Contacts of the helix formed by residues 1505 - 1532 (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 PHE1505 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437A LYS* 5.5 4.1 - - - +
1441A ILE* 4.7 7.0 - - + -
1445A TRP* 4.5 16.8 - + - -
1486A ILE* 3.4 38.1 - - + -
1490A ALA* 3.7 12.8 - - + -
1499A VAL* 3.5 28.5 - - + +
1502A ILE* 3.3 60.4 + - + +
1503A PRO 3.4 0.2 - - - -
1504A ASN* 1.3 75.5 - - - +
1506A ASP* 1.3 69.4 + - - +
1507A THR 3.1 0.7 - - - -
1508A THR* 2.9 15.0 + - - -
1509A LEU* 3.0 43.1 + - + +
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Residues in contact with ASP1506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437A LYS* 4.1 18.1 - - - +
1440A GLU* 3.4 33.1 - - - +
1441A ILE* 3.4 27.4 - - + +
1444A ASN* 4.6 4.5 + - - +
1505A PHE* 1.3 78.7 - - - +
1507A THR* 1.3 64.1 + - - +
1509A LEU* 3.3 4.4 + - - +
1510A LYS* 3.1 41.8 + - - +
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Residues in contact with THR1507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1504A ASN* 3.8 32.0 + - - +
1505A PHE 3.1 0.8 - - - -
1506A ASP* 1.3 78.1 - - - +
1508A THR* 1.3 64.1 + - - +
1510A LYS* 3.4 4.1 + - - +
1511A LEU* 3.0 48.7 + - + +
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Residues in contact with THR1508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1482A GLU* 4.9 15.5 - - + +
1483A TYR* 5.3 1.8 - - - +
1486A ILE* 3.8 36.2 - - + +
1504A ASN* 2.2 32.9 + - - +
1505A PHE 2.9 6.8 + - - -
1507A THR* 1.3 80.5 - - - +
1509A LEU* 1.3 55.4 + - + +
1511A LEU* 3.4 6.2 + - - +
1512A THR* 2.6 44.0 + - - +
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Residues in contact with LEU1509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1441A ILE* 3.8 15.9 - - + +
1444A ASN* 4.1 12.6 - - + -
1445A TRP* 3.6 35.9 - - + -
1448A VAL* 3.5 14.7 - - + +
1483A TYR* 4.2 30.5 - - + -
1486A ILE* 4.5 7.9 - - + -
1505A PHE* 3.0 39.3 + - + +
1506A ASP* 3.8 6.3 - - - +
1508A THR* 1.3 76.8 - - + +
1510A LYS* 1.3 61.5 + - - +
1512A THR* 2.8 6.6 + - - +
1513A ILE* 2.8 31.3 + - - +
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Residues in contact with LYS1510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1440A GLU* 4.9 2.6 + - - +
1444A ASN* 3.3 36.5 + - - +
1506A ASP* 3.1 27.8 + - - +
1507A THR* 3.9 5.6 - - - +
1509A LEU* 1.3 76.3 - - - +
1511A LEU* 1.3 64.9 + - + +
1513A ILE* 3.3 7.9 - - + +
1514A ASP* 3.0 37.8 + - - +
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Residues in contact with LEU1511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1479A LEU* 4.8 1.5 - - - +
1507A THR* 3.0 43.6 + - + +
1508A THR* 3.7 6.7 - - - +
1510A LYS* 1.3 79.7 - - + +
1512A THR* 1.3 58.0 + - - +
1514A ASP* 3.9 6.3 - - - +
1515A SER* 3.1 29.6 + - - -
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Residues in contact with THR1512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1448A VAL* 3.5 26.7 - - + -
1452A TRP* 6.0 1.6 - - + -
1479A LEU* 4.5 21.7 + - + +
1482A GLU* 5.6 3.1 + - - +
1483A TYR* 4.6 17.0 + - + +
1508A THR* 2.6 27.9 + - - +
1509A LEU* 2.8 13.4 + - - +
1511A LEU* 1.3 76.4 - - - +
1513A ILE* 1.3 58.7 + - - -
1515A SER* 3.2 5.9 + - - -
1516A LEU* 2.8 39.6 + - + +
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Residues in contact with ILE1513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1444A ASN* 4.2 14.8 - - - +
1447A GLU* 3.6 31.0 - - + +
1448A VAL* 3.7 16.5 - - + +
1451A TYR* 3.5 40.6 - - + -
1509A LEU 2.8 15.9 + - - +
1510A LYS* 3.3 20.2 - - + +
1512A THR* 1.3 72.7 - - - +
1514A ASP* 1.3 69.8 + - - +
1516A LEU* 3.3 3.3 + - + -
1517A LYS* 2.9 41.4 + - + +
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Residues in contact with ASP1514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1510A LYS* 3.0 28.8 + - - +
1511A LEU* 3.9 7.2 - - - +
