Contacts of the helix formed by residues 1282 - 1319 (chain B) in PDB entry 5TWV
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 GLY1282 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ILE* 6.0 4.9 - - - -
577B PHE* 3.4 27.0 - - - +
1281B VAL* 1.3 77.2 - - - +
1283B LEU* 1.3 59.2 + - - +
1284B GLY 3.3 1.3 - - - -
1285B LEU* 3.1 12.2 + - - +
1286B THR* 2.9 31.5 + - - -
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Residues in contact with LEU1283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B PHE* 3.3 23.5 - - + -
1035B ALA* 5.6 4.9 - - + -
1157B ILE* 5.2 0.7 - - - -
1160B VAL* 5.5 4.5 - - + -
1280B LEU* 3.8 21.3 - - + +
1281B VAL 3.3 1.2 - - - -
1282B GLY* 1.3 78.3 - - - +
1284B GLY* 1.3 57.2 + - - +
1286B THR* 4.9 2.2 - - - -
1287B TYR* 2.9 53.5 + - + +
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Residues in contact with GLY1284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157B ILE* 4.2 21.2 - - - +
1160B VAL* 5.3 4.4 - - - +
1263B ALA* 3.8 14.0 - - - +
1280B LEU 4.2 3.8 + - - -
1281B VAL 4.0 6.2 + - - -
1282B GLY 3.3 0.4 - - - -
1283B LEU* 1.3 78.1 - - - +
1285B LEU* 1.3 57.9 + - - +
1287B TYR 3.7 0.5 - - - -
1288B ALA* 2.8 28.6 + - - +
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Residues in contact with LEU1285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ILE* 5.0 16.2 - - + -
1263B ALA* 5.3 1.8 - - - -
1281B VAL 4.4 3.4 + - - +
1282B GLY* 3.1 18.3 + - - +
1284B GLY* 1.3 76.9 - - - +
1286B THR* 1.3 62.5 + - - +
1287B TYR 3.2 0.2 - - - -
1288B ALA* 3.0 6.6 + - - +
1289B LEU* 3.0 28.2 + - - +
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Residues in contact with THR1286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B PHE* 4.4 21.3 - - - -
580B LEU* 5.9 2.5 - - - -
581B SER* 5.1 11.0 - - - -
1282B GLY 2.9 15.0 + - - -
1283B LEU* 4.4 3.1 - - - -
1285B LEU* 1.3 77.0 - - - +
1287B TYR* 1.3 60.3 + - - +
1289B LEU* 3.6 3.9 + - - +
1290B MET* 2.9 49.1 + - - +
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Residues in contact with TYR1287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B VAL* 5.1 4.5 - - + +
1031B ASP* 3.2 30.3 - - + +
1153B ALA* 4.1 31.4 - - + +
1156B VAL* 4.8 10.8 - - + -
1157B ILE* 4.0 30.1 - - + +
1283B LEU* 2.9 39.0 + - + +
1284B GLY 3.7 1.1 - - - -
1286B THR* 1.3 76.7 - - - +
1288B ALA* 1.3 52.1 + - - +
1290B MET* 3.6 26.7 - - + -
1291B VAL* 2.6 37.7 + - - +
1294B TYR* 5.9 2.5 - + - -
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Residues in contact with ALA1288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256B GLY 4.5 5.9 - - - +
1259B VAL* 4.7 2.8 - - - +
1260B VAL* 3.9 31.6 - - + +
1263B ALA* 3.9 8.1 - - + -
1284B GLY 2.8 21.7 + - - +
1285B LEU* 3.0 9.3 + - - +
1287B TYR* 1.3 77.4 - - - +
1289B LEU* 1.3 60.6 + - - +
1291B VAL* 3.1 5.0 + - - +
1292B SER* 3.0 26.7 + - - -
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Residues in contact with LEU1289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1260B VAL* 5.1 3.1 - - - +
1285B LEU 3.0 13.6 + - - +
1286B THR* 4.1 4.0 - - - +
1288B ALA* 1.3 75.7 - - - +
1290B MET* 1.3 58.8 + - + +
1292B SER* 3.1 9.6 + - - -
1293B ASN* 3.0 24.1 + - - +
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Residues in contact with MET1290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B LEU* 5.9 7.6 - - + +
581B SER* 5.9 3.1 - - - -
584B HIS* 4.3 26.9 - - + -
1286B THR* 2.9 37.6 + - - +
1287B TYR* 3.6 30.7 - - + -
1289B LEU* 1.3 75.5 - - + +
1291B VAL* 1.3 60.4 + - - +
1293B ASN* 3.6 11.7 - - + +
1294B TYR* 2.8 54.9 + - + +
