Contacts of the helix formed by residues 1508 - 1527 (chain A) in PDB entry 5A31
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 GLY1508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1459A GLN* 5.0 1.8 - - - -
1504A ALA 3.0 9.1 + - - -
1505A SER 3.4 4.4 + - - -
1506A VAL 3.2 4.9 - - - -
1507A THR* 1.3 78.4 - - - +
1509A PRO* 1.3 76.6 - - - +
1510A HIS* 3.2 3.1 - - - -
1511A ASN* 3.3 9.5 + - - -
1512A LEU* 3.1 24.6 + - - +
104L ASN* 5.7 1.8 - - - -
106L GLN* 5.9 0.2 - - - -
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Residues in contact with PRO1509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499A LEU* 5.6 0.9 - - - +
1504A ALA* 3.8 15.7 - - + +
1505A SER* 4.2 10.5 - - - +
1508A GLY* 1.3 82.7 - - - +
1510A HIS* 1.3 62.6 + - + +
1512A LEU* 3.4 11.2 + - + +
1513A GLU* 3.3 25.9 + - - +
1549A GLU* 5.1 14.4 - - + -
106L GLN* 4.3 20.6 - - - +
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Residues in contact with HIS1510 (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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1463A TYR* 5.6 0.4 + - - -
1509A PRO* 1.3 80.4 - - + +
1511A ASN* 1.3 68.0 + - - +
1513A GLU* 3.2 9.6 + - - +
1514A THR* 3.2 34.0 + - - -
1549A GLU* 5.5 8.9 - - + +
1551A ASN* 4.7 10.8 + - - -
1554A PHE* 3.8 22.2 - + - -
103L HIS* 4.0 39.0 + + - +
104L ASN* 3.8 30.1 + - + +
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Residues in contact with ASN1511 (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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1459A GLN* 3.1 33.1 + - + +
1462A VAL* 5.1 1.6 - - + -
1463A TYR* 3.4 37.8 + - + +
1507A THR* 3.3 21.1 - - - +
1508A GLY* 3.3 5.8 + - - -
1510A HIS* 1.3 77.7 + - - +
1512A LEU* 1.3 59.0 + - - +
1514A THR* 3.4 1.3 + - - -
1515A CYS* 3.0 28.9 + - - +
100L ASN* 3.9 5.7 + - - -
104L ASN* 3.3 33.7 + - - +
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Residues in contact with LEU1512 (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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1462A VAL* 4.1 12.8 - - + -
1495A PHE* 4.5 7.1 - - + -
1498A TYR* 4.2 39.0 - - + +
1499A LEU* 4.1 18.5 - - + +
1504A ALA* 4.2 11.7 - - + +
1507A THR* 3.4 36.3 - - + +
1508A GLY 3.1 13.4 + - - +
1509A PRO* 3.5 10.5 - - + +
1510A HIS 3.2 0.4 - - - -
1511A ASN* 1.3 74.7 - - - +
1513A GLU* 1.3 67.1 + - - +
1515A CYS* 3.2 16.4 - - - -
1516A LEU* 3.0 23.9 + - - +
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Residues in contact with GLU1513 (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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1499A LEU* 3.1 31.2 - - - +
1509A PRO 3.3 14.8 + - - +
1510A HIS* 3.2 4.2 + - - +
1512A LEU* 1.3 78.1 - - - +
1514A THR* 1.3 53.0 + - - +
1516A LEU* 3.1 12.1 + - - +
1517A SER* 2.8 39.7 + - - +
1545A LYS* 4.3 0.3 + - - -
1549A GLU* 3.6 25.5 - - + +
1550A MET* 3.1 33.1 - - - +
1554A PHE* 3.2 26.7 - - + -
1558A HIS* 6.1 1.8 - - - +
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Residues in contact with THR1514 (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 LEU* 5.1 2.7 - - + -
1463A TYR* 4.0 23.1 + - + +
1510A HIS* 3.2 19.1 + - - -
1511A ASN 3.8 7.2 - - - -
1513A GLU* 1.3 77.2 - - - +
1515A CYS* 1.3 62.2 + - - +
1517A SER* 3.5 3.9 + - - -
1518A VAL* 3.2 25.1 + - + +
1554A PHE* 3.4 24.7 - - - -
1590A PRO* 3.9 23.6 - - + +
1591A HIS* 5.1 5.2 - - + -
1592A PHE* 4.6 3.1 - - + +
