpha-helices in mesophilic + proteins (Kumar et al., 2000) +R PMID:10775659 +A Kumar, S., Tsai, C.J. and Nussinov, R. +T Factors enhancing protein thermostability +J Protein Eng. 13, 179-191 (2000) +C KUMS000103 0.961 FUKS010110 0.861 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 13.4 3.9 3.7 4.6 0.8 4.8 7.8 4.6 3.3 6.5 + 10.6 7.5 3.0 4.5 1.3 3.8 4.6 1.0 3.3 7.1 +// +H TAKK010101 +D Side-chain contribution to protein stability (kJ/mol) (Takano-Yutani, 2001) +R PMID:11579219 +A Takano, K., Yutani, K. +T A new scale for side-chain contribution to protein stability based on the + empirical stability analysis of mutant proteins +J Protein Eng. 14, 525-528 (2001) +C SIMZ760101 0.936 ARGP820101 0.906 JOND750101 0.906 + MEEJ800102 0.891 NOZY710101 0.884 ZHOH040102 0.874 + GOLD730101 0.872 CIDH920102 0.859 ZIMJ680105 0.856 + ZHOH040101 0.846 LEVM760106 0.841 ZIMJ680102 0.840 + CIDH920105 0.840 ROSM880104 0.840 BROC820102 0.839 + BROC820101 0.836 MEEJ810101 0.836 RADA880102 0.830 + PLIV810101 0.822 MEEJ810102 0.819 LEVM760107 0.819 + VENT840101 0.812 WOLS870101 -0.858 BULH740101 -0.865 + PARJ860101 -0.870 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.8 7.3 3.6 4.9 3.0 2.4 4.4 0 11.9 17.2 + 17.0 10.5 11.9 23.0 15.0 2.6 6.9 24.2 17.2 15.3 +// +H FODM020101 +D Propensity of amino acids within pi-helices (Fodje-Al-Karadaghi, 2002) +R PMID:12034854 +A Fodje, M.N. and Al-Karadaghi, S. +T Occurrence, conformational features and amino acid propensities for the + pi-helix +J Protein Eng. 15, 353-358 (2002) +C TANS770104 -0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.70 0.95 1.47 0.87 1.17 0.73 0.96 0.64 1.39 1.29 + 1.44 0.91 0.91 1.34 0.12 0.84 0.74 1.80 1.68 1.20 +// +H NADH010101 +D Hydropathy scale based on self-information values in the two-state model (5% + accessibility) (Naderi-Manesh et al., 2001) +R PMID:11170200 +A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. +T Prediction of protein surface accessibility with information theory +J Proteins 42, 452-459 (2001) +C JURD980101 0.925 KYTJ820101 0.918 NADH010105 0.912 + DESM900102 0.905 NADH010103 0.904 RADA880101 0.902 + NADH010102 0.898 NADH010104 0.895 JANJ780102 0.892 + CHOC760103 0.881 EISD860103 0.868 CIDH920104 0.865 + EISD840101 0.861 BLAS910101 0.855 BASU050103 0.852 + WOLR810101 0.848 JANJ790101 0.847 MANP780101 0.847 + OLSK800101 0.843 RADA880108 0.838 BIOV880101 0.838 + FAUJ830101 0.837 PONP800103 0.833 ROSG850102 0.833 + PONP800102 0.832 CORJ870101 0.827 PONP800101 0.826 + WOLR790101 0.826 ROSM880105 0.825 DESM900101 0.825 + MEIH800103 0.824 PONP800108 0.820 RADA880104 0.819 + MIYS850101 0.815 PONP930101 0.813 NISK800101 0.813 + NISK860101 0.810 JANJ790102 0.808 CHOC760104 0.804 + BIOV880102 0.804 ZHOH040103 0.803 KIDA850101 -0.803 + GUYH850104 -0.804 JANJ780103 -0.804 RACS770102 -0.808 + MIYS990104 -0.810 FAUJ880110 -0.813 MIYS990102 -0.815 + MIYS990101 -0.816 MEIH800102 -0.818 MIYS990105 -0.821 + MIYS990103 -0.825 KRIW790101 -0.827 VHEG790101 -0.827 + FASG890101 -0.838 ENGD860101 -0.843 PRAM900101 -0.843 + GUYH850105 -0.847 GRAR740102 -0.859 MONM990101 -0.860 + OOBM770101 -0.861 PUNT030101 -0.862 GUYH850101 -0.862 + ROSM880101 -0.866 ROSM880102 -0.870 PUNT030102 -0.872 + KUHL950101 -0.898 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 58 -184 -93 -97 116 -139 -131 -11 -73 107 + 95 -24 78 92 -79 -34 -7 59 -11 100 +// +H NADH010102 +D Hydropathy scale based on self-information values in the two-state model (9% + accessibility) (Naderi-Manesh et al., 2001) +R PMID:11170200 +A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. +T Prediction of protein surface accessibility with information theory +J Proteins 42, 452-459 (2001) +C NADH010103 0.986 NADH010104 0.968 JANJ780102 0.949 + ROSG850102 0.948 JANJ790102 0.945 DESM900102 0.933 + JURD980101 0.931 BIOV880101 0.921 PONP800103 0.921 + KYTJ820101 0.920 BIOV880102 0.914 RADA880108 0.911 + CHOC760103 0.910 CORJ870101 0.909 MEIH800103 0.907 + PONP800102 0.901 NADH010101 0.898 FAUJ830101 0.891 + PONP800108 0.890 CASG920101 0.889 EISD840101 0.887 + BASU050103 0.886 DESM900101 0.885 NISK800101 0.881 + PONP930101 0.880 MIYS850101 0.878 NISK860101 0.878 + NADH010105 0.876 PONP800101 0.875 JANJ790101 0.872 + EISD860103 0.872 WARP780101 0.870 ZHOH040103 0.864 + MANP780101 0.863 OLSK800101 0.856 CIDH920104 0.856 + COWR900101 0.848 RADA880101 0.845 ROSM880105 0.845 + WERD780101 0.841 BLAS910101 0.824 RADA880107 0.823 + CORJ870103 0.823 CHOC760104 0.817 CORJ870107 0.812 + BASU050101 0.812 NADH010106 0.808 BASU050102 0.802 + WOEC730101 -0.800 FUKS010104 -0.801 CORJ870108 -0.803 + KARP850102 -0.807 HOPT810101 -0.820 VINM940103 -0.824 + GUYH850102 -0.824 KRIW710101 -0.825 ROSM880101 -0.830 + KUHL950101 -0.836 OOBM770103 -0.838 MEIH800101 -0.847 + VINM940101 -0.859 GUYH850105 -0.867 MIYS990101 -0.870 + ENGD860101 -0.870 PRAM900101 -0.870 MONM990101 -0.871 + MIYS990102 -0.872 PUNT030102 -0.872 KIDA850101 -0.874 + RACS770103 -0.876 ROSM880102 -0.881 GRAR740102 -0.881 + KRIW790102 -0.890 CHOC760102 -0.893 PUNT030101 -0.897 + RACS770102 -0.899 GUYH850101 -0.910 MIYS990104 -0.910 + MIYS990105 -0.923 MIYS990103 -0.923 JANJ780101 -0.924 + MEIH800102 -0.928 KRIW790101 -0.929 FASG890101 -0.929 + JANJ780103 -0.938 OOBM770101 -0.944 GUYH850104 -0.946 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 51 -144 -84 -78 137 -128 -115 -13 -55 106 + 103 -205 73 108 -79 -26 -3 69 11 108 +// +H NADH010103 +D Hydropathy scale based on self-information values in the two-state model (16% + accessibility) (Naderi-Manesh et al., 2001) +R PMID:11170200 +A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. +T Prediction of protein surface accessibility with information theory +J Proteins 42, 452-459 (2001) +C NADH010104 0.996 NADH010102 0.986 ROSG850102 0.958 + BIOV880101 0.939 NADH010105 0.936 PONP800103 0.932 + JANJ780102 0.923 CORJ870101 0.921 RADA880108 0.919 + PONP800102 0.919 CASG920101 0.914 ZHOH040103 0.913 + BIOV880102 0.913 NISK860101 0.910 DESM900102 0.910 + NISK800101 0.908 PONP800108 0.907 NADH010101 0.904 + BASU050103 0.903 MEIH800103 0.901 JURD980101 0.900 + JANJ790102 0.899 FAUJ830101 0.899 PONP930101 0.898 + MIYS850101 0.896 PONP800101 0.894 KYTJ820101 0.885 + CIDH920104 0.885 NADH010106 0.881 WERD780101 0.880 + JANJ790101 0.879 MANP780101 0.878 CHOC760103 0.875 + DESM900101 0.866 BASU050102 0.862 EISD860103 0.855 + BAEK050101 0.853 EISD840101 0.840 BASU050101 0.839 + CORJ870103 0.830 COWR900101 0.825 ROSM880105 0.822 + CORJ870107 0.817 BLAS910101 0.812 WARP780101 0.811 + CIDH920105 0.810 QIAN880122 0.809 RADA880101 0.809 + OLSK800101 0.807 PLIV810101 0.804 GUOD860101 0.803 + CORJ870104 0.802 FUKS010104 -0.805 HOPT810101 -0.805 + RACS770101 -0.807 KUHL950101 -0.807 VINM940102 -0.812 + CORJ870108 -0.812 GUYH850105 -0.815 ENGD860101 -0.815 + PRAM900101 -0.815 KARP850102 -0.834 CHOC760102 -0.840 + RACS770103 -0.851 ROSM880102 -0.857 KIDA850101 -0.859 + KRIW710101 -0.860 OOBM770103 -0.861 MONM990101 -0.862 + PUNT030102 -0.865 GUYH850102 -0.866 MEIH800101 -0.868 + PUNT030101 -0.868 JANJ780101 -0.868 GRAR740102 -0.881 + VINM940103 -0.882 MIYS990101 -0.887 KRIW790102 -0.887 + MIYS990102 -0.889 VINM940101 -0.889 JANJ780103 -0.892 + RACS770102 -0.893 GUYH850104 -0.899 OOBM770101 -0.902 + MEIH800102 -0.916 GUYH850101 -0.916 MIYS990104 -0.938 + MIYS990105 -0.939 MIYS990103 -0.944 FASG890101 -0.945 + KRIW790101 -0.954 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 41 -109 -74 -47 169 -104 -90 -18 -35 104 + 103 -148 77 128 -81 -31 10 102 36 116 +// +H NADH010104 +D Hydropathy scale based on self-information values in the two-state model (20% + accessibility) (Naderi-Manesh et al., 2001) +R PMID:11170200 +A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. +T Prediction of protein surface accessibility with information theory +J Proteins 42, 452-459 (2001) +C NADH010103 0.996 NADH010102 0.968 NADH010105 0.957 + ROSG850102 0.953 BIOV880101 0.937 PONP800103 0.926 + ZHOH040103 0.925 PONP800102 0.917 CASG920101 0.915 + NISK860101 0.915 RADA880108 0.915 NADH010106 0.914 + CORJ870101 0.914 NISK800101 0.909 PONP800108 0.902 + BIOV880102 0.900 BASU050103 0.899 JANJ780102 0.898 + MIYS850101 0.897 NADH010101 0.895 PONP930101 0.895 + FAUJ830101 0.894 PONP800101 0.892 MEIH800103 0.890 + WERD780101 0.890 CIDH920104 0.888 DESM900102 0.886 + BASU050102 0.879 BAEK050101 0.875 MANP780101 0.873 + JURD980101 0.873 JANJ790101 0.871 JANJ790102 0.868 + KYTJ820101 0.856 CHOC760103 0.848 DESM900101 0.843 + EISD860103 0.840 BASU050101 0.837 CORJ870103 0.820 + CIDH920105 0.817 EISD840101 0.809 CORJ870107 0.808 + COWR900101 0.807 PLIV810101 0.806 QIAN880122 0.804 + GUOD860101 0.803 CORJ870108 -0.805 CHOC760102 -0.809 + RACS770101 -0.813 RACS770103 -0.832 JANJ780101 -0.832 + VINM940102 -0.834 KARP850102 -0.835 ROSM880102 -0.839 + KIDA850101 -0.842 PUNT030101 -0.843 MONM990101 -0.848 + PUNT030102 -0.851 JANJ780103 -0.860 OOBM770103 -0.863 + MEIH800101 -0.867 GUYH850104 -0.867 GRAR740102 -0.868 + OOBM770101 -0.871 KRIW710101 -0.874 GUYH850102 -0.879 + KRIW790102 -0.882 RACS770102 -0.883 MIYS990101 -0.885 + MIYS990102 -0.888 VINM940101 -0.891 VINM940103 -0.899 + MEIH800102 -0.900 GUYH850101 -0.910 MIYS990105 -0.934 + MIYS990104 -0.940 MIYS990103 -0.944 FASG890101 -0.944 + KRIW790101 -0.958 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 32 -95 -73 -29 182 -95 -74 -22 -25 106 + 104 -124 82 132 -82 -34 20 118 44 113 +// +H NADH010105 +D Hydropathy scale based on self-information values in the two-state model (25% + accessibility) (Naderi-Manesh et al., 2001) +R PMID:11170200 +A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. +T Prediction of protein surface accessibility with information theory +J Proteins 42, 452-459 (2001) +C NADH010106 0.958 NADH010104 0.957 NADH010103 0.936 + NADH010101 0.912 ZHOH040103 0.890 NADH010102 0.876 + PONP800102 0.869 CIDH920104 0.869 BASU050102 0.869 + BIOV880101 0.867 PONP800103 0.866 ROSG850102 0.865 + NISK860101 0.863 NISK800101 0.860 BASU050103 0.857 + PONP800101 0.853 BAEK050101 0.850 CORJ870101 0.846 + PONP800108 0.845 RADA880108 0.845 MIYS850101 0.844 + JANJ790101 0.843 MANP780101 0.842 PONP930101 0.839 + CASG920101 0.838 WERD780101 0.837 FAUJ830101 0.822 + JURD980101 0.821 DESM900102 0.816 MEIH800103 0.816 + JANJ780102 0.814 BASU050101 0.811 KYTJ820101 0.804 + CIDH920105 0.800 RACS770102 -0.800 MEIH800101 -0.806 + VINM940101 -0.808 VINM940102 -0.809 GRAR740102 -0.812 + MONM990101 -0.815 GUYH850102 -0.826 MIYS990101 -0.837 + MIYS990102 -0.838 KRIW710101 -0.842 GUYH850101 -0.855 + MIYS990105 -0.856 MIYS990104 -0.874 FASG890101 -0.877 + MIYS990103 -0.879 VINM940103 -0.884 KRIW790101 -0.898 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 24 -79 -76 0 194 -87 -57 -28 -31 102 + 103 -9 90 131 -85 -36 34 116 43 111 +// +H NADH010106 +D Hydropathy scale based on self-information values in the two-state model (36% + accessibility) (Naderi-Manesh et al., 2001) +R PMID:11170200 +A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. +T Prediction of protein surface accessibility with information theory +J Proteins 42, 452-459 (2001) +C NADH010105 0.958 NADH010104 0.914 NADH010103 0.881 + ZHOH040103 0.819 NADH010107 0.811 BAEK050101 0.809 + NADH010102 0.808 PONP800103 0.803 VINM940103 -0.813 + KRIW710101 -0.846 KRIW790101 -0.861 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5 -57 -77 45 224 -67 -8 -47 -50 83 + 82 -38 83 117 -103 -41 79 130 27 117 +// +H NADH010107 +D Hydropathy scale based on self-information values in the two-state model (50% + accessibility) (Naderi-Manesh et al., 2001) +R PMID:11170200 +A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. +T Prediction of protein surface accessibility with information theory +J Proteins 42, 452-459 (2001) +C NADH010106 0.811 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -2 -41 -97 248 329 -37 117 -66 -70 28 + 36 115 62 120 -132 -52 174 179 -7 114 +// +H MONM990201 +D Averaged turn propensities in a transmembrane helix (Monne et al., 1999) +R PMID:10543969 +A Monne, M., Nilsson, I., Elofsson, A. and von Heijne, G. +T Turns in transmembrane helices: determination of the minimal length of a + "helical hairpin" and derivation of a fine-grained turn propensity scale +J J. Mol. Biol. 293, 807-814 (1999) +C FINA910101 0.812 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.4 1.5 1.6 1.5 0.7 1.4 1.3 1.1 1.4 0.5 + 0.3 1.4 0.5 0.3 1.6 0.9 0.7 0.9 0.9 0.4 +// +H KOEP990101 +D Alpha-helix propensity derived from designed sequences (Koehl-Levitt, 1999) +R PMID:10535955 +A Koehl, P. and Levitt, M. +T Structure-based conformational preferences of amino acids +J Proc Natl Acad Sci U S A. 96, 12524-12529 (1999) (Pro missing) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.04 -0.30 0.25 0.27 0.57 -0.02 -0.33 1.24 -0.11 -0.26 + -0.38 -0.18 -0.09 -0.01 0. 0.15 0.39 0.21 0.05 -0.06 +// +H KOEP990102 +D Beta-sheet propensity derived from designed sequences (Koehl-Levitt, 1999) +R PMID:10535955 +A Koehl, P. and Levitt, M. +T Structure-based conformational preferences of amino acids +J Proc Natl Acad Sci U S A. 96, 12524-12529 (1999) (Pro!) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.12 0.34 1.05 1.12 -0.63 1.67 0.91 0.76 1.34 -0.77 + 0.15 0.29 -0.71 -0.67 0. 1.45 -0.70 -0.14 -0.49 -0.70 +// +H CEDJ970101 +D Composition of amino acids in extracellular proteins (percent) (Cedano et + al., 1997) +R PMID:9067612 +A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. +T Relation between amino acid composition and cellular location of proteins +J J. Mol. Biol. 266, 594-600 (1997) +C JUKT750101 0.973 DAYM780101 0.970 JOND920101 0.968 + JUNJ780101 0.968 CEDJ970102 0.965 NAKH900101 0.954 + CEDJ970104 0.944 KUMS000102 0.914 FUKS010110 0.889 + CEDJ970103 0.889 FUKS010112 0.882 FUKS010111 0.878 + NAKH900109 0.861 NAKH920107 0.860 NAKH920104 0.859 + NAKH920101 0.850 NAKH920103 0.843 NAKH900102 0.832 + KUMS000101 0.830 NAKH920106 0.826 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.6 4.2 4.6 4.9 2.9 4.0 5.1 7.8 2.1 4.6 + 8.8 6.3 2.5 3.7 4.9 7.3 6.0 1.4 3.6 6.7 +// +H CEDJ970102 +D Composition of amino acids in anchored proteins (percent) (Cedano et al., + 1997) +R PMID:9067612 +A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. +T Relation between amino acid composition and cellular location of proteins +J J. Mol. Biol. 266, 594-600 (1997) +C JOND920101 0.995 NAKH900101 0.988 CEDJ970104 0.976 + CEDJ970101 0.965 FUKS010112 0.946 DAYM780101 0.945 + JUKT750101 0.942 FUKS010110 0.921 JUNJ780101 0.920 + CEDJ970103 0.912 NAKH920103 0.906 NAKH920104 0.905 + NAKH920101 0.898 NAKH920107 0.891 NAKH920106 0.886 + KUMS000102 0.881 NAKH900109 0.865 NAKH900102 0.841 + FUKS010109 0.839 CEDJ970105 0.835 KUMS000101 0.826 + FUKS010111 0.819 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 7.6 5.0 4.4 5.2 2.2 4.1 6.2 6.9 2.1 5.1 + 9.4 5.8 2.1 4.0 5.4 7.2 6.1 1.4 3.2 6.7 +// +H CEDJ970103 +D Composition of amino acids in membrane proteins (percent) (Cedano et al., + 1997) +R PMID:9067612 +A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. +T Relation between amino acid composition and cellular location of proteins +J J. Mol. Biol. 266, 594-600 (1997) +C NAKH900109 0.970 FUKS010106 0.919 CEDJ970102 0.912 + JOND920101 0.911 NAKH900101 0.908 FUKS010105 0.901 + FUKS010108 0.897 CEDJ970101 0.889 NAKH900111 0.865 + FUKS010107 0.860 CEDJ970104 0.854 FUKS010112 0.850 + FUKS010110 0.848 NAKH920105 0.836 JUKT750101 0.835 + NAKH900107 0.820 NAKH900103 0.815 KUMS000102 0.812 + NAKH920108 0.811 DAYM780101 0.807 JUNJ780101 0.806 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.1 4.6 3.7 3.8 2.0 3.1 4.6 7.0 2.0 6.7 + 11.0 4.4 2.8 5.6 4.7 7.3 5.6 1.8 3.3 7.7 +// +H CEDJ970104 +D Composition of amino acids in intracellular proteins (percent) (Cedano et + al., 1997) +R PMID:9067612 +A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. +T Relation between amino acid composition and cellular location of proteins +J J. Mol. Biol. 266, 594-600 (1997) +C JOND920101 0.983 NAKH900101 0.978 CEDJ970102 0.976 + FUKS010112 0.956 FUKS010110 0.956 DAYM780101 0.952 + CEDJ970101 0.944 JUKT750101 0.942 NAKH920106 0.923 + JUNJ780101 0.921 NAKH920101 0.920 KUMS000102 0.908 + FUKS010109 0.901 KUMS000101 0.871 NAKH920104 0.865 + NAKH920103 0.863 NAKH900102 0.860 NAKH920107 0.857 + CEDJ970103 