Contacts of the helix formed by residues 1630 - 1653 (chain A) in PDB entry 3LQJ
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 ALA1630 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1620A THR* 4.4 0.9 - - + -
1625A THR* 3.8 30.3 - - + +
1627A ARG 3.9 0.4 - - - -
1628A HIS* 3.8 10.3 - - + +
1629A PRO* 1.3 72.4 - - - +
1631A GLU* 1.3 67.3 + - - +
1632A TRP* 3.5 33.9 - - + +
1633A ARG* 2.9 28.9 + - + +
1634A LEU* 3.5 4.3 + - - +
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Residues in contact with GLU1631 (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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1617A VAL* 5.3 7.2 - - + +
1620A THR* 5.6 2.0 - - - +
1625A THR* 5.3 0.2 - - - +
1627A ARG 4.8 1.4 + - - -
1629A PRO 3.3 4.3 + - - -
1630A ALA* 1.3 71.8 - - - +
1632A TRP* 1.3 66.5 + - - +
1633A ARG 3.1 0.2 + - - -
1634A LEU* 3.2 20.2 + - - +
1635A ALA* 2.9 29.9 + - + +
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Residues in contact with TRP1632 (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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1600A GLU* 3.8 13.9 + - + -
1602A LEU* 3.8 32.5 - - + -
1610A LEU* 4.4 19.0 - - + +
1613A LEU* 5.0 1.9 - - - +
1617A VAL* 4.5 8.5 - - + -
1618A ALA 3.8 18.5 + - - +
1619A TYR* 3.6 26.4 - + - -
1620A THR* 3.1 40.3 + - + +
1630A ALA* 3.5 23.5 - - + +
1631A GLU* 1.3 79.7 - - - +
1633A ARG* 1.3 106.5 + - + +
1635A ALA* 3.7 7.1 - - - +
1636A LEU* 2.8 45.4 + - + +
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Residues in contact with ARG1633 (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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1600A GLU* 2.9 50.3 + - - +
1601A ASN* 4.6 6.7 + - - +
1602A LEU* 4.5 7.7 - - - +
1629A PRO* 5.1 8.7 - - + -
1630A ALA* 2.9 23.0 + - + +
1632A TRP* 1.3 111.9 - - + +
1634A LEU* 1.3 66.1 + - - +
1636A LEU* 3.2 6.1 + - - +
1637A GLU* 3.0 23.6 + - - +
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Residues in contact with LEU1634 (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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1629A PRO* 5.6 7.3 - - + +
1630A ALA 3.5 5.7 + - - +
1631A GLU* 3.2 17.5 + - - +
1633A ARG* 1.3 78.0 - - - +
1635A ALA* 1.3 63.6 + - - +
1637A GLU* 3.3 13.5 + - + +
1638A LYS* 3.0 61.7 + - + +
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Residues in contact with ALA1635 (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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1613A LEU* 4.3 5.7 - - + +
1617A VAL* 4.0 26.7 - - + -
1631A GLU* 2.9 33.8 + - - +
1632A TRP 3.7 3.8 - - - +
1634A LEU* 1.3 76.8 - - - +
1636A LEU* 1.3 57.4 + - - +
1638A LYS* 3.4 8.7 + - - +
1639A GLU* 2.9 31.6 + - - +
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Residues in contact with LEU1636 (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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1602A LEU* 3.9 26.7 - - + -
1606A MET* 3.0 50.2 - - + +
1609A ILE* 3.7 21.5 - - + -
1610A LEU* 4.1 19.3 - - + +
1613A LEU* 4.5 4.9 - - + +
1632A TRP* 2.8 33.6 + - + +
1633A ARG* 3.4 5.4 - - - +
1635A ALA* 1.3 73.9 - - - +
1637A GLU* 1.3 66.3 + - - +
1639A GLU* 3.2 5.5 + - - +
1640A LEU* 3.2 21.8 + - - +
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Residues in contact with GLU1637 (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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1606A MET* 5.4 2.2 - - - -
1633A ARG 3.0 15.7 + - - +
1634A LEU* 3.7 14.3 - - + +
1636A LEU* 1.3 77.2 - - - +
1638A LYS* 1.3 75.8 + - - +
1640A LEU* 3.5 5.6 + - - +
1641A GLN* 3.1 46.8 + - - +
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Residues in contact with LYS1638 (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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1634A LEU* 3.0 55.8 + - + +
