Contacts of the helix formed by residues 1285 - 1313 (chain A) in PDB entry 3AVR
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 ASP1285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246A ALA* 4.0 8.8 + - - +
1283A VAL* 3.6 3.5 - - + +
1284A SER* 1.3 80.6 + - - +
1286A PRO* 1.3 76.4 - - - +
1287A LYS* 3.5 12.8 + - - +
1288A LEU* 3.0 34.5 + - + +
1289A PHE* 2.9 22.7 + - - +
1392A LEU* 4.0 0.7 - - - -
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Residues in contact with PRO1286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1284A SER 3.4 8.9 - - - +
1285A ASP* 1.3 91.2 - - - +
1287A LYS* 1.3 61.5 + - - +
1289A PHE* 3.3 1.7 + - + +
1290A GLU* 2.9 38.5 + - + +
1392A LEU* 3.7 25.8 - - + -
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Residues in contact with LYS1287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246A ALA* 3.2 26.7 - - + +
1247A CYS* 4.6 3.8 - - - +
1250A LYS* 4.5 11.7 - - - +
1285A ASP* 3.3 11.3 + - - +
1286A PRO* 1.3 79.7 - - - +
1288A LEU* 1.3 61.9 + - - +
1290A GLU* 3.3 7.3 + - - +
1291A MET* 3.1 51.2 + - + +
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Residues in contact with LEU1288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118A LEU* 6.3 0.4 - - + -
1244A LEU* 3.7 51.1 - - + +
1245A THR* 3.7 9.4 - - - +
1246A ALA* 3.9 12.1 - - - +
1249A TYR* 3.5 35.2 - - + -
1277A MET* 5.1 1.3 - - + -
1283A VAL* 4.0 11.2 - - + -
1285A ASP* 3.0 25.0 + - + +
1287A LYS* 1.3 73.9 - - - +
1289A PHE* 1.3 67.4 + - - +
1291A MET* 3.2 3.2 + - - +
1292A ILE* 3.1 39.6 + - + +
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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
----------------------------------------------------------
889A ILE* 6.3 0.7 - - + -
890A TYR* 4.6 11.0 - + - -
1283A VAL* 3.6 14.4 - - + +
1285A ASP 2.9 18.1 + - - +
1286A PRO* 3.6 2.9 - - + +
1288A LEU* 1.3 77.6 - - - +
1290A GLU* 1.3 67.8 + - + +
1292A ILE* 3.3 2.0 + - - +
1293A LYS* 3.0 45.6 + - + +
1390A PHE* 3.5 44.9 - + - -
1391A THR* 3.2 26.2 - - + -
1392A LEU* 3.5 41.5 - - + -
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Residues in contact with GLU1290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A ILE* 3.7 29.9 - - + +
890A TYR* 2.7 29.4 + - + +
1286A PRO* 2.9 29.0 + - + +
1287A LYS* 3.8 6.6 - - - +
1288A LEU 3.2 0.2 - - - -
1289A PHE* 1.3 85.2 - - + +
1291A MET* 1.3 66.2 + - + +
1294A TYR* 3.0 14.3 + - - +
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Residues in contact with MET1291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A EDO 3.7 25.2 + - - +
1246A ALA* 3.7 23.8 - - - +
1249A TYR* 3.6 26.0 - - + -
1250A LYS* 3.6 31.6 - - + +
1287A LYS* 3.1 53.7 + - + +
1288A LEU* 3.2 5.6 + - - +
1290A GLU* 1.3 76.8 - - + +
1292A ILE* 1.3 64.4 + - - +
1294A TYR* 3.4 5.9 + - - +
1295A CYS* 3.1 17.8 + - - +
1298A ARG* 5.4 0.3 + - - -
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Residues in contact with ILE1292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249A TYR* 3.8 22.2 - - + +
