Contacts of the helix formed by residues 1164 - 1186 (chain B) in PDB entry 4DDG
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 ASP1164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047B LEU* 4.5 0.8 - - - +
1160B ALA 3.6 7.5 + - - +
1161B SER* 3.2 14.4 + - - +
1163B ASN* 1.3 78.6 - - - +
1165B GLN* 1.3 68.4 + - - +
1166B SER* 3.2 11.4 + - - -
1167B THR* 2.9 39.6 + - - +
1168B SER* 3.3 22.2 + - - -
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Residues in contact with GLN1165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047B LEU* 3.9 10.3 - - - +
1086B ARG* 3.2 27.8 + - - +
1163B ASN 3.7 3.0 + - - -
1164B ASP* 1.3 77.7 + - - +
1166B SER* 1.3 62.0 + - - +
1168B SER* 3.8 0.9 - - - -
1169B ASP* 2.9 65.4 + - - +
62C PHE* 6.2 2.5 - - + -
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Residues in contact with SER1166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164B ASP* 3.2 8.2 + - - -
1165B GLN* 1.3 79.1 - - - +
1167B THR* 1.3 61.3 + - - +
1169B ASP* 3.9 6.1 - - - -
1170B TYR* 2.9 48.2 + - - +
1C MET* 4.8 23.0 - - - +
62C PHE* 4.8 9.0 - - - -
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Residues in contact with THR1167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141B THR* 3.3 30.6 + - + +
1145B LEU* 4.1 23.6 - - + -
1148B GLN* 5.6 0.7 - - - +
1161B SER* 3.9 19.7 - - - +
1164B ASP* 2.9 23.9 + - - +
1166B SER* 1.3 74.1 + - - +
1168B SER* 1.3 67.2 + - - +
1170B TYR* 3.2 2.6 + - - -
1171B LEU* 3.0 19.8 + - - +
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Residues in contact with SER1168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047B LEU* 4.2 2.2 - - - -
1094B ARG* 2.4 39.6 + - - +
1145B LEU* 5.6 1.1 - - - -
1161B SER 4.4 1.3 + - - -
1162B PHE* 3.2 39.2 + - - +
1164B ASP 3.3 12.3 + - - -
1165B GLN 3.8 1.1 - - - -
1167B THR* 1.3 80.0 - - - +
1169B ASP* 1.3 57.7 + - - +
1171B LEU* 3.1 11.1 + - - +
1172B VAL* 2.9 27.9 + - - +
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Residues in contact with ASP1169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047B LEU* 4.4 0.3 - - - +
1090B ASN* 5.3 0.4 + - - -
1094B ARG* 3.3 26.5 + - - -
1165B GLN* 2.9 47.2 + - - +
1166B SER* 4.1 7.0 - - - +
1168B SER* 1.3 75.6 - - - +
1170B TYR* 1.3 56.2 + - - +
1172B VAL* 3.1 8.1 + - - +
1173B VAL* 2.9 34.4 + - - +
1211B MET* 4.0 20.7 - - + +
62C PHE* 4.3 18.3 - - + -
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Residues in contact with TYR1170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137B ASP* 3.9 29.4 + - + -
1138B PHE* 3.5 35.8 - + + +
1141B THR* 3.8 25.8 - - + +
1166B SER* 2.9 35.9 + - - +
1167B THR 3.5 4.3 - - - +
1169B ASP* 1.3 74.1 - - - +
1171B LEU* 1.3 64.7 + - - +
1173B VAL* 3.2 5.6 + - - +
1174B TYR* 3.0 21.3 + - - +
1C MET* 3.8 28.0 + - + +
5C ARG* 5.6 1.4 - - - +
60C TYR 5.0 0.7 + - - -
61C PRO* 4.4 14.0 - - + +
62C PHE* 3.5 33.2 - + - -
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Residues in contact with LEU1171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093B TYR 4.5 4.5 - - - +
1094B ARG* 5.1 0.9 - - - -
1097B GLY* 4.8 3.4 - - - -
1101B LEU* 4.7 4.0 - - + -
1138B PHE 5.3 1.1 - - - -
1141B THR* 3.8 4.8 - - - +
1142B PHE* 3.6 33.2 - - + +
1145B LEU* 3.6 28.9 - - + -
1162B PHE* 3.6 34.8 - - + -
1167B THR 3.0 12.6 + - - +
1168B SER* 3.2 11.7 - - - +
1170B TYR* 1.3 77.3 - - - +
1172B VAL* 1.3 71.4 + - + +
1174B TYR* 3.1 8.3 + - - +
1175B LEU* 2.9 43.7 + - + +
