Contacts of the helix formed by residues 1424 - 1459 (chain A) in PDB entry 4W8F
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 PHE1424 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1365A PHE* 3.7 33.4 - + + -
1367A ILE* 4.5 22.0 - - + -
1368A GLU* 4.2 25.8 - - + -
1371A LEU* 5.1 4.9 - - + -
1420A TYR 4.4 6.5 - - - -
1421A TYR* 3.1 9.8 + - + +
1423A ILE* 1.3 104.9 - - + +
1425A GLU* 1.3 64.8 + - - +
1426A GLN 3.0 4.7 + - - -
1427A ASP* 3.1 25.0 + - + +
1428A CYS* 3.1 12.0 + - - +
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Residues in contact with GLU1425 (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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1421A TYR* 3.0 34.8 + - + +
1422A LYS* 3.1 36.1 - - - +
1423A ILE 3.2 2.7 - - - +
1424A PHE* 1.3 77.0 - - - +
1426A GLN* 1.3 58.6 + - + +
1428A CYS* 3.2 3.1 + - - +
1429A LEU* 2.7 54.0 + - + +
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Residues in contact with GLN1426 (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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1423A ILE 4.5 4.0 + - - +
1424A PHE 3.1 1.3 - - - -
1425A GLU* 1.3 86.8 - - + +
1427A ASP* 1.3 63.3 + - - +
1429A LEU* 2.9 21.5 + - - +
1430A ASP* 2.7 41.2 + - - +
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Residues in contact with ASP1427 (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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1368A GLU* 5.7 2.3 - - - +
1371A LEU* 4.6 14.8 - - + +
1375A LYS* 3.7 30.1 + - - -
1424A PHE* 3.1 18.5 + - + +
1426A GLN* 1.3 79.1 - - - +
1428A CYS* 1.3 61.7 + - - +
1430A ASP* 4.1 11.9 + - - +
1431A LEU* 3.8 14.7 + - - +
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Residues in contact with CYS1428 (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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1371A LEU* 3.9 19.4 - - + +
1412A LEU* 3.6 38.7 - - - +
1415A MET* 4.0 3.8 - - - -
1421A TYR* 3.2 43.5 - - + +
1424A PHE 3.1 7.7 + - - +
1425A GLU 3.4 2.0 - - - +
1426A GLN 3.0 0.4 - - - -
1427A ASP* 1.3 75.8 - - - +
1429A LEU* 1.3 66.2 + - - +
1431A LEU* 3.0 16.3 + - - +
1432A GLU* 3.0 14.0 + - - +
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Residues in contact with LEU1429 (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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1416A LYS* 4.2 26.9 - - - +
1421A TYR* 4.2 6.1 - - - +
1425A GLU* 2.7 44.4 + - + +
1426A GLN* 2.9 12.3 + - - +
1428A CYS* 1.3 73.1 - - - +
1430A ASP* 1.3 59.1 + - - +
1432A GLU* 3.2 17.6 + - - +
1433A SER* 2.9 34.8 + - - +
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Residues in contact with ASP1430 (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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1426A GLN* 2.7 42.9 + - - +
1427A ASP* 4.1 11.6 - - - +
1429A LEU* 1.3 77.6 - - - +
1431A LEU* 1.3 63.4 + - - +
1433A SER* 3.2 8.0 + - - -
1434A LYS* 3.1 34.3 + - + +
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Residues in contact with LEU1431 (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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1371A LEU* 4.1 19.1 - - + +
1374A ILE* 3.5 35.7 - - + -
1375A LYS* 4.2 31.4 - - + -
1378A TRP* 5.8 2.9 - - + -
1379A LYS* 5.7 3.4 - - - +
1412A LEU* 4.1 12.6 - - + -
1427A ASP 3.8 9.1 + - - +
1428A CYS 3.0 10.5 + - - +
1430A ASP* 1.3 79.0 - - - +