1274A SER* 4.2 20.9 - - - +
1277A MET* 3.5 33.4 - - + -
1278A ALA* 4.9 0.7 - - + -
1283A VAL* 4.0 21.8 - - + -
1288A LEU* 3.1 33.9 + - + +
1291A MET* 1.3 76.8 - - - +
1293A LYS* 1.3 62.9 + - - +
1295A CYS* 3.0 5.5 + - - +
1296A LEU* 3.0 26.8 + - + +
1390A PHE* 3.5 26.0 - - + -
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Residues in contact with LYS1293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A SER* 5.9 0.8 + - - -
890A TYR* 3.5 34.7 + - + +
891A PRO 5.1 0.6 + - - -
1289A PHE* 3.0 30.2 + - + +
1292A ILE* 1.3 76.9 - - - +
1294A TYR* 1.3 57.7 + - - +
1296A LEU* 3.2 9.3 + - + +
1297A LEU* 2.8 27.9 + - - +
1387A TYR* 3.0 53.4 + - + -
1388A ASP* 4.5 6.5 + - - +
1390A PHE* 2.9 39.4 + - + +
1391A THR* 4.7 4.2 - - - +
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Residues in contact with TYR1294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A EDO 4.7 13.7 - - - -
890A TYR* 3.5 23.9 + + - +
914A LEU* 3.9 20.9 - - + +
916A ASP 5.6 1.2 + - - -
918A CYS* 3.9 22.3 - - - -
1290A GLU 3.0 20.2 + - - +
1291A MET* 3.5 4.9 - - - +
1293A LYS* 1.3 78.2 - - - +
1295A CYS* 1.3 62.0 + - - +
1297A LEU* 3.3 4.9 + - + +
1298A ARG* 3.0 53.8 + - + +
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Residues in contact with CYS1295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249A TYR* 3.3 20.0 - - + +
1253A VAL* 5.8 3.4 - - + -
1270A MET* 4.7 4.9 - - - -
1271A VAL* 4.8 7.9 - - - -
1274A SER* 3.7 28.9 - - - -
1275A TRP* 5.5 0.2 - - - -
1291A MET 3.1 7.4 + - - +
1292A ILE 3.0 5.7 + - - +
1294A TYR* 1.3 76.5 - - - +
1296A LEU* 1.3 61.1 + - - +
1298A ARG* 3.4 24.6 + - - +
1299A THR* 2.9 42.7 + - - +
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Residues in contact with LEU1296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274A SER* 3.9 22.4 - - - +
1275A TRP* 3.5 43.5 - - + +
1278A ALA* 3.6 22.2 - - + -
1292A ILE* 3.0 19.8 + - + +
1293A LYS* 3.2 7.6 + - + +
1295A CYS* 1.3 75.1 - - - +
1297A LEU* 1.3 58.9 + - - +
1299A THR* 3.3 4.3 + - - -
1300A LEU* 2.8 33.8 + - - +
1387A TYR* 3.8 25.6 - - + -
1390A PHE* 3.8 27.8 - - + -
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Residues in contact with LEU1297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A TYR* 3.9 25.8 - - + -
891A PRO* 4.0 16.4 - - + -
896A VAL* 3.6 32.8 - - + -
913A ILE* 4.3 9.2 - - + +
914A LEU* 4.1 30.7 - - + -
1293A LYS 2.8 17.1 + - - +
1294A TYR* 3.6 8.1 - - + +
1295A CYS 3.3 0.2 - - - -
1296A LEU* 1.3 76.8 - - - +
1298A ARG* 1.3 64.0 + - - +
1300A LEU* 3.8 1.9 - - + +
1301A LYS* 2.9 28.6 + - + +
1387A TYR* 3.8 19.0 - - + +
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Residues in contact with ARG1298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A EDO 5.1 4.9 + - - -
914A LEU* 4.5 11.4 - - + -
916A ASP* 6.1 3.8 - - - +
918A CYS* 5.1 11.0 - - - -
1253A VAL* 4.4 19.8 - - - +
1257A GLU* 4.0 21.2 + - - +
1291A MET 5.4 0.4 + - - -
1294A TYR* 3.0 58.9 + - + +
1295A CYS* 3.7 29.8 - - - +
1297A LEU* 1.3 77.7 - - - +
1299A THR* 1.3 62.3 + - + +