0.854 CEDJ970105 0.852 NAKH920102 0.834 + NAKH900109 0.821 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 7.9 4.9 4.0 5.5 1.9 4.4 7.1 7.1 2.1 5.2 + 8.6 6.7 2.4 3.9 5.3 6.6 5.3 1.2 3.1 6.8 +// +H CEDJ970105 +D Composition of amino acids in nuclear proteins (percent) (Cedano et al., + 1997) +R PMID:9067612 +A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. +T Relation between amino acid composition and cellular location of proteins +J J. Mol. Biol. 266, 594-600 (1997) +C NAKH920101 0.942 NAKH920106 0.930 NAKH900102 0.903 + NAKH900101 0.860 CEDJ970104 0.852 NAKH920102 0.843 + DAYM780101 0.839 CEDJ970102 0.835 JOND920101 0.834 + JUNJ780101 0.803 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.3 8.7 3.7 4.7 1.6 4.7 6.5 6.3 2.1 3.7 + 7.4 7.9 2.3 2.7 6.9 8.8 5.1 0.7 2.4 5.3 +// +H FUKS010101 +D Surface composition of amino acids in intracellular proteins of thermophiles + (percent) (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C FUKS010102 0.932 FUKS010104 0.885 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 4.47 8.48 3.89 7.05 0.29 2.87 16.56 8.29 1.74 3.30 + 5.06 12.98 1.71 2.32 5.41 4.27 3.83 0.67 2.75 4.05 +// +H FUKS010102 +D Surface composition of amino acids in intracellular proteins of mesophiles + (percent) (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C FUKS010104 0.938 FUKS010101 0.932 VINM940101 0.876 + PARS000102 0.868 HOPT810101 0.854 LEVM760101 0.837 + WOEC730101 0.820 MIYS990104 0.818 MIYS990105 0.813 + VINM940103 0.809 VINM940102 0.808 MIYS990103 0.803 + WERD780101 -0.801 FAUJ830101 -0.805 WIMW960101 -0.808 + BIOV880102 -0.810 RADA880108 -0.815 BIOV880101 -0.820 + CASG920101 -0.831 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.77 6.87 5.50 8.57 0.31 5.24 12.93 7.95 2.80 2.72 + 4.43 10.20 1.87 1.92 4.79 5.41 5.36 0.54 2.26 3.57 +// +H FUKS010103 +D Surface composition of amino acids in extracellular proteins of mesophiles + (percent) (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C GUYH850103 0.874 VINM940102 0.864 GUYH850102 0.848 + KARP850102 0.835 KARP850101 0.834 MEIH800101 0.832 + VINM940101 0.827 MIYS990104 0.822 RACS770101 0.819 + CORJ870108 0.818 FASG890101 0.812 MIYS990103 0.805 + PONP800101 -0.801 CIDH920103 -0.804 PLIV810101 -0.805 + CORJ870107 -0.805 ZHOH040103 -0.808 ROSG850102 -0.808 + BASU050102 -0.809 ROSG850101 -0.819 CIDH920105 -0.821 + CIDH920102 -0.826 MIYS850101 -0.828 CORJ870105 -0.829 + LEVM760106 -0.829 BIOV880101 -0.840 RADA880108 -0.840 + CORJ870106 -0.846 NISK860101 -0.850 CIDH920101 -0.854 + ROBB790101 -0.865 WERD780101 -0.869 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 7.43 4.51 9.12 8.71 0.42 5.42 5.86 9.40 1.49 1.76 + 2.74 9.67 0.60 1.18 5.60 9.60 8.95 1.18 3.26 3.10 +// +H FUKS010104 +D Surface composition of amino acids in nuclear proteins (percent) + (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C FUKS010102 0.938 VINM940101 0.919 FUKS010101 0.885 + HOPT810101 0.884 MIYS990105 0.870 LEVM760101 0.869 + MIYS990104 0.862 KRIW790102 0.853 PARS000102 0.850 + OOBM770103 0.849 MIYS990103 0.845 FASG890101 0.844 + VINM940103 0.838 KRIW790101 0.828 MEIH800102 0.822 + KARP850102 0.822 GUYH850102 0.819 NAKH920106 0.818 + KIDA850101 0.814 VINM940102 0.807 NADH010102 -0.801 + ZHOH040103 -0.803 NADH010103 -0.805 CORJ870101 -0.814 + WERD780101 -0.832 NISK860101 -0.832 FAUJ830101 -0.832 + RADA880108 -0.851 BIOV880101 -0.873 ROSG850102 -0.877 + BIOV880102 -0.887 CASG920101 -0.892 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 5.22 7.30 6.06 7.91 1.01 6.00 10.66 5.81 2.27 2.36 + 4.52 12.68 1.85 1.68 5.70 6.99 5.16 0.56 2.16 4.10 +// +H FUKS010105 +D Interior composition of amino acids in intracellular proteins of thermophiles + (percent) (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C FUKS010106 0.982 NAKH920105 0.929 FUKS010108 0.923 + NAKH900111 0.911 CEDJ970103 0.901 NAKH900109 0.892 + FUKS010107 0.891 NAKH920108 0.890 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.88 3.71 2.35 3.50 1.12 1.66 4.02 6.88 1.88 10.08 + 13.21 3.39 2.44 5.27 3.80 4.10 4.98 1.11 4.07 12.53 +// +H FUKS010106 +D Interior composition of amino acids in intracellular proteins of mesophiles + (percent) (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C FUKS010105 0.982 NAKH900111 0.933 NAKH920105 0.931 + NAKH900109 0.927 FUKS010108 0.927 FUKS010107 0.924 + CEDJ970103 0.919 NAKH920108 0.898 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 10.98 3.26 2.85 3.37 1.47 2.30 3.51 7.48 2.20 9.74 + 12.79 2.54 3.10 4.97 3.42 4.93 5.55 1.28 3.55 10.69 +// +H FUKS010107 +D Interior composition of amino acids in extracellular proteins of mesophiles + (percent) (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C FUKS010106 0.924 NAKH900109 0.903 FUKS010105 0.891 + NAKH900111 0.867 CEDJ970103 0.860 NAKH920105 0.833 + FUKS010108 0.832 NAKH920108 0.817 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.95 3.05 4.84 4.46 1.30 2.64 2.58 8.87 1.99 7.73 + 9.66 2.00 2.45 5.41 3.20 6.03 5.62 2.60 6.15 9.46 +// +H FUKS010108 +D Interior composition of amino acids in nuclear proteins (percent) + (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C NAKH920105 0.968 NAKH900111 0.954 NAKH920108 0.948 + FUKS010106 0.927 FUKS010105 0.923 CEDJ970103 0.897 + NAKH900112 0.896 NAKH900109 0.872 NAKH900103 0.864 + NAKH900105 0.846 FUKS010107 0.832 NAKH900107 0.830 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.26 2.80 2.54 2.80 2.67 2.86 2.67 5.62 1.98 8.95 + 16.46 1.89 2.67 7.32 3.30 6.00 5.00 2.01 3.96 10.24 +// +H FUKS010109 +D Entire chain composition of amino acids in intracellular proteins of + thermophiles (percent) (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C FUKS010110 0.936 CEDJ970104 0.901 KUMS000101 0.894 + FUKS010112 0.890 NAKH900101 0.868 JOND920101 0.861 + KUMS000102 0.850 CEDJ970102 0.839 NAKH920106 0.814 + DAYM780101 0.801 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 7.39 5.91 3.06 5.14 0.74 2.22 9.80 7.53 1.82 6.96 + 9.45 7.81 2.10 3.91 4.54 4.18 4.45 0.90 3.46 8.62 +// +H FUKS010110 +D Entire chain composition of amino acids in intracellular proteins of + mesophiles (percent) (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C CEDJ970104 0.956 KUMS000101 0.947 NAKH900101 0.946 + JOND920101 0.944 KUMS000102 0.943 FUKS010109 0.936 + CEDJ970102 0.921 JUKT750101 0.908 FUKS010112 0.904 + DAYM780101 0.897 CEDJ970101 0.889 JUNJ780101 0.868 + KUMS000104 0.861 NAKH900109 0.853 CEDJ970103 0.848 + NAKH920101 0.833 KUMS000103 0.827 NAKH920106 0.824 + NAKH920107 0.810 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 9.07 4.90 4.05 5.73 0.95 3.63 7.77 7.69 2.47 6.56 + 9.00 6.01 2.54 3.59 4.04 5.15 5.46 0.95 2.96 7.47 +// +H FUKS010111 +D Entire chain composition of amino acids in extracellular proteins of + mesophiles (percent) (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C JUKT750101 0.927 JUNJ780101 0.906 KUMS000102 0.898 + DAYM780101 0.882 CEDJ970101 0.878 NAKH920107 0.841 + JOND920101 0.832 KUMS000101 0.826 CEDJ970102 0.819 + NAKH900101 0.812 MCMT640101 -0.806 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 8.82 3.71 6.77 6.38 0.90 3.89 4.05 9.11 1.77 5.05 + 6.54 5.45 1.62 3.51 4.28 7.64 7.12 1.96 4.85 6.60 +// +H FUKS010112 +D Entire chain compositino of amino acids in nuclear proteins (percent) + (Fukuchi-Nishikawa, 2001) +R PMID:11399062 +A Fukuchi, S. and Nishikawa, K. +T Protein surface amino acid compositions distinctively differ between + thermophilic and mesophilic bacteria +J J. Mol. Biol. 309, 835-843 (2001) +C CEDJ970104 0.956 NAKH900101 0.948 CEDJ970102 0.946 + JOND920101 0.943 NAKH920106 0.921 FUKS010110 0.904 + FUKS010109 0.890 NAKH920104 0.882 CEDJ970101 0.882 + JUKT750101 0.875 NAKH920101 0.856 DAYM780101 0.856 + CEDJ970103 0.850 NAKH920103 0.842 JUNJ780101 0.836 + NAKH920107 0.824 KUMS000102 0.819 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 6.65 5.17 4.40 5.50 1.79 4.52 6.89 5.72 2.13 5.47 + 10.15 7.59 2.24 4.34 4.56 6.52 5.08 1.24 3.01 7.00 +// +H AVBF000101 +D Screening coefficients gamma, local (Avbelj, 2000) +R PMID:10903873 +A Avbelj, F. +T Amino acid conformational preferences and solvation of polar backbone atoms + in peptides and proteins +J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing) +C QIAN880120 0.876 PTIO830102 0.861 KANM800102 0.859 + QIAN880119 0.859 LIFS790101 0.857 QIAN880121 0.855 + CHAM830103 0.843 ROBB760106 0.834 LEVM780105 0.824 + PALJ810104 0.818 PALJ810110 0.816 PRAM900103 0.815 + LEVM780102 0.815 LIFS790103 0.814 AVBF000102 0.805 + LEVM780106 -0.805 GEIM800111 -0.806 QIAN880133 -0.807 + QIAN880132 -0.809 KIMC930101 -0.814 MUNV940104 -0.821 + QIAN880134 -0.822 GEIM800110 -0.825 MUNV940103 -0.917 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.163 0.220 0.124 0.212 0.316 0.274 0.212 0.080 0.315 0.474 + 0.315 0.255 0.356 0.410 NA 0.290 0.412 0.325 0.354 0.515 +// +H AVBF000102 +D Screening coefficients gamma, non-local (Avbelj, 2000) +R PMID:10903873 +A Avbelj, F. +T Amino acid conformational preferences and solvation of polar backbone atoms + in peptides and proteins +J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing) +C FAUJ880102 0.881 LEVM760103 0.816 AVBF000101 0.805 + FAUJ880105 0.802 RACS820110 -0.801 CHAM830101 -0.803 + PALJ810105 -0.815 ISOY800103 -0.821 QIAN880133 -0.823 + LEVM780103 -0.834 PRAM900104 -0.834 QIAN880132 -0.849 + LEVM780106 -0.860 KIMC930101 -0.900 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.236 0.233 0.189 0.168 0.259 0.314 0.306 -0.170 0.256 0.391 + 0.293 0.231 0.367 0.328 NA 0.202 0.308 0.197 0.223 0.436 +// +H AVBF000103 +D Slopes tripeptide, FDPB VFF neutral (Avbelj, 2000) +R PMID:10903873 +A Avbelj, F. +T Amino acid conformational preferences and solvation of polar backbone atoms + in peptides and proteins +J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing) +C AVBF000105 0.965 AVBF000106 0.897 AVBF000107 0.875 + FAUJ880107 0.873 AVBF000108 0.868 AVBF000104 0.865 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.490 -0.429 -0.387 -0.375 -0.352 -0.422 -0.382 -0.647 -0.357 -0.268 + -0.450 -0.409 -0.375 -0.309 NA -0.426 -0.240 -0.325 -0.288 -0.220 +// +H AVBF000104 +D Slopes tripeptides, LD VFF neutral (Avbelj, 2000) +R PMID:10903873 +A Avbelj, F. +T Amino acid conformational preferences and solvation of polar backbone atoms + in peptides and proteins +J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing) +C ONEK900102 0.919 GEOR030109 0.907 FINA910102 0.901 + AVBF000103 0.865 AVBF000107 0.839 AVBF000108 0.819 + BLAM930101 -0.872 ONEK900101 -0.899 BUNA790101 -0.922 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.871 -0.727 -0.741 -0.737 -0.666 -0.728 -0.773 -0.822 -0.685 -0.617 + -0.798 -0.715 -0.717 -0.649 NA -0.679 -0.629 -0.669 -0.655 -0.599 +// +H AVBF000105 +D Slopes tripeptide, FDPB VFF noside (Avbelj, 2000) +R PMID:10903873 +A Avbelj, F. +T Amino acid conformational preferences and solvation of polar backbone atoms + in peptides and proteins +J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing) +C AVBF000103 0.965 AVBF000106 0.939 FAUJ880107 0.931 + AVBF000107 0.879 AVBF000108 0.816 YANJ020101 0.807 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.393 -0.317 -0.268 -0.247 -0.222 -0.291 -0.260 -0.570 -0.244 -0.144 + -0.281 -0.294 -0.274 -0.189 NA -0.280 -0.152 -0.206 -0.155 -0.080 +// +H AVBF000106 +D Slopes tripeptide FDPB VFF all (Avbelj, 2000) +R PMID:10903873 +A Avbelj, F. +T Amino acid conformational preferences and solvation of polar backbone atoms + in peptides and proteins +J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing) +C AVBF000105 0.939 AVBF000103 0.897 FAUJ880107 0.853 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.378 -0.369 -0.245 -0.113 -0.206 -0.290 -0.165 -0.560 -0.295 -0.134 + -0.266 -0.335 -0.260 -0.187 NA -0.251 -0.093 -0.188 -0.147 -0.084 +// +H AVBF000107 +D Slopes tripeptide FDPB PARSE neutral (Avbelj, 2000) +R PMID:10903873 +A Avbelj, F. +T Amino acid conformational preferences and solvation of polar backbone atoms + in peptides and proteins +J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing) +C FAUJ880107 0.884 AVBF000105 0.879 AVBF000103 0.875 + AVBF000104 0.839 AVBF000108 0.832 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.729 -0.535 -0.597 -0.545 -0.408 -0.492 -0.532 -0.860 -0.519 -0.361 + -0.462 -0.508 -0.518 -0.454 NA -0.278 -0.367 -0.455 -0.439 -0.323 +// +H AVBF000108 +D Slopes dekapeptide, FDPB VFF neutral (Avbelj, 2000) +R PMID:10903873 +A Avbelj, F. +T Amino acid conformational preferences and solvation of polar backbone atoms + in peptides and proteins +J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing) +C AVBF000103 0.868 AVBF000107 0.832 AVBF000104 0.819 + AVBF000105 0.816 FAUJ880107 0.802 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.623 -0.567 -0.619 -0.626 -0.571 -0.559 -0.572 -0.679 -0.508 -0.199 + -0.527 -0.581 -0.571 -0.461 NA -0.458 -0.233 -0.327 -0.451 -0.263 +// +H AVBF000109 +D Slopes proteins, FDPB VFF neutral (Avbelj, 2000) +R PMID:10903873 +A Avbelj, F. +T Amino acid conformational preferences and solvation of polar backbone atoms + in peptides and proteins +J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.376 -0.280 -0.403 -0.405 -0.441 -0.362 -0.362 -0.392 -0.345 -0.194 + -0.317 -0.412 -0.312 -0.237 NA -0.374 -0.243 -0.111 -0.171 -0.355 +// +H YANJ020101 +D Side-chain conformation by gaussian evolutionary method (Yang et al., 2002) +R PMID:12142444 +A Yang, J.M., Tsai, C.H., Hwang, M.J., Tsai, H.K., Hwang, J.K. and Kao, C.Y. +T GEM: a Gaussian Evolutionary Method for predicting protein side-chain + conformations +J Protein Sci. 11, 1897-1907 (2002) (Gly Ala missing) +C AVBF000105 0.807 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + NA 0.62 0.76 0.66 0.83 0.59 0.73 NA 0.92 0.88 + 0.89 0.77 0.77 0.92 0.94 0.58 0.73 0.86 0.93 0.88 +// +H MITS020101 +D Amphiphilicity index (Mitaku et al., 2002) +R PMID:12016058 +A Mitaku, S., Hirokawa, T. and Tsuji, T. +T Amphiphilicity index of polar amino acids as an aid in the characterization + of amino acid preference at membrane-water interfaces +J Bioinformatics. 18, 608-616 (2002) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0 2.45 0 0 0 1.25 1.27 0 1.45 0 + 0 3.67 0 0 0 0 0 6.93 5.06 0 +// +H TSAJ990101 +D Volumes including the crystallographic waters using the ProtOr (Tsai et al., + 1999) +R PMID:10388571 +A Tsai, J., Taylor, R., Chothia, C. and Gerstein, M. +T The packing density in proteins: standard radii and volumes +J J. Mol. Biol. 290, 253-266 (1999) (Cyh 112.8) +C TSAJ990102 1.000 CHOC750101 0.995 BIGC670101 0.993 + GOLD730102 0.993 KRIW790103 0.988 FAUJ880103 0.983 + GRAR740103 0.979 CHAM820101 0.977 CHOC760101 0.968 + HARY940101 0.964 PONJ960101 0.960 FASG760101 0.935 + LEVM760105 0.922 ROSG850101 0.914 LEVM760102 0.910 + DAWD720101 0.903 CHAM830106 0.889 FAUJ880106 0.879 + ZHOH040102 0.874 LEVM760107 0.866 RADA880106 0.861 + LEVM760106 0.849 RADA880103 -0.875 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 89.3 190.3 122.4 114.4 102.5 146.9 138.8 63.8 157.5 163.0 + 163.1 165.1 165.8 190.8 121.6 94.2 119.6 226.4 194.6 138.2 +// +H TSAJ990102 +D Volumes not including the crystallographic waters using the ProtOr (Tsai et + al., 1999) +R PMID:10388571 +A Tsai, J., Taylor, R., Chothia, C. and Gerstein, M. +T The packing density in proteins: standard radii and volumes +J J. Mol. Biol. 290, 253-266 (1999) (Cyh 113.7) +C TSAJ990101 1.000 CHOC750101 0.996 BIGC670101 0.992 + GOLD730102 0.991 KRIW790103 0.987 FAUJ880103 0.985 + GRAR740103 0.978 CHAM820101 0.978 CHOC760101 0.972 + HARY940101 0.965 PONJ960101 0.962 FASG760101 0.940 + LEVM760105 0.928 LEVM760102 0.918 ROSG850101 0.909 + DAWD720101 0.905 CHAM830106 0.896 FAUJ880106 0.882 + ZHOH040102 0.867 RADA880106 0.864 LEVM760107 0.861 + LEVM760106 0.841 RADA880103 -0.879 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 90.0 194.0 124.7 117.3 103.3 149.4 142.2 64.9 160.0 163.9 + 164.0 167.3 167.0 191.9 122.9 95.4 121.5 228.2 197.0 139.0 +// +H COSI940101 +D Electron-ion interaction potential values (Cosic, 1994) +R PMID:7851912 +A Cosic, I. +T Macromolecular bioactivity: is it resonant interaction between + macromolecules?