1432A GLU* 1.3 63.3 + - - +
1434A LYS* 3.2 24.9 + - + +
1435A LEU* 2.9 39.9 + - + +
1497A ILE* 6.5 0.4 - - + -
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Residues in contact with GLU1432 (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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1409A LEU* 4.5 8.5 - - + -
1412A LEU* 3.7 27.4 - - + +
1413A VAL* 4.3 13.6 - - + +
1416A LYS* 3.2 39.2 + - - -
1428A CYS* 3.0 14.0 + - - +
1429A LEU* 3.2 19.7 + - - +
1431A LEU* 1.3 76.5 - - - +
1433A SER* 1.3 51.3 + - - +
1435A LEU* 3.3 0.5 + - - +
1436A THR* 2.6 54.9 + - + +
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Residues in contact with SER1433 (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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1429A LEU* 2.9 19.6 + - - +
1430A ASP* 3.2 8.4 + - - -
1432A GLU* 1.3 76.2 - - - +
1434A LYS* 1.3 61.2 + - - +
1436A THR* 2.9 16.6 + - - -
1437A LYS* 3.4 13.9 + - - +
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Residues in contact with LYS1434 (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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1375A LYS* 6.2 1.8 - - - +
1379A LYS* 3.9 24.1 - - - +
1430A ASP* 3.1 26.8 + - + +
1431A LEU* 3.2 23.3 + - + +
1433A SER* 1.3 76.1 - - - +
1435A LEU* 1.3 66.1 + - - +
1437A LYS* 3.2 7.1 + - - +
1438A LEU* 3.1 16.8 + - - +
1497A ILE* 4.5 8.9 - - + +
1500A ILE* 3.9 34.3 - - + +
1501A HIS* 5.2 9.9 - - + +
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Residues in contact with LEU1435 (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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1374A ILE* 3.9 20.9 - - + -
1378A TRP* 3.6 33.4 - - + +
1405A CYS* 3.6 15.6 - - - +
1408A ASP* 4.2 9.9 - - + -
1409A LEU* 3.6 20.9 - - + +
1412A LEU* 3.7 26.7 - - + -
1431A LEU* 2.9 23.8 + - + +
1434A LYS* 1.3 72.6 - - + +
1436A THR* 1.3 62.5 + - - +
1438A LEU* 3.0 7.7 + - + +
1439A SER* 2.8 24.9 + - - -
1497A ILE* 3.8 20.0 - - + -
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Residues in contact with THR1436 (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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1409A LEU* 3.7 20.6 - - + -
1432A GLU* 2.6 42.2 + - + +
1433A SER* 2.9 21.0 + - - -
1435A LEU* 1.3 71.1 - - - +
1437A LYS* 1.3 54.5 + - - +
1439A SER* 3.3 9.3 + - - -
1440A GLU* 3.0 33.4 + - - +
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Residues in contact with LYS1437 (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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1433A SER 3.4 12.3 + - - +
1434A LYS* 3.2 6.6 + - - +
1435A LEU 3.2 0.6 - - - -
1436A THR* 1.3 79.1 + - - +
1438A LEU* 1.3 65.4 + - - +
1440A GLU* 3.6 20.8 - - - +
1441A ILE* 3.2 27.6 + - - +
1499A VAL 5.2 0.2 + - - -
1500A ILE* 2.7 42.9 + - + +
1502A ILE 4.7 6.7 + - - -
1505A PHE* 5.5 1.6 - - - +
1506A ASP* 4.1 29.5 - - - +
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Residues in contact with LEU1438 (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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1378A TRP* 3.9 27.6 - - + -
1405A CYS* 4.2 8.3 - - - -
1434A LYS 3.1 10.4 + - - +
1435A LEU* 3.0 12.2 + - + +
1437A LYS* 1.3 77.2 - - - +
1439A SER* 1.3 51.9 + - - +
1441A ILE* 2.9 22.9 - - + +
1442A GLN* 2.7 63.2 + - + +
1445A TRP* 6.2 2.0 - - + -
1496A THR* 3.9 33.9 - - + +
1497A ILE* 4.0 17.0 - - + -
