Contacts of the helix formed by residues 1165 - 1190 (chain E) in PDB entry 5B2G
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 ALA1165 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151E THR* 4.0 26.0 - - + +
1159E ASP* 4.0 16.2 + - + +
1160E ALA* 5.2 2.7 - - + +
1164E MET* 1.3 77.8 - - - +
1166E SER* 1.3 69.9 + - - +
1167E MET* 3.3 5.4 - - + +
1168E GLY* 3.0 14.4 + - - +
1169E LEU* 3.1 14.2 + - - +
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Residues in contact with SER1166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1154E ARG* 6.3 1.1 - - - -
1165E ALA* 1.3 78.3 - - - +
1167E MET* 1.3 65.6 + - - +
1169E LEU* 3.7 2.9 + - - +
1170E GLN* 3.6 22.3 + - - +
1346E CYS 5.5 1.5 - - - +
1347E SER* 2.8 41.0 + - - +
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Residues in contact with MET1167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147E LYS* 6.1 4.0 - - - +
1165E ALA* 3.3 3.4 - - + +
1166E SER* 1.3 79.0 - - - +
1168E GLY* 1.3 65.3 + - - +
1169E LEU 3.0 1.6 + - - -
1170E GLN* 3.4 37.9 + - - +
1171E VAL* 3.8 11.8 - - - +
1273E ASP* 6.6 0.4 - - + -
1278E ALA* 5.8 6.5 - - - -
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Residues in contact with GLY1168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164E MET* 3.4 25.3 - - - +
1165E ALA* 3.0 18.2 + - - +
1167E MET* 1.3 80.0 - - - +
1169E LEU* 1.3 56.0 + - - +
1171E VAL* 3.3 20.4 - - - +
1172E MET* 5.3 0.2 - - - +
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Residues in contact with LEU1169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164E MET* 3.9 27.8 - - + +
1165E ALA 3.1 12.6 + - - +
1166E SER* 4.4 3.1 - - - +
1167E MET 3.1 1.0 - - - -
1168E GLY* 1.3 77.9 - - - +
1170E GLN* 1.3 63.6 + - - +
1171E VAL 3.2 2.7 - - - -
1172E MET* 3.3 18.3 + - + +
1173E GLY 3.4 6.9 + - - -
1343E LEU* 3.4 36.6 - - + +
1346E CYS* 5.5 14.4 - - + +
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Residues in contact with GLN1170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166E SER* 3.6 13.2 + - - +
1167E MET* 3.4 34.8 + - - +
1169E LEU* 1.3 75.8 - - - +
1171E VAL* 1.3 66.4 + - + +
1173E GLY* 3.1 4.4 + - - +
1174E ILE* 3.1 32.8 + - + +
1278E ALA* 4.7 12.4 - - - +
1281E MET* 4.4 29.9 - - - +
1343E LEU 4.2 15.4 + - - +
1344E LEU* 3.9 14.4 - - + +
1347E SER* 4.4 16.2 - - - -
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Residues in contact with VAL1171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1167E MET 3.8 12.6 - - - +
1168E GLY* 3.3 22.9 - - - +
1170E GLN* 1.3 81.8 - - + +
1172E MET* 1.3 67.8 + - + +
1174E ILE* 3.3 16.3 - - + +
1175E ALA* 3.0 30.5 + - - +
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Residues in contact with MET1172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164E MET* 4.4 20.6 - - + -
1168E GLY 5.3 0.4 - - - +
1169E LEU* 3.3 17.9 + - + +
1170E GLN 3.3 0.2 - - - -
1171E VAL* 1.3 86.2 - - + +
1173E GLY* 1.3 58.4 + - - +
1175E ALA* 4.3 5.4 - - - -
1176E LEU* 3.1 61.7 + - + +
1343E LEU* 4.6 9.6 - - + -
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Residues in contact with GLY1173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169E LEU 3.4 4.9 + - - -
1170E GLN 3.1 7.9 + - - -
1171E VAL 3.1 0.8 - - - -
1172E MET* 1.3 79.9 - - - +
1174E ILE* 1.3 57.3 + - - +
1177E ALA* 2.9 29.3 + - - +
1340E GLY* 3.3 17.2 - - - -
1343E LEU* 3.3 28.5 - - - +
1344E LEU* 4.4 2.5 - - - -
