Contacts of the helix formed by residues 1544 - 1568 (chain A) in PDB entry 2GRC
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 SER1544 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1540A ASN* 3.6 11.6 - - - +
1541A LEU* 2.7 30.5 + - - -
1542A GLU 3.2 1.4 + - - -
1543A GLY* 1.3 79.8 - - - +
1545A LEU* 1.3 65.3 + - - +
1546A ILE* 3.9 3.0 + - - -
1547A TYR* 3.2 17.8 + - - +
1548A GLU* 2.9 23.8 + - - +
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Residues in contact with LEU1545 (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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1479A ARG* 3.8 35.7 - - - +
1484A VAL* 6.0 4.0 - - + -
1543A GLY 3.8 0.8 + - - -
1544A SER* 1.3 73.8 - - - +
1546A ILE* 1.3 71.3 + - + +
1548A GLU* 3.8 2.9 - - - +
1549A ASP* 2.9 56.2 + - - +
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Residues in contact with ILE1546 (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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1484A VAL* 4.2 25.6 - - + -
1485A PHE* 3.6 27.4 - - + -
1536A ALA* 4.6 0.6 - - + +
1540A ASN* 3.6 36.6 - - + +
1544A SER* 3.3 3.1 + - - +
1545A LEU* 1.3 88.0 - - + +
1547A TYR* 1.3 63.8 + - - +
1549A ASP* 3.4 5.1 + - - +
1550A SER* 3.1 21.8 + - - -
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Residues in contact with TYR1547 (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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1536A ALA 4.6 3.6 - - - -
1537A GLN* 3.3 41.1 + - + +
1540A ASN* 3.3 25.8 - - + +
1541A LEU 3.2 6.5 - - - +
1542A GLU* 3.4 42.0 + - + +
1544A SER* 3.2 21.7 + - - +
1546A ILE* 1.3 76.9 - - - +
1548A GLU* 1.3 86.5 + - - +
1550A SER* 2.7 24.4 + - - -
1551A ILE* 3.1 25.7 + - + +
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Residues in contact with GLU1548 (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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1542A GLU* 3.8 6.4 - - - +
1543A GLY* 3.1 34.3 + - - +
1544A SER 2.9 20.7 + - - +
1545A LEU* 4.1 2.7 - - - +
1547A TYR* 1.3 91.7 - - - +
1549A ASP* 1.3 65.3 + - - +
1551A ILE* 3.3 19.4 + - - +
1552A VAL* 3.2 25.7 + - + +
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Residues in contact with ASP1549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1479A ARG* 2.9 45.7 + - - -
1481A LEU* 3.8 38.6 - - + +
1484A VAL* 5.9 1.5 - - + +
1485A PHE* 4.9 2.7 - - + -
1545A LEU* 2.9 29.6 + - - +
1546A ILE* 3.9 5.8 - - - +
1548A GLU* 1.3 77.2 - - - +
1550A SER* 1.3 58.6 + - - +
1552A VAL* 3.2 7.1 + - - +
1553A LEU* 2.9 33.2 + - - +
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Residues in contact with SER1550 (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* 3.9 11.6 - - - -
1533A CYS* 3.4 20.0 + - - -
1536A ALA* 3.6 25.4 - - - +
1537A GLN* 3.0 28.4 + - - +
1546A ILE 3.1 7.7 + - - -
1547A TYR 2.7 19.3 + - - -
1549A ASP* 1.3 78.0 - - - +
1551A ILE* 1.3 60.2 + - - +
1553A LEU* 3.3 7.0 + - - -
1554A GLN* 3.2 19.6 + - - +
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Residues in contact with ILE1551 (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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1537A GLN* 3.6 26.7 - - - +
1547A TYR* 3.1 34.9 + - + +
1548A GLU* 3.3 19.5 + - - +
1550A SER* 1.3 77.9 + - - +
1552A VAL* 1.3 66.0 + - + +
1554A GLN* 3.3 30.6 + - - +
1555A SER* 3.5 5.5 + - - -
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Residues in contact with VAL1552 (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 TYR* 4.2 10.3 - - + +
1481A LEU* 3.6 23.6 - - + -
1548A GLU* 3.2 15.4 + - + +