1499A VAL* 5.0 1.3 - - + -
1500A ILE* 3.8 9.1 - - + +
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Residues in contact with SER1439 (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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1405A CYS* 4.3 5.1 - - - -
1409A LEU* 4.2 18.6 - - - +
1435A LEU 2.8 12.0 + - - -
1436A THR* 3.5 10.6 + - - -
1437A LYS 3.3 0.2 - - - -
1438A LEU* 1.3 77.4 - - - +
1440A GLU* 1.3 63.5 + - - +
1442A GLN* 4.1 12.1 - - - -
1443A VAL* 3.1 34.7 + - - +
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Residues in contact with GLU1440 (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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1436A THR* 3.0 21.9 + - - +
1437A LYS* 3.6 21.5 - - - +
1438A LEU 3.2 0.2 - - - -
1439A SER* 1.3 79.5 - - - +
1441A ILE* 1.3 54.9 + - - +
1443A VAL* 4.2 2.2 + - - +
1444A ASN* 2.5 35.9 + - - +
1506A ASP* 3.4 22.5 - - - +
1510A LYS* 6.0 2.2 - - - +
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Residues in contact with ILE1441 (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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1437A LYS* 3.2 18.4 - - - +
1438A LEU* 2.9 35.7 - - + +
1440A GLU* 1.3 76.8 - - - +
1442A GLN* 1.3 53.1 + - - +
1444A ASN* 3.3 5.0 + - - +
1445A TRP* 2.6 41.6 + - + +
1499A VAL* 3.6 29.8 - - + +
1500A ILE* 3.9 18.4 - - + -
1505A PHE* 4.7 4.5 - - + -
1506A ASP* 3.4 45.1 - - + +
1509A LEU* 3.8 10.3 - - + +
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Residues in contact with GLN1442 (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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1383A TYR* 3.8 26.9 + - + +
1398A TRP* 4.0 5.4 - - + -
1401A LEU* 3.8 24.0 + - - +
1402A GLU* 3.6 27.5 - - + +
1405A CYS* 3.7 11.3 - - - +
1438A LEU* 2.7 54.9 + - + +
1439A SER* 3.4 9.5 + - - +
1441A ILE* 1.3 70.5 - - - +
1443A VAL* 1.3 68.1 + - + +
1445A TRP* 3.0 19.7 + - + +
1446A VAL* 3.1 18.6 + - - +
1496A THR* 4.8 1.0 - - - +
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Residues in contact with VAL1443 (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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1402A GLU* 5.7 7.2 - - + +
1439A SER* 3.1 23.7 + - - +
1440A GLU* 4.2 4.5 - - - +
1442A GLN* 1.3 78.7 - - + +
1444A ASN* 1.3 65.4 + - - +
1446A VAL* 3.3 20.6 - - - +
1447A GLU* 3.5 23.8 - - - +
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Residues in contact with ASN1444 (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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1440A GLU 2.5 27.2 + - - +
1441A ILE* 3.3 6.0 + - - +
1442A GLN 3.1 1.0 - - - -
1443A VAL* 1.3 84.1 - - - +
1445A TRP* 1.3 64.1 + - - +
1446A VAL 3.2 2.8 + - - -
1447A GLU* 3.3 4.9 + - - +
1448A VAL* 3.0 29.4 + - + +
1506A ASP* 4.6 3.7 + - - +
1509A LEU* 4.1 19.5 - - + -
1510A LYS* 3.3 45.4 + - - +
1513A ILE* 4.2 13.0 - - + +
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Residues in contact with TRP1445 (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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1383A TYR* 4.1 22.2 - + - -
1395A VAL* 4.8 2.4 - - + +
1398A TRP* 3.4 25.0 - + + -
1438A LEU* 6.2 0.9 - - + -
1441A ILE* 2.6 27.7 + - + +
1442A GLN* 3.0 6.3 + - + +
1444A ASN* 1.3 73.1 - - - +
1446A VAL* 1.3 61.9 + - - +
1448A VAL* 3.5 3.0 + - - +
1449A GLN* 3.2 18.8 + - - +
1483A TYR* 3.5 29.0 + + - -