--Theory and applications +J IEEE Trans Biomed Eng. 41, 1101-1114 (1994) (values are cited from Protein + Eng. 15:193-203) +C VELV850101 1.000 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.0373 0.0959 0.0036 0.1263 0.0829 0.0761 0.0058 0.0050 0.0242 0.0000 + 0.0000 0.0371 0.0823 0.0946 0.0198 0.0829 0.0941 0.0548 0.0516 0.0057 +// +H PONP930101 +D Hydrophobicity scales (Ponnuswamy, 1993) +R PMID:8419986 +A Ponnuswamy, P.K. +T Hydrophobic characteristics of folded proteins +J Prog Biophys Mol Biol. 59, 57-103 (1993) +C MANP780101 0.967 NISK860101 0.961 CORJ870101 0.960 + NISK800101 0.956 PONP800101 0.945 PONP800108 0.944 + PONP800102 0.934 BASU050103 0.933 BASU050101 0.932 + CIDH920104 0.930 ROSG850102 0.928 CORJ870107 0.923 + CORJ870103 0.920 BASU050102 0.913 BIOV880101 0.912 + CASG920101 0.911 MIYS850101 0.910 PONP800103 0.909 + LIFS790101 0.908 CORJ870104 0.901 CIDH920103 0.899 + NADH010103 0.898 ZHOH040103 0.896 WERD780101 0.895 + NADH010104 0.895 QIAN880121 0.893 RADA880108 0.891 + CIDH920105 0.891 CORJ870106 0.889 NADH010102 0.880 + QIAN880120 0.879 PTIO830102 0.879 CORJ870105 0.878 + BIOV880102 0.877 CHOP780202 0.867 ROBB760106 0.866 + KANM800102 0.866 MEIH800103 0.863 ROBB790101 0.858 + PALJ810104 0.857 BAEK050101 0.856 PONP800107 0.851 + JURD980101 0.849 KYTJ820101 0.844 FAUJ830101 0.843 + NADH010105 0.839 GEIM800107 0.838 QIAN880122 0.837 + QIAN880119 0.836 SWER830101 0.835 DESM900102 0.834 + LIFS790102 0.833 KANM800104 0.833 CORJ870102 0.832 + ROBB760105 0.829 JANJ780102 0.825 CIDH920102 0.820 + PLIV810101 0.819 JANJ790101 0.816 CHOC760103 0.816 + NADH010101 0.813 DESM900101 0.807 GUOD860101 0.802 + GUYH850101 -0.817 VINM940103 -0.818 PUNT030101 -0.820 + KRIW790102 -0.821 PARJ860101 -0.846 PARS000101 -0.849 + GUYH850103 -0.858 MUNV940103 -0.864 VINM940102 -0.869 + RACS770102 -0.871 GRAR740102 -0.872 PUNT030102 -0.872 + MEIH800102 -0.881 RACS770101 -0.886 KARP850102 -0.893 + GUYH850102 -0.897 FASG890101 -0.907 KRIW790101 -0.909 + CORJ870108 -0.912 VINM940101 -0.913 OOBM770103 -0.914 + MIYS990101 -0.916 MEIH800101 -0.916 MIYS990102 -0.919 + MIYS990105 -0.936 MIYS990104 -0.949 MIYS990103 -0.951 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.85 0.20 -0.48 -1.10 2.10 -0.42 -0.79 0 0.22 3.14 + 1.99 -1.19 1.42 1.69 -1.14 -0.52 -0.08 1.76 1.37 2.53 +// +H WILM950101 +D Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/MeCN/H2O (Wilce et + al. 1995) +R +A Wilce, M.C., Aguilar, M.I. and Hearn, M.T. +T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four + new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of + peptides +J Anal Chem. 67, 1210-1219 (1995) +C GUOD860101 0.893 COWR900101 0.860 MEEJ810102 0.849 + VENT840101 0.840 WILM950102 0.838 BLAS910101 0.810 + MIYS990102 -0.822 MIYS990101 -0.822 BULH740101 -0.845 + WOLS870101 -0.851 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.06 -0.85 0.25 -0.20 0.49 0.31 -0.10 0.21 -2.24 3.48 + 3.50 -1.62 0.21 4.80 0.71 -0.62 0.65 2.29 1.89 1.59 +// +H WILM950102 +D Hydrophobicity coefficient in RP-HPLC, C8 with 0.1%TFA/MeCN/H2O (Wilce et al. + 1995) +R +A Wilce, M.C., Aguilar, M.I. and Hearn, M.T. +T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four + new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of + peptides +J Anal Chem. 67, 1210-1219 (1995) +C WILM950101 0.838 MEEJ810102 0.809 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.62 1.26 -1.27 -2.84 0.73 -1.69 -0.45 -1.15 -0.74 4.38 + 6.57 -2.78 -3.12 9.14 -0.12 -1.39 1.81 5.91 1.39 2.30 +// +H WILM950103 +D Hydrophobicity coefficient in RP-HPLC, C4 with 0.1%TFA/MeCN/H2O (Wilce et al. + 1995) +R +A Wilce, M.C., Aguilar, M.I. and Hearn, M.T. +T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four + new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of + peptides +J Anal Chem. 67, 1210-1219 (1995) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -1.64 -3.28 0.83 0.70 9.30 -0.04 1.18 -1.85 7.17 3.02 + 0.83 -2.36 4.26 -1.36 3.12 1.59 2.31 2.61 2.37 0.52 +// +H WILM950104 +D Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/2-PrOH/MeCN/H2O + (Wilce et al. 1995) +R +A Wilce, M.C., Aguilar, M.I. and Hearn, M.T. +T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four + new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of + peptides +J Anal Chem. 67, 1210-1219 (1995) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -2.34 1.60 2.81 -0.48 5.03 0.16 1.30 -1.06 -3.00 7.26 + 1.09 1.56 0.62 2.57 -0.15 1.93 0.19 3.59 -2.58 2.06 +// +H KUHL950101 +D Hydrophilicity scale (Kuhn et al., 1995) +R PMID:8749849 +A Kuhn, L.A., Swanson, C.A., Pique, M.E., Tainer, J.A. and Getzoff, E.D. +T Atomic and residue hydrophilicity in the context of folded protein structures +J Proteins 23, 536-547 (1995) +C ROSM880101 0.962 ROSM880102 0.922 FAUJ880110 0.922 + PRAM900101 0.908 ENGD860101 0.908 KIDA850101 0.882 + OOBM770101 0.876 GRAR740102 0.865 VHEG790101 0.858 + GUYH850105 0.850 PUNT030101 0.844 PUNT030102 0.841 + JANJ780101 0.839 WOEC730101 0.837 GUYH850104 0.835 + GUYH850101 0.827 FAUJ880109 0.827 JANJ780103 0.826 + MEIH800102 0.822 FASG890101 0.821 LEVM760101 0.807 + BASU050103 -0.804 NADH010103 -0.807 BIOV880102 -0.809 + MEIH800103 -0.809 WARP780101 -0.811 JANJ790101 -0.811 + CIDH920104 -0.822 BIOV880101 -0.834 EISD860101 -0.835 + NADH010102 -0.836 RADA880108 -0.839 JANJ790102 -0.844 + RADA880104 -0.847 OLSK800101 -0.849 RADA880107 -0.857 + FAUJ830101 -0.863 DESM900102 -0.863 JACR890101 -0.864 + CHOC760103 -0.865 KYTJ820101 -0.883 JURD980101 -0.884 + JANJ780102 -0.890 EISD860103 -0.894 BLAS910101 -0.894 + ROSM880105 -0.896 WOLR790101 -0.898 WOLR810101 -0.898 + NADH010101 -0.898 EISD840101 -0.907 RADA880101 -0.950 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.78 1.58 1.20 1.35 0.55 1.19 1.45 0.68 0.99 0.47 + 0.56 1.10 0.66 0.47 0.69 1.00 1.05 0.70 1.00 0.51 +// +H GUOD860101 +D Retention coefficient at pH 2 (Guo et al., 1986) +R +A Guo, D., Mant, C.T., Taneja, A.K., Parker, J.M. and Hodges, R.S. +T Prediction of peptide retention times in reversed-phase high-performance + liquid chromatography; I. determination of retention coefficients of amino + acid residues of model synthetic peptides +J J Chromatogr. 359, 499-517 (1986) +C MEEJ810102 0.949 PLIV810101 0.943 MEEJ810101 0.931 + COWR900101 0.920 MIYS850101 0.908 FAUJ830101 0.900 + WILM950101 0.893 ZHOH040103 0.889 ZHOH040101 0.884 + NOZY710101 0.884 BASU050102 0.868 ROSM880104 0.868 + BLAS910101 0.866 MEEJ800102 0.866 CIDH920104 0.860 + CIDH920105 0.858 PONP800107 0.854 SWER830101 0.853 + CORJ870102 0.852 ZIMJ680105 0.850 VENT840101 0.848 + BASU050101 0.847 CIDH920103 0.845 NISK860101 0.840 + EISD860101 0.839 BIOV880101 0.839 BASU050103 0.833 + BROC820101 0.832 CIDH920102 0.831 RADA880102 0.829 + ROSM880105 0.826 BIOV880102 0.817 MANP780101 0.815 + ROBB790101 0.815 RADA880108 0.812 ZHOH040102 0.812 + NAKH900110 0.805 NADH010104 0.803 NADH010103 0.803 + PONP930101 0.802 FASG890101 -0.801 RACS770101 -0.805 + PUNT030101 -0.810 PUNT030102 -0.813 GUYH850103 -0.819 + MIYS990103 -0.828 KIDA850101 -0.828 ROSM880102 -0.829 + MEIH800101 -0.833 OOBM770103 -0.838 MIYS990105 -0.846 + MIYS990104 -0.846 GRAR740102 -0.855 MIYS990102 -0.916 + MIYS990101 -0.917 BULH740101 -0.922 PARJ860101 -0.925 + WOLS870101 -0.955 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 25 -7 -7 2 32 0 14 -2 -26 91 + 100 -26 68 100 25 -2 7 109 56 62 +// +H JURD980101 +D Modified Kyte-Doolittle hydrophobicity scale (Juretic et al., 1998) +R +A Juretic, D., Lucic, B., Zucic, D. and Trinajstic, N. +T Protein transmembrane structure: recognition and prediction by using + hydrophobicity scales through preference functions +J Theoretical and Computational Chemistry, 5, 405-445 (1998) +C KYTJ820101 0.996 CHOC760103 0.967 OLSK800101 0.943 + NADH010102 0.931 JANJ780102 0.928 NADH010101 0.925 + EISD860103 0.901 DESM900102 0.900 NADH010103 0.900 + EISD840101 0.895 RADA880101 0.893 MANP780101 0.887 + WOLR810101 0.881 PONP800103 0.879 JANJ790102 0.879 + NADH010104 0.873 BASU050103 0.871 CHOC760104 0.870 + PONP800102 0.869 JANJ790101 0.868 WOLR790101 0.864 + MEIH800103 0.861 PONP800101 0.858 NAKH920108 0.858 + RADA880108 0.857 PONP800108 0.856 COWR900101 0.855 + ROSG850102 0.854 CORJ870101 0.849 PONP930101 0.849 + RADA880107 0.842 BLAS910101 0.841 BIOV880101 0.840 + MIYS850101 0.837 FAUJ830101 0.833 CIDH920104 0.832 + BASU050101 0.830 DESM900101 0.829 WARP780101 0.827 + KANM800104 0.826 LIFS790102 0.824 RADA880104 0.824 + NADH010105 0.821 ROSM880105 0.818 NISK800101 0.816 + CORJ870104 0.812 NISK860101 0.808 CORJ870103 0.808 + BIOV880102 0.805 CORJ870107 0.804 ARGP820102 0.802 + ARGP820103 0.800 CORJ870108 -0.806 MIYS990104 -0.813 + VHEG790101 -0.814 KRIW790101 -0.824 MIYS990105 -0.829 + MIYS990103 -0.845 CHOC760102 -0.851 ROSM880101 -0.851 + MIYS990101 -0.852 MONM990101 -0.853 JANJ780103 -0.853 + MIYS990102 -0.853 RACS770102 -0.855 FASG890101 -0.857 + ENGD860101 -0.861 PRAM900101 -0.862 JANJ780101 -0.862 + GUYH850101 -0.864 GRAR740102 -0.864 PUNT030102 -0.869 + MEIH800102 -0.879 GUYH850104 -0.880 KUHL950101 -0.884 + PUNT030101 -0.884 ROSM880102 -0.894 GUYH850105 -0.900 + OOBM770101 -0.903 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.10 -5.10 -3.50 -3.60 2.50 -3.68 -3.20 -0.64 -3.20 4.50 + 3.80 -4.11 1.90 2.80 -1.90 -0.50 -0.70 -0.46 -1.3 4.2 +// +H BASU050101 +D Interactivity scale obtained from the contact matrix (Bastolla et al., 2005) +R PMID:15523667 +A Bastolla, U., Porto M., Roman H.E. and Vendruscolo M. +T Principal eigenvector of contact matrices and hydrophobicity profiles in + prote +J Proteins 58, 22-30 (2005) +C BASU050103 0.965 BASU050102 0.946 PONP930101 0.932 + NISK860101 0.926 MANP780101 0.925 SWER830101 0.922 + CORJ870102 0.921 CIDH920104 0.917 ZHOH040103 0.917 + CORJ870107 0.913 CORJ870104 0.910 CIDH920105 0.907 + PTIO830102 0.903 CIDH920103 0.894 PONP800108 0.894 + CORJ870106 0.891 CORJ870103 0.890 CORJ870105 0.888 + MIYS850101 0.888 LIFS790101 0.886 CHOP780202 0.883 + BIOV880101 0.883 PONP800101 0.882 PLIV810101 0.879 + NISK800101 0.876 PALJ810104 0.873 RADA880108 0.867 + PONP800102 0.864 CORJ870101 0.863 CIDH920102 0.858 + VENT840101 0.858 QIAN880120 0.856 KANM800102 0.856 + BLAS910101 0.853 ROBB760105 0.853 FAUJ830101 0.852 + ROBB760106 0.851 ZHOH040101 0.851 KANM800104 0.850 + ROSG850102 0.849 GUOD860101 0.847 GEIM800107 0.847 + ROBB790101 0.845 WERD780101 0.843 PONP800103 0.842 + NADH010103 0.839 CIDH920101 0.839 NADH010104 0.837 + ROSM880104 0.830 JURD980101 0.830 QIAN880121 0.828 + ROSM880105 0.828 KYTJ820101 0.826 PONP800107 0.825 + BIOV880102 0.812 NADH010102 0.812 NADH010105 0.811 + MEEJ810101 0.810 CASG920101 0.806 QIAN880119 0.805 + GUYH850101 -0.807 WOEC730101 -0.811 RACS770102 -0.813 + GUYH850102 -0.815 KRIW790101 -0.821 PUNT030101 -0.822 + MEIH800102 -0.825 PARS000101 -0.835 MUNV940103 -0.846 + OOBM770103 -0.850 RACS770101 -0.850 GUYH850103 -0.852 + BULH740101 -0.854 FASG890101 -0.856 VINM940101 -0.867 + WOLS870101 -0.869 PUNT030102 -0.873 VINM940102 -0.874 + MEIH800101 -0.887 GRAR740102 -0.889 PARJ860101 -0.897 + MIYS990105 -0.900 CORJ870108 -0.916 MIYS990103 -0.918 + MIYS990104 -0.918 MIYS990102 -0.945 MIYS990101 -0.945 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.1366 0.0363 -0.0345 -0.1233 0.2745 0.0325 -0.0484 -0.0464 0.0549 0.4172 + 0.4251 -0.0101 0.1747 0.4076 0.0019 -0.0433 0.0589 0.2362 0.3167 0.4084 +// +H BASU050102 +D Interactivity scale obtained by maximizing the mean of correlation + coefficient over single-domain globular proteins (Bastolla et al., 2005) +R PMID:15523667 +A Bastolla, U., Porto M., Roman H.E. and Vendruscolo M. +T Principal eigenvector of contact matrices and hydrophobicity profiles in + prote +J Proteins 58, 22-30 (2005) +C ZHOH040103 0.978 NISK860101 0.951 ZHOH040101 0.948 + BASU050101 0.946 CIDH920104 0.934 CIDH920105 0.931 + BASU050103 0.925 WERD780101 0.920 CIDH920102 0.914 + PONP930101 0.913 BIOV880101 0.909 MIYS850101 0.904 + BAEK050101 0.898 MEEJ810101 0.898 ROBB790101 0.897 + CIDH920103 0.887 FAUJ830101 0.885 NISK800101 0.884 + CORJ870102 0.881 SWER830101 0.880 PONP800108 0.880 + 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acid sequences +J Bioinformatics 19, 673-674 (2003) +C BAEK050101 0.805 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.058 0.000 0.027 0.016 0.447 -0.073 -0.128 0.331 0.195 0.060 + 0.138 -0.112 0.275 0.240 -0.478 -0.177 -0.163 0.564 0.322 -0.052 +// +H PUNT030101 +D Knowledge-based membrane-propensity scale from 1D_Helix in MPtopo databases + (Punta-Maritan, 2003) +R PMID:12471604 +A Punta, M. and Maritan, A. +T A knowledge-based scale for amino acid membrane propensity +J Proteins 50, 114-121 (2003) +C GUYH850101 0.910 MEIH800102 0.901 PUNT030102 0.899 + RACS770102 0.894 ENGD860101 0.889 PRAM900101 0.889 + MIYS990101 0.888 MIYS990102 0.887 ROSM880101 0.884 + MIYS990105 0.876 VHEG790101 0.876 GRAR740102 0.873 + OOBM770101 0.865 MIYS990103 0.864 ROSM880102 0.861 + MEIH800101 0.860 HOPT810101 0.858 GUYH850105 0.858 + MIYS990104 0.857 KIDA850101 0.856 WOLS870101 0.853 + JANJ780103 0.848 CORJ870108 0.845 FASG890101 0.845 + PARJ860101 0.845 KUHL950101 0.844 GUYH850104 0.840 + MONM990101 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FAUJ830101 -0.908 + ROSM880105 -0.917 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.15 0.32 0.22 0.41 -0.15 0.03 0.30 0.08 0.06 -0.29 + -0.36 0.24 -0.19 -0.22 0.15 0.16 -0.08 -0.28 -0.03 -0.24 +// +H GEOR030101 +D Linker propensity from all dataset (George-Heringa, 2003) +R PMID:12538906 +A George, R.A. and Heringa, J. +T An analysis of protein domain linkers: their classification and role in + protein folding +J Protein Eng. 15, 871-879 (2003) +C GEOR030106 0.938 GEOR030102 0.859 GEOR030103 0.839 + GEOR030104 0.834 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.964 1.143 0.944 0.916 0.778 1.047 1.051 0.835 1.014 0.922 + 1.085 0.944 1.032 1.119 1.299 0.947 1.017 0.895 1 0.955 +// +H GEOR030102 +D Linker propensity from 1-linker dataset (George-Heringa, 2003) +R PMID:12538906 +A George, R.A. and Heringa, J. +T An analysis of protein domain linkers: their classification and role in + protein folding +J Protein Eng. 15, 871-879 (2003) +C GEOR030101 0.859 GEOR030107 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.974 1.129 0.988 0.892 0.972 1.092 1.054 0.845 0.949 0.928 + 1.11 0.946 0.923 1.122 1.362 0.932 1.023 0.879 0.902 0.923 +// +H GEOR030103 +D Linker propensity from 2-linker dataset (George-Heringa, 2003) +R PMID:12538906 +A George, R.A. and Heringa, J. +T An analysis of protein domain linkers: their classification and role in + protein folding +J Protein Eng. 15, 871-879 (2003) +C GEOR030106 0.913 GEOR030101 0.839 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.938 1.137 0.902 0.857 0.6856 0.916 1.139 0.892 1.109 0.986 + 1 0.952 1.077 1.11 1.266 0.956 1.018 0.971 1.157 0.959 +// +H GEOR030104 +D Linker propensity from 3-linker dataset (George-Heringa, 2003) +R PMID:12538906 +A George, R.A. and Heringa, J. +T An analysis of protein domain linkers: their classification and role in + protein folding +J Protein Eng. 15, 871-879 (2003) +C GEOR030106 0.904 GEOR030101 0.834 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.042 1.069 0.828 0.97 0.5 1.111 0.992 0.743 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1.054 0.95 + 1.106 1.003 1.093 1.121 1.314 0.911 0.988 0.939 1.09 0.957 +// +H GEOR030107 +D Linker propensity from long dataset (linker length is greater than 14 + residues) (George-Heringa, 2003) +R PMID:12538906 +A George, R.A. and Heringa, J. +T An analysis of protein domain linkers: their classification and role in + protein folding +J Protein Eng. 15, 871-879 (2003) +C GEOR030102 0.815 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.892 1.154 1.144 0.925 1.035 1.2 1.115 0.917 0.992 0.817 + 0.994 0.944 0.782 1.058 1.309 0.986 1.11 0.841 0.866 0.9 +// +H GEOR030108 +D Linker propensity from helical (annotated by DSSP) dataset (George-Heringa, + 2003) +R PMID:12538906 +A George, R.A. and Heringa, J. +T An analysis of protein domain linkers: their classification and role in + protein folding +J Protein Eng. 15, 871-879 (2003) +C AURR980111 0.846 AURR980112 0.846 AURR980115 0.821 + AURR980110 0.804 AURR980114 0.804 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.092 1.239 0.927 0.919 0.662 1.124 1.199 0.698 1.012 0.912 + 1.276 1.008 1.171 1.09 0.8 0.886 0.832 0.981 1.075 0.908 +// +H GEOR030109 +D Linker propensity from non-helical (annotated by DSSP) dataset + (George-Heringa, 2003) +R PMID:12538906 +A George, R.A. and Heringa, J. +T An analysis of protein domain linkers: their classification and role in + protein folding +J Protein Eng. 15, 871-879 (2003) +C ONEK900102 0.908 AVBF000104 0.907 FINA910102 0.890 + ISOY800104 0.812 MUNV940101 0.801 CHOP780213 0.800 + FAUJ880113 -0.848 ONEK900101 -0.884 BLAM930101 -0.889 + BUNA790101 -0.901 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.843 1.038 0.956 0.906 0.896 0.968 0.9 0.978 1.05 0.946 + 0.885 0.893 0.878 1.151 1.816 1.003 1.189 0.852 0.945 0.999 +// +H ZHOH040101 +D The stability scale from the knowledge-based atom-atom potential (Zhou-Zhou, + 2004) +R PMID:14696193 +A Zhou, H. and Zhou, Y. +T Quantifying the effect of burial of amino acid residues on protein stability +J Proteins 54, 315-322 (2004) +C BASU050102 0.948 CIDH920102 0.939 MEEJ810101 0.935 + ZHOH040103 0.935 NOZY710101 0.932 MEEJ810102 0.922 + ZHOH040102 0.910 CIDH920105 0.904 ROSG850101 0.904 + GUOD860101 0.884 LEVM760106 0.883 ROBB790101 0.872 + NISK860101 0.871 PLIV810101 0.864 CORJ870102 0.862 + SWER830101 0.860 WERD780101 0.859 CIDH920104 0.858 + ROSM880104 0.858 VENT840101 0.858 CIDH920101 0.855 + MIYS850101 0.855 LEVM760107 0.855 BASU050101 0.851 + TAKK010101 0.846 ARGP820101 0.841 FAUJ830101 0.841 + JOND750101 0.841 MEEJ800102 0.838 CIDH920103 0.829 + RADA880102 0.828 BIOV880101 0.825 WIMW960101 0.821 + GOLD730101 0.817 BASU050103 0.813 SIMZ760101 0.808 + LIFS790103 0.801 MIYS990103 -0.824 MEIH800101 -0.827 + KARP850101 -0.833 VINM940101 -0.833 GUYH850102 -0.836 + MIYS990105 -0.838 PARS000101 -0.845 WOLS870101 -0.858 + OOBM770103 -0.862 MIYS990104 -0.864 WEBA780101 -0.865 + MIYS990102 -0.870 MIYS990101 -0.871 BULH740101 -0.876 + GUYH850103 -0.882 VINM940102 -0.899 PARJ860101 -0.912 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 2.18 2.71 1.85 1.75 3.89 2.16 1.89 1.17 2.51 4.50 + 4.71 2.12 3.63 5.88 2.09 1.66 2.18 6.46 5.01 3.77 +// +H ZHOH040102 +D The relative stability scale extracted from mutation experiments (Zhou-Zhou, + 2004) +R PMID:14696193 +A Zhou, H. and Zhou, Y. +T Quantifying the effect of burial of amino acid residues on protein stability +J Proteins 54, 315-322 (2004) +C ROSG850101 0.930 ZHOH040101 0.910 LEVM760106 0.905 + NOZY710101 0.897 BIGC670101 0.884 KRIW790103 0.884 + GOLD730102 0.882 ZIMJ680102 0.878 TSAJ990101 0.874 + TAKK010101 0.874 GRAR740103 0.872 TSAJ990102 0.867 + CIDH920102 0.862 CHOC750101 0.856 LEVM760107 0.843 + VENT840101 0.831 HARY940101 0.830 CHAM820101 0.826 + PONJ960101 0.823 CIDH920105 0.818 FAUJ880103 0.816 + SIMZ760101 0.814 GUOD860101 0.812 CIDH920101 0.811 + PLIV810101 0.809 MEEJ800102 0.808 BASU050102 0.808 + MEEJ810101 0.804 WEBA780101 -0.807 PARJ860101 -0.854 + BULH740101 -0.860 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.79 3.20 2.83 2.33 2.22 2.37 2.52 0.70 3.06 4.59 + 4.72 2.50 3.91 4.84 2.45 1.82 2.45 5.64 4.46 3.67 +// +H ZHOH040103 +D Buriability (Zhou-Zhou, 2004) +R PMID:14696193 +A Zhou, H. and Zhou, Y. +T Quantifying the effect of burial of amino acid residues on protein stability +J Proteins 54, 315-322 (2004) +C BASU050102 0.978 NISK860101 0.946 BIOV880101 0.941 + CIDH920104 0.941 ZHOH040101 0.935 FAUJ830101 0.933 + BASU050103 0.927 CIDH920105 0.926 NADH010104 0.925 + WERD780101 0.923 MEEJ810101 0.921 BASU050101 0.917 + MIYS850101 0.914 NADH010103 0.913 CIDH920102 0.909 + RADA880108 0.904 ROSG850102 0.903 MEEJ810102 0.902 + CASG920101 0.900 PONP930101 0.896 BIOV880102 0.891 + NADH010105 0.890 GUOD860101 0.889 PLIV810101 0.889 + NISK800101 0.888 PONP800108 0.887 BAEK050101 0.884 + CIDH920103 0.881 ROBB790101 0.872 NADH010102 0.864 + MANP780101 0.864 CORJ870101 0.864 SWER830101 0.863 + CORJ870102 0.863 PONP800103 0.861 PONP800102 0.858 + PONP800101 0.847 BLAS910101 0.846 CIDH920101 0.845 + NOZY710101 0.842 ROSM880105 0.839 ROSM880104 0.826 + CORJ870106 0.822 CORJ870107 0.822 MEIH800103 0.820 + NADH010106 0.819 CORJ870103 0.819 LIFS790101 0.815 + PTIO830102 0.813 RADA880102 0.813 CORJ870104 0.809 + VENT840101 0.807 NADH010101 0.803 FUKS010104 -0.803 + FUKS010103 -0.808 PUNT030101 -0.809 LEVM760101 -0.811 + CORJ870108 -0.821 BULH740101 -0.828 HOPT810101 -0.829 + RACS770102 -0.832 RACS770101 -0.835 KARP850102 -0.836 + GUYH850101 -0.839 KARP850101 -0.846 PARS000101 -0.846 + PUNT030102 -0.847 MEIH800102 -0.848 KIDA850101 -0.851 + WOLS870101 -0.870 GUYH850103 -0.879 VINM940103 -0.882 + GRAR740102 -0.895 PARJ860101 -0.897 MEIH800101 -0.898 + KRIW790101 -0.905 OOBM770103 -0.907 FASG890101 -0.910 + GUYH850102 -0.912 VINM940101 -0.922 MIYS990101 -0.926 + MIYS990102 -0.927 MIYS990103 -0.933 MIYS990105 -0.939 + VINM940102 -0.939 MIYS990104 -0.954 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 13.4 8.5 7.6 8.2 22.6 8.5 7.3 7.0 11.3 20.3 + 20.8 6.1 15.7 23.9 9.9 8.2 10.3 24.5 19.5 19.5 +// +H BAEK050101 +D Linker index (Bae et al., 2005) +R PMID:15746283 +A Bae, K., Mallick, B.K. and Elsik, C.G. +T Prediction of protein inter-domain linker regions by a hidden Markov model +J Bioinformatics 21, ??-?? (2005) +C CASG920101 0.919 BASU050102 0.898 WERD780101 0.895 + NISK860101 0.886 ZHOH040103 0.884 NISK800101 0.881 + NADH010104 0.875 ROSG850102 0.868 CORJ870101 0.862 + PONP930101 0.856 BIOV880101 0.853 NADH010103 0.853 + NADH010105 0.850 QIAN880121 0.836 PONP800108 0.833 + PONP800102 0.818 PONP800101 0.812 CIDH920104 0.809 + NADH010106 0.809 BASU050103 0.806 SUYM030101 0.805 + OOBM770103 -0.810 PARS000101 -0.821 KARP850102 -0.839 + FASG890101 -0.859 KRIW790101 -0.860 MIYS990105 -0.871 + VINM940102 -0.873 MIYS990103 -0.877 MIYS990104 -0.892 + VINM940101 -0.896 VINM940103 -0.906 GUYH850102 -0.907 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.0166 -0.0762 -0.0786 -0.1278 0.5724 -0.1051 -0.1794 -0.0442 0.1643 0.2758 + 0.2523 -0.2134 0.0197 0.3561 -0.4188 -0.1629 -0.0701 0.3836 0.2500 0.1782 +// +H HARY940101 +D Mean volumes of residues buried in protein interiors (Harpaz et al., 1994) +R PMID: 7922041 +A Harpaz, Y., Gerstein, M. and Chothia, C. +T Volume changes on protein folding +J Structure 2, 641-649 (1994) (Disulfide bonded cysteine, 103.5) +C PONJ960101 0.989 TSAJ990102 0.965 TSAJ990101 0.964 + CHOC750101 0.961 BIGC670101 0.960 GOLD730102 0.959 + KRIW790103 0.956 FAUJ880103 0.951 CHOC760101 0.946 + GRAR740103 0.946 CHAM820101 0.933 LEVM760105 0.919 + FASG760101 0.910 FAUJ880106 0.909 LEVM760102 0.905 + DAWD720101 0.900 CHAM830106 0.894 ROSG850101 0.869 + RADA880106 0.846 ZHOH040102 0.830 LEVM760106 0.829 + LEVM760107 0.815 RADA880103 -0.840 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 90.1 192.8 127.5 117.1 113.2 149.4 140.8 63.8 159.3 164.9 + 164.6 170.0 167.7 193.5 123.1 94.2 120.0 197.1 231.7 139.1 +// +H PONJ960101 +D Average volumes of residues (Pontius et al., 1996) +R PMID: 8950272 +A Pontius, J., Richelle, J. and Wodak, S.J. +T Deviations from standard atomic volumes as a quality measure for protein + crystal structures +J J. Mol. Biol 264, 121-136 (1996) (Disulfide bonded cysteine, 102.4) +C HARY940101 0.989 CHOC750101 0.966 FAUJ880103 0.963 + TSAJ990102 0.962 CHOC760101 0.961 TSAJ990101 0.960 + BIGC670101 0.950 GOLD730102 0.947 FASG760101 0.945 + KRIW790103 0.943 CHAM820101 0.938 GRAR740103 0.937 + LEVM760102 0.930 LEVM760105 0.928 CHAM830106 0.917 + FAUJ880106 0.913 DAWD720101 0.873 ROSG850101 0.862 + RADA880106 0.860 LEVM760107 0.827 ZHOH040102 0.823 + RADA880103 -0.873 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 91.5 196.1 138.3 135.2 114.4 156.4 154.6 67.5 163.2 162.6 + 163.4 162.5 165.9 198.8 123.4 102.0 126.0 209.8 237.2 138.4 +// +H DIGM050101 +D Hydrostatic pressure asymmetry index, PAI (Di Giulio, 2005) +R PMID: 15716096 +A Di Giulio M. +T A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: + barophily in the physicochemical properties of amino acids and in the genetic + code +J Gene 346, 1-6 (2005) +C +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.076 1.361 1.056 1.290 0.753 0.729 1.118 1.346 0.985 0.926 + 1.054 1.105 0.974 0.869 0.820 1.342 0.871 0.666 0.531 1.131 +// +H WOLR790101 +D Hydrophobicity index (Wolfenden et al., 1979) +R PMID:493962 +A Wolfenden, R.V., Cullis, P.M. and Southgate, C.C.F. +T Water, protein folding, and the genetic code +J Science 206, 575-577 (1979) +C WOLR810101 0.996 RADA880101 0.933 RADA880104 0.926 + EISD840101 0.909 JACR890101 0.906 RADA880107 0.905 + RADA880105 0.903 KYTJ820101 0.869 JURD980101 0.864 + OLSK800101 0.859 CHOC760103 0.857 CHOC760104 0.851 + JANJ780102 0.833 NADH010101 0.826 JANJ790102 0.818 + JANJ780103 -0.806 GUYH850104 -0.815 OOBM770101 -0.831 + CHOC760102 -0.834 ROSM880102 -0.836 VHEG790101 -0.844 + JANJ780101 -0.856 ENGD860101 -0.877 PRAM900101 -0.877 + ROSM880101 -0.887 KUHL950101 -0.898 GUYH850105 -0.908 + FAUJ880109 -0.920 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.12 -2.55 -0.83 -0.83 0.59 -0.78 -0.92 1.20 -0.93 1.16 + 1.18 -0.80 0.55 0.67 0.54 -0.05 -0.02 -0.19 -0.23 1.13 +// +H OLSK800101 +D Average internal preferences (Olsen, 1980) +R PMID:7378453 +A Olsen, K.W. +T Internal residue criteria for predicting three-dimensional protein structures +J Biochim. Biophys. Acta 622, 259-267 (1980) +C CHOC760103 0.981 JURD980101 0.943 KYTJ820101 0.942 + JANJ780102 0.905 EISD860103 0.881 RADA880107 0.874 + CHOC760104 0.872 JANJ790102 0.870 WOLR810101 0.869 + EISD840101 0.869 WOLR790101 0.859 NADH010102 0.856 + DESM900102 0.849 NADH010101 0.843 RADA880101 0.840 + JANJ790101 0.828 MEIH800103 0.826 WARP780101 0.818 + LIFS790102 0.818 MANP780101 0.817 RADA880104 0.814 + NADH010103 0.807 PONP800103 0.801 ENGD860101 -0.805 + PRAM900101 -0.806 ROSM880101 -0.806 FAUJ880109 -0.821 + GUYH850101 -0.823 PUNT030101 -0.838 JANJ780103 -0.845 + RACS770102 -0.845 ROSM880102 -0.847 KUHL950101 -0.849 + MEIH800102 -0.858 JANJ780101 -0.858 GUYH850104 -0.871 + OOBM770101 -0.878 CHOC760102 -0.886 GUYH850105 -0.927 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.38 0.00 0.37 0.52 1.43 0.22 0.71 1.34 0.66 2.32 + 1.47 0.15 1.78 1.72 0.85 0.86 0.89 0.82 0.47 1.99 +// +H KIDA850101 +D Hydrophobicity-related index (Kidera et al., 1985) +R +A Kidera, A., Konishi, Y., Oka, M., Ooi, T. and Scheraga, A. +T Statistical Analysis of the Physical Properties of the 20 Naturally Occuring + Amino Acids +J J. Prot. Chem. 4, 23-55 (1985) +C ROSM880101 0.933 ROSM880102 0.920 LEVM760101 0.915 + KUHL950101 0.882 HOPT810101 0.881 GRAR740102 0.881 + PRAM900101 0.866 ENGD860101 0.866 MIYS990105 0.865 + FASG890101 0.861 PUNT030101 0.856 WOLS870101 0.852 + GUYH850104 0.848 JANJ780101 0.843 OOBM770101 0.843 + JANJ780103 0.842 MEIH800102 0.834 GUYH850101 0.834 + MIYS990104 0.822 MIYS990101 0.817 MIYS990102 0.817 + FUKS010104 0.814 PARJ860101 0.809 WOEC730101 0.807 + PUNT030102 0.807 MIYS990103 0.805 CHOC760102 0.804 + NADH010101 -0.803 CIDH920105 -0.803 RADA880104 -0.805 + BASU050103 -0.806 NAKH900110 -0.808 MEIH800103 -0.813 + CASG920101 -0.817 MEEJ800102 -0.823 GUOD860101 -0.828 + JANJ780102 -0.828 MIYS850101 -0.831 EISD860103 -0.832 + JACR890101 -0.836 CIDH920104 -0.836 RADA880107 -0.837 + PLIV810101 -0.841 NADH010104 -0.842 ROSG850102 -0.849 + MEEJ810101 -0.850 MEEJ810102 -0.851 ZHOH040103 -0.851 + JANJ790102 -0.858 NADH010103 -0.859 COWR900101 -0.868 + NADH010102 -0.874 RADA880108 -0.875 RADA880101 -0.883 + EISD860101 -0.890 BIOV880102 -0.892 BIOV880101 -0.893 + EISD840101 -0.900 BLAS910101 -0.901 ROSM880105 -0.922 + FAUJ830101 -0.946 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.27 1.87 0.81 0.81 -1.05 1.10 1.17 -0.16 0.28 -0.77 + -1.10 1.70 -0.73 -1.43 -0.75 0.42 0.63 -1.57 -0.56 -0.40 +// +H GUYH850102 +D Apparent partition energies calculated from Wertz-Scheraga index (Guy, 1985) +R PMID:3978191 +A Guy, H.R. +T Amino acid side-chain partition energies and distribution of residues in + soluble proteins +J Biophys. J. 47, 61-70 (1985) +C MIYS990104 0.928 VINM940101 0.924 MIYS990103 0.914 + MIYS990105 0.912 FASG890101 0.909 VINM940102 0.905 + OOBM770103 0.904 MEIH800101 0.899 VINM940103 0.895 + KARP850102 0.882 KRIW790101 0.878 MIYS990102 0.868 + GUYH850103 0.866 MIYS990101 0.865 RACS770101 0.859 + MEIH800102 0.856 RACS770102 0.853 FUKS010103 0.848 + KRIW790102 0.841 PARS000101 0.839 PARJ860101 0.836 + CORJ870108 0.821 RACS770103 0.821 FUKS010104 0.819 + KARP850101 0.811 KRIW710101 0.811 GRAR740102 0.806 + GUYH850101 0.805 PLIV810101 -0.802 CORJ870105 -0.804 + MEEJ810101 -0.813 BASU050101 -0.815 NADH010102 -0.824 + NADH010105 -0.826 CORJ870106 -0.830 CORJ870107 -0.834 + ZHOH040101 -0.836 CORJ870103 -0.841 CIDH920101 -0.843 + BASU050103 -0.845 MANP780101 -0.850 MEIH800103 -0.854 + CIDH920102 -0.855 PONP800103 -0.856 FAUJ830101 -0.857 + ROBB790101 -0.862 NADH010103 -0.866 CIDH920103 -0.871 + PONP800108 -0.873 PONP800101 -0.873 PONP800102 -0.874 + NADH010104 -0.879 CORJ870101 -0.883 MIYS850101 -0.884 + CIDH920105 -0.892 CIDH920104 -0.894 PONP930101 -0.897 + RADA880108 -0.902 BIOV880102 -0.903 BAEK050101 -0.907 + BASU050102 -0.911 ZHOH040103 -0.912 NISK800101 -0.914 + BIOV880101 -0.922 ROSG850102 -0.925 CASG920101 -0.941 + NISK860101 -0.950 WERD780101 -0.976 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.05 0.12 0.29 0.41 -0.84 0.46 0.38 0.31 -0.41 -0.69 + -0.62 0.57 -0.38 -0.45 0.46 0.12 0.38 -0.98 -0.25 -0.46 +// +H GUYH850103 +D Apparent partition energies calculated from Robson-Osguthorpe index (Guy, + 1985) +R PMID:3978191 +A Guy, H.R. +T Amino acid side-chain partition energies and distribution of residues in + soluble proteins +J Biophys. J. 47, 61-70 (1985) (Gly missing) +C OOBM770103 0.906 PARJ860101 0.897 MIYS990102 0.888 + MIYS990101 0.886 MIYS990105 0.883 MIYS990104 0.879 + VINM940102 0.875 FUKS010103 0.874 MEIH800101 0.873 + GUYH850102 0.866 VINM940101 0.860 FASG890101 0.860 + MIYS990103 0.857 RACS770101 0.844 WOLS870101 0.836 + CORJ870108 0.831 GRAR740102 0.831 PARS000101 0.822 + BULH740101 0.820 CORJ870103 -0.804 JOND750101 -0.807 + ROSM880104 -0.807 PONP800102 -0.808 ARGP820101 -0.808 + CORJ870104 -0.809 MEEJ800102 -0.809 CORJ870101 -0.815 + BIOV880102 -0.818 GUOD860101 -0.819 LEVM760106 -0.822 + PONP800101 -0.822 MEEJ810102 -0.823 PONP800108 -0.828 + NISK800101 -0.828 CORJ870105 -0.830 MANP780101 -0.833 + CORJ870107 -0.833 CORJ870106 -0.837 SWER830101 -0.839 + CORJ870102 -0.839 ROSG850102 -0.844 CASG920101 -0.846 + BASU050101 -0.852 CIDH920101 -0.854 BASU050103 -0.854 + PONP930101 -0.858 MEEJ810101 -0.864 FAUJ830101 -0.870 + RADA880108 -0.870 WERD780101 -0.876 ZHOH040103 -0.879 + PLIV810101 -0.881 ZHOH040101 -0.882 BIOV880101 -0.890 + CIDH920103 -0.890 MIYS850101 -0.897 CIDH920102 -0.904 + BASU050102 -0.904 CIDH920104 -0.906 NISK860101 -0.914 + CIDH920105 -0.927 ROBB790101 -0.999 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.54 -0.16 0.38 0.65 -1.13 0.05 0.38 NA -0.59 -2.15 + -1.08 0.48 -0.97 -1.51 -0.22 0.65 0.27 -1.61 -1.13 -0.75 +// +H GUYH850104 +D Apparent partition energies calculated from Janin index (Guy, 1985) +R PMID:3978191 +A Guy, H.R. +T Amino acid side-chain partition energies and distribution of residues in + soluble proteins +J Biophys. J. 47, 61-70 (1985) +C JANJ780101 0.989 JANJ780103 0.983 CHOC760102 0.970 + OOBM770101 0.966 GUYH850105 0.908 MEIH800102 0.892 + ENGD860101 0.881 PRAM900101 0.881 FASG890101 0.872 + GUYH850101 0.857 ROSM880102 0.856 KRIW790102 0.849 + RACS770102 0.849 KIDA850101 0.848 PUNT030101 0.840 + RACS770103 0.839 KUHL950101 0.835 KRIW790101 0.822 + MIYS990105 0.821 ROSM880101 0.814 FAUJ880109 0.812 + MIYS990103 0.805 NADH010101 -0.804 PONP800108 -0.807 + WOLR790101 -0.815 FAUJ830101 -0.816 CASG920101 -0.819 + DESM900101 -0.824 PONP800102 -0.824 WOLR810101 -0.826 + JACR890101 -0.827 CORJ870101 -0.830 RADA880101 -0.831 + EISD860103 -0.835 BIOV880101 -0.844 CHOC760104 -0.845 + PONP800103 -0.845 RADA880108 -0.847 MEIH800103 -0.854 + BIOV880102 -0.855 JANJ790101 -0.862 NADH010104 -0.867 + KYTJ820101 -0.869 OLSK800101 -0.871 JURD980101 -0.880 + WARP780101 -0.882 ROSG850102 -0.891 EISD840101 -0.892 + DESM900102 -0.896 RADA880107 -0.896 NADH010103 -0.899 + CHOC760103 -0.907 NADH010102 -0.946 JANJ780102 -0.968 + JANJ790102 -0.999 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.31 1.30 0.49 0.58 -0.87 0.70 0.68 -0.33 0.13 -0.66 + -0.53 1.79 -0.38 -0.45 0.34 0.10 0.21 -0.27 0.40 -0.62 +// +H