1549A ASP* 3.2 8.2 + - - +
1551A ILE* 1.3 80.5 - - + +
1553A LEU* 1.3 58.5 + - - +
1555A SER* 2.5 29.3 + - - +
1556A VAL* 2.9 22.3 + - + +
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Residues in contact with LEU1553 (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 VAL* 3.9 37.1 - - + +
1472A TYR* 5.0 2.0 - - + -
1481A LEU* 3.9 23.6 - - + +
1482A SER* 3.9 18.2 - - - +
1485A PHE* 3.6 37.2 - - + -
1507A PHE* 4.6 9.6 - - + -
1529A VAL* 5.1 2.2 - - + +
1532A LEU* 5.2 0.2 - - + -
1533A CYS* 4.2 11.9 - - - -
1549A ASP 2.9 16.8 + - - +
1550A SER* 3.3 7.6 + - - +
1552A VAL* 1.3 76.5 - - - +
1554A GLN* 1.3 56.3 + - - +
1556A VAL* 3.6 9.8 - - + +
1557A PHE* 2.9 29.8 + - - +
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Residues in contact with GLN1554 (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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1529A VAL* 5.7 0.4 - - - -
1530A MET* 3.7 34.3 + - + +
1533A CYS* 3.5 17.3 - - + +
1534A GLN* 4.7 1.6 - - - +
1537A GLN* 2.7 38.8 + - - +
1550A SER 3.2 11.2 + - - +
1551A ILE* 3.3 20.3 - - - +
1552A VAL 3.2 0.4 - - - -
1553A LEU* 1.3 77.0 - - - +
1555A SER* 1.3 61.6 + - - +
1557A PHE* 3.4 4.5 + - - +
1558A THR* 3.2 23.9 + - - -
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Residues in contact with SER1555 (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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1551A ILE 3.5 3.9 + - - -
1552A VAL* 2.5 30.9 + - - +
1554A GLN* 1.3 76.9 - - - +
1556A VAL* 1.3 61.3 + - - +
1558A THR* 3.2 8.2 + - - -
1559A SER* 2.9 34.5 + - - -
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Residues in contact with VAL1556 (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 VAL* 4.2 14.4 - - + +
1472A TYR* 3.8 61.0 - - + -
1552A VAL* 2.9 26.2 + - + +
1553A LEU* 3.3 12.3 + - + +
1555A SER* 1.3 73.3 - - - +
1557A PHE* 1.3 60.6 + - - +
1559A SER* 3.3 5.4 + - - +
1560A VAL* 2.8 50.9 + - + +
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Residues in contact with PHE1557 (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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1465A ILE* 3.6 27.5 - - + +
1466A VAL* 5.3 2.0 - - + -
1469A VAL* 3.6 18.1 - - + +
1522A LEU* 4.7 2.0 - - + -
1525A LEU* 4.0 15.3 - - + -
1526A GLU* 3.2 52.3 - - + -
1529A VAL* 3.7 37.2 - - + -
1530A MET* 4.0 17.7 - - + -
1553A LEU 2.9 13.8 + - - +
1554A GLN 3.6 8.3 - - - +
1555A SER 3.3 0.2 - - - -
1556A VAL* 1.3 76.3 - - - +
1558A THR* 1.3 60.6 + - - +
1560A VAL* 3.8 0.7 - - - +
1561A ARG* 2.8 42.7 + - + +
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Residues in contact with THR1558 (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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1526A GLU* 4.6 7.4 + - - -
1530A MET* 4.2 10.9 - - - +
1554A GLN 3.2 12.3 + - - -
1555A SER* 3.6 10.3 - - - +
1556A VAL 3.2 0.2 - - - -
1557A PHE* 1.3 81.8 - - - +
1559A SER* 1.3 65.8 + - - +
1561A ARG* 3.4 3.6 + - - +
1562A GLN* 3.1 46.6 + - - +
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Residues in contact with SER1559 (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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1555A SER* 2.9 18.6 + - - -
1556A VAL* 3.8 6.3 - - - -
1558A THR* 1.3 77.9 - - - +
1560A VAL* 1.3 66.1 + - - +
1562A GLN* 3.3 10.2 + - - +
1563A LYS* 3.0 27.6 + - - +
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Residues in contact with VAL1560 (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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1465A ILE* 3.8 15.7 - - + +