1487A THR* 3.8 12.5 - - + +
1490A ALA* 4.0 22.0 - - + -
1491A PHE* 3.4 43.3 - + - -
1496A THR* 5.0 2.2 - - + -
1499A VAL* 4.1 25.1 - - + -
1505A PHE* 4.5 13.9 - + - -
1509A LEU* 3.6 18.3 - - + +
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Residues in contact with VAL1446 (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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1398A TRP* 3.3 54.2 - - + +
1402A GLU* 5.0 11.2 - - - +
1442A GLN 3.1 9.5 + - - +
1443A VAL* 3.3 20.4 - - - +
1445A TRP* 1.3 76.7 - - - +
1447A GLU* 1.3 73.1 + - + +
1449A GLN* 3.2 4.2 + - - +
1450A PHE* 2.9 28.6 + - + +
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Residues in contact with GLU1447 (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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1443A VAL* 3.5 27.7 - - - +
1444A ASN* 3.3 6.8 + - - +
1446A VAL* 1.3 84.0 - - + +
1448A VAL* 1.3 66.9 + - - +
1450A PHE* 4.2 9.2 - - + -
1451A TYR* 2.9 48.5 + - + +
1513A ILE* 3.8 18.5 - - + +
1517A LYS* 5.7 1.9 - - - +
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Residues in contact with VAL1448 (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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1444A ASN 3.0 24.6 + - - +
1445A TRP* 3.6 6.7 - - - +
1447A GLU* 1.3 76.3 - - - +
1449A GLN* 1.3 62.6 + - - +
1452A TRP* 3.1 26.9 + - + +
1483A TYR* 3.8 28.5 - - + -
1509A LEU* 3.5 34.1 - - + +
1512A THR* 3.5 25.6 - - + -
1513A ILE* 3.7 21.3 - - + +
1516A LEU* 3.5 4.7 - - + +
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Residues in contact with GLN1449 (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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1392A LEU* 5.2 0.7 - - + -
1393A LYS 4.5 1.0 - - - +
1394A LEU* 3.4 23.3 - - + +
1395A VAL* 2.9 53.7 + - - +
1398A TRP* 3.5 12.8 - - + +
1445A TRP* 3.2 9.2 + - - +
1446A VAL* 3.5 9.4 - - - +
1448A VAL* 1.3 77.3 - - - +
1450A PHE* 1.3 67.5 + - - +
1452A TRP* 3.1 6.2 + - + +
1453A LEU* 2.9 44.6 + - + +
1483A TYR* 3.8 22.2 + - - +
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Residues in contact with PHE1450 (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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1446A VAL* 2.9 19.7 + - + +
1447A GLU* 3.4 8.0 + - + +
1449A GLN* 1.3 77.7 - - - +
1451A TYR* 1.3 89.1 + + - +
1453A LEU* 3.4 7.6 + - + +
1454A ASP* 3.1 30.3 + - + +
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Residues in contact with TYR1451 (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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1447A GLU* 2.9 41.2 + - + +
1450A PHE* 1.3 97.7 - + - +
1452A TRP* 1.3 65.1 + - - +
1454A ASP* 3.3 6.8 + - + +
1455A LEU* 2.9 28.5 + - + +
1513A ILE* 3.5 16.6 - - + -
1516A LEU* 3.9 17.9 - - + -
1517A LYS* 3.7 41.6 + - + +
1520A LYS* 4.7 26.9 - - + -
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Residues in contact with TRP1452 (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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1388A HIS* 3.2 37.2 - + - -
1390A SER 5.0 0.9 - - - -
1392A LEU* 4.0 24.2 - - + -
1394A LEU* 5.0 0.2 - - + -
1448A VAL 3.1 21.5 + - - +
1449A GLN* 3.5 5.4 - - - +
1451A TYR* 1.3 75.1 - - - +
1453A LEU* 1.3 97.8 + - + +
1455A LEU* 3.0 6.3 + - - +
1456A TYR* 2.8 42.7 + + + +
1476A PHE* 3.5 25.1 - + - -
1479A LEU* 5.5 1.3 - - + -
1480A THR* 3.1 50.2 + - + +