1513A ILE* 1.3 91.0 - - - +
1515A SER* 1.3 57.3 + - - +
1517A LYS* 3.4 11.3 + - - +
1518A MET* 3.0 28.9 + - - +
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Residues in contact with SER1515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475A LYS* 3.4 28.3 + - - +
1479A LEU* 3.3 34.1 - - - +
1511A LEU 3.1 19.3 + - - -
1512A THR 3.2 1.3 + - - -
1514A ASP* 1.3 74.6 - - - +
1516A LEU* 1.3 66.6 + - - +
1518A MET* 3.1 9.2 + - - +
1519A ILE* 3.0 23.9 + - - +
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Residues in contact with LEU1516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1448A VAL* 3.5 28.3 - - - +
1451A TYR* 3.9 15.0 - - + -
1452A TRP* 3.6 26.2 - - + +
1455A LEU* 3.8 19.0 - - + +
1476A PHE* 4.1 19.3 - - + -
1479A LEU* 3.7 23.6 - - + -
1512A THR* 2.8 32.8 + - + +
1513A ILE* 3.7 4.9 - - - +
1515A SER* 1.3 76.4 - - - +
1517A LYS* 1.3 58.4 + - - +
1519A ILE* 2.9 9.3 + - + +
1520A LYS* 2.8 28.8 + - - +
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Residues in contact with LYS1517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1447A GLU* 5.7 2.0 - - - +
1451A TYR* 3.7 36.5 + - + +
1513A ILE* 2.9 35.7 + - + +
1514A ASP* 3.6 11.7 - - - +
1516A LEU* 1.3 75.7 - - - +
1518A MET* 1.3 57.3 + - - +
1520A LYS* 3.8 7.3 - - - +
1521A SER* 2.9 31.7 + - - -
----------------------------------------------------------
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Residues in contact with MET1518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475A LYS* 4.6 15.7 - - + +
1514A ASP 3.0 15.8 + - - +
1515A SER* 3.4 13.0 - - - +
1516A LEU 3.1 0.4 - - - -
1517A LYS* 1.3 75.9 - - - +
1519A ILE* 1.3 58.3 + - + +
1521A SER* 3.8 8.4 - - - -
1522A SER* 3.1 26.9 + - - -
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Residues in contact with ILE1519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1455A LEU* 3.9 11.0 - - + -
1459A LEU* 3.7 24.5 - - + -
1472A GLU* 3.4 37.0 - - + +
1475A LYS* 4.0 13.9 - - + -
1476A PHE* 4.0 17.7 - - + +
1479A LEU* 3.9 26.9 - - + -
1515A SER 3.0 12.9 + - - +
1516A LEU* 2.9 10.6 + - + +
1518A MET* 1.3 76.5 - - + +
1520A LYS* 1.3 66.9 + - - +
1522A SER* 2.9 7.3 + - - -
1523A LEU* 2.8 24.7 + - + +
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Residues in contact with LYS1520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451A TYR* 4.7 18.4 - - + -
1454A ASP* 3.1 29.4 + - - +
1455A LEU* 4.4 19.8 - - + +
1458A ILE* 5.7 4.9 - - - +
1516A LEU 2.8 18.2 + - - +
1517A LYS* 3.8 8.7 - - - +
1519A ILE* 1.3 74.3 - - - +
1521A SER* 1.3 64.0 + - - +
1523A LEU* 3.4 10.1 + - + +
1524A SER* 3.1 25.3 + - - -
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Residues in contact with SER1521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517A LYS 2.9 19.2 + - - -
1518A MET* 3.8 10.6 - - - -
1520A LYS* 1.3 76.9 - - - +
1522A SER* 1.3 58.5 + - - +
1524A SER* 3.3 7.2 + - - -
1525A THR* 2.9 38.1 + - - -
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Residues in contact with SER1522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1471A LEU* 6.0 0.3 - - - +
1472A GLU* 2.3 37.0 + - - -
1518A MET* 3.1 16.8 + - - -
1519A ILE* 2.9 6.8 + - - -
1521A SER* 1.3 79.4 - - - +
1523A LEU* 1.3 51.7 + - - +
1525A THR* 3.2 7.7 + - - -
1526A PHE* 2.7 34.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU1523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1455A LEU* 4.0 23.6 - - + -
1458A ILE* 3.8 30.5 - - + -
1459A LEU* 4.4 11.7 - - + -
1465A ILE* 5.9 0.4 - - + -
1469A LEU* 3.7 28.3 - - + -
1472A GLU* 4.6 6.5 + - + +
1519A ILE* 2.8 10.4 + - + +
1520A LYS* 3.6 12.6 - - + +
1522A SER* 1.3 74.6 - - - +
1524A SER* 1.3 66.1 + - - +
1526A PHE* 3.1 11.5 + - + +
1527A LEU* 3.0 45.5 + - + +
1546A LEU* 5.2 6.1 - - + -
----------------------------------------------------------
