Contacts of the helix formed by residues 1272 - 1293 (chain A) in PDB entry 3F2B
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 PRO1272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A GLY 4.1 11.7 - - - -
895A SER* 4.2 6.3 - - - -
898A SER* 5.1 1.1 - - - +
962A THR* 4.0 14.4 - - + -
1212A CYS* 4.5 0.2 - - - -
1213A ARG* 3.4 29.8 - - + +
1214A ASP* 3.4 5.6 - - - +
1271A PHE* 1.3 88.5 - - + +
1273A LYS* 1.3 67.7 + - - +
1274A ALA 4.4 3.1 - - - +
1275A HIS* 2.9 21.6 + - + +
1276A ALA 3.2 8.1 + - - -
1456A DGT 3.2 36.6 - - - +
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Residues in contact with LYS1273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A GLY 4.8 7.7 + - - -
935A SER* 6.5 0.4 - - - -
956A HIS* 3.2 26.9 + - + +
957A ASP* 4.0 9.9 + - - +
958A ILE* 3.4 27.8 - - + -
1176A SER* 6.1 3.8 - - - -
1179A VAL* 4.2 22.4 - - + -
1212A CYS* 3.8 22.4 - - + +
1214A ASP* 2.7 28.6 + - + +
1215A ASP* 4.4 15.0 + - - -
1272A PRO* 1.3 71.6 - - - +
1274A ALA* 1.3 58.4 + - - +
1276A ALA* 3.1 8.2 + - - +
1277A ALA* 2.8 30.9 + - + +
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Residues in contact with ALA1274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A ARG 5.8 0.2 - - - -
894A GLY 3.9 8.5 - - - +
895A SER* 4.8 1.1 - - - +
897A GLY* 3.3 42.8 - - - +
898A SER* 3.6 11.9 - - - +
910A VAL* 3.6 9.6 - - + +
958A ILE* 3.8 15.8 - - + +
1272A PRO* 3.0 1.8 + - + +
1273A LYS* 1.3 77.5 - - - +
1275A HIS* 1.3 57.8 + - - +
1277A ALA* 4.5 0.2 - - - -
1278A ALA* 3.0 29.6 + - - +
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Residues in contact with HIS1275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A ARG* 3.4 12.7 - - + +
894A GLY 3.0 29.5 + - - +
1271A PHE* 3.4 37.1 - + + -
1272A PRO* 2.9 16.7 + - + +
1274A ALA* 1.3 76.3 - - - +
1276A ALA* 1.3 64.9 + - - +
1277A ALA 3.1 0.2 + - - -
1278A ALA* 3.2 5.1 + - - +
1279A TYR* 2.9 66.7 + + - +
1456A DGT 3.3 40.1 + - + +
6T G 6.1 0.2 + - - -
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Residues in contact with ALA1276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A VAL* 3.8 26.7 - - + +
1182A SER* 3.6 21.7 + - - +
1183A GLY* 4.3 3.4 - - - +
1212A CYS* 5.8 2.2 - - + -
1271A PHE* 4.1 13.9 - - + -
1272A PRO 3.2 4.1 + - - +
1273A LYS* 3.1 13.1 + - - +
1275A HIS* 1.3 79.6 - - - +
1277A ALA* 1.3 57.7 + - - +
1279A TYR* 3.4 1.2 + - - -
1280A VAL* 2.9 36.6 + - - +
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Residues in contact with ALA1277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A VAL* 4.4 8.5 - - + -
956A HIS* 4.3 31.2 - - + +
1175A PHE* 3.6 8.5 - - + -
1179A VAL* 4.0 19.9 - - + +
1273A LYS* 2.8 20.2 + - + +
1274A ALA* 3.9 4.3 - - - +
1276A ALA* 1.3 71.6 - - - +
1278A ALA* 1.3 68.1 + - - +
1280A VAL 3.4 0.2 + - - -
1281A LEU* 2.9 25.9 + - - +
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Residues in contact with ALA1278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A SER* 3.5 43.5 - - - +
893A ARG* 4.4 1.8 - - - +
910A VAL* 3.7 10.7 - - + +
1274A ALA 3.0 18.1 + - - +
1275A HIS* 3.5 6.1 - - - +
1277A ALA* 1.3 79.2 - - - +
1279A TYR* 1.3 65.2 + - + +
1281A LEU* 3.3 5.1 + - - +
1282A MET* 3.1 28.0 + - - +
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Residues in contact with TYR1279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A SER 3.9 12.8 - - - -
893A ARG* 3.4 26.0 + - + -
977A ASN* 3.3 30.3 + - - -
1102A HIS* 3.4 17.1 - + - -
1104A ASP* 5.0 8.4 - - - +
1156A PRO* 5.5 1.3 - - + +
1157A GLU* 3.2 41.0 - - + +
1158A PHE* 5.8 1.1 - - - -
1182A SER* 5.0 5.8 - - - +