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Residues in contact with CYS1515 (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 LEU* 5.1 0.4 - - - -
1462A VAL* 3.7 22.2 - - + +
1463A TYR* 4.3 9.6 - - + -
1466A ALA* 3.7 26.5 - - + +
1495A PHE* 3.4 28.3 - - + -
1511A ASN 3.0 18.3 + - - +
1512A LEU* 3.2 20.4 - - - -
1514A THR* 1.3 80.0 - - - +
1516A LEU* 1.3 57.0 + - - +
1518A VAL* 3.5 3.1 + - - +
1519A VAL* 3.0 28.5 + - - +
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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
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1492A ALA* 4.5 9.0 - - + +
1495A PHE* 4.1 22.2 - - + -
1496A MET* 4.3 18.6 - - + -
1499A LEU* 4.3 13.5 - - + -
1512A LEU 3.0 18.9 + - - +
1513A GLU* 3.4 20.9 - - - +
1515A CYS* 1.3 74.7 - - - +
1517A SER* 1.3 67.5 + - - +
1518A VAL 3.1 1.8 - - - -
1519A VAL* 3.1 16.4 - - + +
1520A LEU* 3.0 29.2 + - + +
1538A LEU* 5.3 1.6 - - + -
1542A LEU* 4.0 33.4 - - + -
1550A MET* 6.4 0.2 - - - -
1558A HIS* 4.8 4.9 - - - +
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Residues in contact with SER1517 (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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1513A GLU 2.8 22.3 + - - -
1514A THR* 3.7 2.7 - - - -
1516A LEU* 1.3 74.8 - - - +
1518A VAL* 1.3 57.0 + - - +
1520A LEU* 3.7 5.8 - - - +
1521A LEU* 3.0 34.7 + - - +
1554A PHE* 3.7 14.2 - - - -
1557A ALA* 4.0 10.9 - - - +
1558A HIS* 3.6 23.9 + - - -
1592A PHE* 3.6 26.0 - - - -
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Residues in contact with VAL1518 (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 LEU* 4.1 7.9 - - + -
1466A ALA* 3.8 23.6 - - + +
1470A LEU* 3.5 33.3 - - + +
1514A THR* 3.2 17.1 + - + +
1515A CYS* 3.7 4.0 - - - +
1516A LEU 3.1 0.4 - - - -
1517A SER* 1.3 79.1 - - - +
1519A VAL* 1.3 65.3 + - - +
1521A LEU* 3.3 9.2 + - + +
1522A SER* 2.9 25.1 + - - -
1588A LEU 5.4 0.2 - - - +
1590A PRO* 3.4 40.6 - - + +
1592A PHE* 4.4 5.6 - - + -
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Residues in contact with VAL1519 (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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1469A CYS* 3.4 33.7 - - + -
1488A LEU* 4.1 16.1 - - + +
1491A PHE* 4.1 21.1 - - + -
1492A ALA* 4.4 8.3 - - + +
1495A PHE* 3.8 19.1 - - + -
1515A CYS 3.0 18.9 + - - +
1516A LEU* 3.1 29.4 - - + +
1518A VAL* 1.3 76.6 - - - +
1520A LEU* 1.3 57.5 + - - +
1522A SER* 3.3 3.8 + - - -
1523A LEU* 2.9 25.7 + - + +
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Residues in contact with LEU1520 (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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1492A ALA* 5.1 1.8 - - + -
1516A LEU* 3.0 22.7 + - + +
1517A SER 3.7 3.4 - - - +
1519A VAL* 1.3 76.2 - - - +
1521A LEU* 1.3 65.4 + - - +
1523A LEU* 3.2 15.0 + - + +
1524A ALA* 3.0 21.3 + - - +
1535A VAL* 4.5 11.2 - - + -
1538A LEU* 3.9 32.8 - - + -
1539A CYS* 4.6 11.0 - - - -
1542A LEU* 3.4 30.5 - - + -
1557A ALA 5.5 0.4 - - - +
1558A HIS* 3.9 19.7 - - + -
1561A ALA* 4.1 16.8 - - + -
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Residues in contact with LEU1521 (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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1470A LEU* 5.9 2.9 - - + -
1517A SER 3.0 22.8 + - - +
1518A VAL* 3.3 8.3 + - + +
1520A LEU* 1.3 75.6 - - - +
1522A SER* 1.3 58.4 + - - +
1524A ALA* 3.4 1.9 + - - +
1525A MET* 2.8 40.4 + - + +
1557A ALA* 3.7 12.8 - - + +
1560A MET* 3.9 14.4 - - + +
