Contacts of the helix formed by residues 965 - 987 (chain A) in PDB entry 5B16
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 965 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A LEU* 3.3 20.9 - - - +
896A ALA* 3.4 20.5 + - - +
898A THR 3.0 20.0 + - - +
899A HIS* 4.8 6.1 + - - -
900A PRO* 3.5 17.7 - - - +
964A HIS* 1.3 71.7 - - - +
966A GLU* 1.3 55.6 + - - +
967A ARG 3.1 2.9 - - - -
968A LEU* 3.2 6.7 + - - +
969A GLU* 2.7 38.1 + - - +
1042A ASN* 4.4 4.8 - - - +
1043A CYS* 3.5 29.3 - - - +
1046A ALA* 3.6 10.1 - - + +
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Residues in contact with GLU 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A PRO* 4.6 13.6 - - + +
961A ARG* 3.4 37.1 + - - +
964A HIS* 3.3 29.4 + - + +
965A ASN* 1.3 82.2 + - - +
967A ARG* 1.3 57.6 + - + +
969A GLU* 3.7 19.5 - - - +
970A PHE* 2.9 29.5 + - - +
1170A HIS* 5.4 0.2 - - - +
1171A GLU* 4.0 32.8 + - + +
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Residues in contact with ARG 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A LEU* 5.5 3.8 - - + -
961A ARG 5.5 1.6 - - - +
962A ILE* 4.6 26.2 + - - +
964A HIS* 4.9 5.6 - - + +
965A ASN 3.1 1.3 - - - -
966A GLU* 1.3 78.0 - - + +
968A LEU* 1.3 60.0 + - + +
970A PHE* 3.0 10.6 + - - +
971A LEU* 2.9 26.0 + - - +
1163A PHE* 3.0 62.6 + - + +
1166A PHE 3.4 5.1 + - - -
1167A PRO* 2.7 39.6 + - - +
1168A ASP* 4.7 0.6 - - - +
1169A HIS 3.3 22.5 + - - -
1170A HIS* 4.3 11.0 - - - +
1171A GLU* 4.6 1.1 - - - +
1174A LEU* 3.4 18.9 - - - +
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Residues in contact with LEU 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892A LEU* 3.9 17.5 - - + -
895A LEU* 3.8 22.2 - - + -
896A ALA* 3.6 33.4 - - + +
965A ASN* 3.2 6.5 + - - +
967A ARG* 1.3 79.6 - - + +
969A GLU* 1.3 57.0 + - - +
971A LEU* 3.8 6.5 - - + -
972A GLY 2.9 19.8 + - - -
1045A GLN 3.2 10.9 - - - +
1046A ALA* 3.4 18.8 - - + +
1049A GLY* 3.9 5.1 - - - -
1050A ALA* 3.9 27.4 - - + +
1053A LEU* 4.5 3.6 - - + -
1163A PHE* 3.5 28.5 - - + -
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Residues in contact with GLU 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965A ASN* 2.7 19.2 + - - +
966A GLU* 3.7 23.0 - - - +
968A LEU* 1.3 76.3 - - - +
970A PHE* 1.3 60.8 + - - +
973A ASP* 2.9 31.9 + - - +
1042A ASN* 3.0 54.4 + - + +
1045A GLN* 3.5 17.8 + - - +
1046A ALA* 3.8 8.9 - - + +
1171A GLU* 6.1 0.9 - - - +
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Residues in contact with PHE 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A GLU 2.9 19.7 + - - +
967A ARG* 3.0 6.7 + - - +
969A GLU* 1.3 76.9 - - - +
971A LEU* 1.3 61.9 + - - +
973A ASP* 3.9 13.3 - - + +
974A ALA* 4.0 2.1 + - - +
1159A THR* 3.3 35.8 + - + +
1162A LEU* 5.1 3.6 - - + -
1163A PHE* 5.3 2.7 - + - -
1171A GLU* 4.7 12.6 - - + -
1174A LEU* 3.6 48.9 - - + -
1175A THR* 3.8 24.7 - - - -
1178A ARG* 3.5 47.2 + - + -
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Residues in contact with LEU 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967A ARG 2.9 13.3 + - - +
968A LEU* 3.9 9.6 - - + +
970A PHE* 1.3 77.4 - - - +
972A GLY* 1.3 60.0 + - - +
974A ALA* 3.1 8.1 + - - +
975A VAL* 2.9 34.6 + - + +
1049A GLY 3.6 24.2 - - - +
1052A TYR* 4.1 17.0 - - + -
1053A LEU* 4.5 10.5 - - + -
1156A LEU* 5.1 3.1 - - + +
1159A THR* 3.7 22.0 - - + +
1160A GLU* 3.9 26.7 - - + +
1163A PHE* 4.2 30.1 - - + -
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Residues in contact with GLY 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968A LEU 2.9 10.7 + - - -
969A GLU 3.3 1.3 + - - -