1483A TYR* 4.6 18.5 - + + -
1484A LYS* 5.7 0.2 - - - -
1512A THR* 6.0 1.3 - - + -
1516A LEU* 3.6 19.0 - - + +
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Residues in contact with LEU1453 (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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1388A HIS* 5.1 4.5 - - + +
1394A LEU* 3.5 40.6 - - + -
1449A GLN* 2.9 30.4 + - + +
1450A PHE* 3.6 6.7 - - + +
1452A TRP* 1.3 109.7 - - + +
1454A ASP* 1.3 62.8 + - - +
1455A LEU 3.4 0.2 + - - -
1456A TYR* 3.4 14.3 + - + +
1457A GLY* 4.0 3.6 + - - -
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Residues in contact with ASP1454 (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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1450A PHE* 3.1 25.4 + - + +
1451A TYR* 3.6 11.6 - - + +
1453A LEU* 1.3 77.9 - - - +
1455A LEU* 1.3 63.7 + - - +
1456A TYR 3.6 0.2 + - - -
1457A GLY* 4.1 3.6 + - - -
1458A ILE* 3.7 17.7 - - - +
1520A LYS* 3.1 34.9 + - - +
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Residues in contact with LEU1455 (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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1451A TYR* 2.9 21.4 + - + +
1452A TRP 3.0 0.6 + - - +
1454A ASP* 1.3 79.4 - - - +
1456A TYR* 1.3 62.8 + - - +
1457A GLY 3.3 0.2 - - - -
1458A ILE* 3.1 9.5 + - + +
1459A LEU* 2.9 44.7 + - + +
1476A PHE* 3.6 16.6 - - + -
1516A LEU* 3.8 43.1 - - + +
1519A ILE* 3.9 17.7 - - + -
1520A LYS* 4.4 24.5 - - + +
1523A LEU* 4.0 18.4 - - + -
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Residues in contact with TYR1456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1388A HIS* 3.4 30.3 - + - -
1389A SER* 3.9 8.3 + - - -
1390A SER* 3.5 18.6 + - - -
1452A TRP* 2.8 34.7 + + + +
1453A LEU* 3.4 9.6 + - + +
1455A LEU* 1.3 76.4 - - - +
1457A GLY* 1.3 62.1 + - - +
1460A GLY* 3.1 45.3 + - - -
1461A GLU* 3.5 33.5 + - + +
1476A PHE* 3.9 19.7 - + + -
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Residues in contact with GLY1457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1453A LEU 4.0 5.9 + - - -
1454A ASP 4.1 2.4 + - - -
1455A LEU 3.3 0.6 - - - -
1456A TYR* 1.3 81.7 - - - +
1458A ILE* 1.3 68.0 + - - +
1461A GLU* 4.1 24.5 + - - +
1462A ASN* 4.9 5.2 + - - +
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Residues in contact with ILE1458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1454A ASP* 3.7 21.8 - - - +
1455A LEU* 3.1 9.3 + - + +
1457A GLY* 1.3 81.7 - - - +
1459A LEU* 1.3 64.0 + - + +
1462A ASN 5.7 0.7 - - - -
1465A ILE* 3.4 27.8 - - + +
1520A LYS* 5.7 4.3 - - - +
1523A LEU* 3.8 31.0 - - + -
1546A LEU* 4.1 28.5 - - + -
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Residues in contact with LEU1459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1455A LEU* 2.9 24.9 + - + +
1456A TYR 3.3 0.2 + - - -
1458A ILE* 1.3 84.7 - - + +
1460A GLY* 1.3 57.2 + - - +
1461A GLU 3.1 3.9 + - - -
1462A ASN 3.9 4.6 - - - +
1465A ILE* 5.8 1.6 - - + -
1466A GLN* 2.7 38.0 - - - +
1469A LEU* 4.8 11.0 - - + -
1472A GLU* 4.1 15.7 - - + +
1473A THR* 4.0 20.0 - - + +
1476A PHE* 3.7 37.0 - - + -
1519A ILE* 3.7 28.9 - - + -
1523A LEU* 4.4 12.3 - - + -
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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) + - + + + + + -
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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