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Residues in contact with ILE1174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170E GLN* 3.1 8.2 + - + +
1171E VAL* 3.3 22.2 - - + +
1173E GLY* 1.3 73.5 - - - +
1175E ALA* 1.3 64.5 + - - +
1177E ALA* 3.8 6.9 - - - +
1178E VAL* 3.0 37.7 + - + +
1261E SER* 3.8 37.5 - - - +
1281E MET* 5.0 8.7 - - + -
1288E PHE* 5.1 0.7 - - + -
1344E LEU* 3.4 30.1 - - + -
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Residues in contact with ALA1175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1171E VAL 3.0 19.6 + - - +
1172E MET* 4.0 9.0 - - - +
1174E ILE* 1.3 80.0 - - + +
1176E LEU* 1.3 68.3 + - + +
1178E VAL* 3.5 4.8 + - - +
1179E LEU* 3.2 28.2 + - + +
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Residues in contact with LEU1176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1172E MET* 3.1 51.6 + - + +
1173E GLY 3.9 2.5 - - - +
1175E ALA* 1.3 81.8 - - + +
1177E ALA* 1.3 61.4 + - - +
1179E LEU* 3.4 14.8 + - + -
1180E GLY 3.1 3.1 + - - -
1336E LEU* 2.8 49.8 - - + +
1339E LEU* 3.9 31.9 - - + -
1340E GLY* 4.3 3.4 - - - +
1343E LEU* 5.3 4.3 - - + -
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Residues in contact with ALA1177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173E GLY 2.9 19.9 + - - +
1174E ILE* 3.8 4.0 - - - +
1175E ALA 3.2 0.2 - - - -
1176E LEU* 1.3 78.1 - - - +
1178E VAL* 1.3 62.1 + - - +
1180E GLY 3.3 0.3 + - - -
1181E TRP* 3.1 18.7 + - - +
1288E PHE* 3.4 45.1 - - + -
1336E LEU 4.1 5.4 + - - -
1337E LEU* 3.1 17.4 - - - +
1340E GLY* 4.1 6.7 - - - -
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Residues in contact with VAL1178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174E ILE* 3.0 23.8 + - + +
1175E ALA* 3.9 5.8 - - - +
1176E LEU 3.3 0.2 - - - -
1177E ALA* 1.3 73.0 - - + +
1179E LEU* 1.3 68.4 + - + +
1181E TRP* 3.1 16.0 + - + +
1182E LEU* 3.0 37.8 + - + +
1258E VAL* 4.1 29.4 - - + -
1261E SER* 5.5 5.2 - - - +
1288E PHE* 5.3 1.8 - - + -
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Residues in contact with LEU1179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175E ALA* 3.2 17.5 + - + +
1176E LEU* 3.5 22.0 - - + +
1177E ALA 3.3 0.2 - - - -
1178E VAL* 1.3 80.2 - - + +
1180E GLY* 1.3 51.4 + - - +
1182E LEU* 3.2 18.9 + - + +
1183E ALA* 2.7 34.9 + - - +
1336E LEU* 3.6 14.6 - - + -
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Residues in contact with GLY1180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176E LEU 3.1 3.0 + - - -
1177E ALA 3.3 4.2 + - - -
1178E VAL 3.2 0.2 - - - -
1179E LEU* 1.3 75.9 - - - +
1181E TRP* 1.3 57.1 + - - +
1183E ALA* 3.9 5.6 - - - -
1184E VAL* 2.9 27.4 + - - +
1333E ALA* 3.4 18.9 - - - +
1336E LEU* 2.9 27.1 - - - +
1337E LEU* 3.9 11.4 - - - +
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Residues in contact with TRP1181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177E ALA 3.1 12.8 + - - +
1178E VAL* 3.4 11.7 - - + +
1180E GLY* 1.3 75.3 - - - +
1182E LEU* 1.3 90.3 + - + +
1184E VAL* 3.0 28.9 - - + +
1185E MET* 3.1 37.8 + - + +
1251E ILE* 2.9 28.6 + - + +
1254E ALA* 3.5 28.0 - - + -
1255E ALA* 3.6 21.0 - - + +
1258E VAL* 4.1 33.4 - - + -
1337E LEU* 3.8 3.7 - - + +
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Residues in contact with LEU1182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1178E VAL* 3.0 29.3 + - + +
1179E LEU* 3.6 19.5 - - + +
1181E TRP* 1.3 93.4 - - + +
1183E ALA* 1.3 56.9 + - - +
1185E MET* 3.6 26.7 + - + +
1186E LEU* 3.0 27.4 + - - +