971A LEU* 1.3 74.7 - - - +
973A ASP* 1.3 58.6 + - - +
974A ALA 3.3 0.2 - - - -
975A VAL* 3.6 4.9 - - - -
976A VAL* 2.9 36.9 + - - +
1045A GLN* 3.2 29.8 - - - -
1048A ILE* 4.2 0.4 - - - -
1049A GLY* 3.8 11.2 - - - -
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Residues in contact with ASP 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A GLU* 2.9 17.0 + - - +
970A PHE* 3.9 10.1 - - + +
972A GLY* 1.3 78.4 - - - +
974A ALA* 1.3 57.6 + - - +
976A VAL* 4.0 1.6 - - - +
977A GLU* 2.9 44.8 + - - +
1004A VAL* 5.1 4.9 - - - +
1045A GLN* 2.9 30.2 + - - +
1155A GLN* 5.3 5.1 + - - +
1178A ARG* 5.9 2.5 - - - +
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Residues in contact with ALA 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970A PHE 4.0 0.6 + - - +
971A LEU 3.1 9.2 + - - +
973A ASP* 1.3 76.5 - - - +
975A VAL* 1.3 61.0 + - - +
977A GLU* 3.6 6.4 - - - +
978A PHE* 2.9 30.8 + - - +
1152A SER 5.1 0.9 - - - +
1155A GLN* 4.0 11.2 - - + +
1156A LEU* 3.6 26.8 - - + +
1159A THR* 3.5 31.9 - - + +
1178A ARG* 4.9 1.7 - - - +
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Residues in contact with VAL 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A LEU* 2.9 25.7 + - + +
972A GLY* 3.6 11.2 - - - +
973A ASP 3.2 0.2 - - - -
974A ALA* 1.3 74.2 - - - +
976A VAL* 1.3 61.2 + - - +
978A PHE* 3.1 4.4 + - - +
979A LEU* 2.9 42.9 + - + +
1048A ILE* 4.0 31.4 - - + +
1049A GLY* 4.3 1.1 - - - -
1052A TYR* 3.6 42.4 - - + -
1057A LEU* 5.4 0.7 - - + -
1060A ALA* 4.2 4.3 - - + -
1156A LEU* 3.9 12.3 - - + -
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Residues in contact with VAL 976 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A GLY 2.9 23.3 + - - +
973A ASP* 4.0 3.8 - - - +
975A VAL* 1.3 74.1 - - - +
977A GLU* 1.3 55.3 + - - +
979A LEU* 3.8 5.9 - - - +
980A THR* 2.5 41.8 + - + +
1004A VAL* 4.4 20.9 - - + -
1009A LEU* 4.6 9.9 - - + -
1044A PHE* 4.6 5.2 - - + -
1045A GLN* 4.5 13.5 - - + +
1048A ILE* 3.7 30.1 - - + -
1064A PHE* 4.0 27.6 - - + -
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Residues in contact with GLU 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A ASP* 2.9 28.8 + - - +
974A ALA* 3.6 8.7 - - - +
976A VAL* 1.3 78.2 - - - +
978A PHE* 1.3 54.3 + - - +
980A THR* 2.8 15.5 + - - -
981A SER* 2.7 28.1 + - - -
1000A ARG* 3.5 35.9 + - - +
1004A VAL* 3.8 21.3 - - - +
1152A SER* 3.5 11.2 - - - +
1155A GLN* 3.8 21.0 + - - +
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Residues in contact with PHE 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974A ALA 2.9 18.4 + - - +
975A VAL 3.1 3.1 + - - +
977A GLU* 1.3 75.2 - - - +
979A LEU* 1.3 75.3 + - + +
981A SER* 3.3 0.5 + - - -
982A VAL* 2.9 54.3 + - + +
1057A LEU* 3.9 25.4 - - + -
1061A LYS* 4.9 3.6 - - - -
1149A LEU* 5.0 1.1 - - + -
1152A SER* 3.2 14.8 + - - +
1153A ILE* 3.5 38.8 - - + -
1156A LEU* 3.4 27.8 - - + -
1229A TYR* 3.5 35.2 - + - -
1234A LEU* 4.0 8.1 - - + -
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Residues in contact with LEU 979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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975A VAL* 2.9 19.9 + - + +
976A VAL* 3.8 3.6 - - - +
978A PHE* 1.3 84.4 - - + +
980A THR* 1.3 63.0 + - - +
982A VAL* 3.9 2.3 - - - +
983A HIS* 2.9 41.0 + - + +
1048A ILE* 3.9 13.9 - - + -
1057A LEU* 3.8 22.0 - - + -
1060A ALA* 3.4 34.3 - - + +
1061A LYS* 3.6 31.6 - - + +
1064A PHE* 3.7 23.3 - - + -
1078A TRP* 4.9 0.2 - - - -
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Residues in contact with THR 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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976A VAL* 2.5 29.8 + - + +
