Contacts of the helix formed by residues 1187 - 1208 (chain B) in PDB entry 1VDV
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 ASN1187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B ARG 3.5 7.3 - - - +
577B LEU* 2.6 33.2 + - - +
1044B THR* 4.3 2.8 - - - +
1045B LYS* 4.4 8.8 - - - +
1048B GLN* 3.1 22.3 + - - +
1185B SER* 3.0 6.7 + - - -
1186B LEU* 1.3 81.9 - - - +
1188B PRO* 1.3 62.3 - - - +
1189B ALA* 3.0 13.3 + - - +
1190B ILE* 2.9 37.3 + - + +
1191B ASP* 2.9 27.2 + - - -
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Residues in contact with PRO1188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LEU* 4.1 2.2 - - + -
560B PHE* 3.6 47.8 - - + -
561B GLN 5.3 0.9 - - - +
574B GLY* 3.3 27.1 - - - +
575B ARG 3.5 6.1 - - - +
576B PRO* 3.9 11.9 - - + -
1185B SER* 3.0 13.7 - - - +
1187B ASN* 1.3 85.6 - - - +
1189B ALA* 1.3 57.4 + - - +
1191B ASP* 3.8 0.9 - - + -
1192B ILE* 2.9 35.9 + - - +
1243B LEU* 3.9 9.9 - - + -
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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
----------------------------------------------------------
109B HIS* 3.4 51.6 - - + +
195B LEU* 3.6 13.9 - - + +
576B PRO* 3.8 12.6 - - + -
577B LEU 4.6 0.7 - - - +
1187B ASN* 3.0 10.6 + - - +
1188B PRO* 1.3 80.8 - - - +
1190B ILE* 1.3 60.1 + - + +
1192B ILE* 4.1 1.4 - - - +
1193B GLY* 3.0 24.6 + - - -
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Residues in contact with ILE1190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B HIS* 5.4 4.3 - - + +
112B GLN* 5.9 4.4 - - + -
577B LEU 4.2 2.2 - - - +
578B PRO* 5.2 0.4 - - + -
579B HIS* 4.1 33.4 - - + +
1039B GLY 6.0 0.4 - - - +
1040B GLN 3.2 27.1 - - - +
1041B GLY* 4.6 12.3 - - - +
1044B THR* 5.1 4.7 - - + -
1045B LYS* 3.8 20.2 - - + +
1187B ASN* 2.9 39.5 + - + +
1189B ALA* 1.3 77.6 - - + +
1191B ASP* 1.3 57.9 + - - +
1193B GLY* 3.2 3.3 + - - -
1194B GLN* 2.9 31.6 + - + +
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Residues in contact with ASP1191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B LYS* 2.7 31.8 + - - -
1182B VAL* 4.1 10.9 - - + +
1185B SER* 2.5 37.3 + - - +
1186B LEU 4.0 3.3 + - - -
1187B ASN 2.9 12.9 + - - +
1188B PRO* 4.1 2.9 - - + +
1190B ILE* 1.3 73.9 - - - +
1192B ILE* 1.3 64.5 + - - +
1194B GLN* 3.2 7.3 + - - +
1195B VAL* 3.0 28.4 + - - +
1243B LEU* 4.4 9.4 - - + -
1256B SER* 5.9 0.9 - - - -
1257B LYS 5.1 3.1 - - - +
1259B VAL* 3.4 20.1 - - + +
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Residues in contact with ILE1192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ARG* 4.3 0.9 - - - +
195B LEU* 3.9 20.4 - - + -
558B GLN* 3.7 38.1 - - + -
559B LEU 4.6 3.4 - - - +
560B PHE* 4.2 13.0 - - + -
1188B PRO 2.9 22.9 + - - +
1189B ALA 4.1 2.2 - - - +
1191B ASP* 1.3 74.8 - - - +
1193B GLY* 1.3 59.1 + - - +
1195B VAL* 3.2 7.4 + - - +
1196B GLU* 2.9 50.8 + - + +
1241B VAL* 4.2 13.9 - - + +
1243B LEU* 3.9 26.5 - - + -
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Residues in contact with GLY1193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B HIS* 6.1 2.5 - - - -
112B GLN* 3.2 26.3 + - - -
151B THR 4.3 1.9 - - - +
155B PRO* 6.3 2.2 - - - -
1189B ALA 3.0 16.3 + - - -
1190B ILE* 3.5 6.1 - - - -
1191B ASP 3.1 0.2 - - - -
1192B ILE* 1.3 79.5 - - - +
1194B GLN* 1.3 55.7 + - - +
1196B GLU* 4.1 9.2 - - - +
1197B GLY* 2.9 23.9 + - - -
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Residues in contact with GLN1194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLN* 3.2 27.3 + - - -
912B ARG* 3.3 9.4 + - - +
1040B GLN* 3.5 21.2 + - - +
1045B LYS* 5.5 0.4 - - - +
