Contacts of the helix formed by residues 1644 - 1667 (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 ILE1644 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1588A GLU* 3.1 19.5 - - + +
1589A VAL 3.3 26.0 - - - +
1590A LEU* 4.0 17.7 - - + -
1619A VAL* 4.3 8.3 - - + -
1622A GLN* 3.0 32.6 + - - +
1643A TYR* 1.3 78.1 - - - +
1645A PHE* 1.3 66.7 + - - +
1646A GLN* 4.0 19.1 - - + -
1647A ALA* 3.5 14.0 + - + +
1648A ILE* 3.4 11.8 + - - +
1697A LYS* 4.2 2.0 - - - +
1762A TYR* 3.7 31.2 - - + -
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Residues in contact with PHE1645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1588A GLU* 2.4 18.5 + - - +
1644A ILE* 1.3 70.7 - - - +
1646A GLN* 1.3 67.0 + - - +
1648A ILE* 3.0 6.8 - - - +
1649A LEU* 3.0 51.4 + - + +
1697A LYS* 3.7 20.2 - - + +
1700A ALA* 3.4 29.8 - - + -
1701A LEU* 3.5 36.3 - - + -
1763A ILE* 5.9 2.2 - - + -
1764A GLY 3.3 17.7 - - - +
1765A ILE* 3.4 23.6 - - + -
1766A PRO* 4.3 10.3 - - + -
1768A ARG* 3.8 18.8 - - - -
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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
----------------------------------------------------------
1619A VAL* 3.5 26.9 - - + +
1644A ILE* 3.5 15.8 - - + +
1645A PHE* 1.3 86.5 - - + +
1647A ALA* 1.3 60.5 - - - +
1649A LEU* 3.5 8.0 + - + +
1650A LEU* 3.2 23.3 + - + +
1758A TYR* 2.8 33.8 + - + +
1760A PHE 4.0 1.2 + - - -
1761A GLU 3.2 17.4 + - - -
1762A TYR* 3.4 5.2 - - + -
1763A ILE* 2.6 46.5 + - + +
1764A GLY 4.1 7.2 + - - +
1814A GLY* 4.3 0.4 - - - -
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Residues in contact with ALA1647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1619A VAL* 4.3 4.7 - - + +
1622A GLN* 3.4 24.7 - - + +
1623A PHE* 3.4 37.1 - - - +
1626A CYS* 4.6 0.7 - - - -
1643A TYR* 4.6 4.3 - - + -
1644A ILE* 3.5 14.2 + - + +
1645A PHE 3.1 0.8 + - - -
1646A GLN* 1.3 80.8 - - - +
1648A ILE* 1.3 52.3 - - - +
1650A LEU* 5.1 0.2 - - - -
1651A SER* 2.2 38.5 + - - -
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Residues in contact with ILE1648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1626A CYS* 3.6 12.5 - - - -
1630A LEU* 4.8 0.7 - - + +
1636A ILE* 3.6 26.2 - - + -
1639A VAL* 3.8 11.7 - - + -
1640A VAL* 3.4 46.0 - - + +
1643A TYR* 4.8 4.5 - - + +
1644A ILE 3.4 12.3 + - - +
1645A PHE* 3.0 23.6 - - - +
1647A ALA* 1.3 78.6 - - - +
1649A LEU* 1.3 57.4 + - - +
1651A SER* 3.4 7.4 - - - -
1652A ALA* 3.1 25.5 + - - +
1697A LYS* 4.7 3.8 - - + -
1701A LEU* 3.7 21.8 - - + +
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Residues in contact with LEU1649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1645A PHE* 3.0 51.9 + - + +
1646A GLN* 3.6 9.2 - - + +
1648A ILE* 1.3 74.6 - - - +
1650A LEU* 1.3 62.7 + - + +
1651A SER 3.0 1.6 - - - -
1652A ALA* 3.0 7.1 + - + +
1653A GLN* 2.9 38.2 + - + +
1701A LEU* 4.1 8.3 - - + -
1704A GLU* 3.4 41.1 - - + +
1758A TYR* 6.1 0.9 - - - +
1763A ILE* 6.0 4.9 - - + -
1768A ARG* 3.9 16.6 - - - +
1811A GLN 6.0 2.2 - - - +
1812A ASN* 6.5 0.9 - - - -
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Residues in contact with LEU1650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1619A VAL* 6.5 0.2 - - + -
1623A PHE* 3.5 33.4 - - + -
1646A GLN 3.2 13.0 + - - +
1647A ALA* 5.1 0.2 - - - -
1649A LEU* 1.3 79.0 - - + +
1651A SER* 1.3 63.1 + - - +
1653A GLN* 3.4 21.3 - - - +
1654A VAL* 2.9 39.1 + - + +
1734A PHE* 3.7 18.6 - - + -
1747A VAL* 3.9 13.7 - - + -
1758A TYR* 3.6 51.1 - - + +
1760A PHE* 4.2 4.9 - - + -
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Residues in contact with SER1651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623A PHE* 3.7 16.0 + - - -