1271A PHE* 5.4 4.0 - + + -
1275A HIS* 2.9 56.8 + + + +
1276A ALA* 4.2 3.6 - - - +
1278A ALA* 1.3 75.3 - - - +
1280A VAL* 1.3 64.0 + - + +
1282A MET* 3.2 9.3 + - + +
1283A ALA* 2.9 22.4 + - - +
6T G 5.4 5.1 + - - -
7T G 5.7 0.2 - - - -
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Residues in contact with VAL1280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133A PHE* 6.3 0.2 - - + -
1158A PHE* 4.2 11.2 - - + -
1175A PHE* 3.7 22.4 - - + -
1178A LEU* 3.8 35.7 - - + +
1179A VAL* 3.9 12.3 - - + -
1182A SER* 3.7 24.2 - - - -
1276A ALA 2.9 26.4 + - - +
1277A ALA 3.9 2.7 - - - +
1279A TYR* 1.3 77.9 - - - +
1281A LEU* 1.3 61.8 + - - +
1283A ALA* 3.1 8.4 + - + +
1284A VAL* 2.9 27.0 + - + +
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Residues in contact with LEU1281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A GLU* 4.0 26.7 - - + +
910A VAL* 6.1 0.9 - - + -
937A PHE* 4.0 26.2 - - + -
1122A ILE 6.0 0.4 - - - +
1124A THR* 4.2 15.7 - - + -
1175A PHE* 3.8 13.9 - - + -
1277A ALA 2.9 18.6 + - - +
1278A ALA* 3.6 8.1 - - - +
1280A VAL* 1.3 75.8 - - - +
1282A MET* 1.3 63.3 + - + +
1284A VAL* 3.5 3.0 + - + +
1285A ARG* 3.1 66.7 + - + +
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Residues in contact with MET1282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A LEU* 5.5 7.6 - - - -
891A GLY* 4.6 14.4 - - - -
892A SER* 4.6 18.6 - - - +
909A GLU* 4.6 10.1 - - + +
1104A ASP* 3.6 37.0 - - + +
1105A PRO 5.8 0.4 - - - -
1108A ILE* 4.5 16.4 - - + -
1278A ALA* 3.1 26.7 + - + +
1279A TYR* 3.2 11.4 + - + +
1280A VAL 3.1 0.4 - - - -
1281A LEU* 1.3 84.5 - - + +
1283A ALA* 1.3 65.6 + - - +
1285A ARG* 3.4 24.5 + - - +
1286A ILE* 3.1 29.6 + - - +
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Residues in contact with ALA1283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133A PHE* 4.6 5.4 - - + -
1155A ILE* 4.1 20.7 - - + +
1156A PRO* 4.2 19.2 - - + +
1157A GLU* 6.5 0.2 - - + -
1158A PHE* 4.2 18.2 - - + -
1279A TYR 2.9 13.4 + - - +
1280A VAL* 3.1 13.9 + - + +
1282A MET* 1.3 77.6 - - - +
1284A VAL* 1.3 57.3 + - + +
1286A ILE* 3.3 3.3 + - - +
1287A ALA* 2.8 29.0 + - - +
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Residues in contact with VAL1284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122A ILE* 5.0 2.5 - - + -
1123A PRO 4.0 20.6 - - - +
1124A THR* 4.2 19.3 - - + -
1129A VAL* 3.9 7.2 - - + +
1130A MET* 4.2 25.1 - - + -
1133A PHE* 4.3 9.0 - - + -
1175A PHE* 4.8 5.8 - - + -
1178A LEU* 4.3 17.0 - - + -
1280A VAL* 2.9 23.5 + - + +
1281A LEU* 4.0 6.3 - - - +
1282A MET 3.2 0.4 - - - -
1283A ALA* 1.3 73.1 - - - +
1285A ARG* 1.3 67.6 + - - +
1287A ALA* 3.2 7.0 + - - +
1288A TYR* 2.9 22.3 + - - +
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Residues in contact with ARG1285 (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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889A LEU* 6.1 2.2 - - - +
909A GLU* 2.8 42.2 + - - -
1108A ILE* 4.1 26.5 - - + +
1119A PRO* 3.3 27.6 + - + +
1120A LYS* 4.0 23.3 + - - +
1122A ILE* 3.8 20.4 + - + +
1281A LEU* 3.1 46.5 + - + +
1282A MET* 3.4 21.8 + - - +
1284A VAL* 1.3 76.4 - - - +
1286A ILE* 1.3 63.0 + - + +
1288A TYR* 3.1 18.4 + - - +
1289A PHE* 3.3 13.7 - - + -
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Residues in contact with ILE1286 (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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1104A ASP* 3.9 24.2 - - - +
1107A VAL* 4.0 29.8 - - + -
1108A ILE* 4.1 22.2 - - + -
1111A LEU* 5.1 3.8 - - + -
1155A ILE* 4.2 7.9 - - + -
1156A PRO* 4.0 18.4 - - + -