1190B ILE* 2.9 25.5 + - + +
1191B ASP 3.2 7.8 + - - +
1193B GLY* 1.3 73.4 - - - +
1195B VAL* 1.3 61.1 + - - +
1197B GLY* 5.0 0.2 - - - -
1198B ALA* 2.9 34.9 + - - +
1259B VAL* 3.8 32.7 - - + +
1260B GLY* 3.7 7.4 - - - -
1263B PRO* 4.5 0.8 - - - +
4003B MTE 2.8 42.3 + - - +
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Residues in contact with VAL1195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178B ILE* 4.0 28.5 - - + -
1180B MET* 3.9 27.1 - - + -
1191B ASP 3.0 19.9 + - - +
1192B ILE* 3.5 10.8 - - - +
1194B GLN* 1.3 78.2 - - - +
1196B GLU* 1.3 57.6 + - - +
1199B PHE* 2.9 31.9 + - - +
1241B VAL* 3.9 20.9 - - + -
1243B LEU* 4.6 7.6 - - + -
1259B VAL* 3.9 12.1 - - + -
1263B PRO* 3.8 17.2 - - + +
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Residues in contact with GLU1196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B THR 3.8 13.0 - - - +
152B GLY* 4.3 1.3 - - - -
154B ARG* 2.7 59.0 + - - +
155B PRO* 3.8 9.5 - - - +
558B GLN* 4.7 1.4 - - - +
1192B ILE* 2.9 28.6 + - - +
1193B GLY* 4.1 4.7 - - - +
1195B VAL* 1.3 73.0 - - - +
1197B GLY* 1.3 66.7 + - - +
1199B PHE* 3.4 5.6 + - - +
1200B VAL* 3.0 30.0 + - - +
1239B PHE* 4.1 18.5 - - + +
1241B VAL* 3.8 28.0 - - + +
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Residues in contact with GLY1197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG 4.8 2.1 - - - +
150B CYS 3.0 28.4 - - - +
151B THR 3.8 6.9 + - - -
152B GLY 4.1 1.6 - - - -
912B ARG* 4.0 7.9 - - - -
1193B GLY 2.9 13.6 + - - -
1194B GLN 4.0 0.2 - - - -
1196B GLU* 1.3 78.0 - - - +
1198B ALA* 1.3 61.6 + - - +
1200B VAL* 3.4 3.5 + - - +
1201B GLN* 3.1 25.5 + - - +
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Residues in contact with ALA1198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912B ARG* 3.6 30.7 - - - +
1194B GLN 2.9 19.5 + - - +
1197B GLY* 1.3 72.9 - - - +
1199B PHE* 1.3 64.9 + - - +
1201B GLN* 3.1 2.8 + - - +
1202B GLY 2.9 18.7 + - - -
1260B GLY 3.9 5.4 - - - +
1263B PRO* 3.9 8.3 - - + -
1264B LEU* 3.5 35.2 - - + +
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Residues in contact with PHE1199 (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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1158B ALA* 4.5 1.3 - - + -
1160B SER* 3.9 1.1 - - - -
1176B THR* 3.6 35.4 - - + -
1178B ILE* 3.5 23.1 - - + -
1195B VAL* 2.9 20.3 + - + +
1196B GLU* 3.6 5.6 - - - +
1198B ALA* 1.3 76.7 - - - +
1200B VAL* 1.3 63.4 + - + +
1202B GLY* 3.2 2.6 + - - -
1203B LEU* 2.8 35.7 + - + +
1236B PRO* 4.5 5.8 - - + -
1239B PHE* 3.9 17.9 - + - -
1263B PRO 4.1 10.2 + - - +
1264B LEU 4.5 1.6 - - - -
1266B LEU* 3.1 28.9 - - + -
1267B GLY* 3.4 18.1 - - - -
1269B SER* 3.8 4.0 - - - -
1270B VAL* 3.9 22.9 - - + -
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Residues in contact with VAL1200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B CYS 6.0 0.4 - - - +
152B GLY* 3.5 31.6 - - - +
153B TYR* 4.8 4.9 - - + -
1196B GLU 3.0 17.4 + - - +
1197B GLY 3.9 3.6 - - - +
1199B PHE* 1.3 84.7 - - + +
1201B GLN* 1.3 61.1 + - + +
1203B LEU* 3.1 13.4 + - + +
1204B GLY 2.8 23.6 + - - -
1230B PRO* 3.4 31.9 - - + +
1235B ILE* 4.1 15.7 - - + -
1236B PRO* 5.4 0.4 - - + -
1239B PHE* 4.5 6.7 - - + -
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Residues in contact with GLN1201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG* 3.2 57.3 - - - +
739B GLN* 3.2 14.9 + - - +
741B HIS 4.0 0.8 + - - -
798B PHE* 3.4 30.1 - - - -
911B PHE* 3.9 14.4 - - + -
912B ARG* 3.0 38.7 + - - +
1197B GLY 3.1 12.4 + - - +
1198B ALA 3.6 7.0 - - - +
1200B VAL* 1.3 76.7 - - + +
1202B GLY* 1.3 57.8 + - - +