977A GLU* 2.8 17.5 + - - -
979A LEU* 1.3 73.7 - - - +
981A SER* 1.3 60.6 + - - +
983A HIS* 4.2 0.2 - - - +
984A LEU* 2.9 35.9 + - - +
1000A ARG* 4.0 13.0 - - - +
1003A ILE* 3.7 30.1 - - + -
1004A VAL* 4.0 8.5 - - + +
1064A PHE* 3.5 26.2 - - + -
1078A TRP* 4.5 8.1 - - + -
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Residues in contact with SER 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977A GLU 2.7 25.2 + - - -
978A PHE 3.6 1.6 - - - -
979A LEU 3.3 0.2 - - - -
980A THR* 1.3 77.0 - - - +
982A VAL* 1.3 57.8 - - - +
984A LEU 3.7 0.2 - - - -
985A TYR* 2.9 31.6 + - - +
1000A ARG* 3.7 8.2 + - - +
1148A PHE* 3.3 40.1 - - - -
1149A LEU* 4.3 5.8 - - - -
1152A SER* 3.0 28.4 + - - -
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Residues in contact with VAL 982 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A PHE* 2.9 58.9 + - + +
979A LEU* 3.9 3.4 - - - +
981A SER* 1.3 70.3 - - - +
983A HIS* 1.3 61.4 + - + +
985A TYR* 3.0 3.7 + - - +
986A TYR* 2.9 49.8 + - + -
1061A LYS* 5.1 5.2 - - - +
1081A TYR* 4.1 19.3 - - + +
1149A LEU* 3.7 18.6 - - + -
1229A TYR* 3.6 16.2 - - + +
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Residues in contact with HIS 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A LEU* 2.9 34.5 + - + +
982A VAL* 1.3 77.5 - - + +
984A LEU* 1.3 63.3 + - - +
987A LEU* 3.1 35.9 + - + +
1061A LYS* 4.2 32.0 + - + +
1064A PHE* 5.5 0.2 - + - -
1078A TRP* 2.8 73.7 + + + -
1079A LEU* 4.3 6.7 - - + -
1081A TYR* 3.3 33.0 - + - +
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Residues in contact with LEU 984 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980A THR* 2.9 22.6 + - - +
981A SER* 4.1 3.1 - - - +
983A HIS* 1.3 74.6 - - - +
985A TYR* 1.3 60.2 + - - +
988A PHE* 3.4 30.6 - - + +
996A LEU* 3.7 25.9 - - + +
999A TYR* 3.6 15.0 - - + -
1000A ARG* 3.5 39.9 - - + +
1003A ILE* 3.8 12.1 - - + -
1078A TRP* 4.0 16.8 - - + -
1148A PHE* 5.4 0.9 - - + -
735B LEU* 3.8 32.3 - - + -
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Residues in contact with TYR 985 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981A SER 2.9 19.3 + - - +
982A VAL* 3.0 6.3 + - - +
984A LEU* 1.3 78.4 - - - +
986A TYR* 1.3 86.0 + + - +
987A LEU 3.6 0.2 + - - -
988A PHE 3.7 6.1 - - - +
989A PRO* 4.1 1.4 - - - +
996A LEU* 4.1 20.4 - - + -
1084A HIS* 3.5 24.8 + + - -
1126A ARG* 4.5 0.9 + - - -
1145A ARG* 3.5 66.7 + - + -
1146A MET* 3.6 13.5 - - + +
1148A PHE* 4.7 1.1 - + + -
1149A LEU* 3.8 25.4 - - + -
1230A ILE* 3.3 35.1 - - + +
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Residues in contact with TYR 986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982A VAL* 2.9 41.0 + - + +
985A TYR* 1.3 95.1 - + - +
987A LEU* 1.3 61.0 + - - +
988A PHE 3.2 3.7 + - - -
989A PRO* 3.5 17.1 - - - +
1081A TYR* 3.4 40.2 - + + -
1082A PRO* 3.2 33.9 - - - +
1083A LEU* 4.2 5.8 - - + +
1084A HIS* 4.0 31.0 - + + -
1087A GLN* 5.5 1.3 - - - -
1149A LEU* 5.0 0.4 - - + -
1229A TYR* 4.3 13.4 - + - -
1230A ILE* 3.2 40.0 + - + +
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Residues in contact with LEU 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983A HIS* 3.1 21.7 + - + +
986A TYR* 1.3 76.2 - - - +
988A PHE* 1.3 80.1 + - + +
989A PRO* 3.6 5.4 - - - +
1077A VAL* 3.2 33.4 - - + +
1078A TRP* 3.7 33.0 - - + +
1081A TYR* 3.8 8.1 - - + -
1082A PRO* 3.6 24.2 - - + -
739B MET* 3.6 24.9 - - + -
741B ARG* 5.6 0.2 + - - -
742B LEU* 3.4 22.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il