1635A ALA* 3.7 7.9 - - - +
1637A GLU* 1.3 85.1 + - - +
1639A GLU* 1.3 58.2 + - - +
1641A GLN* 3.3 4.7 + - - +
1642A ILE* 2.8 51.8 + - + +
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Residues in contact with GLU1639 (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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1609A ILE* 3.9 11.4 - - + -
1612A ASN* 6.5 0.2 - - + -
1613A LEU* 3.5 31.9 - - + +
1614A PRO* 5.2 7.4 - - - +
1635A ALA 2.9 18.4 + - - +
1636A LEU 3.2 5.8 + - - +
1638A LYS* 1.3 76.8 - - - +
1640A LEU* 1.3 59.7 + - - +
1642A ILE* 4.5 10.7 - - - +
1643A SER* 2.6 52.6 + - - +
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Residues in contact with LEU1640 (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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1605A GLU* 5.3 0.7 - - - +
1606A MET* 4.7 12.1 - - + -
1609A ILE* 3.7 31.6 - - + +
1636A LEU 3.2 10.2 + - - +
1637A GLU* 3.9 7.6 - - - +
1638A LYS 3.3 0.2 - - - -
1639A GLU* 1.3 79.4 - - - +
1641A GLN* 1.3 82.9 + - - +
1643A SER* 3.7 2.9 - - - -
1644A LEU* 3.0 43.2 + - + +
1720A TYR 4.6 0.2 - - - +
1721A THR* 3.6 28.7 - - - +
1722A SER* 4.3 1.8 - - - +
1723A VAL* 3.7 25.8 - - + +
1766A PHE* 4.5 2.9 - - + -
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Residues in contact with GLN1641 (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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1637A GLU* 3.1 32.7 + - - +
1638A LYS* 3.3 7.9 + - - +
1640A LEU* 1.3 98.2 - - - +
1642A ILE* 1.3 59.9 + - + +
1644A LEU* 3.4 11.6 + - - +
1645A LYS* 3.0 29.1 + - - +
1715A MET* 4.5 19.6 - - - +
1718A GLY* 4.9 7.9 - - - -
1720A TYR* 3.1 28.7 + - - +
1721A THR* 4.9 0.6 - - - +
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Residues in contact with ILE1642 (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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1638A LYS* 2.8 42.8 + - + +
1639A GLU* 3.9 12.3 - - - +
1641A GLN* 1.3 73.5 - - + +
1643A SER* 1.3 59.2 + - - +
1645A LYS* 3.3 7.6 + - + +
1646A GLN* 2.8 34.3 + - + +
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Residues in contact with SER1643 (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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1639A GLU* 2.6 41.4 + - - +
1640A LEU 3.7 0.4 - - - -
1642A ILE* 1.3 73.4 - - - +
1644A LEU* 1.3 66.4 + - - +
1646A GLN* 3.2 10.0 + - - +
1647A VAL* 3.1 27.4 + - - +
1765A VAL* 3.4 19.3 + - - +
1766A PHE* 3.4 29.4 - - - -
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Residues in contact with LEU1644 (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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1640A LEU* 3.0 44.8 + - + +
1641A GLN* 3.7 17.0 - - - +
1643A SER* 1.3 75.1 - - - +
1645A LYS* 1.3 58.3 + - - +
1647A VAL* 3.3 4.5 + - - +
1648A LEU* 3.0 28.4 + - - +
1715A MET* 3.9 14.1 - - + -
1720A TYR* 3.8 31.4 - - + +
1722A SER 4.5 4.3 - - - +
1723A VAL* 4.4 7.2 - - - -
1726A PHE* 3.6 35.7 - - + -
1766A PHE* 3.9 21.8 - - + -
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Residues in contact with LYS1645 (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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1641A GLN 3.0 17.9 + - - +
1642A ILE* 3.6 8.3 - - + +
1644A LEU* 1.3 75.0 - - - +
1646A GLN* 1.3 58.1 + - - +
1648A LEU* 4.5 1.3 - - + +
1649A THR* 2.8 51.9 + - - +
1712A LYS* 6.3 2.0 - - - +
1715A MET* 3.7 17.9 - - - -
1716A ASP* 4.7 15.7 + - - +
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Residues in contact with GLN1646 (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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1642A ILE* 2.8 21.4 + - + +