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Residues in contact with ALA1183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179E LEU 2.7 17.2 + - - +
1180E GLY* 3.4 1.8 - - - +
1181E TRP 3.1 0.2 - - - -
1182E LEU* 1.3 76.0 - - - +
1184E VAL* 1.3 59.0 + - - +
1186E LEU* 3.4 7.7 + - + +
1187E CYS* 2.9 22.0 + - - +
1329E VAL* 3.2 22.2 - - + +
1332E ALA* 5.1 1.1 - - + -
1333E ALA* 3.3 30.7 - - + +
1336E LEU* 5.3 3.4 - - + -
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Residues in contact with VAL1184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180E GLY 2.9 15.6 + - - +
1181E TRP* 3.0 34.3 - - + +
1183E ALA* 1.3 73.2 - - - +
1185E MET* 1.3 61.8 + - - +
1186E LEU 3.2 0.2 - - - -
1187E CYS* 3.2 8.6 + - + +
1188E CYS* 2.9 27.0 + - - +
1247E VAL* 4.6 11.2 - - + +
1250E SER* 3.9 11.0 - - - +
1251E ILE* 4.4 16.6 - - + +
1254E ALA* 5.3 0.9 - - + -
1295E VAL* 3.3 35.7 - - + -
1333E ALA* 3.4 11.2 - - + +
1337E LEU* 4.9 4.7 - - + -
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Residues in contact with MET1185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181E TRP* 3.1 49.4 + - + +
1182E LEU* 3.6 34.8 - - + +
1184E VAL* 1.3 75.4 - - - +
1186E LEU* 1.3 58.2 + - - +
1188E CYS* 3.2 8.3 + - - +
1189E ALA* 2.9 30.4 + - - +
1251E ILE* 3.8 29.8 - - + -
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Residues in contact with LEU1186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182E LEU 3.0 19.5 + - - +
1183E ALA* 3.4 7.9 - - + +
1185E MET* 1.3 75.1 - - - +
1187E CYS* 1.3 58.6 + - - +
1189E ALA* 3.8 6.5 - - + -
1190E LEU* 3.0 63.5 + - + +
1329E VAL* 4.1 19.3 - - + -
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Residues in contact with CYS1187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183E ALA 2.9 15.0 + - - +
1184E VAL* 3.4 15.0 - - - +
1186E LEU* 1.3 77.2 - - - +
1188E CYS* 1.3 59.0 + - - +
1190E LEU* 3.7 6.5 - - - +
1193E TRP* 3.1 52.4 + - - -
1247E VAL* 5.7 2.9 - - - -
1295E VAL* 5.3 2.9 - - - -
1299E VAL* 4.3 6.1 - - - -
1326E SER* 3.7 28.5 - - - +
1329E VAL* 4.1 3.8 - - + +
1330E GLY* 4.0 22.9 - - - +
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Residues in contact with CYS1188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184E VAL 2.9 13.7 + - - +
1185E MET 3.5 8.5 - - - +
1186E LEU 3.2 0.2 - - - -
1187E CYS* 1.3 79.8 - - - +
1189E ALA* 1.3 60.0 + - - +
1190E LEU 3.8 3.5 + - - +
1213E LEU* 4.5 7.4 - - - +
1214E TRP* 3.1 65.9 + - - -
1247E VAL* 3.7 27.8 - - + -
1248E ILE* 5.4 2.2 - - - -
1251E ILE* 3.9 17.0 - - + -
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Residues in contact with ALA1189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1185E MET 2.9 16.7 + - - +
1186E LEU* 3.3 7.6 + - + +
1188E CYS* 1.3 77.2 - - - +
1190E LEU* 1.3 65.0 + - + +
1191E PRO* 3.6 5.9 - - - +
1214E TRP* 5.2 3.1 - - - -
1215E MET* 4.8 12.5 - - - +
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Residues in contact with LEU1190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186E LEU* 3.0 49.4 + - + +
1187E CYS 3.7 10.6 + - - +
1188E CYS 3.5 3.1 - - - +
1189E ALA* 1.3 78.7 - - + +
1191E PRO* 1.3 67.6 - - + +
1192E MET* 3.1 38.6 + - + -
1193E TRP* 3.8 9.7 + - - -
1212E GLY* 4.7 0.5 - - - -
1213E LEU 4.7 1.4 + - - -
1325E ALA* 5.6 0.2 - - + -
1326E SER* 4.3 13.5 - - - +
1329E VAL* 4.7 15.3 - - + -
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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