GUYH850105 +D Apparent partition energies calculated from Chothia index (Guy, 1985) +R PMID:3978191 +A Guy, H.R. +T Amino acid side-chain partition energies and distribution of residues in + soluble proteins +J Biophys. J. 47, 61-70 (1985) +C CHOC760102 0.946 FAUJ880109 0.927 JANJ780101 0.923 + GUYH850104 0.908 JANJ780103 0.885 OOBM770101 0.874 + ROSM880102 0.874 PRAM900101 0.867 ENGD860101 0.867 + PUNT030101 0.858 KUHL950101 0.850 ROSM880101 0.849 + VHEG790101 0.845 GUYH850101 0.843 MEIH800102 0.811 + RADA880105 -0.809 EISD860103 -0.812 NADH010103 -0.815 + DESM900102 -0.818 CHOC760104 -0.822 YUTK870101 -0.841 + NADH010101 -0.847 NADH010102 -0.867 KYTJ820101 -0.883 + JACR890101 -0.887 JANJ780102 -0.898 RADA880104 -0.899 + RADA880101 -0.899 JURD980101 -0.900 WOLR790101 -0.908 + JANJ790102 -0.913 WOLR810101 -0.916 OLSK800101 -0.927 + CHOC760103 -0.933 EISD840101 -0.951 RADA880107 -0.953 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.27 2.00 0.61 0.50 -0.23 1.00 0.33 -0.22 0.37 -0.80 + -0.44 1.17 -0.31 -0.55 0.36 0.17 0.18 0.05 0.48 -0.65 +// +H ROSM880104 +D Hydropathies of amino acid side chains, neutral form (Roseman, 1988) +R PMID:3398047 +A Roseman, M.A. +T Hydrophilicity of Polar Amino Acid Side-chains is Markedly Reduced by + Flanking Peptide Bonds +J J. Mol. Biol. 200, 513-522 (1988) (Arg Pro missing) +C MEEJ810101 0.911 CIDH920105 0.886 MEEJ810102 0.885 + ARGP820101 0.872 JOND750101 0.872 GUOD860101 0.868 + PLIV810101 0.866 CIDH920103 0.866 CIDH920104 0.860 + CIDH920102 0.859 ZHOH040101 0.858 SIMZ760101 0.855 + NOZY710101 0.847 BASU050102 0.846 SWER830101 0.844 + CORJ870102 0.844 TAKK010101 0.840 BASU050101 0.830 + VENT840101 0.829 ZHOH040103 0.826 MIYS850101 0.824 + GOLD730101 0.808 ROBB790101 0.807 BLAS910101 0.802 + NISK860101 0.801 GUYH850103 -0.807 MIYS990102 -0.839 + MIYS990101 -0.843 WOLS870101 -0.870 BULH740101 -0.884 + PARJ860101 -0.896 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.39 NA -1.91 -0.71 0.25 -1.30 -0.18 0.00 -0.60 1.82 + 1.82 0.32 0.96 2.27 NA -1.24 -1.00 2.13 1.47 1.30 +// +H ROSM880105 +D Hydropathies of amino acid side chains, pi-values in pH 7.0 (Roseman, 1988) +R PMID:3398047 +A Roseman, M.A. +T Hydrophilicity of Polar Amino Acid Side-chains is Markedly Reduced by + Flanking Peptide Bonds +J J. Mol. Biol. 200, 513-522 (1988) (Pro missing) +C BLAS910101 0.954 EISD860101 0.948 FAUJ830101 0.937 + RADA880101 0.933 EISD840101 0.923 BIOV880101 0.874 + BIOV880102 0.871 RADA880102 0.870 BASU050103 0.864 + JACR890101 0.863 PLIV810101 0.862 RADA880108 0.861 + NAKH900110 0.859 ZIMJ680105 0.857 CIDH920104 0.855 + NADH010102 0.845 MIYS850101 0.844 SWER830101 0.843 + CIDH920105 0.843 CORJ870102 0.841 MEEJ800102 0.841 + ZHOH040103 0.839 ROSG850102 0.838 NISK860101 0.836 + CIDH920103 0.832 BASU050101 0.828 GUOD860101 0.826 + NADH010101 0.825 DESM900102 0.825 NADH010103 0.822 + JURD980101 0.818 COWR900101 0.817 CASG920101 0.814 + PONP800108 0.808 KYTJ820101 0.806 JANJ790102 0.805 + MEEJ810102 0.804 MANP780101 0.803 MEEJ810101 0.802 + EISD860103 0.801 MEIH800101 -0.802 FAUJ880110 -0.803 + VINM940101 -0.818 MEIH800102 -0.821 FASG890101 -0.822 + OOBM770101 -0.824 OOBM770103 -0.828 MIYS990103 -0.829 + GUYH850101 -0.832 MIYS990104 -0.841 MIYS990102 -0.854 + MIYS990101 -0.854 ROSM880102 -0.871 PARJ860101 -0.871 + MIYS990105 -0.873 KUHL950101 -0.896 WOLS870101 -0.899 + VHEG790101 -0.901 WOEC730101 -0.902 ENGD860101 -0.912 + PRAM900101 -0.912 PUNT030102 -0.917 KIDA850101 -0.922 + PUNT030101 -0.922 GRAR740102 -0.924 ROSM880101 -0.951 + LEVM760101 -0.954 HOPT810101 -0.955 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.39 -3.95 -1.91 -3.81 0.25 -1.30 -2.91 0.00 -0.64 1.82 + 1.82 -2.77 0.96 2.27 NA -1.24 -1.00 2.13 1.47 1.30 +// +H JACR890101 +D Weights from the IFH scale (Jacobs-White, 1989) +R PMID:2742845 +A Jacobs, R. and White, S.H. +T The nature of the hydrophobic bonding of small peptides at the bilayer + interface: implications for the insertion of transbilayer helices +J Biochemistry 28, 3421-3437 (1989) +C EISD840101 0.938 RADA880101 0.936 WOLR810101 0.908 + WOLR790101 0.906 RADA880107 0.895 RADA880104 0.868 + ROSM880105 0.863 JANJ790102 0.840 EISD860101 0.827 + BLAS910101 0.819 CHOC760102 -0.803 JANJ780103 -0.809 + PUNT030101 -0.812 OOBM770101 -0.812 HOPT810101 -0.816 + GUYH850104 -0.827 LEVM760101 -0.832 ZIMJ680103 -0.835 + KIDA850101 -0.836 ROSM880102 -0.837 KUHL950101 -0.864 + JANJ780101 -0.865 EISD860102 -0.871 GUYH850105 -0.887 + FAUJ880109 -0.889 ROSM880101 -0.892 VHEG790101 -0.903 + ENGD860101 -0.948 PRAM900101 -0.948 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.18 -5.40 -1.30 -2.36 0.27 -1.22 -2.10 0.09 -1.48 0.37 + 0.41 -2.53 0.44 0.50 -0.20 -0.40 -0.34 -0.01 -0.08 0.32 +// +H COWR900101 +D Hydrophobicity index, 3.0 pH (Cowan-Whittaker, 1990) +R PMID:2134053 +A Cowan, R. and Whittaker, R.G. +T Hydrophobicity indices for amino acid residues as determined by + high-performance liquid chromatography +J Peptide Res. 3, 75-80 (1990) +C GUOD860101 0.920 BLAS910101 0.885 FAUJ830101 0.876 + EISD860103 0.868 EISD840101 0.863 WILM950101 0.860 + PLIV810101 0.857 JURD980101 0.855 MEEJ810102 0.849 + NADH010102 0.848 KYTJ820101 0.845 RADA880101 0.840 + NADH010103 0.825 MIYS850101 0.824 MEEJ810101 0.823 + CHOC760103 0.820 RADA880104 0.818 ROSM880105 0.817 + RADA880107 0.810 NADH010104 0.807 CIDH920104 0.803 + BULH740101 -0.804 MIYS990102 -0.825 MIYS990101 -0.826 + ROSM880101 -0.849 GRAR740102 -0.854 KIDA850101 -0.868 + WOLS870101 -0.883 ROSM880102 -0.897 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.42 -1.56 -1.03 -0.51 0.84 -0.96 -0.37 0.00 -2.28 1.81 + 1.80 -2.03 1.18 1.74 0.86 -0.64 -0.26 1.46 0.51 1.34 +// +H BLAS910101 +D Scaled side chain hydrophobicity values (Black-Mould, 1991) +R PMID:2042744 +A Black, S.D. and Mould D.R. +T Development of Hydrophobicity Parameters to Analyze Proteins Which Bear Post- + or Cotranslational Modifications +J Analytical Biochemistry 193, 72-82 (1991) +C ROSM880105 0.954 FAUJ830101 0.923 RADA880101 0.922 + EISD860101 0.911 SWER830101 0.887 COWR900101 0.885 + CORJ870102 0.884 EISD840101 0.884 CIDH920104 0.881 + BASU050103 0.878 PLIV810101 0.871 GUOD860101 0.866 + ZIMJ680105 0.855 NADH010101 0.855 BASU050101 0.853 + CIDH920105 0.852 MEEJ800102 0.849 ZHOH040103 0.846 + JURD980101 0.841 CIDH920103 0.838 BIOV880101 0.838 + KYTJ820101 0.836 MEEJ810101 0.831 MEEJ810102 0.830 + EISD860103 0.830 MIYS850101 0.829 RADA880108 0.826 + RADA880102 0.826 NADH010102 0.824 GOLD730101 0.821 + JACR890101 0.819 NADH010103 0.812 PONP800108 0.810 + WILM950101 0.810 BIOV880102 0.809 BASU050102 0.807 + CIDH920102 0.805 NISK860101 0.803 ROSM880104 0.802 + MANP780101 0.802 NAKH900110 0.801 MIYS990103 -0.806 + MIYS990104 -0.818 VHEG790101 -0.847 MIYS990105 -0.848 + MIYS990102 -0.854 MIYS990101 -0.857 BULH740101 -0.860 + ENGD860101 -0.864 PRAM900101 -0.864 PUNT030101 -0.865 + PARJ860101 -0.870 HOPT810101 -0.877 PUNT030102 -0.877 + ROSM880102 -0.884 LEVM760101 -0.889 KUHL950101 -0.894 + KIDA850101 -0.901 WOEC730101 -0.902 WOLS870101 -0.930 + ROSM880101 -0.940 GRAR740102 -0.950 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.616 0.000 0.236 0.028 0.680 0.251 0.043 0.501 0.165 0.943 + 0.943 0.283 0.738 1.000 0.711 0.359 0.450 0.878 0.880 0.825 +// +H CASG920101 +D Hydrophobicity scale from native protein structures (Casari-Sippl, 1992) +R PMID:1569551 +A Casari, G. and Sippl, M. +T Structure-derived Hydrophobic Potential. Hydrophobic Potential Derived from + X-ray Structures of Globular Proteins is able to Identify Native Folds +J J. Mol. Biol. 224, 725-732 (1992) +C ROSG850102 0.952 CORJ870101 0.947 NISK860101 0.938 + BIOV880101 0.935 NISK800101 0.935 WERD780101 0.927 + BAEK050101 0.919 BIOV880102 0.919 NADH010104 0.915 + NADH010103 0.914 PONP930101 0.911 RADA880108 0.903 + CIDH920104 0.903 PONP800108 0.901 ZHOH040103 0.900 + PONP800102 0.889 NADH010102 0.889 MEIH800103 0.881 + PONP800103 0.879 FAUJ830101 0.875 PONP800101 0.874 + BASU050102 0.873 DESM900102 0.869 MIYS850101 0.863 + BASU050103 0.860 CIDH920105 0.859 JANJ780102 0.853 + ROBB790101 0.850 MANP780101 0.848 NADH010105 0.838 + JANJ790101 0.828 CIDH920103 0.827 JANJ790102 0.822 + CORJ870103 0.821 ROSM880105 0.814 CORJ870107 0.813 + DESM900101 0.806 BASU050101 0.806 CIDH920102 0.802 + RACS770101 -0.807 KRIW710101 -0.808 VINM940104 -0.810 + PUNT030101 -0.811 KIDA850101 -0.817 GUYH850104 -0.819 + JANJ780103 -0.825 PARS000101 -0.826 FUKS010102 -0.831 + PUNT030102 -0.831 MIYS990101 -0.834 GUYH850101 -0.836 + OOBM770101 -0.838 MIYS990102 -0.838 HOPT810101 -0.839 + RACS770103 -0.846 GUYH850103 -0.846 RACS770102 -0.849 + GRAR740102 -0.850 PARS000102 -0.859 KRIW790102 -0.865 + VINM940102 -0.874 MEIH800101 -0.875 MEIH800102 -0.879 + FUKS010104 -0.892 KARP850102 -0.901 KRIW790101 -0.911 + OOBM770103 -0.914 VINM940103 -0.915 MIYS990103 -0.915 + FASG890101 -0.924 MIYS990104 -0.931 MIYS990105 -0.937 + GUYH850102 -0.941 VINM940101 -0.947 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.2 -0.7 -0.5 -1.4 1.9 -1.1 -1.3 -0.1 0.4 1.4 + 0.5 -1.6 0.5 1.0 -1.0 -0.7 -0.4 1.6 0.5 0.7 +// +H CORJ870101 +D NNEIG index (Cornette et al., 1987) +R PMID:3656427 +A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and + DeLisi, C. +T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic + Structures in Proteins +J J. Mol. Biol. 196, 659-685, (1987) +C NISK800101 0.976 PONP800108 0.969 PONP930101 0.960 + PONP800102 0.954 ROSG850102 0.948 CASG920101 0.947 + PONP800103 0.944 PONP800101 0.939 NISK860101 0.935 + NADH010103 0.921 MANP780101 0.918 BIOV880101 0.917 + NADH010104 0.914 NADH010102 0.909 MEIH800103 0.902 + DESM900102 0.901 BASU050103 0.897 CIDH920104 0.896 + RADA880108 0.895 JANJ790101 0.891 CORJ870103 0.889 + JANJ780102 0.885 BIOV880102 0.882 CORJ870107 0.878 + WERD780101 0.873 DESM900101 0.870 ZHOH040103 0.864 + BASU050101 0.863 CORJ870104 0.863 BAEK050101 0.862 + MIYS850101 0.861 BASU050102 0.855 JURD980101 0.849 + KYTJ820101 0.848 NADH010105 0.846 FAUJ830101 0.845 + QIAN880121 0.842 KANM800102 0.839 KANM800104 0.833 + CORJ870106 0.829 ROBB760106 0.829 NADH010101 0.827 + CIDH920105 0.827 QIAN880122 0.826 LIFS790101 0.826 + JANJ790102 0.825 CIDH920103 0.822 CHOC760103 0.822 + GEIM800107 0.821 ROBB790101 0.819 CORJ870105 0.818 + CHOP780202 0.815 ROBB760105 0.809 EISD860103 0.809 + QIAN880120 0.802 WARP780101 0.800 VINM940104 -0.805 + KRIW710101 -0.812 FUKS010104 -0.814 GUYH850103 -0.815 + MUNV940103 -0.817 GUYH850101 -0.820 JANJ780103 -0.826 + GUYH850104 -0.830 RACS770103 -0.832 VINM940103 -0.837 + RACS770102 -0.837 KRIW790102 -0.838 WOEC730101 -0.841 + VINM940102 -0.847 PARS000102 -0.850 MIYS990101 -0.854 + MEIH800101 -0.855 MIYS990102 -0.859 PUNT030102 -0.860 + KARP850102 -0.865 CORJ870108 -0.866 OOBM770101 -0.875 + MEIH800102 -0.878 GUYH850102 -0.883 GRAR740102 -0.890 + KRIW790101 -0.902 OOBM770103 -0.907 FASG890101 -0.921 + VINM940101 -0.924 MIYS990104 -0.932 MIYS990103 -0.936 + MIYS990105 -0.937 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 50.76 48.66 45.80 43.17 58.74 46.09 43.48 50.27 49.33 57.30 + 53.89 42.92 52.75 53.45 45.39 47.24 49.26 53.59 51.79 56.12 +// +H CORJ870102 +D SWEIG index (Cornette et al., 1987) +R PMID:3656427 +A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and + DeLisi, C. +T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic + Structures in Proteins +J J. Mol. Biol. 196, 659-685, (1987) +C SWER830101 1.000 BASU050101 0.921 CIDH920105 0.890 + BASU050103 0.889 MIYS850101 0.887 BLAS910101 0.884 + CORJ870104 0.881 CORJ870107 0.881 BASU050102 0.881 + PLIV810101 0.873 CIDH920102 0.872 NISK860101 0.864 + CIDH920103 0.864 ZHOH040103 0.863 ZHOH040101 0.862 + CORJ870103 0.860 CIDH920104 0.860 CIDH920101 0.855 + PTIO830102 0.854 GUOD860101 0.852 CORJ870105 0.848 + CORJ870106 0.845 ROSM880104 0.844 ROSM880105 0.841 + NOZY710101 0.838 VENT840101 0.837 BIOV880101 0.837 + ROBB790101 0.835 PONP930101 0.832 FAUJ830101 0.831 + ZIMJ680105 0.828 QIAN880120 0.825 RADA880108 0.823 + EISD860101 0.822 CHOP780202 0.822 RADA880102 0.821 + MANP780101 0.818 LIFS790101 0.815 PALJ810104 0.809 + MEEJ810101 0.807 WERD780101 0.804 MUNV940103 -0.802 + RACS770101 -0.802 VINM940102 -0.812 VINM940101 -0.817 + WOEC730101 -0.828 MEIH800101 -0.829 OOBM770103 -0.832 + PUNT030101 -0.835 GUYH850103 -0.839 PARS000101 -0.848 + MIYS990103 -0.877 MIYS990105 -0.882 CORJ870108 -0.883 + WOLS870101 -0.885 MIYS990104 -0.886 PARJ860101 -0.892 + GRAR740102 -0.893 MIYS990102 -0.920 MIYS990101 -0.922 + BULH740101 -0.923 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.414 -0.584 -0.916 -1.310 0.162 -0.905 -1.218 -0.684 -0.630 1.237 + 1.215 -0.670 1.020 1.938 -0.503 -0.563 -0.289 0.514 1.699 0.899 +// +H CORJ870103 +D PRIFT index (Cornette et al., 1987) +R PMID:3656427 +A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and + DeLisi, C. +T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic + Structures in Proteins +J J. Mol. Biol. 196, 659-685, (1987) +C CORJ870104 0.988 CORJ870107 0.969 PONP930101 0.920 + PONP800101 0.917 NISK860101 0.914 PONP800102 0.907 + MANP780101 0.906 MIYS850101 0.892 BASU050101 0.890 + PONP800103 0.889 CORJ870101 0.889 NISK800101 0.886 + ROSG850102 0.883 WERD780101 0.882 MEIH800103 0.880 + CORJ870106 0.880 CORJ870105 0.880 RADA880108 0.876 + BIOV880101 0.876 PONP800108 0.873 BASU050103 0.867 + SWER830101 0.862 CORJ870102 0.860 CIDH920103 0.856 + BASU050102 0.845 CIDH920104 0.841 BIOV880102 0.840 + CIDH920105 0.838 NADH010103 0.830 CIDH920101 0.825 + NADH010102 0.823 CASG920101 0.821 PONP800106 0.821 + NADH010104 0.820 ZHOH040103 0.819 DESM900102 0.815 + DESM900101 0.812 QIAN880122 0.808 JURD980101 0.808 + KYTJ820101 0.806 ROBB790101 0.804 PUNT030101 -0.802 + GUYH850103 -0.804 PARJ860101 -0.807 KRIW790102 -0.812 + GUYH850101 -0.813 PARS000101 -0.815 RACS770103 -0.827 + KRIW790101 -0.830 GRAR740102 -0.836 OOBM770103 -0.839 + GUYH850102 -0.841 VINM940101 -0.848 KARP850102 -0.850 + RACS770102 -0.852 MEIH800102 -0.855 RACS770101 -0.870 + MEIH800101 -0.871 FASG890101 -0.876 MIYS990101 -0.911 + MIYS990102 -0.913 MIYS990104 -0.920 MIYS990105 -0.923 + MIYS990103 -0.930 CORJ870108 -0.959 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.96 0.75 -1.94 -5.68 4.54 -5.30 -3.86 -1.28 -0.62 5.54 + 6.81 -5.62 4.76 5.06 -4.47 -1.92 -3.99 0.21 3.34 5.39 +// +H CORJ870104 +D PRILS index (Cornette et al., 1987) +R PMID:3656427 +A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and + DeLisi, C. +T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic + Structures in Proteins +J J. Mol. Biol. 196, 659-685, (1987) +C CORJ870103 0.988 CORJ870107 0.973 PONP800101 0.913 + BASU050101 0.910 MANP780101 0.908 PONP800102 0.901 + NISK860101 0.901 PONP930101 0.901 CORJ870105 0.895 + MIYS850101 0.892 CORJ870106 0.889 PONP800103 0.884 + SWER830101 0.883 CORJ870102 0.881 RADA880108 0.880 + BASU050103 0.877 NISK800101 0.868 BIOV880101 0.867 + CORJ870101 0.863 PONP800108 0.861 ROSG850102 0.860 + CIDH920103 0.857 MEIH800103 0.856 WERD780101 0.850 + PONP800106 0.842 CIDH920101 0.840 BASU050102 0.838 + CIDH920105 0.838 CIDH920104 0.832 PLIV810101 0.821 + BIOV880102 0.815 KYTJ820101 0.812 JURD980101 0.812 + ZHOH040103 0.809 ROBB760106 0.808 ROBB790101 0.807 + ROBB760105 0.803 NADH010103 0.802 PARS000101 -0.800 + KRIW790101 -0.801 PUNT030101 -0.804 GUYH850103 -0.809 + OOBM770103 -0.814 GUYH850101 -0.815 PARJ860101 -0.823 + VINM940101 -0.826 KARP850102 -0.830 RACS770102 -0.838 + MEIH800102 -0.840 GRAR740102 -0.850 RACS770101 -0.860 + MEIH800101 -0.862 FASG890101 -0.865 MIYS990104 -0.905 + MIYS990105 -0.908 MIYS990103 -0.919 MIYS990101 -0.919 + MIYS990102 -0.920 CORJ870108 -0.972 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.26 0.08 -0.46 -1.30 0.83 -0.83 -0.73 -0.40 -0.18 1.10 + 1.52 -1.01 1.09 1.09 -0.62 -0.55 -0.71 -0.13 0.69 1.15 +// +H CORJ870105 +D ALTFT index (Cornette et al., 1987) +R PMID:3656427 +A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and + DeLisi, C. +T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic + Structures in Proteins +J J. Mol. Biol. 196, 659-685, (1987) +C CORJ870106 0.991 CORJ870107 0.968 NISK860101 0.901 + CORJ870104 0.895 BASU050101 0.888 CORJ870103 0.880 + MIYS850101 0.879 PONP930101 0.878 BEGF750102 0.878 + PONP800101 0.867 ROSG850102 0.864 BIOV880101 0.859 + WERD780101 0.858 QIAN880120 0.858 