Contacts of the helix formed by residues 1169 - 1193 (chain B) in PDB entry 4E70
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 ALA1169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165B CYS 4.5 2.2 - - - -
1166B SER 5.4 0.2 - - - -
1167B GLU 3.8 3.8 + - - -
1168B ASP* 1.3 73.2 + - - +
1170B ASN* 1.3 59.1 + - - +
1172B SER* 3.4 6.9 + - - -
1173B GLN* 2.9 32.9 + - - +
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Residues in contact with ASN1170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124B HIS* 4.4 13.5 + - - -
1168B ASP* 3.3 8.8 + - - +
1169B ALA* 1.3 77.9 - - - +
1171B PHE* 1.3 64.9 + - - +
1173B GLN* 3.3 11.7 + - - +
1174B LEU* 3.0 46.1 + - - +
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Residues in contact with PHE1171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121B CYS* 3.7 41.3 - - - -
1124B HIS* 3.7 29.6 - + + +
1126B HIS* 3.8 23.8 - + + -
1127B LEU* 4.0 21.3 - - + -
1152B PHE* 5.2 0.7 - + - -
1161B VAL* 4.0 14.8 - - + -
1164B VAL* 4.8 4.9 - - + -
1165B CYS* 3.8 29.6 - - - -
1168B ASP* 3.1 29.5 + - - +
1170B ASN* 1.3 80.2 - - - +
1172B SER* 1.3 62.3 + - - +
1174B LEU* 3.3 7.8 + - + +
1175B PHE* 3.1 24.1 + + - +
1329B PHE* 5.9 0.2 - + - -
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Residues in contact with SER1172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165B CYS* 3.4 46.5 + - - +
1168B ASP 2.9 9.4 + - - -
1169B ALA* 3.6 6.7 - - - -
1171B PHE* 1.3 78.8 - - - +
1173B GLN* 1.3 61.9 + - - +
1175B PHE* 3.3 4.0 + - - +
1176B SER* 3.0 31.1 + - - -
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Residues in contact with GLN1173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1169B ALA 2.9 18.5 + - - +
1170B ASN* 3.3 10.4 + - - +
1172B SER* 1.3 73.4 - - - +
1174B LEU* 1.3 60.7 + - + +
1176B SER* 3.3 6.5 + - - -
1177B GLU* 2.8 65.6 + - + +
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Residues in contact with LEU1174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117B SER* 3.5 38.1 - - - +
1120B PHE* 3.8 39.0 - - + +
1121B CYS* 3.9 13.8 - - + +
1124B HIS* 4.7 6.5 - - + -
1170B ASN* 3.0 42.2 + - - +
1171B PHE* 3.5 11.4 - - - +
1173B GLN* 1.3 77.8 - - + +
1175B PHE* 1.3 56.9 + - - +
1177B GLU* 3.4 4.7 + - - +
1178B GLY* 2.9 26.2 + - - -
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Residues in contact with PHE1175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118B LEU* 5.0 1.6 - - + -
1121B CYS* 3.9 16.5 - - - -
1161B VAL* 4.7 7.6 - - + -
1165B CYS* 4.4 17.9 - - - -
1171B PHE* 3.1 17.9 + + + +
1172B SER* 3.6 9.9 - - - +
1173B GLN 3.3 0.2 - - - -
1174B LEU* 1.3 75.5 - - - +
1176B SER* 1.3 64.7 + - - +
1178B GLY* 3.1 2.6 + - - -
1179B MET* 3.0 55.3 + - + +
1272B ASP* 6.0 0.4 - - - -
1329B PHE* 3.6 37.9 - + - -
1330B LEU* 5.2 3.8 - - + -
1402B N7I 4.0 25.4 - + + -
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Residues in contact with SER1176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172B SER* 3.0 22.0 + - - -
1173B GLN* 3.7 6.5 - - - -
1175B PHE* 1.3 76.3 - - - +
1177B GLU* 1.3 62.9 + - - +
1179B MET* 3.3 7.4 + - - +
1180B ALA* 3.1 23.8 + - - +
1211B THR* 6.5 0.9 - - - -
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Residues in contact with GLU1177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114B ASN 5.6 0.7 - - - +
1117B SER* 2.7 35.5 + - - +
1173B GLN* 2.8 59.9 + - + +
1174B LEU* 4.3 5.4 - - - +
1176B SER* 1.3 73.9 - - - +
1178B GLY* 1.3 58.2 + - - +
1180B ALA* 3.4 7.2 + - - +
1181B GLY* 3.0 26.3 + - - -