1626A CYS* 3.3 21.1 - - - -
1627A LEU* 3.3 25.0 - - - +
1630A LEU* 3.8 11.0 - - - -
1647A ALA 2.2 31.2 + - - -
1648A ILE 3.4 7.9 - - - -
1650A LEU* 1.3 77.7 - - - +
1652A ALA* 1.3 63.9 + - - +
1655A MET* 2.9 22.6 + - - +
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Residues in contact with ALA1652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1630A LEU* 4.4 6.0 - - - +
1636A ILE* 5.1 2.9 - - + -
1648A ILE 3.1 10.4 + - - +
1649A LEU* 3.0 11.5 + - + +
1651A SER* 1.3 78.7 - - - +
1653A GLN* 1.3 57.8 + - - +
1655A MET* 4.0 5.9 - - - +
1656A TRP* 2.8 34.7 + - - +
1701A LEU* 5.6 2.0 - - + -
1704A GLU* 6.3 0.7 - - + -
1705A TYR* 3.8 35.7 - - + +
1708A PHE* 3.7 12.3 - - + -
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Residues in contact with GLN1653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1649A LEU* 2.9 28.8 + - + +
1650A LEU* 3.4 21.2 - - - +
1651A SER 3.1 0.2 - - - -
1652A ALA* 1.3 76.7 - - - +
1654A VAL* 1.3 62.4 + - - +
1656A TRP* 3.6 3.3 - - - +
1657A THR* 3.0 27.7 + - - -
1704A GLU* 3.0 40.6 + - - +
1708A PHE* 3.9 10.5 - - + -
1734A PHE* 3.1 54.2 - - + -
1758A TYR* 5.5 0.2 - - - -
1768A ARG* 4.6 1.0 - - - +
1771A TYR* 4.2 1.6 + - - -
1812A ASN* 4.5 10.2 + - - +
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Residues in contact with VAL1654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623A PHE* 4.2 10.1 - - + -
1627A LEU* 4.4 14.6 - - + -
1631A LYS* 6.1 2.5 - - - +
1650A LEU* 2.9 35.2 + - + +
1651A SER 4.0 1.8 - - - +
1653A GLN* 1.3 75.3 - - - +
1655A MET* 1.3 65.4 + - - +
1657A THR* 3.4 4.7 + - - +
1658A GLU* 3.1 21.3 + - + +
1734A PHE* 3.2 33.0 - - + +
1735A TYR* 4.5 2.5 - - - +
1736A GLN* 4.0 27.1 - - + +
1747A VAL* 4.7 6.7 - - + -
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Residues in contact with MET1655 (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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1627A LEU* 3.9 10.9 - - + +
1630A LEU* 3.9 42.2 - - + +
1631A LYS* 4.1 22.2 - - + +
1651A SER 2.9 16.0 + - - +
1652A ALA* 4.0 4.9 - - - +
1654A VAL* 1.3 75.2 - - - +
1656A TRP* 1.3 72.5 + - + +
1658A GLU* 3.1 12.4 + - - +
1659A LEU* 2.9 47.9 + - + +
1672A TYR* 4.7 3.8 - - - +
1679A LYS* 4.5 17.7 - - - +
1705A TYR* 4.6 8.1 - - - +
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Residues in contact with TRP1656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1652A ALA 2.8 20.9 + - - +
1653A GLN* 3.6 6.1 - - - +
1655A MET* 1.3 78.9 - - + +
1657A THR* 1.3 73.4 + - - +
1659A LEU* 2.7 23.6 + - - +
1660A VAL* 2.8 25.4 + - + +
1672A TYR* 3.6 31.6 - + - +
1707A HIS* 4.1 21.3 - + - -
1708A PHE* 3.5 57.1 - + + +
1711A VAL* 4.0 21.8 - - + -
1712A ILE* 3.9 12.9 - - + +
1728A TRP* 3.7 28.3 - + - -
1731A VAL* 4.4 4.3 - - + -
1732A GLN 4.0 18.4 - - - -
1734A PHE* 5.2 4.5 - + - -
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Residues in contact with THR1657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1653A GLN 3.0 10.1 + - - -
1654A VAL 3.4 0.9 - - - +
1656A TRP* 1.3 87.9 - - - +
1658A GLU* 1.3 65.1 + - - +
1660A VAL* 3.5 9.6 - - - +
1661A GLU* 3.0 29.9 + - + +
1728A TRP* 4.3 2.2 - - + -
1733A LYS* 3.4 12.8 - - + +
1734A PHE 2.9 45.6 + - - +
1735A TYR* 3.8 34.8 - - + +
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Residues in contact with GLU1658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1631A LYS* 3.1 38.4 + - - +
1654A VAL* 3.1 9.4 + - + +
1655A MET* 3.1 11.6 + - - +
1657A THR* 1.3 82.8 - - + +
1659A LEU* 1.3 64.2 + - + +
1661A GLU* 3.3 19.0 - - + +
