Contacts of the helix formed by residues 1657 - 1683 (chain A) in PDB entry 2KBB
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 GLY1657 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656A PRO* 1.3 75.0 - - - +
1658A GLN* 1.3 55.6 + - - +
1659A LEU* 3.1 7.0 - - - +
1660A GLU* 3.1 19.8 + - - +
1661A CYS* 2.8 42.9 + - - -
1724A ALA 4.1 3.8 + - - -
1727A LEU* 3.9 16.4 - - - -
1728A GLY* 4.3 5.1 - - - -
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Residues in contact with GLN1658 (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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1650A ILE 4.0 6.1 - - - +
1651A ASP* 3.2 35.0 - - + +
1652A PRO* 4.5 0.7 - - + -
1653A PHE* 3.5 20.9 - - + +
1655A ALA* 2.8 28.6 - - - +
1656A PRO 3.4 2.1 - - - +
1657A GLY* 1.3 74.2 - - - +
1659A LEU* 1.3 62.4 + - - +
1662A GLU* 3.4 18.5 + - - +
1780A LYS* 2.9 43.5 + - + +
1781A GLU 3.7 6.3 + - - -
1783A GLY* 2.8 38.4 + - - +
1785A ASN* 5.2 0.8 - - - +
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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
----------------------------------------------------------
1649A GLY* 3.2 39.9 - - - +
1650A ILE 4.5 2.6 + - - -
1651A ASP* 4.9 5.6 - - + +
1655A ALA 4.9 0.6 + - - -
1656A PRO* 6.1 0.4 - - + -
1657A GLY 3.1 3.7 - - - +
1658A GLN* 1.3 79.7 - - - +
1660A GLU* 1.3 81.3 - - + +
1662A GLU* 3.1 3.6 + - - +
1663A THR* 2.9 39.7 + - + +
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Residues in contact with GLU1660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1657A GLY* 3.1 15.6 + - - +
1659A LEU* 1.3 100.4 - - + +
1661A CYS* 1.3 57.3 + - - +
1663A THR* 2.8 18.9 + - - -
1664A ALA* 3.0 20.8 + - - +
1728A GLY* 3.6 34.3 - - - +
1731A VAL* 3.4 8.7 - - + +
1732A SER* 4.1 12.6 + - - -
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Residues in contact with CYS1661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1657A GLY 2.8 28.7 + - - +
1660A GLU* 1.3 73.6 - - - +
1662A GLU* 1.3 57.3 + - - +
1664A ALA* 3.3 1.9 + - - +
1665A ILE* 2.8 35.3 + - - +
1727A LEU* 3.8 11.2 - - - -
1731A VAL* 3.7 28.9 - - - -
1776A LEU* 3.6 10.7 - - - +
1779A ALA* 3.8 28.5 - - - -
1780A LYS* 3.6 22.2 - - + -
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Residues in contact with GLU1662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1649A GLY* 2.6 30.8 + - - +
1650A ILE* 2.8 31.4 + - - +
1658A GLN 3.4 9.3 + - - +
1659A LEU 3.1 4.0 + - - +
1661A CYS* 1.3 76.9 - - - +
1663A THR* 1.3 64.4 + - - +
1665A ILE* 3.3 12.1 + - + +
1666A ALA* 3.2 21.0 + - - +
1780A LYS* 2.7 44.7 + - + +
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Residues in contact with THR1663 (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 GLY* 3.8 11.9 - - - +
1659A LEU* 2.9 35.4 + - + +
1660A GLU* 2.8 26.7 + - - -
1662A GLU* 1.3 78.3 - - - +
1664A ALA* 1.3 59.5 + - - +
1666A ALA* 3.5 15.2 + - - +
1667A ALA* 3.5 10.4 + - - +
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Residues in contact with ALA1664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1660A GLU 3.0 18.6 + - - +
1661A CYS 3.7 0.7 - - - +
1663A THR* 1.3 73.6 + - - +
1665A ILE* 1.3 56.8 + - - +
1666A ALA 3.2 0.4 - - - -
1667A ALA* 3.0 8.7 + - - +
1668A LEU* 2.7 36.4 + - - +
1731A VAL* 3.4 22.2 - - + -
1735A ALA* 3.9 16.3 - - + +
1776A LEU* 3.7 13.9 - - + -
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Residues in contact with ILE1665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1661A CYS 2.8 25.7 + - - +
1662A GLU* 3.4 17.7 - - + +
1664A ALA* 1.3 75.8 - - - +
1666A ALA* 1.3 54.6 + - - +
1669A ASN* 2.8 42.4 + - - +
1773A LEU* 3.8 15.0 - - + +
1776A LEU* 3.6 21.1 - - + +
1777A TYR* 3.7 62.4 - - + +
1780A LYS* 4.3 11.0 - - + +
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Residues in contact with ALA1666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1662A GLU 3.2 11.6 + - - +
1663A THR* 3.5 12.6 - - - +
1664A ALA 3.2 0.6 - - - -
1665A ILE* 1.3 79.6 - - - +
1667A ALA* 1.3 60.3 + - - +
1669A ASN* 3.8 5.4 - - - +
1670A SER* 3.3 20.3 + - - -
1673A ARG* 5.8 0.5 + - - -
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Residues in contact with ALA1667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1663A THR 3.5 7.9 + - - +