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Residues in contact with GLY1178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114B ASN 6.0 1.8 - - - -
1115B ALA* 6.5 0.2 - - - -
1117B SER* 3.9 1.1 - - - -
1118B LEU* 3.9 34.3 - - - +
1174B LEU 2.9 16.0 + - - -
1175B PHE 3.1 4.0 + - - -
1177B GLU* 1.3 77.8 - - - +
1179B MET* 1.3 66.9 + - - +
1181B GLY* 3.5 1.0 + - - -
1182B ASP* 3.2 22.0 + - - +
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Residues in contact with MET1179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118B LEU* 3.7 26.5 - - + -
1175B PHE* 3.0 48.6 + - + +
1176B SER* 3.3 6.7 + - - +
1178B GLY* 1.3 77.2 - - - +
1180B ALA* 1.3 57.4 + - - +
1182B ASP* 3.2 4.8 + - - +
1183B SER* 2.9 34.3 + - - +
1267B LYS* 4.0 2.6 + - - +
1268B TRP* 3.8 30.5 - - + +
1402B N7I 3.8 24.7 - - + -
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Residues in contact with ALA1180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112B PRO 5.3 0.2 - - - -
1176B SER 3.1 16.6 + - - +
1177B GLU* 3.7 7.6 - - - +
1179B MET* 1.3 77.1 - - - +
1181B GLY* 1.3 63.1 + - - +
1183B SER* 3.2 5.7 + - - -
1184B TRP* 3.0 11.6 + - - +
1211B THR* 4.4 15.7 - - + +
1213B ASN* 2.9 33.5 + - - +
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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
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13A GLN* 4.6 1.6 - - - +
1112B PRO 3.8 20.2 - - - -
1113B TYR* 3.9 16.0 - - - +
1114B ASN 4.6 9.4 - - - -
1177B GLU 3.0 15.9 + - - -
1178B GLY* 3.5 1.8 + - - -
1179B MET 3.3 0.2 - - - -
1180B ALA* 1.3 76.6 - - - +
1182B ASP* 1.3 61.4 + - - +
1184B TRP* 3.3 16.3 + - - +
1185B LEU* 3.6 4.3 + - - +
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Residues in contact with ASP1182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.4 0.2 - - - +
13A GLN* 2.9 29.4 + - - +
17A TRP* 3.7 5.1 - - + -
1118B LEU* 5.7 3.4 - - + -
1178B GLY 3.2 14.8 + - - +
1179B MET 3.2 7.2 + - - +
1181B GLY* 1.3 75.2 - - - +
1183B SER* 1.3 58.3 + - - +
1185B LEU* 3.2 4.3 + - - +
1186B PHE* 2.8 25.9 + - - +
1267B LYS* 2.8 25.6 + - - -
1268B TRP* 3.5 18.2 - - + -
1361B ARG* 2.8 40.5 + - - -
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Residues in contact with SER1183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179B MET* 2.9 16.2 + - - +
1180B ALA* 3.2 7.8 + - - -
1182B ASP* 1.3 75.8 - - - +
1184B TRP* 1.3 54.0 + - - +
1186B PHE* 4.4 1.8 - - - +
1187B SER* 2.8 39.5 + - - -
1213B ASN* 3.8 15.9 - - - +
1214B THR* 3.4 20.1 + - - -
1267B LYS* 2.8 30.8 + - - +
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Residues in contact with TRP1184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.9 26.9 - - + -
1112B PRO* 3.5 44.6 - - + +
1113B TYR* 3.5 30.1 - + + -
1180B ALA 3.0 12.3 + - - +
1181B GLY 3.3 12.1 - - - +
1182B ASP 3.1 0.2 - - - -
1183B SER* 1.3 76.9 - - - +
1185B LEU* 1.3 72.6 + - + +
1187B SER* 3.2 9.5 + - - -
1188B ARG* 2.9 74.9 + - - +
1213B ASN* 4.0 19.0 - - - +
1241B GLN* 5.7 3.4 - - - -
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Residues in contact with LEU1185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 3.9 21.0 - - - +
9A LEU* 3.9 39.0 - - + -
10A LEU* 4.0 11.4 - - + +
13A GLN* 3.7 33.9 - - + +
1106B LEU* 4.1 6.1 - - + -
1113B TYR* 3.5 25.1 - - + -
1181B GLY 3.6 2.2 + - - +
1182B ASP 3.2 6.3 + - - +
1184B TRP* 1.3 98.9 - - + +
1186B PHE* 1.3 65.1 + - - +
1188B ARG* 3.2 5.2 + - - +
1189B ALA* 3.1 21.7 + - - +