1204B GLY* 3.2 0.7 + - - -
1205B LEU* 2.9 23.0 + - - +
1230B PRO* 5.2 0.2 - - - -
1264B LEU* 4.0 9.2 - - + -
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Residues in contact with GLY1202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1198B ALA 2.9 10.5 + - - -
1199B PHE 3.6 1.1 - - - -
1201B GLN* 1.3 75.5 - - - +
1203B LEU* 1.3 64.2 + - - +
1205B LEU* 3.0 4.0 + - - +
1206B PHE* 2.9 36.0 + - - -
1264B LEU* 3.5 37.2 - - - +
1267B GLY* 4.3 2.0 - - - -
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Residues in contact with LEU1203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171B HIS* 5.3 0.2 - - - +
1173B ASN* 3.7 12.6 - - - +
1199B PHE* 2.8 32.2 + - + +
1200B VAL* 3.2 19.3 - - + +
1202B GLY* 1.3 75.6 - - - +
1204B GLY* 1.3 55.9 + - - +
1206B PHE* 3.6 0.8 + - - -
1207B THR* 2.6 50.5 + - + +
1208B LEU* 5.4 2.9 - - + -
1230B PRO* 4.9 4.3 - - + -
1234B SER* 3.6 29.4 - - - +
1235B ILE* 4.6 1.6 - - - -
1236B PRO* 4.5 8.5 - - + -
1267B GLY* 4.1 10.8 - - - +
1270B VAL* 3.7 33.4 - - + -
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Residues in contact with GLY1204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200B VAL 2.8 10.3 + - - -
1201B GLN 3.2 1.5 + - - -
1202B GLY 3.1 0.2 - - - -
1203B LEU* 1.3 75.5 - - - +
1205B LEU* 1.3 64.7 + - - +
1208B LEU* 3.0 12.3 + - - -
1209B GLU* 2.9 48.7 + - - -
1230B PRO* 3.6 16.4 - - - -
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Residues in contact with LEU1205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B ILE* 4.5 9.2 - - + -
737B GLY 3.9 11.9 - - - +
738B GLY 3.9 21.3 - - - +
739B GLN* 3.6 24.7 - - + +
839B ARG* 3.7 29.2 - - - +
917B PRO* 4.2 11.0 - - + -
1201B GLN 2.9 14.4 + - - +
1202B GLY 3.0 7.8 + - - +
1204B GLY* 1.3 78.4 - - - +
1206B PHE* 1.3 86.8 + - + +
1209B GLU* 4.1 6.3 - - - +
1264B LEU* 4.4 5.8 - - + -
1298B SER* 3.5 3.3 + - - -
1299B PRO* 3.3 19.4 - - - +
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Residues in contact with PHE1206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B ILE* 3.5 25.4 - - + -
917B PRO* 4.2 6.3 - - + -
921B PHE* 3.6 24.2 - + + -
1202B GLY* 2.9 26.9 + - - +
1203B LEU 4.4 0.4 - - - +
1205B LEU* 1.3 94.4 - - + +
1207B THR* 1.3 65.8 + - + +
1264B LEU* 4.6 1.6 - - + -
1265B PHE* 3.8 33.2 - + - -
1267B GLY 3.9 2.7 - - - +
1268B ALA* 3.6 35.2 - - + -
1271B PHE* 3.3 23.7 - - + -
1298B SER* 3.4 15.9 - - - -
1299B PRO* 3.4 3.5 - - - +
1300B ALA 2.8 19.4 + - - -
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Residues in contact with THR1207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171B HIS* 4.5 8.1 - - - -
1203B LEU* 2.6 30.4 + - + +
1204B GLY 3.4 0.6 + - - -
1205B LEU 3.6 0.2 + - - -
1206B PHE* 1.3 91.2 - - + +
1208B LEU* 1.3 81.5 + - - +
1270B VAL* 4.1 15.5 - - + -
1271B PHE* 4.4 6.7 - - - +
1274B ILE* 3.8 23.8 - - + -
1299B PRO* 3.8 5.8 - - - +
1300B ALA* 3.3 23.9 - - + +
1301B THR* 3.6 11.1 - - - -
1302B PRO* 4.6 2.9 - - - +
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Residues in contact with LEU1208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B SER* 4.5 22.4 - - - +
426B ARG* 4.2 14.8 - - + -
1171B HIS* 4.4 14.1 - - + -
1173B ASN* 6.0 1.1 - - - +
1203B LEU* 4.8 3.8 - - + +
1204B GLY* 3.0 9.3 + - - +
1207B THR* 1.3 111.5 + - - +
1209B GLU* 1.3 65.3 + - - +
1210B GLU* 3.6 3.3 + - - +
1228B LYS* 3.4 25.7 + - + +
1230B PRO* 4.0 22.2 - - + -
1234B SER* 3.6 28.0 - - - +
1299B PRO* 4.3 0.4 - - - +
1301B THR* 4.5 11.0 - - - +
1302B PRO* 6.1 0.7 - - + -
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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