1301A LYS* 3.7 5.2 - - - +
1302A GLN* 3.0 45.3 + - - +
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Residues in contact with THR1299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271A VAL* 3.8 34.5 - - + +
1275A TRP* 3.0 27.5 + - - -
1295A CYS* 2.9 25.0 + - - +
1296A LEU 3.3 1.9 + - - -
1298A ARG* 1.3 78.6 - - + +
1300A LEU* 1.3 62.3 + - - +
1302A GLN* 3.7 17.3 - - - +
1303A CYS* 2.9 35.5 + - - -
1339A PHE* 5.0 4.9 - - - -
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Residues in contact with LEU1300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A SER* 4.3 15.7 - - - -
896A VAL* 4.3 15.9 - - + -
1275A TRP* 4.0 11.6 - - + -
1296A LEU 2.8 22.1 + - - +
1297A LEU* 3.8 2.9 - - - +
1299A THR* 1.3 72.4 + - - +
1301A LYS* 1.3 63.0 + - - +
1303A CYS* 3.3 4.9 + - - +
1304A GLN* 3.0 40.0 + - - +
1380A MET* 3.7 29.8 - - + -
1383A LEU* 4.0 22.4 - - + -
1384A MET* 4.5 3.8 - - + -
1387A TYR* 3.9 35.7 - - + -
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Residues in contact with LYS1301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A VAL* 4.0 14.8 - - + +
899A ALA* 5.6 4.0 - - - -
900A CYS* 3.7 17.7 - - - +
913A ILE* 4.1 20.9 - - + +
914A LEU* 3.5 36.6 + - + +
916A ASP* 4.2 21.8 + - - +
1297A LEU* 2.9 19.0 + - + +
1298A ARG* 3.7 5.6 - - - +
1300A LEU* 1.3 76.9 - - - +
1302A GLN* 1.3 58.2 + - + +
1304A GLN 3.4 0.2 + - - -
1305A THR* 2.8 42.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN1302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A ASP 6.0 0.2 + - - -
1298A ARG* 3.0 39.4 + - - +
1299A THR* 3.3 19.8 + - - +
1301A LYS* 1.3 76.8 - - + +
1303A CYS* 1.3 57.8 + - - +
1305A THR* 3.7 5.0 - - - +
1306A LEU* 3.0 30.5 + - - +
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Residues in contact with CYS1303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299A THR* 2.9 20.8 + - - +
1300A LEU* 3.7 6.3 - - - +
1302A GLN* 1.3 79.4 - - - +
1304A GLN* 1.3 58.1 + - - +
1306A LEU* 3.5 1.9 + - - -
1307A ARG* 2.9 29.6 + - - +
1339A PHE* 3.8 33.7 - - - -
1340A ASP* 3.7 22.4 - - - +
1341A LEU* 3.7 12.8 - - + +
1380A MET* 4.0 16.1 - - + +
1383A LEU* 4.8 3.4 - - + -
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Residues in contact with GLN1304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A SER 4.1 2.4 + - - -
896A VAL* 3.2 28.2 - - - +
897A LEU* 3.2 48.9 - - + +
900A CYS* 3.9 10.0 - - + -
1300A LEU* 3.0 25.3 + - - +
1303A CYS* 1.3 76.9 - - - +
1305A THR* 1.3 58.4 + - - +
1307A ARG* 3.4 4.3 + - - +
1308A GLU* 2.9 36.2 + - - +
1380A MET* 3.5 33.8 - - + -
1384A MET* 3.9 17.4 - - - +
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Residues in contact with THR1305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A CYS* 3.3 22.9 - - - +
1301A LYS* 2.8 33.4 + - - +
1302A GLN* 3.7 6.1 - - - +
1304A GLN* 1.3 78.9 - - - +
1306A LEU* 1.3 62.1 + - - +
1308A GLU* 3.4 4.3 + - - +
1309A ALA* 3.0 23.4 + - + +
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Residues in contact with LEU1306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1302A GLN 3.0 17.3 + - - +