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Residues in contact with VAL1291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1153B ALA* 5.8 4.5 - - + +
1154B LEU* 5.9 5.6 - - + -
1256B GLY* 5.9 0.4 - - - -
1259B VAL* 6.0 5.6 - - + -
1287B TYR 2.6 25.7 + - - +
1288B ALA* 3.1 10.0 + - - +
1290B MET* 1.3 77.7 - - - +
1292B SER* 1.3 58.0 + - - +
1294B TYR* 3.2 12.9 + - + +
1295B LEU* 2.9 26.0 + - - +
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Residues in contact with SER1292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252B MET 4.9 3.9 - - - +
1253B GLU* 4.9 13.3 - - - -
1256B GLY* 3.9 29.8 - - - -
1257B ALA* 4.7 0.9 - - - -
1288B ALA 3.0 12.2 + - - -
1289B LEU* 3.1 10.1 + - - -
1291B VAL* 1.3 74.0 - - - +
1293B ASN* 1.3 59.0 + - - +
1295B LEU* 3.3 9.9 + - - +
1296B ASN* 3.0 26.5 + - - +
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Residues in contact with ASN1293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1289B LEU 3.0 13.3 + - - +
1290B MET* 3.6 15.9 - - + +
1291B VAL 3.3 0.2 - - - -
1292B SER* 1.3 77.9 - - - +
1294B TYR* 1.3 58.0 + - + +
1296B ASN* 3.1 6.1 + - - +
1297B TRP* 2.9 60.3 + - + +
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Residues in contact with TYR1294 (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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1024B HIS* 5.6 1.4 - - - -
1146B SER* 4.7 6.7 - - - +
1149B LEU* 3.2 49.9 - - + +
1150B CYS* 3.7 22.2 - - + +
1153B ALA* 3.7 20.1 - - + +
1154B LEU 5.6 0.2 - - - -
1287B TYR* 5.9 3.0 - + - -
1290B MET* 2.8 45.8 + - + +
1291B VAL* 3.2 9.8 + - - +
1293B ASN* 1.3 78.5 - - + +
1295B LEU* 1.3 54.4 + - - +
1297B TRP* 5.2 5.4 - + + -
1298B MET* 2.6 40.5 + - - +
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Residues in contact with LEU1295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150B CYS* 5.9 0.4 - - - -
1252B MET* 4.4 18.2 - - + +
1256B GLY* 5.7 2.9 - - - -
1291B VAL 2.9 13.3 + - - +
1292B SER* 3.7 11.0 - - - +
1294B TYR* 1.3 76.7 - - - +
1296B ASN* 1.3 58.6 + - - +
1298B MET* 4.0 4.0 - - - +
1299B VAL* 2.9 31.2 + - - +
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Residues in contact with ASN1296 (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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1249B GLU* 6.1 4.3 - - - -
1252B MET* 4.5 13.4 - - + +
1253B GLU* 5.9 2.9 - - + +
1292B SER 3.0 13.5 + - - +
1293B ASN* 3.1 12.0 + - - +
1295B LEU* 1.3 74.9 - - - +
1297B TRP* 1.3 65.2 + - + +
1299B VAL* 3.2 3.7 + - - +
1300B ARG* 3.0 30.4 + - - +
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Residues in contact with TRP1297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B THR* 5.6 11.9 - - - -
1146B SER* 3.9 12.4 - - - -
1293B ASN* 2.9 54.1 + - + +
1294B TYR* 4.9 5.4 - + + +
1296B ASN* 1.3 77.3 - - + +
1298B MET* 1.3 50.2 + - - +
1300B ARG* 4.6 7.2 - - + +
1301B ASN* 2.6 40.6 + - - +
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Residues in contact with MET1298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146B SER* 4.3 11.6 - - - +
1147B THR* 5.2 3.4 - - - +
1150B CYS* 4.5 14.1 - - + -
1294B TYR 2.6 25.6 + - - +
1295B LEU* 4.0 5.2 - - - +
1297B TRP* 1.3 77.6 - - - +
1299B VAL* 1.3 58.7 + - - +
1301B ASN* 3.8 3.9 - - - +
1302B LEU* 2.9 27.9 + - - +
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Residues in contact with VAL1299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182B PHE* 5.0 14.2 - - + -
1248B LEU* 5.8 5.8 - - + +
1252B MET* 5.1 8.7 - - + -
1295B LEU 2.9 20.2 + - - +
1296B ASN* 3.7 3.8 - - - +
1298B MET* 1.3 75.4 - - - +
1300B ARG* 1.3 60.6 + - - +
1302B LEU* 3.0 9.3 + - - +
1303B ALA* 2.9 24.9 + - - +