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Residues in contact with SER1524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1520A LYS* 3.1 13.2 + - - -
1521A SER* 3.5 10.8 - - - -
1523A LEU* 1.3 80.2 - - - +
1525A THR* 1.3 63.4 + - - +
1527A LEU* 3.8 8.0 - - - +
1528A GLU* 3.1 27.1 + - - +
1542A ASN* 6.1 1.6 - - - +
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Residues in contact with THR1525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1521A SER* 2.9 24.3 + - - -
1522A SER* 3.5 7.1 - - - -
1524A SER* 1.3 74.4 - - - +
1526A PHE* 1.3 66.9 + - - +
1528A GLU* 3.3 5.3 + - + +
1529A ARG* 2.9 67.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE1526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1465A ILE* 5.0 10.8 - - + -
1468A PHE* 5.0 11.7 - - + -
1469A LEU* 4.0 42.8 - - + -
1472A GLU* 5.1 1.3 - - - +
1522A SER* 2.7 20.7 + - - +
1523A LEU* 3.1 9.6 + - + +
1525A THR* 1.3 74.7 - - - +
1527A LEU* 1.3 75.1 + - + +
1529A ARG* 3.3 8.2 + - + +
1530A GLN* 3.0 55.0 + - + +
1546A LEU* 5.1 0.9 - - + -
1549A ILE* 5.1 12.3 - - + -
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Residues in contact with LEU1527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1523A LEU* 3.0 33.2 + - + +
1524A SER* 3.8 7.0 - - - +
1526A PHE* 1.3 84.7 - - + +
1528A GLU* 1.3 58.8 + - - +
1530A GLN* 2.7 24.6 + - + +
1531A ARG* 2.9 22.5 + - - +
1542A ASN* 3.3 41.1 - - + +
1545A LEU* 3.8 22.7 - - + -
1546A LEU* 3.5 35.0 - - + -
----------------------------------------------------------
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Residues in contact with GLU1528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524A SER* 3.1 18.2 + - - +
1525A THR* 3.9 5.4 - - + +
1527A LEU* 1.3 78.7 - - - +
1529A ARG* 1.3 61.6 + - + +
1531A ARG* 3.8 13.4 + - - +
1532A ARG* 2.9 52.4 + - - +
1538A TYR* 3.3 28.9 + - + -
1884A GLU* 2.5 29.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG1529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1525A THR* 2.9 45.5 + - + +
1526A PHE* 3.6 8.1 - - + +
1528A GLU* 1.3 77.0 - - + +
1530A GLN* 1.3 62.5 + - - +
1532A ARG* 3.5 20.1 + - - +
1533A GLN* 3.8 16.1 + - - +
----------------------------------------------------------
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Residues in contact with GLN1530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1526A PHE* 3.0 42.4 + - + +
1527A LEU* 2.7 17.6 + - + +
1529A ARG* 1.3 77.0 - - - +
1531A ARG* 1.3 61.3 + - - +
1532A ARG 3.4 0.2 + - - -
1533A GLN* 3.5 16.2 + - - +
1537A PHE* 3.8 12.3 - - + -
1545A LEU* 3.9 15.5 - - + -
1549A ILE* 3.0 37.3 - - + +
1603A GLN* 3.6 8.0 - - - +
1605A GLN* 3.2 25.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG1531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1527A LEU* 2.9 24.1 + - - +
1528A GLU* 4.0 12.1 - - - +
1530A GLN* 1.3 76.8 - - - +
1532A ARG* 1.3 58.0 + - - +
1533A GLN 3.0 0.4 - - - -
1534A PHE 2.9 31.9 + - - +
1535A PRO* 3.1 3.3 - - - +
1537A PHE* 3.5 34.3 - - + -
1538A TYR* 3.7 34.3 - - + +
1541A GLY* 3.7 17.2 - - - +
1542A ASN* 2.5 37.9 + - - +
1545A LEU* 3.2 31.1 - - + +
1833A ARG* 3.9 23.7 - - - +
----------------------------------------------------------
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Residues in contact with ARG1532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1528A GLU* 2.9 35.4 + - - +
1529A ARG* 3.5 15.8 + - - +
1530A GLN 3.3 1.2 - - - -
1531A ARG* 1.3 75.7 - - - +
1533A GLN* 1.3 66.0 + - - +
1534A PHE* 3.4 0.4 - - - -
1535A PRO* 4.4 8.7 - - - +
1538A TYR* 2.9 21.9 + - - +
1840A GLN* 3.8 22.3 - - - +
1884A GLU* 3.7 12.7 + - - +
1885A GLU 3.1 26.8 + - - +
1886A THR* 4.5 3.2 - - - +
1887A PRO* 5.3 6.5 - - - +
----------------------------------------------------------
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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