1303A CYS* 3.9 4.0 - - - +
1305A THR* 1.3 73.9 - - - +
1307A ARG* 1.3 66.6 + - - +
1309A ALA* 3.1 8.8 + - + +
1310A LEU* 2.9 45.4 + - + +
1341A LEU* 3.8 24.0 - - + +
1343A PHE* 3.9 25.8 - - + -
1359A GLN* 3.2 41.1 - - + +
1363A ARG* 4.8 1.1 - - - +
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Residues in contact with ARG1307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1303A CYS 2.9 18.9 + - - +
1304A GLN* 3.7 5.8 - - - +
1306A LEU* 1.3 76.8 - - - +
1308A GLU* 1.3 64.5 + - + +
1310A LEU* 3.5 2.9 + - - +
1311A ILE* 3.2 46.2 + - + +
1317A ILE* 3.8 30.9 + - + +
1341A LEU* 4.1 11.8 - - + +
1376A GLU* 2.8 43.0 + - - -
1380A MET* 4.3 26.2 - - - +
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Residues in contact with GLU1308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A LEU* 4.7 9.4 - - + +
900A CYS* 4.3 21.5 - - + +
901A ARG* 4.1 37.0 + - + +
1304A GLN 2.9 23.0 + - - +
1305A THR* 3.7 5.2 - - - +
1307A ARG* 1.3 75.8 - - + +
1309A ALA* 1.3 65.1 + - - +
1311A ILE* 3.4 12.7 + - - +
1312A ALA* 2.9 24.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA1309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305A THR* 3.0 16.0 + - + +
1306A LEU* 3.5 15.3 - - + +
1308A GLU* 1.3 77.4 - - - +
1310A LEU* 1.3 63.1 + - + +
1312A ALA* 3.1 9.6 + - - +
1313A ALA* 3.0 22.4 + - - +
1359A GLN* 5.8 0.7 - - - +
1363A ARG* 5.7 5.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU1310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306A LEU* 2.9 39.4 + - + +
1307A ARG* 3.8 5.2 - - - +
1308A GLU 3.3 0.2 - - - -
1309A ALA* 1.3 76.0 - - - +
1311A ILE* 1.3 57.9 + - - +
1313A ALA* 3.0 15.2 + - + +
1315A LYS* 3.0 45.9 + - + +
1317A ILE* 4.3 18.8 - - + -
1341A LEU* 4.7 4.3 - - + -
1343A PHE* 4.1 12.6 - - + -
1363A ARG* 4.3 12.3 - - - +
1369A LEU* 4.1 26.2 - - + -
1374A VAL* 4.1 25.8 - - + -
----------------------------------------------------------
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Residues in contact with ILE1311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1307A ARG* 3.2 47.3 + - + +
1308A GLU* 3.9 13.0 - - - +
1310A LEU* 1.3 76.5 - - - +
1312A ALA* 1.3 59.3 + - - +
1314A GLY* 2.9 18.7 + - - +
1315A LYS 4.3 7.0 - - - +
1317A ILE* 4.3 11.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA1312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1308A GLU 2.9 19.0 + - - +
1309A ALA* 3.4 9.4 - - - +
1311A ILE* 1.3 76.6 - - - +
1313A ALA* 1.3 57.8 + - - +
1314A GLY 3.3 1.2 + - - -
----------------------------------------------------------
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Residues in contact with ALA1313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309A ALA 3.0 11.1 + - - +
1310A LEU* 3.0 14.2 + - + +
1312A ALA* 1.3 77.5 - - - +
1314A GLY* 1.3 59.5 + - - +
1315A LYS* 3.1 9.9 + - + +
----------------------------------------------------------
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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