RADA880108 0.854 + MANP780101 0.853 BASU050103 0.852 SWER830101 0.848 + CORJ870102 0.848 PONP800102 0.841 BASU050102 0.834 + NISK800101 0.834 CIDH920103 0.832 LIFS790101 0.830 + CIDH920101 0.828 MEIH800103 0.827 PLIV810101 0.827 + ROBB790101 0.827 BIOV880102 0.823 CIDH920105 0.822 + PONP800103 0.821 CORJ870101 0.818 PONP800107 0.812 + QIAN880119 0.810 PONP800108 0.801 GUYH850102 -0.804 + VINM940102 -0.807 GEIM800110 -0.807 GUYH850101 -0.810 + CHOP780203 -0.815 PUNT030102 -0.817 FASG890101 -0.821 + MUNV940103 -0.829 FUKS010103 -0.829 GUYH850103 -0.830 + OOBM770103 -0.833 KARP850102 -0.834 PUNT030101 -0.834 + PARJ860101 -0.837 RACS770102 -0.839 MEIH800102 -0.839 + MIYS990105 -0.867 VINM940101 -0.873 RACS770101 -0.876 + PARS000101 -0.878 MEIH800101 -0.883 MIYS990104 -0.885 + MIYS990103 -0.894 MIYS990101 -0.897 MIYS990102 -0.898 + CORJ870108 -0.967 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.73 -1.03 -5.29 -6.13 0.64 -0.96 -2.90 -2.67 3.03 5.04 + 4.91 -5.99 3.34 5.20 -4.32 -3.00 -1.91 0.51 2.87 3.98 +// +H CORJ870106 +D ALTLS index (Cornette et al., 1987) +R PMID:3656427 +A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and + DeLisi, C. +T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic + Structures in Proteins +J J. Mol. Biol. 196, 659-685, (1987) +C CORJ870105 0.991 CORJ870107 0.963 NISK860101 0.908 + BASU050101 0.891 CORJ870104 0.889 PONP930101 0.889 + PONP800101 0.887 MIYS850101 0.884 CORJ870103 0.880 + WERD780101 0.878 ROSG850102 0.878 BIOV880101 0.870 + MANP780101 0.867 QIAN880120 0.866 PONP800102 0.864 + RADA880108 0.863 BASU050102 0.859 BASU050103 0.858 + NISK800101 0.857 BEGF750102 0.853 CORJ870102 0.845 + SWER830101 0.845 PONP800103 0.840 CIDH920103 0.837 + LIFS790101 0.836 ROBB790101 0.834 CIDH920101 0.832 + CORJ870101 0.829 CIDH920105 0.826 ZHOH040103 0.822 + MEIH800103 0.822 PLIV810101 0.820 BIOV880102 0.818 + PONP800108 0.813 PTIO830102 0.809 PONP800106 0.807 + QIAN880121 0.806 QIAN880119 0.803 PONP800107 0.800 + CHOP780216 -0.803 GEIM800110 -0.812 CHOP780203 -0.813 + PUNT030102 -0.814 PARJ860101 -0.820 KRIW790101 -0.825 + OOBM770103 -0.826 GUYH850102 -0.830 VINM940102 -0.830 + PUNT030101 -0.833 GUYH850101 -0.833 MEIH800102 -0.835 + GUYH850103 -0.837 RACS770102 -0.839 FASG890101 -0.841 + FUKS010103 -0.846 MUNV940103 -0.848 KARP850102 -0.870 + RACS770101 -0.879 MIYS990105 -0.879 VINM940101 -0.881 + MEIH800101 -0.882 PARS000101 -0.891 MIYS990101 -0.898 + MIYS990102 -0.899 MIYS990104 -0.902 MIYS990103 -0.909 + CORJ870108 -0.968 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -1.35 -3.89 -10.96 -11.88 4.37 -1.34 -4.56 -5.82 6.54 10.93 + 9.88 -11.92 7.47 11.35 -10.86 -6.21 -4.83 1.80 7.61 8.20 +// +H CORJ870107 +D TOTFT index (Cornette et al., 1987) +R PMID:3656427 +A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and + DeLisi, C. +T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic + Structures in Proteins +J J. Mol. Biol. 196, 659-685, (1987) +C CORJ870104 0.973 CORJ870103 0.969 CORJ870105 0.968 + CORJ870106 0.963 NISK860101 0.928 PONP930101 0.923 + PONP800101 0.923 BASU050101 0.913 MIYS850101 0.911 + MANP780101 0.908 PONP800102 0.905 ROSG850102 0.898 + RADA880108 0.889 BIOV880101 0.889 WERD780101 0.887 + PONP800103 0.884 NISK800101 0.884 MEIH800103 0.883 + BASU050103 0.883 SWER830101 0.883 CORJ870102 0.881 + CORJ870101 0.878 CIDH920103 0.866 PONP800108 0.859 + BASU050102 0.855 BIOV880102 0.850 CIDH920105 0.848 + CIDH920101 0.843 QIAN880120 0.840 CIDH920104 0.835 + PONP800106 0.834 ROBB790101 0.832 BEGF750102 0.831 + PLIV810101 0.829 ZHOH040103 0.822 LIFS790101 0.820 + ROBB760106 0.819 DESM900102 0.819 NADH010103 0.817 + DESM900101 0.815 CASG920101 0.813 NADH010102 0.812 + PTIO830102 0.810 NADH010104 0.808 QIAN880121 0.806 + PONP800107 0.805 JURD980101 0.804 KYTJ820101 0.801 + ROBB760105 0.800 FUKS010103 -0.805 RACS770103 -0.808 + PUNT030102 -0.810 VINM940102 -0.811 KRIW790102 -0.816 + MUNV940103 -0.832 KRIW790101 -0.832 GUYH850103 -0.833 + GUYH850102 -0.834 PARJ860101 -0.838 GRAR740102 -0.840 + GUYH850101 -0.841 PUNT030101 -0.848 OOBM770103 -0.851 + PARS000101 -0.865 KARP850102 -0.866 MEIH800102 -0.871 + RACS770102 -0.871 FASG890101 -0.871 VINM940101 -0.877 + MEIH800101 -0.897 RACS770101 -0.898 MIYS990105 -0.918 + MIYS990104 -0.924 MIYS990101 -0.929 MIYS990102 -0.930 + MIYS990103 -0.937 CORJ870108 -0.996 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.56 -0.26 -2.87 -4.31 1.78 -2.31 -2.35 -1.35 0.81 3.83 + 4.09 -4.08 3.11 3.67 -3.22 -1.85 -1.97 -0.11 2.17 3.31 +// +H CORJ870108 +D TOTLS index (Cornette et al., 1987) +R PMID:3656427 +A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and + DeLisi, C. +T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic + Structures in Proteins +J J. Mol. Biol. 196, 659-685, (1987) +C MIYS990103 0.933 MIYS990102 0.929 MIYS990101 0.928 + MIYS990104 0.918 MIYS990105 0.909 RACS770101 0.891 + MEIH800101 0.889 FASG890101 0.872 KARP850102 0.868 + RACS770102 0.863 VINM940101 0.862 MEIH800102 0.860 + PARS000101 0.854 GUYH850101 0.851 PUNT030101 0.845 + GRAR740102 0.838 KRIW790101 0.833 GUYH850103 0.831 + PARJ860101 0.831 MUNV940103 0.830 OOBM770103 0.829 + GUYH850102 0.821 FUKS010103 0.818 PUNT030102 0.810 + VINM940102 0.810 KYTJ820101 -0.802 NADH010102 -0.803 + NADH010104 -0.805 JURD980101 -0.806 DESM900101 -0.809 + DESM900102 -0.811 ROBB760105 -0.811 LIFS790101 -0.811 + PTIO830102 -0.812 NADH010103 -0.812 ROBB760106 -0.820 + ZHOH040103 -0.821 BEGF750102 -0.825 ROBB790101 -0.829 + CIDH920104 -0.829 BIOV880102 -0.831 QIAN880120 -0.834 + PLIV810101 -0.838 CIDH920105 -0.843 CIDH920101 -0.845 + PONP800108 -0.853 BASU050102 -0.855 PONP800106 -0.859 + CIDH920103 -0.864 CORJ870101 -0.866 MEIH800103 -0.870 + WERD780101 -0.878 NISK800101 -0.880 BASU050103 -0.883 + CORJ870102 -0.883 SWER830101 -0.884 BIOV880101 -0.886 + PONP800103 -0.889 ROSG850102 -0.890 RADA880108 -0.893 + MIYS850101 -0.910 PONP800102 -0.911 MANP780101 -0.911 + PONP930101 -0.912 BASU050101 -0.916 NISK860101 -0.920 + PONP800101 -0.928 CORJ870103 -0.959 CORJ870105 -0.967 + CORJ870106 -0.968 CORJ870104 -0.972 CORJ870107 -0.996 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 1.37 1.33 6.29 8.93 -4.47 3.88 4.04 3.39 -1.65 -7.92 + -8.68 7.70 -7.13 -7.96 6.25 4.08 4.02 0.79 -4.73 -6.94 +// +H MIYS990101 +D Relative partition energies derived by the Bethe approximation + (Miyazawa-Jernigan, 1999) +R PMID:10336383 +A Miyazawa, S. and Jernigan, R. L. +T Self-consistent estimation of inter-residue protein contact energies based on + an equilibrium mixture approximation of residues +J Proteins 34, 49-68 (1999) +C MIYS990102 1.000 MIYS990103 0.957 MIYS990104 0.954 + MIYS990105 0.951 PARJ860101 0.944 MEIH800101 0.940 + CORJ870108 0.928 FASG890101 0.926 RACS770101 0.920 + RACS770102 0.917 MEIH800102 0.913 WOLS870101 0.912 + GRAR740102 0.903 GUYH850101 0.891 PUNT030101 0.888 + OOBM770103 0.887 GUYH850103 0.886 BULH740101 0.884 + PUNT030102 0.881 VINM940101 0.880 KRIW790101 0.870 + GUYH850102 0.865 VINM940102 0.841 PARS000101 0.830 + KARP850102 0.825 KRIW790102 0.821 ROSM880102 0.819 + KIDA850101 0.817 VINM940103 0.817 WOEC730101 0.805 + HOPT810101 0.803 ZIMJ680105 -0.801 CHOC760103 -0.803 + DESM900102 -0.809 LIFS790101 -0.811 NADH010101 -0.816 + ARGP820103 -0.817 VENT840101 -0.821 NOZY710101 -0.821 + WILM950101 -0.822 COWR900101 -0.826 EISD860101 -0.827 + EISD860103 -0.829 PTIO830102 -0.833 CASG920101 -0.834 + RADA880102 -0.837 NADH010105 -0.837 KYTJ820101 -0.840 + ROSM880104 -0.843 CIDH920101 -0.847 JURD980101 -0.852 + MEEJ810102 -0.854 CORJ870101 -0.854 ROSM880105 -0.854 + BLAS910101 -0.857 NISK800101 -0.860 PONP800108 -0.866 + MEEJ810101 -0.867 NADH010102 -0.870 ZHOH040101 -0.871 + PONP800103 -0.871 CIDH920102 -0.872 PONP800102 -0.874 + PONP800107 -0.877 ROBB790101 -0.883 PONP800101 -0.883 + NADH010104 -0.885 NADH010103 -0.887 MEIH800103 -0.891 + CORJ870105 -0.897 CORJ870106 -0.898 CIDH920103 -0.900 + BIOV880102 -0.901 FAUJ830101 -0.907 CORJ870103 -0.911 + WERD780101 -0.912 ROSG850102 -0.913 MANP780101 -0.913 + CIDH920104 -0.915 PONP930101 -0.916 CIDH920105 -0.916 + GUOD860101 -0.917 CORJ870104 -0.919 CORJ870102 -0.922 + SWER830101 -0.923 ZHOH040103 -0.926 CORJ870107 -0.929 + RADA880108 -0.932 BASU050102 -0.935 BASU050103 -0.940 + PLIV810101 -0.944 BASU050101 -0.945 BIOV880101 -0.947 + NISK860101 -0.957 MIYS850101 -0.977 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.02 0.44 0.63 0.72 -0.96 0.56 0.74 0.38 0.00 -1.89 + -2.29 1.01 -1.36 -2.22 0.47 0.55 0.25 -1.28 -0.88 -1.34 +// +H MIYS990102 +D Optimized relative partition energies - method A (Miyazawa-Jernigan, 1999) +R PMID:10336383 +A Miyazawa, S. and Jernigan, R. L. +T Self-consistent estimation of inter-residue protein contact energies based on + an equilibrium mixture approximation of residues +J Proteins 34, 49-68 (1999) +C MIYS990101 1.000 MIYS990103 0.958 MIYS990104 0.956 + MIYS990105 0.953 PARJ860101 0.942 MEIH800101 0.941 + FASG890101 0.929 CORJ870108 0.929 RACS770101 0.921 + RACS770102 0.919 MEIH800102 0.916 WOLS870101 0.910 + GRAR740102 0.903 GUYH850101 0.892 OOBM770103 0.891 + GUYH850103 0.888 PUNT030101 0.887 VINM940101 0.883 + PUNT030102 0.882 BULH740101 0.880 KRIW790101 0.873 + GUYH850102 0.868 VINM940102 0.842 PARS000101 0.830 + KARP850102 0.828 KRIW790102 0.826 VINM940103 0.818 + ROSM880102 0.818 KIDA850101 0.817 WOEC730101 0.805 + HOPT810101 0.804 CHOP780202 -0.801 CHOC760103 -0.805 + DESM900102 -0.811 LIFS790101 -0.813 ARGP820103 -0.814 + NADH010101 -0.815 NOZY710101 -0.819 VENT840101 -0.820 + WILM950101 -0.822 EISD860101 -0.824 COWR900101 -0.825 + EISD860103 -0.831 RADA880102 -0.834 PTIO830102 -0.834 + NADH010105 -0.838 CASG920101 -0.838 ROSM880104 -0.839 + KYTJ820101 -0.840 CIDH920101 -0.846 MEEJ810102 -0.853 + JURD980101 -0.853 ROSM880105 -0.854 BLAS910101 -0.854 + CORJ870101 -0.859 NISK800101 -0.863 MEEJ810101 -0.866 + PONP800108 -0.869 ZHOH040101 -0.870 CIDH920102 -0.870 + NADH010102 -0.872 PONP800103 -0.875 PONP800102 -0.877 + PONP800107 -0.879 ROBB790101 -0.885 PONP800101 -0.886 + NADH010104 -0.888 NADH010103 -0.889 MEIH800103 -0.893 + CORJ870105 -0.898 CORJ870106 -0.899 CIDH920103 -0.899 + BIOV880102 -0.902 FAUJ830101 -0.908 CORJ870103 -0.913 + WERD780101 -0.914 CIDH920105 -0.915 MANP780101 -0.915 + GUOD860101 -0.916 CIDH920104 -0.916 ROSG850102 -0.916 + PONP930101 -0.919 CORJ870102 -0.920 CORJ870104 -0.920 + SWER830101 -0.921 ZHOH040103 -0.927 CORJ870107 -0.930 + RADA880108 -0.934 BASU050102 -0.936 BASU050103 -0.940 + PLIV810101 -0.942 BASU050101 -0.945 BIOV880101 -0.948 + NISK860101 -0.960 MIYS850101 -0.978 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + 0.00 0.07 0.10 0.12 -0.16 0.09 0.12 0.06 0.00 -0.31 + -0.37 0.17 -0.22 -0.36 0.08 0.09 0.04 -0.21 -0.14 -0.22 +// +H MIYS990103 +D Optimized relative partition energies - method B (Miyazawa-Jernigan, 1999) +R PMID:10336383 +A Miyazawa, S. and Jernigan, R. L. +T Self-consistent estimation of inter-residue protein contact energies based on + an equilibrium mixture approximation of residues +J Proteins 34, 49-68 (1999) +C MIYS990104 0.995 MIYS990105 0.984 MIYS990102 0.958 + FASG890101 0.957 MIYS990101 0.957 VINM940101 0.951 + KRIW790101 0.944 CORJ870108 0.933 MEIH800101 0.923 + MEIH800102 0.917 GUYH850102 0.914 OOBM770103 0.908 + RACS770102 0.908 GUYH850101 0.907 GRAR740102 0.904 + KARP850102 0.901 KRIW790102 0.899 VINM940102 0.895 + RACS770101 0.887 VINM940103 0.886 PUNT030102 0.881 + PARS000101 0.879 PUNT030101 0.864 PARJ860101 0.859 + GUYH850103 0.857 KRIW710101 0.856 FUKS010104 0.845 + RACS770103 0.840 MUNV940103 0.831 OOBM770101 0.827 + HOPT810101 0.825 WOEC730101 0.824 WOLS870101 0.815 + MONM990101 0.809 KIDA850101 0.805 GUYH850104 0.805 + FUKS010103 0.805 FUKS010102 0.803 GEIM800107 -0.803 + JANJ790102 -0.804 BLAS910101 -0.806 PONP800106 -0.807 + PALJ810104 -0.811 PTIO830102 -0.820 KANM800102 -0.823 + ZHOH040101 -0.824 CHOP780202 -0.825 NADH010101 -0.825 + GUOD860101 -0.828 QIAN880120 -0.829 ROSM880105 -0.829 + KYTJ820101 -0.833 JANJ780102 -0.834 ROBB760106 -0.836 + LIFS790101 -0.838 QIAN880121 -0.838 CIDH920101 -0.838 + JURD980101 -0.845 CIDH920102 -0.845 ROBB790101 -0.854 + DESM900101 -0.854 PLIV810101 -0.861 CIDH920103 -0.870 + DESM900102 -0.876 BAEK050101 -0.877 CORJ870102 -0.877 + SWER830101 -0.878 NADH010105 -0.879 CIDH920105 -0.886 + FAUJ830101 -0.893 CORJ870105 -0.894 CIDH920104 -0.902 + MEIH800103 -0.906 CORJ870106 -0.909 CASG920101 -0.915 + BASU050101 -0.918 MANP780101 -0.918 CORJ870104 -0.919 + PONP800108 -0.920 NADH010102 -0.923 BIOV880102 -0.923 + BASU050102 -0.924 CORJ870103 -0.930 ZHOH040103 -0.933 + CORJ870101 -0.936 CORJ870107 -0.937 NISK800101 -0.938 + WERD780101 -0.938 PONP800101 -0.940 PONP800103 -0.943 + BASU050103 -0.943 NADH010104 -0.944 NADH010103 -0.944 + PONP800102 -0.946 RADA880108 -0.950 PONP930101 -0.951 + MIYS850101 -0.952 BIOV880101 -0.962 ROSG850102 -0.966 + NISK860101 -0.974 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.03 0.09 0.13 0.17 -0.36 0.13 0.23 0.09 -0.04 -0.33 + -0.38 0.32 -0.30 -0.34 0.20 0.10 0.01 -0.24 -0.23 -0.29 +// +H MIYS990104 +D Optimized relative partition energies - method C (Miyazawa-Jernigan, 1999) +R PMID:10336383 +A Miyazawa, S. and Jernigan, R. L. +T Self-consistent estimation of inter-residue protein contact energies based on + an equilibrium mixture approximation of residues +J Proteins 34, 49-68 (1999) +C MIYS990103 0.995 MIYS990105 0.990 VINM940101 0.965 + MIYS990102 0.956 MIYS990101 0.954 FASG890101 0.949 + KRIW790101 0.945 OOBM770103 0.931 GUYH850102 0.928 + MEIH800101 0.925 VINM940102 0.922 CORJ870108 0.918 + GRAR740102 0.910 KARP850102 0.909 MEIH800102 0.903 + PARS000101 0.903 VINM940103 0.898 RACS770102 0.892 + GUYH850101 0.889 KRIW790102 0.889 RACS770101 0.884 + GUYH850103 0.879 PARJ860101 0.877 PUNT030102 0.874 + FUKS010104 0.862 PUNT030101 0.857 HOPT810101 0.843 + KRIW710101 0.837 RACS770103 0.833 WOLS870101 0.830 + MUNV940103 0.827 WOEC730101 0.827 FUKS010103 0.822 + KARP850101 0.822 KIDA850101 0.822 FUKS010102 0.818 + OOBM770101 0.806 LEVM760101 0.801 KYTJ820101 -0.800 + MEEJ810102 -0.807 KANM800102 -0.808 NADH010101 -0.810 + PALJ810104 -0.810 JANJ780102 -0.811 JURD980101 -0.813 + ROBB760106 -0.815 PTIO830102 -0.818 BLAS910101 -0.818 + DESM900101 -0.828 CHOP780202 -0.829 MEEJ810101 -0.831 + QIAN880121 -0.832 QIAN880120 -0.833 ROSM880105 -0.841 + LIFS790101 -0.843 GUOD860101 -0.846 DESM900102 -0.854 + CIDH920101 -0.860 ZHOH040101 -0.864 PLIV810101 -0.869 + NADH010105 -0.874 CIDH920102 -0.877 ROBB790101 -0.877 + CIDH920103 -0.883 CORJ870105 -0.885 CORJ870102 -0.886 + SWER830101 -0.887 BAEK050101 -0.892 MEIH800103 -0.894 + CORJ870106 -0.902 CORJ870104 -0.905 FAUJ830101 -0.906 + CIDH920105 -0.908 MANP780101 -0.909 NADH010102 -0.910 + CIDH920104 -0.916 BASU050101 -0.918 PONP800108 -0.918 + CORJ870103 -0.920 PONP800101 -0.924 CORJ870107 -0.924 + PONP800103 -0.929 PONP800102 -0.930 CASG920101 -0.931 + BIOV880102 -0.932 CORJ870101 -0.932 BASU050103 -0.938 + NISK800101 -0.938 NADH010103 -0.938 NADH010104 -0.940 + BASU050102 -0.942 RADA880108 -0.943 WERD780101 -0.949 + PONP930101 -0.949 MIYS850101 -0.953 ZHOH040103 -0.954 + ROSG850102 -0.962 BIOV880101 -0.965 NISK860101 -0.980 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.04 0.07 0.13 0.19 -0.38 0.14 0.23 0.09 -0.04 -0.34 + -0.37 0.33 -0.30 -0.38 0.19 0.12 0.03 -0.33 -0.29 -0.29 +// +H MIYS990105 +D Optimized relative partition energies - method D (Miyazawa-Jernigan, 1999) +R PMID:10336383 +A Miyazawa, S. and Jernigan, R. L. +T Self-consistent estimation of inter-residue protein contact energies based on + an equilibrium mixture approximation of residues +J Proteins 34, 49-68 (1999) +C MIYS990104 0.990 MIYS990103 0.984 FASG890101 0.959 + MIYS990102 0.953 VINM940101 0.952 MIYS990101 0.951 + OOBM770103 0.936 GRAR740102 0.928 KRIW790101 0.925 + MEIH800102 0.914 GUYH850102 0.912 MEIH800101 0.912 + CORJ870108 0.909 GUYH850101 0.895 RACS770102 0.893 + VINM940102 0.891 KARP850102 0.888 KRIW790102 0.887 + GUYH850103 0.883 VINM940103 0.880 PARJ860101 0.878 + PARS000101 0.877 PUNT030101 0.876 PUNT030102 0.874 + FUKS010104 0.870 RACS770101 0.866 KIDA850101 0.865 + HOPT810101 0.862 RACS770103 0.852 WOEC730101 0.849 + OOBM770101 0.844 WOLS870101 0.838 LEVM760101 0.828 + GUYH850104 0.821 JANJ780103 0.816 FUKS010102 0.813 + KRIW710101 0.801 EISD860103 -0.815 MEEJ810102 -0.817 + KYTJ820101 -0.818 JANJ790102 -0.820 NADH010101 -0.821 + JURD980101 -0.829 DESM900101 -0.832 ZHOH040101 -0.838 + MEEJ810101 -0.839 JANJ780102 -0.846 GUOD860101 -0.846 + BLAS910101 -0.848 CIDH920101 -0.849 NADH010105 -0.856 + CIDH920102 -0.859 CORJ870105 -0.867 PLIV810101 -0.869 + BAEK050101 -0.871 ROSM880105 -0.873 DESM900102 -0.875 + CIDH920103 -0.876 CORJ870106 -0.879 CORJ870102 -0.882 + SWER830101 -0.883 ROBB790101 -0.885 BASU050101 -0.900 + CIDH920105 -0.901 MANP780101 -0.906 CORJ870104 -0.908 + CIDH920104 -0.916 CORJ870107 -0.918 PONP800101 -0.918 + BASU050102 -0.919 MEIH800103 -0.919 FAUJ830101 -0.920 + NADH010102 -0.923 CORJ870103 -0.923 PONP800102 -0.927 + PONP800108 -0.927 BASU050103 -0.928 PONP800103 -0.928 + NADH010104 -0.934 NISK800101 -0.935 WERD780101 -0.936 + PONP930101 -0.936 CASG920101 -0.937 CORJ870101 -0.937 + ZHOH040103 -0.939 NADH010103 -0.939 BIOV880102 -0.947 + RADA880108 -0.950 MIYS850101 -0.951 ROSG850102 -0.968 + NISK860101 -0.972 BIOV880101 -0.975 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.02 0.08 0.10 0.19 -0.32 0.15 0.21 -0.02 -0.02 -0.28 + -0.32 0.30 -0.25 -0.33 0.11 0.11 0.05 -0.27 -0.23 -0.23 +// +H ENGD860101 +D Hydrophobicity index (Engelman et al., 1986) +R PMID:3521657 +A Engelman, D.M., Steitz, T.A. and Goldman, A. +T Identifying Nonpolar Transbilayer Helices in Amino Acid Sequences of Membrane + Proteins +J Ann.Rev.Biophys.Biophys.Chem. 15, 321-353 (1986) +C PRAM900101 1.000 ROSM880101 0.917 VHEG790101 0.909 + KUHL950101 0.908 OOBM770101 0.907 JANJ780101 0.901 + ROSM880102 0.891 PUNT030101 0.889 JANJ780103 0.884 + HOPT810101 0.882 GUYH850104 0.881 LEVM760101 0.881 + WOEC730101 0.871 PUNT030102 0.870 GUYH850105 0.867 + KIDA850101 0.866 GRAR740102 0.855 ZIMJ680103 0.854 + CHOC760102 0.826 MONM990101 0.820 GUYH850101 0.820 + FAUJ880109 0.814 RADA880104 -0.803 OLSK800101 -0.805 + CHOC760103 -0.813 NADH010103 -0.815 WARP780101 -0.827 + EISD860103 -0.831 NADH010101 -0.843 KYTJ820101 -0.850 + FAUJ830101 -0.853 JANJ780102 -0.860 JURD980101 -0.861 + EISD860101 -0.862 BLAS910101 -0.864 RADA880107 -0.865 + NADH010102 -0.870 WOLR790101 -0.877 WOLR810101 -0.887 + JANJ790102 -0.890 DESM900102 -0.890 ROSM880105 -0.912 + RADA880101 -0.932 EISD840101 -0.936 JACR890101 -0.948 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -1.6 12.3 4.8 9.2 -2.0 4.1 8.2 -1.0 3.0 -3.1 + -2.8 8.8 -3.4 -3.7 0.2 -0.6 -1.2 -1.9 0.7 -2.6 +// +H FASG890101 +D Hydrophobicity index (Fasman, 1989) +R +A Fasman, G.D. +T Prediction of Protein Structure and the Principles of Protein Conformation +J Plenum, New York 1989, page 457, Table XVII +C MIYS990105 0.959 MIYS990103 0.957 MEIH800102 0.951 + MIYS990104 0.949 RACS770102 0.935 GUYH850101 0.934 + MIYS990102 0.929 MIYS990101 0.926 MEIH800101 0.919 + KRIW790101 0.914 GUYH850102 0.909 VINM940101 0.904 + KRIW790102 0.882 GUYH850104 0.872 RACS770101 0.872 + GRAR740102 0.872 CORJ870108 0.872 KARP850102 0.871 + OOBM770103 0.869 VINM940103 0.868 OOBM770101 0.868 + KRIW710101 0.865 KIDA850101 0.861 GUYH850103 0.860 + PUNT030102 0.853 PUNT030101 0.845 FUKS010104 0.844 + RACS770103 0.842 ROSM880102 0.839 JANJ780103 0.838 + VINM940102 0.836 PARJ860101 0.825 KUHL950101 0.821 + JANJ780101 0.813 FUKS010103 0.812 GUOD860101 -0.801 + DESM900101 -0.808 CORJ870105 -0.821 ROSM880105 -0.822 + PONP800106 -0.823 NADH010101 -0.838 CORJ870106 -0.841 + KYTJ820101 -0.844 CIDH920103 -0.846 CHOC760103 -0.849 + BASU050101 -0.856 JURD980101 -0.857 PLIV810101 -0.858 + BAEK050101 -0.859 CIDH920105 -0.860 ROBB790101 -0.860 + EISD860103 -0.863 CORJ870104 -0.865 CORJ870107 -0.871 + JANJ790102 -0.875 CORJ870103 -0.876 NADH010105 -0.877 + DESM900102 -0.879 BASU050102 -0.881 JANJ790101 -0.885 + CIDH920104 -0.903 JANJ780102 -0.903 MANP780101 -0.904 + PONP930101 -0.907 ZHOH040103 -0.910 FAUJ830101 -0.911 + PONP800108 -0.913 BASU050103 -0.915 CORJ870101 -0.921 + NISK800101 -0.923 MEIH800103 -0.924 CASG920101 -0.924 + WERD780101 -0.926 BIOV880102 -0.928 NADH010102 -0.929 + PONP800101 -0.932 PONP800103 -0.936 MIYS850101 -0.938 + PONP800102 -0.944 NADH010104 -0.944 NADH010103 -0.945 + NISK860101 -0.949 ROSG850102 -0.976 RADA880108 -0.977 + BIOV880101 -0.982 +I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V + -0.21 2.11 0.96 1.36 -6.04 1.52 2.30 0.00 -1.23 -4.81 + -4.68 3.88 -3.66 -4.65 0.75 1.74 0.78 -3.32 -1.01 -3.50 +// diff --git a/src/data/project_training.txt b/src/data/project_training.txt new file mode 100755 index 0000000..b774f11 --- /dev/null +++ b/src/data/project_training.txt @@ -0,0 +1,727 @@ +Peptide IC50.nM. class +NFFHASLAY 64.1 1 +YQKKNASVY 330 1 +AAFLDDNAF 106.43 1 +IQNKLSSTF 24 1 +KLAEIFQPF 101.91 1 +FAAAAARTL 296 1 +MQQSGDEAF 200.3 1 +KLRKKSSFY 88.9 1 +GLGGDASAY 299.95 1 +LQKVPHTRY 476.05 1 +IQAGVDRFY 189 1 +FQVNRFTGY 9.7 1 +YFRNSGMTY 85.27 1 +TVSPSAPTY 67.5 1 +KTIQGGLGW 237 1 +VMLDWGIEL 267 1 +KLEGKIVQY 125.5 1 +RMGAAVTPY 98.8 1 +SQHNYRPGY 22 1 +RGRAATMAL 86.88 1 +QLFIKDYRY 73 1 +FQLYSDLAH 68.2 1 +FVFEATKLY 17.7 1 +SQLEMCEKY 299.1 1 +KVAAAGVSY 165 1 +YVRGYLRGY 151.85 1 +MQLQLNCAY 112.3 1 +LLKPGGVQW 386 1 +YLCEDTITY 196.5 1 +VAGGTSSVY 129 1 +WQFGPSTYY 16 1 +ALEPGFKDY 482.05 1 +IQGTLAKAY 215.15 1 +TTFPVNGGY 164.7 1 +ILSPHNVVT 228 1 +KIFEYGFTF 228.75 1 +GLVECNNHY 181.7 1 +LLRDKDGVY 69.3 1 +AFMATNKAY 94.4 1 +AVLLHEESM 429.35 1 +LMLADHPEY 312.6 1 +LSDDAVVCY 473.7 1 +FTERSDKSY 496.6 1 +ITAGYNRYY 108.47 1 +FVSVYFSDY 250.4 1 +FLFMDRDAL 86 1 +SSLPSYAAY 52.57 1 +GQWDGWVWL 205.5 1 +RLFFIDWEY 296 1 +FSVQRNLPF 45 1 +KLQLKGMSY 110.5 1 +LQIPFAMQM 180.5 1 +YLAGAGLAF 10.4 1 +LMQWWSDYV 234.2 1 +SQKHFDTWW 472.9 1 +YQHLHTAPK 398.65 1 +QQYHRFGLY 7 1 +IVFATAARY 160.3 1 +KMTPWSAYW 56.89 1 +VVAVGGLAI 144.3 1 +FVIGGMTGV 249.3 1 +KQIANELNY 112.1 1 +LAEQFSGEY 374.45 1 +NQQVTNSKY 80.3 1 +NLKLYGAEF 132.9 1 +RQLESRLGY 146.1 1 +AQAVMEMTY 55.5 1 +KIISEIGQL 222.7 1 +YTAVVPLVY 409.5 1 +KQFDTYNLW 241.5 1 +YMIKLAKEV 360.85 1 +FVRQCFNPM 171 1 +AENGWGFYF 284.65 1 +KQINPPTVY 66 1 +HTAEIQQFF 90.58 1 +VQQESSFVM 67.38 1 +PQVLGGLSF 475.4 1 +AQIDNYNKF 1 1 +RLAELIGPA 332.5 1 +IQTHCEVGY 285.1 1 +QLQANRRAY 23 1 +IQVNKGVAY 102.5 1 +KTIECSKEL 468.35 1 +YLDDPDLKY 436.53 1 +FQHERLGQF 20.4 1 +QARQMVQAM 316 1 +QQSEARRML 109.4 1 +KQYNVTQAF 87.07 1 +ISLEAGQRF 363.25 1 +NIRQAGVQY 14 1 +LQSLENVAY 161 1 +ALMEITSRY 90.5 1 +VMKRNFIDF 84.39 1 +LLVAPAYSF 137 1 +WQQWDRQSL 126.6 1 +TVLDVGDAY 170 1 +RLYYDSMSY 129.95 1 +NQECWDSVF 372.7 1 +ILGDTAWDF 273.5 1 +AQLYAYAGF 71.6 1 +VQGYERIMY 271.15 1 +RLKTATYTF 93.81 1 +SVKERGPAY 178.9 1 +KSNEKNMDF 215.2 1 +SQEAEFTGY 94 1 +GMFGGCFAA 161 1 +YQPEREKVY 79.5 1 +IQRDQVTDY 239.15 1 +GMHHLYREY 134.9 1 +LQKGGVIVY 478.17 1 +KSCLPACVY 482 1 +AMIDRLHQT 272.8 1 +RMYGISPWT 454.85 1 +GVIMPNGSY 29 1 +TQFESLKIY 210.9 1 +IIMEEGNSI 243 1 +QAFEAGIDF 76.6 1 +WSILRQRCW 93.37 1 +IMDEPTSSL 172.6 1 +KTFSAHNLF 92 1 +GMKRSFYVY 402.5 1 +RVMAPRALL 102.5 1 +RLKPVGSAY 357.35 1 +AQNAISTTF 89 1 +YTYPCIPEY 126 1 +GQTGVIADY 129 1 +VQLQEYDTY 199.1 1 +EQNWDWNRY 128.6 1 +VVQDPKNVY 173.5 1 +GLVRALTAF 254.8 1 +FHMDPSGTF 464.65 1 +YQYPRDTHY 33.5 1 +KVYWAGIEF 132.6 1 +AQRPAKYSY 132.8 1 +RMLPKLAEF 82.48 1 +IMGIPYCNY 43 1 +YMTLQAVTF 354.2 1 +ELYPTVNTY 227.8 1 +RTWHYCGSY 68 1 +FLRGRAYGI 187.45 1 +VMETENALF 300.95 1 +TSNPKTPKY 393.3 1 +WQFAIHYSF 130.3 1 +TMLYNKMEF 118 1 +TLASIGTAF 341.6 1 +HERPVILSL 169.05 1 +IMYDSGAKY 33.7 1 +VIQLNRKSY 105 1 +EQFPNATAF 42.33 1 +KVMALPIPH 451.55 1 +WSFLEDRVY 41.98 1 +IAQLNRPAM 324.4 1 +GQFGSGWTW 137.7 1 +ILGPPGSVY 40.68 1 +SQIETGTPF 14 1 +LLWYRRGTF 359.7 1 +ALSTGAGAY 435.9 1 +VQLDWQGDY 162.05 1 +KLIADSIDF 67.5 1 +YIFRNTINM 298.45 1 +LLFLPKAAY 99.4 1 +GMMGGLWKY 31.3 1 +ILGRYLPEF 150.5 1 +AMAAAAAPY 294.4 1 +ILLRKGHVF 114.93 1 +VLFKTESGF 11.8 1 +ITFHNQRDF 146.4 1 +IMDASSFTL 138.5 1 +TMKEGWIVY 179.5 1 +GMKAFTAAV 59 1 +AMFEEQNQW 16.7 1 +MSNEGSYFF 64 1 +KQFKQDAKY 172.7 1 +ELNITSATY 458.6 1 +NQLYLTVSF 411.5 1 +STGPLHGCK 20000 0 +RLWNGRRCR 20000 0 +VKKLWGHLP 20000 0 +ATTHSWIPK 20000 0 +AIQIQMFEA 20000 0 +GSFKEYVFW 5692 0 +QATAQAAAY 6054.5 0 +WASRELERF 20000 0 +EKPKFLPDL 20000 0 +TFDVAPSRL 20000 0 +NSDYMMWVG 20000 0 +MTNRQFHQK 20000 0 +PSEVSPIAQ 20000 0 +RLRQLPKKK 20000 0 +KRFQPFQQF 20000 0 +GPGHKARVL 20000 0 +YRYTYRCHR 20000 0 +ARADGILRF 20000 0 +KTTFKPNTW 20000 0 +SVPEPAAGI 20000 0 +DFDGTPRLY 20000 0 +GRPNCFQIV 20000 0 +YFSGIMVRL 20000 0 +RRATAILRK 20000 0 +WMLGTGVYL 2947 0 +HIPEVCLKW 20000 0 +FIKDYRYTY 2746 0 +YRYGFVANF 3268 0 +IVDCLTEMY 1091.5 0 +FVDGVPFVV 20000 0 +IPRRIRQGL 20000 0 +YGDTEAICR 20000 0 +YFFVKWIGK 20000 0 +ETIEEPAVE 20000 0 +WAGIWGGKL 20000 0 +APYFATVRL 20000 0 +TYYPQVVLG 20000 0 +ILGETAWDF 524.7 0 +RYFSVTRPL 20000 0 +EHAGVISVL 20000 0 +RRVSGCVSV 20000 0 +ETIFTVLAL 20000 0 +ASSWAPTQK 20000 0 +SHEGEGIPL 20000 0 +AHGWSTFYL 20000 0 +FLADYRGKT 20000 0 +LSDHQDLKW 20000 0 +DAYRRIHSL 20000 0 +GPRRAAWRI 20000 0 +DISPTNIPL 20000 0 +ATFSRPGSL 3287 0 +SKGETVNPL 20000 0 +DTDISQLHH 20000 0 +GYTPGQQFY 20000 0 +GVPPKVVSY 2559.3 0 +FPRGQGVPI 20000 0 +STDHIPILY 20000 0 +KNDAVYIGY 20000 0 +AEFWDVFLS 20000 0 +FKNSVFYSV 20000 0 +ILYVSCNPA 747.5 0 +SSEQTFMYY 1416 0 +KTQEPPQVA 20000 0 +VVDKYFDCY 20000 0 +RLITVYVQA 20000 0 +RNEQGQTLW 20000 0 +AIKCVDIVK 20000 0 +SEYKAAGYL 20000 0 +RQIQVEGLK 1874 0 +GHLENNPAL 20000 0 +SRWGYQVKH 20000 0 +FSDARLAKL 20000 0 +RSFAERLDR 20000 0 +DLAAGVDVV 20000 0 +NGYRWQHQI 20000 0 +GVFELSDEK 20000 0 +RPPEVDGNR 20000 0 +ISYTYNDNW 20000 0 +SYLIRALTL 20000 0 +KVCRTLLAK 20000 0 +KTPWDRFCK 20000 0 +THADVPVVL 20000 0 +ALGYTTEEI 20000 0 +EADPTGHSY 13540 0 +RPPIFIRRL 20000 0 +YHFDPVHHL 20000 0 +DRYPANAIV 20000 0 +VMLLDIDYF 726.05 0 +AITTPQMTL 13950 0 +ATLLSQVEV 20000 0 +HLGGFVHAC 20000 0 +RMGVKSQLL 1279.5 0 +RPWMLDKYF 20000 0 +KLMPICMDV 2541 0 +GRGQILLGK 20000 0 +QQLEADYTF 1025.15 0 +TPVWHVTSA 20000 0 +AVLQSGFRK 20000 0 +TAVPWNASW 20000 0 +KMSEYKGPV 6666.5 0 +MRVLHLDLK 20000 0 +DTKCKNNYF 20000 0 +YATVAGHEG 10453.5 0 +NPNSPSITY 5622.5 0 +RIKQIINMW 20000 0 +EIPGSPGSY 20000 0 +GTLSYDNLK 20000 0 +ASDRISGIL 5163 0 +RRRIGEIFK 20000 0 +VHTQKKDLY 20000 0 +ARYGIFLPF 3085.33 0 +ICDDVLSKY 20000 0 +AVAVHDFFK 20000 0 +RPRIRLSAP 20000 0 +HFQKDAKVL 2656 0 +DLPPAIAAE 10000 0 +SRKKGFLGL 20000 0 +GVKGFSFKY 20000 0 +ERSDKSYEH 20000 0 +RFEAYGWQV 20000 0 +RPKSNIVLL 20000 0 +MEIYIWDHD 20000 0 +KGPDKLQVY 2419 0 +GYSFSIPGY 547.6 0 +WLWVSSSDM 1373.5 0 +RAPKVRLSL 7169 0 +HRDGKPRYL 20000 0 +FRNQVKIRR 20000 0 +NESGRLIDF 20000 0 +WGKEAVNHF 1717.9 0 +IAIPAHVRL 1807 0 +GEVGLDLTV 20000 0 +GRNSRFPDK 20000 0 +NRRFVNVVP 20000 0 +SSSLTSLLK 20000 0 +STHMENILK 20000 0 +QLQCHQIAI 7264.5 0 +LMTAISQGI 1997.5 0 +SADPLASLL 20000 0 +FPRSAERAG 20000 0 +ARLGKGYMF 20000 0 +EGFLKAAMF 20000 0 +CLWLLTLGL 20000 0 +IHESVIGQL 20000 0 +DPSMLRTTA 20000 0 +RRGPEQTQG 20000 0 +NMERKLNLS 20000 0 +GLENGLNYI 20000 0 +LPYPDPSRI 20000 0 +KSAQVPLPL 1031.85 0 +NSDDYTADE 20000 0 +WTDLYTSMS 20000 0 +RYQRMTGGY 1345.5 0 +GHYTHITAK 20000 0 +KCDICTDEY 20000 0 +KRMGVQMQR 20000 0 +CHKGWGVSV 20000 0 +KEKGPIFRD 20000 0 +ALWEIQQVV 869.15 0 +PPSGKGGNY 20000 0 +GRNSFEVRV 20000 0 +IRNLVKRYK 20000 0 +LPEFERRTL 20000 0 +HLAGFIHAC 2278.5 0 +VRFPNITNL 20000 0 +ITDVQDMDP 20000 0 +VMTEGRHAV 3695.5 0 +KLQWLFAAL 797.8 0 +MKWGMEMRR 20000 0 +RRKTNLYGF 20000 0 +DSDPMDGCE 20000 0 +RVFNNYMPY 560.95 0 +RPVSPGKDI 20000 0 +ATISYRIKL 20000 0 +NANPDCKTI 20000 0 +PPQATAKYL 20000 0 +RTRFFCIPK 10000 0 +FLPGQYMNI 20000 0 +RVDFCGKGY 1087.15 0 +SSECQGEML 20000 0 +ATHKAPQPA 20000 0 +RYDYANLCQ 20000 0 +FAANPNSQV 20000 0 +IHKPRPPAT 20000 0 +QTHFPQFYW 41510 0 +MPASWVMRI 20000 0 +ATPQDLNTM 20000 0 +LVMAPRTVL 731 0 +RVNKGTGVK 4454 0 +IASLTGWQW 16000 0 +ATNNVFRLK 20000 0 +CQTYKWETF 10000 0 +KLFIRQEEV 14890 0 +RLYEWQHVS 2569 0 +EIIELTRTL 20000 0 +YLDADREFL 20000 0 +GMDPRMCSL 20000 0 +GRSLEDDIR 20000 0 +YTPLNYSKF 1425.5 0 +GVNACQVGV 20000 0 +SQEDNHFSL 2791 0 +RPRGHREFC 20000 0 +RPYGKFRAM 20000 0 +ASDPSFPDI 20000 0 +MVDESMMMS 20000 0 +RVRIERGPR 20000 0 +DIIRAHPWF 16615 0 +GRRATAILR 20000 0 +ADFKLFFRW 20000 0 +APTGDLPRA 20000 0 +HHIPNGVVW 20000 0 +DWSGYSGSF 10000 0 +TLVPQEHYV 20000 0 +YTDDYPMYK 20000 0 +AAGLPAIFV 20000 0 +VVISKKDTY 20000 0 +VNGVKGIQF 20000 0 +AYSPFAFKK 20000 0 +SPAIFQSSM 20000 0 +AYLLQHLDL 20000 0 +VTTEVAFGL 20000 0 +WRDDSRGRW 20000 0 +TTRAWFDKK 20000 0 +ALIVAIWDK 20000 0 +DLSNSMRDF 20000 0 +FRKEFTKLE 20000 0 +DTFGVIDTM 20000 0 +HRIQEELFY 6287 0 +VMGGNAAEA 20000 0 +EVWGMRWPI 20000 0 +RRRQWASCM 20000 0 +IRHENRMVL 20000 0 +AEHDPWWAV 20000 0 +EFIYWDWLY 20000 0 +EHFYWGSVF 1890 0 +YIALGRARV 20000 0 +GYLNACGHF 20000 0 +EISGLRPGE 20000 0 +VGYVDDTQF 571.5 0 +ERLQICQRK 20000 0 +AEIDRSFKP 20000 0 +KLGDQFGRK 20000 0 +IVLLCYGGW 6176 0 +PAHKSQLVW 20000 0 +IAFCNWAFV 20000 0 +TVANNPDDK 20000 0 +FPEHIFPAL 20000 0 +EEIDWIKTD 20000 0 +EFDNYRGTI 20000 0 +EEVWRDPYL 20000 0 +EEFTMVGRR 20000 0 +ALASFLFGF 745 0 +VFLPNTHNL 20000 0 +RPLLARMPE 20000 0 +FGSGWTWVV 20000 0 +HIMPNSFRV 20000 0 +CADGTRHTY 1259.4 0 +GRDHVRVTL 20000 0 +ASLPTTIAK 20000 0 +LPLIVDTAA 20000 0 +GPATAQMAL 20000 0 +IPLTEEAEL 20000 0 +SSNVANYQK 20000 0 +ITGQIIFGF 20000 0 +EAFPYEITE 20000 0 +RFSFNCSMK 20000 0 +KLFAAETLK 21275 0 +KTFPPTEPK 20000 0 +PTKCGENLY 2359 0 +DFPIFNQRY 20000 0 +TSSDTYACW 20000 0 +NAHEGQLVI 20000 0 +SRALLLNKY 16495 0 +EPIVGAETF 20000 0 +AIKPITDQF 20000 0 +KLRQGNTLV 20000 0 +SEGDDDGSR 20000 0 +PSSKPDWFY 15155 0 +GKFFAQAFL 20000 0 +LLKDLMPFV 9230 0 +EKFFPSSSY 1116 0 +GLKRGGVLL 919.05 0 +SRLKPSSFK 20000 0 +KSDGTGTIY 847.8 0 +FPVTPQVPL 20000 0 +ELLSHVGQA 20000 0 +RQFVSNNGK 1970.5 0 +FTDGVCLFW 20000 0 +SPRTLNAWV 20000 0 +ATDFKFAMY 4097.5 0 +HVPTRGTAM 5000 0 +MRIPVERTL 20000 0 +AMVPLVMVI 833.5 0 +FIFGKMGAG 20000 0 +AFASLQDML 20000 0 +FPREGVFVF 2137.5 0 +VTFQGKFKK 20000 0 +EVIPYTPAM 4763.5 0 +YQTDSGCWY 1342.8 0 +QPEWFRNVL 20000 0 +KYDDRIQSQ 20000 0 +PEIRRWIIF 20000 0 +MEFEPFQSL 2652 0 +YLGPTIRVW 1223 0 +NWDWGVFFK 20000 0 +YSDIPRLKK 20000 0 +YFSDVSAPV 704.5 0 +VPAPAGPIV 20000 0 +LTLKPCHAL 20000 0 +STEIGLLVG 20000 0 +EVMPVSMAK 20000 0 +DYIYLPLLK 20000 0 +ILHCANFNV 20000 0 +PTDYMSSKL 20000 0 +RLLRMNNEN 20000 0 +YPKCDLVEL 20000 0 +FMHSAAPIT 1923.5 0 +TMPELAWAV 20000 0 +CTDDNALAY 20000 0 +KVIQPRVEK 20000 0 +AIPYFYKGK 20000 0 +ETVNFVPNY 20000 0 +GLYEAIEEC 20000 0 +IIANARIEV 10625 0 +PSEDEQQGH 20000 0 +QTPGVKIAP 20000 0 +YPAEITLTW 20000 0 +APIEHIASM 20000 0 +FHLRSRFAF 20000 0 +VPRVHNQPQ 20000 0 +TLAAAANSY 570.8 0 +KTTIKFHPW 20000 0 +AANEIRISK 20000 0 +FFGWEGVGV 20000 0 +LTDDMIAAY 635.9 0 +DQFSIPIRY 579.2 0 +TVNVILRPK 20000 0 +RGINDRNFW 20000 0 +NMAPEKVDF 1541 0 +DPSGAYFAW 20000 0 +SLAIDAYPL 1076.7 0 +SALNHTKKW 20000 0 +MSSAMSMMH 2580.5 0 +YLHRDIFDI 8639 0 +DMYDQQLSV 20000 0 +AISAQVAAY 1270.7 0 +YQRPFGGQS 3714.5 0 +LFMSHVKSV 15245 0 +QTSTLYDFY 1709.5 0 +CYDLMSFLE 20000 0 +MGRDIKVQF 2000 0 +SMELPSFGV 20000 0 +ATQPVHWFL 20000 0 +RRFQHKDGH 20000 0 +YFDPANGKF 20000 0 +RHIAIQVCY 1731.5 0 +ISNQEPLKL 20000 0 +NMLREGLSP 20000 0 +MTMRRRLFK 20000 0 +RLEDVFAGK 20000 0 +ASHFISNSW 11397.5 0 +DPRDDLSGM 20000 0 +DYPDDFMDK 20000 0 +HEKGINPNY 541 0 +EEQTDPKTL 20000 0 +WYETVKVNY 20000 0 +GSDGGLDDY 20000 0 +LYQPSSGCY 1074.5 0 +GLAGLQTDV 20000 0 +RKAGVNQAK 20000 0 +KMQRMLLEK 40280 0 +RRTPRVSWK 20000 0 +RRHWGGNVL 20000 0 +DYVPTNKWV 20000 0 +EIKFNDITF 20000 0 +FLHPKHWGT 20000 0 +VRDPKTSEI 20000 0 +NLGDKQDTF 5000 0 +ETFNTPAMY 554.45 0 +TCDGNTFTY 20000 0 +ISNYICVAW 2929.33 0 +GKIKGKYSY 20000 0 +LPHQPLATY 2352.5 0 +ALYWALMES 20000 0 +VLPPLSADL 20000 0 +DLNKVIQFL 20000 0 +ELDEIGEDV 20000 0 +VTDGGEVGE 20000 0 +FADINGKLY 3140 0 +ITWETPMIW 20000 0 +EHGIVIRAF 20000 0 +LIFPAFFLC 20000 0 +LLTEVETYV 20000 0 +ADLRFASEF 930.35 0 +NLEPGTFDL 20000 0 +RSEVELCIY 6276 0 +SYINRTGTF 584 0 +TPYDINQML 20000 0 +EEMATKADY 1455 0 +SYPPPPASF 10000 0 +DLLENLQAY 2687 0 +RRVRDNMTK 20000 0 +APRQPGLMA 20000 0 +NPDIVIYQY 20000 0 +FMSLQSGDV 20000 0 +VLWAHGFEL 617.4 0 +NILVAGNLI 20000 0 +RVRQLDESI 1093.5 0 +EVHIYYLEK 20000 0 +ALMRWRHPR 20000 0 +FLILCSVLL 20000 0 +STDTRHIPQ 20000 0 +AEGTGITHL 20000 0 +KIRLGFHWK 20000 0 +APRTVALTA 20000 0 +RRQWVLAFR 20000 0 +ISEPMFHQG 20000 0 +AYGSRFHEW 98055 0 +RPPGCTFPA 20000 0 +FRYMNSQGL 20000 0 +NPALRMKWM 20000 0 +LLQEKYGLI 20000 0 +CFMYSDFHF 20000 0 +RHYSASFKK 20000 0 +MSDIFHALV 20000 0 +RDALGRTAL 20000 0 +MCFHQHLMY 1436 0 +ASYRLCLYR 20000 0 +NPKTPKYKF 20000 0 +FYKRKAMAW 20000 0 +AQKLATKPV 715.6 0 +KMVGTVQRV 662.4 0 +YIFWIRTPR 20845 0 +TIPTNIPTL 20000 0 +YINMAWNLV 20000 0 +NPVPVGNIY 20000 0 +KLNHHKPPT 20000 0 +SVKEKDMTK 5000 0 +IVAWTRTAT 20000 0 +AYYWNQNGF 25085 0 +YHGEAMAIG 20000 0 +KRVDWSVEY 2720.5 0 +GVFKVWHPI 20000 0 +VVNYDNSTK 20000 0 +LYDYKENRF 20000 0 +SRDKTIIMW 20000 0 +PVDEYITTY 20000 0 +WPWNAREDV 20000 0 +YYLEKANKI 20000 0 +KAVRGDLNF 929 0 +SRARIKTRL 20000 0 +IYYLEKANK 20000 0 +THYPTQNRF 20000 0 +VSPLAVTWW 2198 0 +AMHYIRHRA 20000 0 +EEIRRIWRQ 20000 0 +KPRSPVVEL 20000 0 +FAAFYFVFI 20000 0 +HFDDVANGF 20000 0 +FTFDNSKFV 20000 0 +SVMPAWQEK 20000 0 +LGYPFAWFL 20000 0 +IHDHGEQLF 20000 0 +RPMTYKAAL 20000 0 +ISVQPLWEW 20000 0 +AMAETGCDA 661.03 0 +FRISGRGGK 20000 0 +HPDIVIYQY 1510 0 +ILKGKFQTA 5723 0 +ISSGETRSF 3604.9 0 +RPASAGAML 20000 0 +TSPDLSFSL 84550 0 +KTNDFAPAW 5000 0 +WMQELRAGA 2636.5 0 +LVYNHCEHG 20000 0 +TYQWIIRNW 20000 0 +KLLQICMWF 16605 0 +YAEISFMLW 20000 0 +LLPYPIAGC 20000 0 +PLWESATEV 20000 0 +DFIGKTIGF 20000 0 +RRQGNIYPK 20000 0 +GSDKQVVGQ 20000 0 +GSEDRDLLY 20000 0 +AEFPVGSTA 20000 0 +FVRSSNLKF 8000 0 +IADMGHLKY 4093.5 0 +IIMFDAEKL 3350 0 +LSEEIGLDL 20000 0 +LMPLARFWL 5779 0 +MKWMMAMKY 20000 0 +EPEPHILLF 20000 0 +TMKFKGTVD 20000 0 +ILWGYGFLQ 20000 0 +GLMWLSYFV 20000 0 +FPGEKRVSK 20000 0 +AFGLFWLVW 20000 0 +ETDVMTRGQ 20000 0 +QHTRRVSVL 20000 0 +KVGVYKMHK 20000 0 +KLPRMFLPK 20000 0 +APRALLLLL 20000 0 +SPRYIFTML 20000 0 +PLVQQEDDK 20000 0 +TVYPKTHYV 2011 0 +QYDDLHKKF 47520 0 +SYGNANVSF 1140 0 +EEDLPVTWR 20000 0 +FHNNWGATL 20000 0 +APILVVSGI 20000 0 +KFFPSSSYR 20000 0 +LMAEDLANV 7686 0 +HEGEGIPLY 20000 0 +AVDPAKAYK 20000 0 +SRIGAWASK 20000 0 +HSSVAGGLW 20000 0 +SRYWEPEFY 20000 0 +RLTGREGAV 20000 0 +SPADERAVA 5000 0 +IAGFIEGGW 20000 0 +WPISAILWF 20000 0 +PHYNNPWNT 20000 0 +IPSINVHHY 20000 0 +IYSAEFKNY 19990 0 +IVDYVTAYG 20000 0 +RTDPVIDNI 20000 0 +ERPAFGIQK 20000 0 +DVSPLMHLF 22195 0 +QPQQSPQFF 20000 0 +HPLSHFVNL 20000 0 +KLWAQCVQL 20000 0 +KTNFQNHKG 20000 0 +VPPTNSINK 10000 0 +GRLQSLQTY 20000 0 +DYAMHGTVF 3804 0 +RPRHQGVMV 20000 0 +IQCAGSEEK 20000 0 +GRYSVRYVR 20000 0 +RPQLGVGDV 20000 0 +RTGDIGCFK 20000 0 +VMCIQMKYV 20000 0 +RLFFKCIYR 20000 0 +TFMYVFSTF 694.7 0 +AYQQGVKTL 94965 0 +VLTGNLQTL 20000 0 +TPKGPKVKY 20000 0 +RMFLAMITY 1224 0 +YQYIFLSFF 3064 0 +EIPQFMIGL 20000 0 +LIPDGDGEV 20000 0 +PPIPVGDIY 20000 0 diff --git a/src/main.py b/src/main.py new file mode 100755 index 0000000..d7f2024 --- /dev/null +++ b/src/main.py @@ -0,0 +1,84 @@ +#!