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Residues in contact with VAL1172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B ASN* 3.7 31.2 - - + -
1093B TYR* 4.0 10.3 - - + +
1094B ARG* 3.8 43.3 - - - +
1168B SER 2.9 18.9 + - - +
1169B ASP* 3.1 8.7 + - - +
1171B LEU* 1.3 81.9 - - + +
1173B VAL* 1.3 63.6 + - - +
1175B LEU* 3.2 6.8 + - - +
1176B ARG* 2.9 31.9 + - - +
1211B MET* 3.8 11.2 - - + -
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Residues in contact with VAL1173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138B PHE* 3.7 40.2 - - + -
1169B ASP 2.9 21.3 + - - +
1170B TYR 3.4 7.4 - - - +
1172B VAL* 1.3 75.7 - - - +
1174B TYR* 1.3 58.6 + - - +
1176B ARG* 3.2 8.6 + - - +
1177B LEU* 2.9 35.4 + - + +
1209B GLU 5.7 2.2 - - - +
1211B MET* 3.6 29.4 - - + -
62C PHE* 4.6 6.1 - - + -
94C SER* 5.8 0.2 - - - +
95C PRO* 4.1 21.3 - - + -
96C ALA 5.2 1.6 - - - +
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Residues in contact with TYR1174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121B SER* 2.7 24.9 + - - -
1122B LYS* 3.4 11.0 + - - -
1125B LEU* 4.0 14.7 - - + +
1135B ILE* 4.3 7.6 - - + -
1138B PHE* 3.9 20.8 - - + +
1139B HIS* 3.1 44.5 + - + -
1142B PHE* 3.4 38.8 - + + -
1170B TYR 3.0 13.4 + - - +
1171B LEU 3.6 7.0 - - - +
1173B VAL* 1.3 76.0 - - - +
1175B LEU* 1.3 58.3 + - - +
1177B LEU* 3.1 12.5 + - + +
1178B LEU* 2.9 52.6 + - + +
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Residues in contact with LEU1175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093B TYR* 3.4 42.2 - - + +
1096B PHE* 4.8 4.5 - - + -
1097B GLY* 4.1 12.3 - - - +
1142B PHE* 4.4 14.8 - - + -
1171B LEU* 2.9 37.4 + - + +
1172B VAL 3.2 7.1 + - - +
1174B TYR* 1.3 75.0 - - - +
1176B ARG* 1.3 53.1 + - - +
1178B LEU* 3.4 13.3 + - + +
1179B THR* 2.6 37.3 + - - -
1223B LEU* 3.7 23.9 - - + +
1227B LEU* 4.2 17.0 - - + -
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Residues in contact with ARG1176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089B GLY 3.5 8.3 + - - -
1090B ASN* 2.7 30.5 + - - -
1093B TYR* 3.3 43.2 + - + -
1172B VAL* 2.9 22.0 + - - +
1173B VAL* 3.4 9.9 - - - +
1175B LEU* 1.3 77.3 - - - +
1177B LEU* 1.3 58.7 + - + +
1179B THR* 3.2 9.1 + - - -
1180B SER* 2.9 25.8 + - - -
1207B GLU 4.4 2.0 + - - -
1208B VAL* 3.1 41.9 + - - +
1209B GLU* 3.9 11.2 - - - +
1210B PRO 3.6 18.3 + - - -
1211B MET* 4.0 11.7 - - - +
1212B CYS 3.6 4.4 - - - +
1213B LYS 2.8 29.6 + - - -
1214B GLU 5.0 0.6 + - - -
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Residues in contact with LEU1177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125B LEU* 3.7 18.5 - - + +
1130B PHE* 3.8 30.9 - - + -
1135B ILE* 3.9 31.0 - - + -
1138B PHE* 4.5 7.0 - - + -
1173B VAL* 2.9 27.7 + - + +
1174B TYR* 3.1 17.2 + - + +
1176B ARG* 1.3 74.7 - - + +
1178B LEU* 1.3 59.9 + - - +
1180B SER* 3.4 4.4 + - - -
1181B GLY* 2.9 26.0 + - - -
1209B GLU* 4.4 14.8 - - + +
94C SER* 4.8 2.5 - - - +
96C ALA* 3.8 25.1 - - + -
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Residues in contact with LEU1178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121B SER* 3.6 32.1 - - - +
1125B LEU* 4.0 16.8 - - + -
1142B PHE* 4.4 2.5 - - + -
1174B TYR* 2.9 41.6 + - + +
1175B LEU* 3.6 19.7 - - + +
1177B LEU* 1.3 72.3 - - - +
1179B THR* 1.3 66.6 + - - +
1181B GLY* 3.1 0.9 + - - -
1182B TYR* 2.9 26.3 + - - +
1185B ARG* 5.4 1.4 + - - +
1223B LEU* 4.2 7.0 - - + -
1226B ALA* 4.2 13.2 - - + +
1227B LEU* 3.7 31.0 - - + -