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Residues in contact with ARG1300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182B PHE* 5.9 2.2 - - - -
1248B LEU* 6.4 1.8 - - + -
1296B ASN 3.0 16.1 + - - +
1297B TRP* 4.7 7.9 - - + +
1299B VAL* 1.3 73.3 - - - +
1301B ASN* 1.3 61.2 + - - +
1303B ALA* 3.1 10.2 + - + +
1304B ASP* 2.9 27.4 + - - +
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Residues in contact with ASN1301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139B THR 5.1 1.6 - - - +
1142B CYS* 4.5 5.4 - - + +
1143B LEU* 4.2 27.9 - - + +
1146B SER* 4.2 6.3 - - - -
1297B TRP* 2.6 25.7 + - + +
1298B MET* 4.0 4.9 - - - +
1300B ARG* 1.3 76.0 - - - +
1302B LEU* 1.3 58.3 + - - +
1304B ASP* 3.8 6.4 - - - +
1305B MET* 2.9 30.1 + - - +
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Residues in contact with LEU1302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179B GLN* 6.4 2.0 - - + -
1298B MET 2.9 20.7 + - - +
1299B VAL* 3.0 9.2 + - - +
1301B ASN* 1.3 76.3 - - - +
1303B ALA* 1.3 58.5 + - - +
1305B MET* 3.6 6.2 + - - +
1306B GLU* 2.9 27.2 + - - +
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Residues in contact with ALA1303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182B PHE* 4.7 16.8 - - + -
1186B SER* 5.3 7.4 - - - -
1299B VAL 2.9 12.3 + - - +
1300B ARG* 3.1 12.3 + - - +
1302B LEU* 1.3 75.9 - - - +
1304B ASP* 1.3 60.9 + - - +
1306B GLU* 3.0 8.9 + - - +
1307B ILE* 3.0 29.1 + - - +
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Residues in contact with ASP1304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139B THR* 4.1 21.1 - - - -
1300B ARG 2.9 15.8 + - - +
1301B ASN* 4.0 7.0 - - - +
1303B ALA* 1.3 76.5 - - - +
1305B MET* 1.3 58.1 + - - +
1307B ILE* 4.4 4.0 - - - +
1308B GLN* 2.9 33.8 + - - +
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Residues in contact with MET1305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139B THR* 5.1 5.1 - - - +
1140B LEU* 6.5 0.4 - - - -
1143B LEU* 4.5 15.7 - - + -
1301B ASN 2.9 18.7 + - - +
1302B LEU* 3.8 7.4 - - - +
1304B ASP* 1.3 74.1 - - - +
1306B GLU* 1.3 53.5 + - - +
1308B GLN* 4.6 2.5 - - - -
1309B LEU* 2.6 40.0 + - - +
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Residues in contact with GLU1306 (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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1183B ARG* 6.1 4.0 - - + +
1187B ARG* 6.0 7.0 - - + -
1302B LEU 2.9 15.7 + - - +
1303B ALA* 3.0 12.5 + - - +
1305B MET* 1.3 75.4 - - - +
1307B ILE* 1.3 60.0 + - - +
1309B LEU* 3.7 4.0 - - - +
1310B GLY* 2.9 21.5 + - - -
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Residues in contact with ILE1307 (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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1190B GLN* 5.5 11.2 - - + -
1303B ALA 3.0 13.4 + - - +
1304B ASP* 4.4 3.6 - - - +
1306B GLU* 1.3 74.1 - - - +
1308B GLN* 1.3 61.3 + - - +
1310B GLY* 2.9 16.1 + - - +
1311B ALA* 2.9 12.5 + - - +
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Residues in contact with GLN1308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135B HIS* 5.2 7.4 - - + +
1136B ILE* 5.3 9.9 - - + +
1139B THR* 4.9 11.4 - - - -
1304B ASP 2.9 21.4 + - - +
1305B MET* 4.6 2.7 - - - -
1307B ILE* 1.3 74.0 - - - +
1309B LEU* 1.3 60.4 + - - +
1311B ALA* 3.0 12.1 + - + +
1312B VAL* 2.9 26.3 + - - +
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Residues in contact with LEU1309 (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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1305B MET* 2.6 25.2 + - - +
1306B GLU* 3.7 5.8 - - - +
1308B GLN* 1.3 75.6 - - - +
1310B GLY* 1.3 57.6 + - - +