1468A ALA* 3.5 35.4 - - + +
1469A VAL* 4.3 5.4 - - + -
1472A TYR* 6.3 0.4 - - + -
1556A VAL* 2.8 36.1 + - + +
1557A PHE 3.9 2.2 - - - +
1559A SER* 1.3 76.3 - - - +
1561A ARG* 1.3 64.8 + - - +
1563A LYS* 3.3 6.9 + - - +
1564A ILE* 3.1 40.4 + - + +
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Residues in contact with ARG1561 (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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1465A ILE* 4.1 24.9 - - + +
1522A LEU* 3.7 36.7 - - - +
1523A ASN* 4.2 10.3 - - - +
1526A GLU* 2.9 30.6 + - - +
1557A PHE* 2.8 30.1 + - + +
1558A THR* 3.7 5.4 - - - +
1560A VAL* 1.3 77.6 - - - +
1562A GLN* 1.3 59.9 + - + +
1564A ILE* 3.4 1.4 + - - +
1565A GLU* 2.9 63.3 + - - +
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Residues in contact with GLN1562 (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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1558A THR* 3.1 35.3 + - + +
1559A SER* 3.8 7.4 - - - +
1561A ARG* 1.3 80.0 - - + +
1563A LYS* 1.3 66.9 + - - +
1565A GLU* 4.5 4.0 - - - +
1566A LYS* 2.9 41.5 + - + +
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Residues in contact with LYS1563 (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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1559A SER* 3.0 19.0 + - - +
1560A VAL* 3.8 7.0 - - - +
1562A GLN* 1.3 75.8 - - - +
1564A ILE* 1.3 59.9 + - + +
1566A LYS* 3.9 6.8 - - + +
1567A GLU* 3.0 44.1 + - - +
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Residues in contact with ILE1564 (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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1461A LYS* 4.0 30.3 - - + +
1464A LYS* 3.9 20.2 - - + +
1465A ILE* 3.5 42.4 - - + +
1468A ALA* 5.2 1.3 - - + -
1560A VAL* 3.1 30.4 + - + +
1561A ARG 3.8 3.1 - - - +
1563A LYS* 1.3 74.9 - - + +
1565A GLU* 1.3 67.5 + - + +
1567A GLU* 3.3 18.9 + - - +
1568A ASP* 3.1 23.8 + - - +
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Residues in contact with GLU1565 (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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1461A LYS* 4.9 11.9 + - + +
1522A LEU* 3.3 29.7 - - + +
1561A ARG* 2.9 52.0 + - - +
1562A GLN* 4.2 3.6 - - - +
1564A ILE* 1.3 78.8 - - + +
1566A LYS* 1.3 65.2 + - + +
1568A ASP* 3.2 18.1 + - - +
1569A ASP 3.2 13.7 + - - +
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Residues in contact with LYS1566 (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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1562A GLN* 2.9 33.3 + - + +
1563A LYS* 3.9 5.8 - - + +
1565A GLU* 1.3 73.1 - - + +
1567A GLU* 1.3 62.0 + - - +
1569A ASP* 2.9 28.4 + - - +
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Residues in contact with GLU1567 (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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1563A LYS* 3.0 33.3 + - - +
1564A ILE* 3.4 21.7 - - - +
1566A LYS* 1.3 76.9 - - - +
1568A ASP* 1.3 58.8 + - - +
1569A ASP* 2.7 19.8 - - - +
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Residues in contact with ASP1568 (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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1461A LYS* 3.2 41.6 - - + +
1564A ILE* 3.1 15.9 + - - +
1565A GLU* 3.2 11.3 + - - +
1567A GLU* 1.3 77.0 - - - +
1569A ASP* 1.3 67.6 + - - +
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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
------------------------------------------------------------
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