1643A SER* 3.3 15.6 + - - +
1645A LYS* 1.3 77.5 - - - +
1647A VAL* 1.3 63.6 + - + +
1649A THR* 3.8 4.5 - - - -
1650A ALA* 3.3 19.9 + - - +
1761A GLN* 4.9 9.7 + - - +
1764A ARG* 5.2 7.9 - - - +
1765A VAL* 4.1 29.1 - - + +
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Residues in contact with VAL1647 (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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1643A SER 3.1 15.2 + - - +
1644A LEU* 3.6 6.5 - - - +
1646A GLN* 1.3 73.2 - - - +
1648A LEU* 1.3 66.9 + - - +
1650A ALA* 3.1 6.4 + - - +
1651A LEU* 3.0 21.9 + - + +
1726A PHE* 4.1 7.6 - - + -
1758A PHE* 4.0 20.2 - - + -
1761A GLN* 4.1 21.2 - - + +
1762A MET* 3.9 31.9 - - + -
1765A VAL* 3.5 29.4 - - + -
1766A PHE* 4.4 3.1 - - + -
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Residues in contact with LEU1648 (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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1644A LEU 3.0 17.4 + - - +
1645A LYS* 4.0 2.9 - - + +
1647A VAL* 1.3 75.9 - - - +
1649A THR* 1.3 58.9 + - - +
1651A LEU* 3.0 20.5 + - + +
1652A LEU* 2.8 43.5 + - + +
1708A LEU* 4.5 7.9 - - + +
1711A VAL* 4.1 20.0 - - + -
1712A LYS* 3.4 41.1 - - + +
1715A MET* 3.6 29.2 - - + -
1726A PHE* 4.2 4.6 - - + -
1730A ILE* 4.6 4.7 - - + -
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Residues in contact with THR1649 (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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1645A LYS* 2.8 43.4 + - - +
1646A GLN* 3.8 5.8 - - - -
1648A LEU* 1.3 72.3 - - - +
1650A ALA* 1.3 59.6 + - - +
1652A LEU* 3.3 10.3 + - - +
1653A ASN* 2.9 49.0 + - - +
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Residues in contact with ALA1650 (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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1646A GLN 3.3 10.5 + - - +
1647A VAL 3.1 9.9 + - - +
1649A THR* 1.3 80.6 - - - +
1651A LEU* 1.3 63.0 + - - +
1653A ASN* 3.5 4.5 + - - +
1654A SER* 3.4 23.7 + - - -
1757A PHE* 3.6 20.0 - - + -
1761A GLN* 4.1 19.7 - - + +
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Residues in contact with LEU1651 (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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1647A VAL* 3.0 17.3 + - + +
1648A LEU* 3.0 17.6 + - + +
1650A ALA* 1.3 78.4 - - - +
1652A LEU* 1.3 54.7 + - - +
1654A SER 3.5 1.6 + - - -
1657A THR* 2.3 48.4 + - + +
1708A LEU* 4.4 15.9 - - + -
1726A PHE* 5.3 0.7 - - + -
1730A ILE* 4.1 24.0 - - + -
1734A ILE* 5.7 0.2 - - + -
1754A VAL* 4.3 16.6 - - + +
1757A PHE* 4.0 24.4 - - + -
1758A PHE* 3.7 37.5 - - + -
1761A GLN* 6.1 2.0 - - + -
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Residues in contact with LEU1652 (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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1648A LEU* 2.8 33.2 + - + +
1649A THR* 3.7 8.1 - - - +
1651A LEU* 1.3 80.0 - - - +
1653A ASN* 1.3 63.6 + - - +
1654A SER 3.2 6.3 + - - +
1657A THR* 3.9 5.4 + - - -
1661A LEU* 3.7 34.8 - - + +
1708A LEU* 3.8 28.0 - - + +
1709A GLU* 4.7 5.4 - - + +
1712A LYS* 3.5 35.4 - - + -
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Residues in contact with ASN1653 (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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1649A THR* 2.9 39.2 + - - +
1650A ALA* 3.5 5.4 + - - +
1651A LEU 3.4 0.2 - - - -
1652A LEU* 1.3 80.1 - - - +
1654A SER* 1.3 57.6 + - - +
1655A ARG 4.1 0.5 + - - -
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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) + - + + + + + -
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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