1561A ALA* 3.6 34.3 - - + +
1564A LEU* 4.3 9.3 - - + +
1588A LEU* 4.5 27.6 - - + +
1592A PHE* 3.9 29.2 - - + -
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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
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1469A CYS 3.7 9.6 - - - -
1470A LEU* 2.8 40.8 + - - +
1473A GLY* 3.9 5.0 - - - -
1488A LEU* 3.8 9.0 - - - -
1518A VAL 2.9 14.3 + - - -
1519A VAL* 3.3 9.3 - - - -
1520A LEU 3.2 0.2 - - - -
1521A LEU* 1.3 76.1 - - - +
1523A LEU* 1.3 57.5 + - - +
1525A MET* 3.2 11.7 + - - +
1526A VAL* 2.7 38.6 + - - +
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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
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1485A PHE* 3.7 24.0 - - + -
1488A LEU* 3.7 28.0 - - + +
1489A HIS* 4.3 7.6 - - - +
1492A ALA* 4.0 16.2 - - + -
1519A VAL 2.9 12.6 + - - +
1520A LEU* 3.2 17.5 - - + +
1522A SER* 1.3 76.9 - - - +
1524A ALA* 1.3 61.4 + - - +
1526A VAL* 3.2 17.8 - - + +
1527A MET* 3.3 4.5 - - - +
1535A VAL* 3.6 27.1 - - + -
1538A LEU* 3.8 28.7 - - + -
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Residues in contact with ALA1524 (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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1520A LEU 3.0 12.9 + - - +
1521A LEU 3.7 6.5 - - - +
1523A LEU* 1.3 76.2 - - - +
1525A MET* 1.3 51.5 + - - +
1527A MET 2.7 9.9 + - - +
1528A ALA* 2.7 35.5 + - - -
1535A VAL* 4.4 5.3 - - + +
1561A ALA* 3.4 35.4 - - + +
1564A LEU* 4.1 7.2 - - + -
1565A LEU* 4.1 18.4 - - + -
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Residues in contact with MET1525 (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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1470A LEU* 5.0 4.7 - - + +
1473A GLY 4.1 0.9 - - - +
1474A PHE* 4.0 43.3 - - + -
1477A ALA* 3.1 23.6 - - + +
1478A GLY 3.4 4.0 + - - -
1521A LEU* 2.8 38.8 + - + +
1522A SER* 3.6 16.8 - - - +
1524A ALA* 1.3 72.0 - - - +
1526A VAL* 1.4 58.5 + - - +
1528A ALA* 3.8 9.1 - - - +
1564A LEU* 3.7 18.1 - - + +
1574A LEU* 3.9 20.0 - - + -
1584A LEU* 4.7 5.6 - - + -
1588A LEU* 3.6 34.1 - - + -
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Residues in contact with VAL1526 (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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1472A LEU 4.6 0.2 - - - -
1473A GLY* 3.6 22.6 + - - +
1476A PHE* 2.9 26.0 - - + +
1477A ALA* 4.0 1.1 - - - +
1478A GLY 3.2 4.0 + - - -
1480A GLU 2.9 22.0 + - - -
1481A ASN 5.0 3.8 - - - +
1484A ALA* 4.2 17.9 - - + -
1485A PHE* 4.7 18.4 - - + +
1488A LEU* 3.7 14.8 - - + -
1522A SER 2.7 23.5 + - - +
1523A LEU* 3.2 19.5 - - + +
1524A ALA 3.2 0.4 + - - -
1525A MET* 1.4 71.8 - - - +
1527A MET* 1.3 72.8 + - + +
1528A ALA 3.5 0.2 - - - -
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Residues in contact with MET1527 (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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1480A GLU* 3.6 39.0 - - + +
1485A PHE* 3.4 38.6 - - + -
1523A LEU* 3.3 18.2 - - + +
1524A ALA 2.7 8.5 + - - +
1526A VAL* 1.3 84.1 - - + +
1528A ALA* 1.3 60.9 + - - +
1529A GLY 3.7 1.2 + - - -
1530A SER* 3.9 10.0 - - - +
1532A ASN* 3.4 35.4 - - - +
1535A VAL* 3.7 17.0 - - + -
1565A LEU* 3.5 13.9 - - + +
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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
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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