/usr/bin/python + +from optparse import OptionParser, OptionGroup +import tools +from sklearn.externals import joblib + + +DEBUG = False + +# print debug messages and errors +def debug(s): + if DEBUG: + print("DEBUG: " + s) + + +def error(s): + print("ERROR: " + s) + + +# read the input file and parse the lines +def parseAndReadInput(s): + try: + source = s + datei = open(source, "r") + lines = datei.read().splitlines() + new_lines = [] + for line in lines: + # remove whitespace and tab + new_line = line.replace(' ','') + new_line = new_line.replace('\t','') + if(len(new_line) == 9): + new_lines.append(new_line) + debug("Got input: %s" % new_lines) + return new_lines + except Exception as e: + error("Couldn't read input file: %s" % str(e)) + return None + + +# main method with menu +if __name__ == '__main__': + # build menu structure + usage = "\nCopyright (C) 2016 App, Krumm, Spaeth - Use at your own risk!\n" + \ + "description: this is an SVM based MHC-I predictor \n\n" + \ + "Input file required." + + parser = OptionParser(usage) + parser.add_option("-d", "--debug", + action="store_true", dest="debug", default=False) + + option_group = OptionGroup(parser, "Open input file") + option_group.add_option("--input", dest="input", + help="path to the input file") + option_group.add_option("--output", dest="output", + help="name of the generated output file") + parser.add_option_group(option_group) + + (options, args) = parser.parse_args() + + DEBUG = options.debug + + # if input is given: + # set input path, read and parse input, execute svm + if options.input and options.output: + debug("Reading input file: " + options.input) + input_list = parseAndReadInput(options.input) + features = tools.prep.prepareData(input_list) + try: + debug("Loading existing svm...") + svm = joblib.load('svm/svm.pkl') + except Exception as e: + error("Couldn't load svm file: %s \n +" + "-> First execute tools/svm.py to generate a svm." % str(e)) + # save prediction in file + predicted_labels = tools.svm_methods.svmPredict(svm, features) + try: + out_file = open("%s" % options.output, "w+") + for x in range(0, len(input_list)): + out_file.write("%s\t%s\n" % (input_list[x], predicted_labels[x])) + debug("Generated output file %s" %options.output) + except Exception as e: + error("Could't create output file: %s" % str(e)) + else: + error("No input and output given!") diff --git a/src/selector/__init__.py b/src/selector/__init__.py new file mode 100755 index 0000000..e69de29 diff --git a/src/selector/selector.pkl b/src/selector/selector.pkl new file mode 100755 index 0000000..29b1d7d Binary files /dev/null and b/src/selector/selector.pkl differ diff --git a/src/selector/selector.pkl_01.npy b/src/selector/selector.pkl_01.npy new file 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import SelectPercentile, f_classif + +# Lädt Trainingsdaten von training_data.txt +trainingData, ligands, labels = project_training_parser.parseProjectTraining() + + +# Gibt Trainingsdaten aus +# Out: Trainingsdaten +def getTrainingData(): + return trainingData + + +# Gibt Liganden der Trainingsdaten aus +# Out: Liganden des Trainingsdatensatzes +def getLigands(): + return ligands + + +# Gibt Labels der Trainingsdaten aus +# Out: Labels des Trainingsdatensatzes +def getLabels(): + return labels + + +# Gibt Liste mit Features für die Trainingsdaten aus +# Out: Features für Aminosäuren +def getFeaturesForAS(x): + features_for_as = [] + for feature in total_aaindex_parser.getFeaturesforAAX(): + features_for_as.append(feature[x]) + return features_for_as + + +# Weist jeder Aminosäure seine Features zu +# Out: Dictionary das jeder Aminosäure seine Eigenschaften zuweist +def setAllFeatures(): + aas = ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"] + feature_dic = {} + for x in range(0, len(aas)): + feature_dic.update({aas[x]: getFeaturesForAS(x)}) + return feature_dic + + +# Stellt Peptide als Feature-Vektor dar +# In: Liganden und Features +# Out: Liganden als Feature-Vektor +def featureLigands(ligands, features): + a = setAllFeatures() + number_of_features = len(a["A"]) + ligands_featured = [] + for x in range(0, len(ligands)): + peptide = [] + for y in range(0, number_of_features): + for char in ligands[x]: + peptide.append(features[char][y]) + ligands_featured.append(peptide) + return ligands_featured + + +# Bereitet Trainingsdaten für SVM auf +# Out: Skalierte und Selektierte Features und Labels der Trainingsdaten +def prepareTrainingData(): + # Einlesen der Trainingsdaten und casten in Numpy Array + labels = np.array(getLabels()) + features = np.array(featureLigands(getLigands(), setAllFeatures())) + # Skalierung der Trainingsdaten mit MinMaxScaler + scaler = preprocessing.MinMaxScaler() + scaled_features = scaler.fit_transform(features) + # Feature Selection mit 10 Percentil + selector = SelectPercentile(f_classif, percentile=10) + selector.fit(scaled_features, labels) + # Speichere Selektor um ihn bei INPUT später auch zu verwenden + joblib.dump(selector, '../selector/selector.pkl') + selected_features = selector.transform(scaled_features) + return selected_features, labels + + +# Bereitet Input-Daten fuer SVM auf +# In: Liganden aus Input +# Out: Skalierte und Selektierte Feature-Vektoren des Inputs +def prepareData(ligands): + # Skalierung mit MinMaxScaler + scaler = preprocessing.MinMaxScaler() + scaled_features = scaler.fit_transform(np.array(featureLigands(ligands, setAllFeatures()))) + # Feature Selection mit Selektor aus Trainingsvorgängen + selector = joblib.load('selector/selector.pkl') + selected_features = selector.transform(scaled_features) + return selected_features diff --git a/src/tools/project_training_parser.py b/src/tools/project_training_parser.py new file mode 100755 index 0000000..27c06f3 --- /dev/null +++ b/src/tools/project_training_parser.py @@ -0,0 +1,28 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- + +import os + + +# Lädt Trainingsdatensatz in einen Array +# Out: Trainingsdaten, Liganden und Labels +def parseProjectTraining(): + training_data = [] + source = "data/project_training.txt" + if not os.path.isfile(source): + source = "../data/project_training.txt" + input_file = open(source, "r") + ligands = [] + labels_str = [] + input_file.next() + for line in input_file: + ligands.append(line.split(None, 1)[0]) + labels_str.append(line[-2]) + input_file.close() + labels = [] + for i in range(len(labels_str)): + labels.append(int(labels_str[i])) + for x in range(0, len(ligands)): + training_data.append([ligands[x], labels[x]]) + + return training_data, ligands, labels diff --git a/src/tools/svm.py b/src/tools/svm.py new file mode 100755 index 0000000..cfcb461 --- /dev/null +++ b/src/tools/svm.py @@ -0,0 +1,21 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- + +# Eine neue SVM wird erstellt und in das SVM-Verzeichnis gespeichert +# Die SVM wird auf dem kompletten Datensatz trainiert + +import prep +import svm_methods +from sklearn.externals import joblib + +# Bereite Daten für SVM auf +features, labels = prep.prepareTrainingData() +# Grid-Search für kompletten Trainingsdatensatz +svm = svm_methods.svmGridFit(features, labels) +# Sage Labels für Trainingsdatensatz vorraus +# predicted_labels = svm_methods.svmPredict(svm, features) +# Zeige Ergebnisse der Vorhersage an +# svm_methods.showResults(predicted_labels, labels) +# svm_methods.plotROC(predicted_labels, labels) +# Speichere SVM +joblib.dump(svm, '../svm/svm.pkl') diff --git a/src/tools/svm_cv.py b/src/tools/svm_cv.py new file mode 100755 index 0000000..0d8ca6e --- /dev/null +++ b/src/tools/svm_cv.py @@ -0,0 +1,30 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- + +# Führt eine Stratified 10-Fold Kreuzvalidierung auf den Trainingsdaten aus, um die Qualität zu beurteilen +import tools.svm_methods as svm_methods + +meanAUC = 0 +meanFPR = 0 +meanTPR = 0 +counter = 0 +#Führe Kreuzvalidierung durch (10 Stratified-KFold) +for ligands_train, ligands_test, labels_train, labels_test in svm_methods.skfCV(): + #Grid-Search jeweils für die 10 Datensätze + svm = svm_methods.svmGridFit(ligands_train, labels_train) + #Vorhersage der Labels für die jeweils 10 Datensätze + predicted_labels = svm_methods.svmPredict(svm, ligands_test) + #Zeige AUC für die jeweils 10 Datensätze + print(svm_methods.getAUC(predicted_labels, labels_test)) + #Berechne mittleren AUC + meanAUC = meanAUC+svm_methods.getAUC(predicted_labels, labels_test) + fpr, tpr = svm_methods.getFprTpr(predicted_labels, labels_test) + meanFPR = meanFPR+fpr + meanTPR = meanTPR+tpr + counter = counter + 1 +#Zeige Mittleren AUC Wert der 10 Durchgänge +meanAUC = meanAUC/counter +meanFPR = meanFPR/counter +meanTPR = meanTPR/counter +print("MEAN AUC: %s" % (meanAUC)) +svm_methods.plotMeanROC(meanFPR, meanTPR) \ No newline at end of file diff --git a/src/tools/svm_methods.py b/src/tools/svm_methods.py new file mode 100755 index 0000000..1877a56 --- /dev/null +++ b/src/tools/svm_methods.py @@ -0,0 +1,121 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- + +import tools.prep as prep +from sklearn.svm import SVC +from sklearn.model_selection import StratifiedKFold +from sklearn.model_selection import GridSearchCV +from sklearn.metrics import roc_curve, auc +import matplotlib.pyplot as plt + + +# Hier befinden sich die Methoden zum erstellen und trainieren einer SVM + +# 10-Stratified-KFold Kreuzvalidierung der Daten +# Out: Jeweils Folds des Datensatzes +def skfCV(): + # Liest aufbereitete Trainingsdaten ein + features, labels = prep.prepareTrainingData() + # Initialisiere SKF mit 10 Folds + skf = StratifiedKFold(labels, n_folds=10) + # Teile Datensatz in Folds auf + for train, test in skf: + features_train, features_test, labels_train, labels_test = features[train], features[test], labels[train], \ + labels[test] + yield features_train, features_test, labels_train, labels_test + + +# SVM mit Grid-Search +# In: Features und Labels +# Out: SVM mit bestem Parameter +def svmGridFit(features, labels): + param_grid = [{'C': [1, 10, 20, 30, 40, 50, 100, 500, 750, 1000], 'gamma': [0.1, 0.01, 0.001, 0.002, 0.003, 0.005]}] + svm = SVC(kernel='rbf', cache_size=1000, class_weight='balanced') + clf = GridSearchCV(svm, param_grid=param_grid, cv=10, scoring='roc_auc') + clf.fit(features, labels) + # print "Best parameters: %s" % clf.best_params_ + return clf + + +# Vorhersage der Labels für Input +# In: Input-Features +# Out: Vorhergesagte Labels +def svmPredict(clf, input): + pred_labels = clf.predict(input) + return pred_labels + + +# Zeigt Anzahl der Binder und Nicht-Binder an +# In: Labels +# Out: Binder, nicht-Binder +def showBinder(labels): + binder = 0 + nonBinder = 0 + for p in labels: + if p == 1: + binder = binder + 1 + else: + nonBinder = nonBinder + 1 + return binder, nonBinder + + +# Gibt FPR und TPR einer Vorhersage heraus +# In: Vorhergesagt Labels, Test Labels +# Out: FPR, TPR +def getFprTpr(pred_labels, test_labels): + fpr, tpr, thresholds = roc_curve(test_labels, pred_labels) + return fpr, tpr + + +# Plottet ROC Kurve aus FPR und TPR +# In: False Positive Rate, True Positiv Rate +# Out: ROC-Plot +def plotMeanROC(fpr, tpr): + roc_auc = auc(fpr, tpr) + plt.title('Receiver Operating Characteristic') + plt.plot(fpr, tpr, 'b', label='AUC = %0.2f' % roc_auc) + plt.legend(loc='lower right') + plt.plot([0, 1], [0, 1], 'r--') + plt.xlim([-0.1, 1.2]) + plt.ylim([-0.1, 1.2]) + plt.ylabel('True Positive Rate') + plt.xlabel('False Positive Rate') + print("ROC-Curve plotted") + plt.show() + + +# Plottet ROC Kurve von der Vorhersage +# In: Vorhergesagte Labels, Test Labels +# Out: ROC-Plot +def plotROC(pred_labels, test_labels): + false_positive_rate, true_positive_rate, thresholds = roc_curve(test_labels, pred_labels) + roc_auc = auc(false_positive_rate, true_positive_rate) + plt.title('Receiver Operating Characteristic') + plt.plot(false_positive_rate, true_positive_rate, 'b', label='AUC = %0.2f' % roc_auc) + plt.legend(loc='lower right') + plt.plot([0, 1], [0, 1], 'r--') + plt.xlim([-0.1, 1.2]) + plt.ylim([-0.1, 1.2]) + plt.ylabel('True Positive Rate') + plt.xlabel('False Positive Rate') + print("ROC-Curve plotted") + plt.show() + + +# Gibt Ergebnisse der Vorhersage aus +# In: Vorhergesagte Labels, Testlabels +# Out: Zeigt Anzahl der Binder, nicht-Binder und AUC an +def showResults(pred_labels, test_labels): + binder, nonBinder = showBinder(pred_labels) + false_positive_rate, true_positive_rate, thresholds = roc_curve(test_labels, pred_labels) + roc_auc = auc(false_positive_rate, true_positive_rate) + print("SVM predicted %s binder and %s nonBinder. AUC = %s" % (binder, nonBinder, roc_auc)) + + +# Ermittelt AUC der Vorhersage +# In: Vorhergesagte Labels, Testlabels +# Out: AUC der Vorhersage +def getAUC(pred_labels, test_labels): + false_positive_rate, true_positive_rate, thresholds = roc_curve(test_labels, pred_labels) + roc_auc = auc(false_positive_rate, true_positive_rate) + return roc_auc diff --git a/src/tools/total_aaindex_parser.py b/src/tools/total_aaindex_parser.py new file mode 100755 index 0000000..43e8cb3 --- /dev/null +++ b/src/tools/total_aaindex_parser.py @@ -0,0 +1,41 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- + +import os + + +# Lädt alle Eigenschaften der aaindex1.txt in eine Liste +# Out: Liste mit aaIndex-Eigenschaften +def parseAaIndex(): + source = "data/aaindex1.txt" + if not os.path.isfile(source): + source = "../data/aaindex1.txt" + input_file = open(source, "r") + lines = input_file.read().splitlines() + totalaaIndex = [] + counter = 0 + for i in range(len(lines)): + if lines[i][0] == "I": + bothLines = lines[i + 1] + lines[i + 2] + partielaaIndex = bothLines.split() + totalaaIndex.append(partielaaIndex) + counter += 1 + input_file.close() + return totalaaIndex + + +# Entfernt Eigenschaften in denen NA vorkommt und Floatet die Liste +# Out: neue Liste der aaIndex-Eigenschaftens +def getFeaturesforAAX(): + a = parseAaIndex() + rmv = [] + for feature in a: + if 'NA' in feature: + rmv.append(feature) + for feature in rmv: + a.remove(feature) + lst = [] + for feature in a: + b = map(float, feature) + lst.append(b) + return lst