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Residues in contact with PHE1186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.9 19.0 - - + +
1182B ASP* 2.8 30.1 + - - +
1183B SER 4.3 0.7 - - - +
1185B LEU* 1.3 73.6 - - - +
1187B SER* 1.3 60.3 + - - +
1189B ALA* 3.2 3.1 + - - +
1190B LEU* 2.8 43.7 + - + -
1214B THR* 6.0 1.6 - - + -
1267B LYS* 4.2 19.5 - - + -
1301B ALA* 3.6 34.3 - - + -
1357B VAL* 3.8 29.4 - - + -
1358B GLY 4.0 2.5 - - - -
1361B ARG* 3.6 51.4 - - + -
1362B VAL 4.6 0.9 - - - -
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Residues in contact with SER1187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1183B SER 2.8 23.0 + - - -
1184B TRP 3.2 7.4 + - - -
1186B PHE* 1.3 80.7 - - - +
1188B ARG* 1.3 59.9 + - - +
1190B LEU* 3.2 10.3 + - - +
1191B VAL* 3.0 36.2 + - - +
1213B ASN 3.9 1.2 + - - -
1214B THR* 3.9 25.1 + - - -
1217B VAL* 3.3 31.5 - - - +
1218B ILE* 5.7 0.4 - - - -
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Residues in contact with ARG1188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.1 9.0 + - - +
3A ALA* 4.9 4.9 - - - +
6A ALA* 3.8 21.1 - - + -
1184B TRP* 2.9 83.3 + - - +
1185B LEU 3.2 8.3 + - - +
1187B SER* 1.3 82.5 + - - +
1189B ALA* 1.3 59.8 + - - +
1191B VAL* 3.6 7.0 - - + +
1192B SER* 3.5 21.1 + - - -
1216B LYS* 6.3 0.2 - - - +
1217B VAL* 3.3 36.5 - - + +
1220B GLU* 4.8 7.1 + - - -
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Residues in contact with ALA1189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA 5.4 0.2 - - - -
6A ALA* 4.4 1.5 - - - +
7A VAL* 3.8 32.3 - - + +
10A LEU* 3.5 31.6 - - + -
1185B LEU 3.1 9.4 + - - +
1186B PHE 3.6 3.6 - - - +
1188B ARG* 1.3 77.4 - - - +
1190B LEU* 1.3 57.9 + - - +
1192B SER* 3.2 1.6 + - - -
1193B LYS* 2.8 34.3 + - - +
1357B VAL* 3.8 8.7 - - + +
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Residues in contact with LEU1190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186B PHE* 2.8 43.5 + - + +
1187B SER* 3.2 6.5 + - - +
1189B ALA* 1.3 72.5 - - - +
1191B VAL* 1.3 59.5 + - + +
1194B CYS* 2.9 47.3 + - + +
1198B PHE* 3.9 22.6 - - + -
1214B THR* 4.8 17.5 - - + -
1218B ILE* 4.9 6.1 - - + -
1265B LEU* 4.9 14.1 - - + -
1267B LYS* 6.1 0.4 - - + -
1301B ALA* 5.0 2.0 - - + -
1357B VAL* 3.8 26.2 - - + +
1363B LEU* 4.2 18.8 - - + -
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Residues in contact with VAL1191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1187B SER 3.0 20.4 + - - +
1188B ARG* 3.6 9.0 - - - +
1190B LEU* 1.3 78.2 - - + +
1192B SER* 1.3 62.1 + - - +
1195B ARG* 3.5 24.3 + - - +
1198B PHE* 4.2 11.0 - - + -
1217B VAL* 4.0 17.9 - - + -
1218B ILE* 4.1 23.3 - - + -
1221B THR* 3.5 25.6 - - + +
1222B PHE* 3.6 28.2 - - + -
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Residues in contact with SER1192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.3 33.4 - - - +
7A VAL* 5.2 3.1 - - - +
1188B ARG 3.5 11.2 + - - -
1189B ALA* 3.2 5.1 + - - -
1190B LEU 3.1 0.6 - - - -
1191B VAL* 1.3 80.1 - - - +
1193B LYS* 1.3 67.7 + - - +
1194B CYS 3.2 2.3 + - - -
1195B ARG* 3.6 13.5 + - - +
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Residues in contact with LYS1193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.9 36.3 - - + +
1189B ALA 2.8 22.3 + - - +
1192B SER* 1.3 76.5 - - - +
1194B CYS* 1.3 63.9 + - - +
1195B ARG 3.9 0.7 + - - -
1355B THR* 3.9 12.6 - - - +
1356B PRO 3.8 18.6 - - - +
1357B VAL* 3.7 22.4 - - - +
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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