1662A LYS* 3.3 31.1 + - - +
1735A TYR* 6.2 0.4 - - - -
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Residues in contact with LEU1659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655A MET* 2.9 36.5 + - + +
1656A TRP 2.7 13.8 + - - +
1658A GLU* 1.3 72.0 - - + +
1660A VAL* 1.3 57.2 + - - +
1661A GLU 3.0 4.9 + - - -
1662A LYS* 3.1 28.1 + - + +
1663A CYS* 2.8 30.8 + - - +
1672A TYR* 3.2 41.3 - - + +
1675A GLU* 5.8 1.8 - - - +
1679A LYS* 6.0 0.4 - - - +
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Residues in contact with VAL1660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656A TRP* 2.8 42.2 + - + +
1657A THR* 3.5 3.8 - - - +
1659A LEU* 1.3 73.8 - - - +
1661A GLU* 1.3 55.6 + - - +
1663A CYS* 3.6 9.2 - - + -
1664A LEU* 3.0 27.5 + - + +
1669A PHE* 4.8 6.1 - - + -
1672A TYR* 4.0 7.5 - - + -
1712A ILE* 4.5 12.1 - - + -
1715A LEU* 3.5 32.1 - - + -
1728A TRP* 3.0 37.2 - - + -
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Residues in contact with GLU1661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1657A THR* 3.0 27.0 + - + +
1658A GLU* 3.3 10.5 - - - +
1659A LEU 3.0 0.6 - - - -
1660A VAL* 1.3 76.6 - - - +
1662A LYS* 1.3 63.8 + - - +
1664A LEU* 3.3 23.6 + - - +
1665A GLN* 3.6 5.7 + - - +
1728A TRP* 4.1 20.8 + - + +
1735A TYR* 2.6 38.3 + - + +
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Residues in contact with LYS1662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658A GLU* 3.3 29.7 + - - +
1659A LEU* 3.1 28.5 + - + +
1661A GLU* 1.3 74.5 - - - +
1663A CYS* 1.3 60.1 + - + +
1664A LEU 3.0 5.4 - - - -
1665A GLN* 3.1 7.9 + - - +
1666A THR* 3.0 36.0 + - + +
1668A GLN* 4.9 10.1 - - - +
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Residues in contact with CYS1663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1659A LEU 2.8 18.5 + - - +
1660A VAL* 3.6 13.5 - - + +
1662A LYS* 1.3 81.4 - - + +
1664A LEU* 1.3 52.7 + - - +
1666A THR* 3.5 7.0 - - - -
1667A ASN* 2.8 31.5 + - - -
1668A GLN* 3.2 31.8 + - + +
1669A PHE* 3.4 33.2 - - - -
1672A TYR* 4.0 20.4 - - + -
1712A ILE* 5.4 0.7 - - - -
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Residues in contact with LEU1664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1660A VAL 3.0 20.9 + - - +
1661A GLU* 3.3 15.3 - - - +
1662A LYS 3.0 0.4 - - - -
1663A CYS* 1.3 76.3 - - - +
1665A GLN* 1.3 64.2 + - - +
1667A ASN* 3.3 16.1 + - - +
1669A PHE* 3.6 25.1 - - + -
1715A LEU* 4.0 14.6 - - + -
1721A LYS* 3.4 14.7 - - + +
1724A ALA* 4.0 22.0 - - + +
1725A ARG* 5.2 9.6 - - + +
1728A TRP* 3.4 43.3 - - + +
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Residues in contact with GLN1665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1661A GLU 3.6 7.0 + - - +
1662A LYS* 3.1 10.6 + - - +
1664A LEU* 1.3 78.6 - - - +
1666A THR* 1.3 64.2 + - + +
1667A ASN* 3.3 5.2 - - - +
1721A LYS* 3.2 28.7 + - - +
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Residues in contact with THR1666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1662A LYS* 3.0 19.2 + - + +
1663A CYS* 3.5 3.1 - - - -
1665A GLN* 1.3 79.1 - - + +
1667A ASN* 1.3 77.0 + - - +
1668A GLN* 3.4 32.5 + - + +
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Residues in contact with ASN1667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1663A CYS 2.8 16.2 + - - -
1664A LEU 3.3 10.0 + - - +
1665A GLN 3.3 11.8 - - - +
1666A THR* 1.3 84.5 - - - +
1668A GLN* 1.3 55.1 + - - +
1669A PHE* 3.0 35.0 + - + -
1670A SER 5.0 0.2 + - - -
1721A LYS* 3.8 23.0 + - - +
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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