1282A MET 3.1 18.5 + - - +
1283A ALA* 3.7 3.6 - - - +
1285A ARG* 1.3 72.6 - - - +
1287A ALA* 1.3 67.4 + - - +
1289A PHE* 2.9 20.3 + - - +
1290A LYS* 3.0 9.5 + - - +
1297A TYR* 3.6 29.5 - - + -
1305A ARG* 4.3 2.7 - - - +
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Residues in contact with ALA1287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1129A VAL* 3.4 19.7 - - + -
1132A ILE* 3.9 19.5 - - + -
1133A PHE* 4.3 8.5 - - + -
1155A ILE* 3.9 13.7 - - + +
1283A ALA 2.8 17.8 + - - +
1284A VAL* 3.4 6.7 - - - +
1286A ILE* 1.3 76.3 - - - +
1288A TYR* 1.3 64.2 + - - +
1290A LYS* 2.9 15.0 + - - +
1291A VAL* 3.1 17.3 + - - +
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Residues in contact with TYR1288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117A ILE* 4.5 19.6 - - + +
1122A ILE* 3.6 46.2 - - + -
1123A PRO* 4.2 17.9 - - + -
1126A ASP* 4.2 5.4 - - + -
1129A VAL* 3.8 19.7 - - + -
1284A VAL 2.9 7.8 + - - +
1285A ARG 3.2 11.2 - - - +
1286A ILE 3.0 0.2 - - - -
1287A ALA* 1.3 77.8 - - - +
1289A PHE* 1.3 64.9 + + - +
1291A VAL* 4.0 0.2 - - - -
1292A HIS* 3.0 54.9 + + + +
1293A HIS* 4.2 20.2 + + - -
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Residues in contact with PHE1289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108A ILE* 5.4 4.5 - - + -
1111A LEU* 3.5 54.3 - - + -
1112A GLN* 4.7 2.0 - - + -
1115A SER* 3.2 31.4 - - - -
1117A ILE* 4.4 16.8 - - + -
1119A PRO* 5.0 6.7 - - + -
1122A ILE* 3.5 27.4 - - + -
1285A ARG 3.3 14.8 - - - -
1286A ILE* 2.9 9.8 + - + +
1288A TYR* 1.3 77.4 - + - +
1290A LYS* 1.3 67.1 + - - +
1291A VAL 3.0 2.2 - - - -
1293A HIS* 2.9 56.3 + + + +
1296A LEU* 4.9 0.4 - - + -
1297A TYR* 4.0 6.3 - - + -
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Residues in contact with LYS1290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132A ILE* 4.1 11.9 - - + -
1139A LEU* 4.2 11.7 - - + -
1151A GLY 2.9 27.8 + - - +
1152A THR 3.6 0.2 - - - -
1153A ILE 2.5 36.0 + - - +
1155A ILE* 4.1 4.0 - - + -
1286A ILE 3.0 8.0 + - - +
1287A ALA* 2.9 15.3 + - - +
1289A PHE* 1.3 77.5 - - - +
1291A VAL* 1.3 57.1 + - - +
1294A PRO* 3.8 4.0 - - - +
1297A TYR* 3.6 36.9 - - + +
1298A TYR* 4.3 0.9 - - - -
1351A GLU* 2.8 40.1 + - - -
1355A ARG* 2.3 39.3 + - - +
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Residues in contact with VAL1291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128A ASP* 4.0 23.8 - - + +
1129A VAL* 4.2 8.1 - - + -
1132A ILE* 3.6 30.5 - - + -
1138A PRO* 4.1 15.1 - - + +
1139A LEU* 4.2 7.6 - - + -
1287A ALA 3.1 13.9 + - - +
1288A TYR 4.1 2.7 - - - +
1289A PHE 3.0 0.2 - - - -
1290A LYS* 1.3 81.8 - - + +
1292A HIS* 1.3 86.5 + - + +
1293A HIS 3.5 0.2 - - - -
1294A PRO* 3.7 9.2 - - - +
1355A ARG* 4.1 10.2 + - - +
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Residues in contact with HIS1292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126A ASP* 3.0 24.2 + - - -
1128A ASP* 4.9 11.9 - - + -
1129A VAL* 4.0 9.1 - - + +
1288A TYR* 3.0 49.4 + + + +
1291A VAL* 1.3 91.5 + - + +
1293A HIS* 1.3 85.6 + - + +
1294A PRO* 3.4 5.0 - - - +
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Residues in contact with HIS1293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115A SER* 5.2 2.9 - - - -
1117A ILE* 3.5 26.3 - - + +
1288A TYR* 4.2 12.7 + + - -
1289A PHE* 2.9 35.8 + + + +
1292A HIS* 1.3 98.1 + - + +
1294A PRO* 1.3 67.2 - - - +
1295A LEU 3.4 2.0 - - - -
1296A LEU* 3.1 39.9 + - + +
1297A TYR 3.1 9.5 + - - -
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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