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Residues in contact with THR1179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093B TYR* 3.4 20.3 - - + +
1175B LEU 2.6 21.6 + - - -
1176B ARG* 3.2 11.0 + - - -
1178B LEU* 1.3 76.3 - - - +
1180B SER* 1.3 56.4 + - - +
1182B TYR* 3.5 0.7 + - - -
1183B LEU* 2.9 38.4 + - + +
1208B VAL* 4.1 13.2 - - + -
1219B HIS* 3.7 32.3 - - + +
1222B ALA* 3.9 15.6 - - + +
1223B LEU* 3.7 16.6 - - - +
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Residues in contact with SER1180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130B PHE* 4.2 2.3 - - - -
1176B ARG 2.9 13.9 + - - -
1177B LEU* 3.7 5.2 - - - -
1179B THR* 1.3 78.1 - - - +
1181B GLY* 1.3 56.3 + - - +
1183B LEU* 3.3 1.6 + - - +
1184B GLN* 2.9 45.0 + - - +
1204B CYS* 3.2 17.0 - - - +
1208B VAL* 3.7 8.9 - - - +
1209B GLU* 2.9 41.6 + - - -
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Residues in contact with GLY1181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125B LEU* 3.9 11.7 - - - -
1128B GLN* 2.8 42.1 + - - -
1130B PHE* 4.4 6.2 - - - -
1177B LEU 2.9 15.3 + - - -
1178B LEU 3.1 3.8 + - - -
1180B SER* 1.3 75.8 - - - +
1182B TYR* 1.3 58.4 + - - +
1184B GLN* 3.2 2.4 + - - -
1185B ARG* 2.9 14.3 + - - +
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Residues in contact with TYR1182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178B LEU 2.9 14.9 + - - +
1179B THR 4.2 1.3 - - - +
1181B GLY* 1.3 74.5 - - - +
1183B LEU* 1.3 62.9 + - - +
1185B ARG* 3.9 30.0 - - - +
1186B GLU* 3.1 54.9 + - + +
1190B PHE* 3.8 22.9 - + - -
1222B ALA* 3.7 17.7 - - - +
1225B GLN* 3.5 47.3 + - + +
1226B ALA* 3.8 22.0 - - + -
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Residues in contact with LEU1183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179B THR* 2.9 31.6 + - + +
1180B SER 3.5 4.9 - - - +
1181B GLY 3.2 0.2 - - - -
1182B TYR* 1.3 78.7 - - - +
1184B GLN* 1.3 56.8 + - - +
1187B SER* 3.2 25.6 + - - -
1190B PHE* 3.6 46.3 - - + -
1200B VAL* 3.6 9.2 - - + +
1203B PHE* 4.2 15.9 - - + -
1204B CYS* 3.6 20.9 - - - -
1208B VAL* 4.1 17.9 - - + -
1218B ILE* 4.1 12.3 - - + +
1219B HIS* 5.3 2.7 - - - -
1222B ALA* 3.7 15.3 - - + -
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Residues in contact with GLN1184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128B GLN* 3.9 12.5 - - + +
1130B PHE* 4.1 13.7 - - - -
1180B SER* 2.9 38.2 + - - +
1181B GLY* 3.9 3.4 - - - +
1183B LEU* 1.3 73.6 - - - +
1185B ARG* 1.3 66.0 + - - +
1186B GLU 3.4 0.2 - - - -
1187B SER* 3.1 23.8 + - - -
1200B VAL* 4.2 2.9 - - + -
1201B LYS* 3.4 45.5 - - + +
1204B CYS* 3.8 15.7 - - - +
1209B GLU* 3.6 10.7 + - - -
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Residues in contact with ARG1185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124B ASP* 3.9 29.8 + - - +
1125B LEU* 5.5 2.2 - - - +
1128B GLN* 2.9 45.0 + - - +
1178B LEU* 5.4 0.8 + - - +
1181B GLY* 2.9 10.7 + - - +
1182B TYR* 3.7 40.8 - - - +
1184B GLN* 1.3 79.1 - - - +
1186B GLU* 1.3 71.8 + - + +
1187B SER* 3.2 2.8 + - - -
1188B LYS* 5.7 2.9 - - - +
1226B ALA* 5.5 4.6 + - - +
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Residues in contact with GLU1186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182B TYR* 3.1 45.2 + - + +
1183B LEU 3.8 1.6 - - - -
1185B ARG* 1.3 87.7 - - + +
1187B SER* 1.3 50.9 + - - +
1188B LYS* 3.2 5.5 - - - +
1189B PHE* 2.6 44.2 + - + +
1190B PHE* 3.6 23.0 + - + -
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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