1312B VAL* 3.6 8.5 + - - +
1313B LYS* 2.9 28.5 + - - +
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Residues in contact with GLY1310 (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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1306B GLU 2.9 15.8 + - - -
1307B ILE* 2.9 7.9 + - - -
1309B LEU* 1.3 77.4 - - - +
1311B ALA* 1.3 56.7 + - - +
1313B LYS* 3.3 8.4 + - - +
1314B ARG* 2.9 28.1 + - - +
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Residues in contact with ALA1311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128B ASP* 4.6 8.6 - - - +
1131B THR* 5.6 6.3 - - - -
1132B ILE* 4.8 20.7 - - + +
1307B ILE 2.9 10.9 + - - +
1308B GLN* 3.0 13.4 + - - +
1310B GLY* 1.3 74.6 - - - +
1312B VAL* 1.3 60.2 + - - +
1314B ARG* 3.2 13.4 + - - +
1315B ILE* 2.9 25.1 + - - +
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Residues in contact with VAL1312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004B TYR* 3.7 37.0 - - + -
1132B ILE* 5.3 5.5 - - + +
1308B GLN 2.9 14.2 + - - +
1309B LEU* 4.0 8.1 - - - +
1311B ALA* 1.3 76.1 - - - +
1313B LYS* 1.3 58.5 + - - +
1315B ILE* 3.2 10.7 + - + +
1316B HIS* 2.9 26.2 + - - +
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Residues in contact with LYS1313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309B LEU 2.9 19.5 + - - +
1310B GLY* 3.6 9.2 - - - +
1311B ALA 3.2 0.2 - - - -
1312B VAL* 1.3 73.2 - - - +
1314B ARG* 1.3 60.8 + - - +
1316B HIS* 3.4 8.4 + - - +
1317B ALA* 2.9 27.2 + - - +
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Residues in contact with ARG1314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124B ARG* 3.7 47.4 - - + +
1127B SER* 4.7 5.8 - - - -
1128B ASP* 4.6 5.7 - - + +
1310B GLY 2.9 15.4 + - - +
1311B ALA* 3.3 13.4 - - - +
1313B LYS* 1.3 75.4 - - - +
1315B ILE* 1.3 59.1 + - - +
1317B ALA* 3.1 9.8 + - + +
1318B LEU* 2.9 26.3 + - - +
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Residues in contact with ILE1315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128B ASP* 4.5 17.4 - - + +
1132B ILE* 5.6 4.3 - - + -
1311B ALA 2.9 13.0 + - - +
1312B VAL* 3.2 12.8 + - + +
1314B ARG* 1.3 77.6 - - - +
1316B HIS* 1.3 59.6 + - - +
1318B LEU* 3.3 19.6 + - - +
1319B LEU* 4.0 4.5 + - - +
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Residues in contact with HIS1316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B LYS* 3.7 36.0 + - + +
1312B VAL 2.9 16.5 + - - +
1313B LYS* 3.8 8.3 - - - +
1314B ARG 3.2 0.2 - - - -
1315B ILE* 1.3 75.7 - - - +
1317B ALA* 1.3 62.2 + - - +
1318B LEU 3.2 0.8 + - - -
1319B LEU* 3.5 23.2 + - + +
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Residues in contact with ALA1317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313B LYS 2.9 18.1 + - - +
1314B ARG* 3.1 12.5 + - + +
1316B HIS* 1.3 75.6 - - - +
1318B LEU* 1.3 62.8 + - - +
1319B LEU* 3.3 4.1 + - - -
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Residues in contact with LEU1318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101B LEU* 6.0 4.0 - - + -
1105B ILE* 6.1 1.2 - - - +
1124B ARG* 5.7 6.3 - - + +
1125B PHE* 5.1 21.8 - - + +
1128B ASP* 6.2 0.7 - - + -
1314B ARG 2.9 10.7 + - - +
1315B ILE* 3.4 14.8 - - - +
1316B HIS 3.2 0.8 - - - -
1317B ALA* 1.3 77.4 - - - +
1319B LEU* 1.3 60.6 + - - +
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Residues in contact with LEU1319 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1104B ARG* 6.0 7.6 - - + -
1315B ILE 4.0 4.7 + - - +
1316B HIS* 3.5 21.7 + - + +
1317B ALA 3.3 5.6 - - - -
1318B LEU* 1.3 83.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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