1664A ALA* 3.0 11.5 + - - +
1666A ALA* 1.3 78.4 - - - +
1668A LEU* 1.3 64.8 + - - +
1670A SER* 3.1 17.9 + - - -
1671A CYS* 3.2 12.1 + - - +
1735A ALA* 5.4 7.9 - - + +
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Residues in contact with LEU1668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1664A ALA 2.7 18.7 + - - +
1667A ALA* 1.3 71.2 - - - +
1669A ASN* 1.3 65.0 + - - +
1671A CYS* 2.9 45.5 - - - -
1672A LEU* 3.0 11.8 + - + +
1734A MET* 6.2 0.2 - - + -
1735A ALA* 5.6 6.7 - - + +
1738A PHE* 4.0 27.8 - - + -
1769A ALA* 3.9 10.8 - - + +
1772A ALA* 3.4 13.2 - - + -
1773A LEU* 3.2 46.0 - - + +
1776A LEU* 3.4 19.3 - - + -
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Residues in contact with ASN1669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1665A ILE* 2.8 23.9 + - - +
1666A ALA* 3.8 7.4 - - - +
1668A LEU* 1.3 76.4 - - - +
1670A SER* 1.3 61.1 + - - +
1672A LEU* 3.2 11.1 + - - +
1673A ARG* 3.2 53.0 + - - +
1773A LEU* 4.0 16.4 - - + +
1777A TYR* 4.3 16.0 + - - -
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Residues in contact with SER1670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1666A ALA 3.3 10.4 + - - -
1667A ALA* 3.1 15.1 + - - -
1669A ASN* 1.3 80.4 - - - +
1671A CYS* 1.3 54.6 + - - +
1673A ARG* 3.3 17.7 + - - +
1674A ASP* 3.1 25.5 + - - +
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Residues in contact with CYS1671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1667A ALA 3.2 8.0 + - - +
1668A LEU* 2.9 50.0 + - - -
1670A SER* 1.3 73.7 - - - +
1672A LEU* 1.3 65.6 + - - +
1674A ASP* 3.5 7.4 - - - +
1675A LEU* 2.8 34.5 + - - +
1738A PHE* 4.7 8.1 - - - +
1739A GLU* 5.4 3.8 - - - -
1742A THR* 3.1 28.7 - - + +
1769A ALA* 4.2 7.9 - - - -
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Residues in contact with LEU1672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1668A LEU* 3.0 32.1 + - + +
1669A ASN* 3.3 14.1 - - - +
1671A CYS* 1.3 78.4 - - - +
1673A ARG* 1.3 57.5 - - + +
1675A LEU* 3.4 2.9 + - - +
1676A ASP* 2.8 32.2 + - - +
1766A LYS* 3.5 30.1 - - + +
1769A ALA* 3.5 33.9 - - + +
1770A GLU* 3.3 32.8 - - + +
1773A LEU* 4.4 14.6 - - + -
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Residues in contact with ARG1673 (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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1666A ALA 5.8 0.4 + - - -
1669A ASN* 3.2 41.3 + - - +
1670A SER* 3.6 17.0 - - - +
1671A CYS 3.3 0.2 - - - -
1672A LEU* 1.3 76.6 - - + +
1674A ASP* 1.3 57.0 + - - +
1676A ASP* 3.4 6.8 + - - +
1677A GLN* 2.9 38.4 + - + +
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Residues in contact with ASP1674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1670A SER 3.1 14.1 + - - +
1671A CYS* 3.5 9.6 - - - +
1672A LEU 3.3 0.2 - - - -
1673A ARG* 1.3 78.6 - - - +
1675A LEU* 1.3 56.1 + - - +
1677A GLN* 3.4 4.7 + - - +
1678A ALA* 2.9 25.3 + - - +
1742A THR* 3.8 13.1 - - + +
1743A LEU* 5.6 7.0 - - - +
1746A VAL* 3.3 24.9 - - - +
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Residues in contact with LEU1675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1671A CYS 2.8 18.6 + - - +
1672A LEU* 3.7 3.4 - - - +
1674A ASP* 1.3 73.8 - - - +
1676A ASP* 1.3 66.0 - - - +
1678A ALA* 3.1 13.2 + - - +
1679A SER* 3.1 15.2 + - - -
1742A THR* 3.6 43.7 - - + +
1745A ALA* 3.7 20.0 - - + -
1746A VAL* 3.8 6.7 - - + -
1762A LEU* 4.0 16.0 - - + +
1765A THR* 3.8 10.5 - - + +
1766A LYS* 3.5 41.9 - - + +
1769A ALA* 4.2 9.6 - - + -
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Residues in contact with ASP1676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1672A LEU 2.8 19.1 + - - +
1673A ARG* 3.7 6.6 - - - +
1674A ASP 3.3 0.2 - - - -
1675A LEU* 1.3 76.1 - - - +
1677A GLN* 1.3 73.5 + - - +
1679A SER* 3.6 5.4 + - - -
1680A LEU* 3.4 19.9 + - - +
1766A LYS* 3.8 27.9 - - - +
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Residues in contact with GLN1677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1673A ARG* 2.9 23.8 + - + +
1674A ASP* 3.8 5.6 - - - +
1676A ASP* 1.3 87.8 + - - +
1678A ALA* 1.3 56.1 + - - +
1680A LEU* 3.2 27.2 + - - +
1681A ALA* 2.7 37.5 + - - +
1687A LEU* 5.4 0.7 - - - -
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Residues in contact with ALA1678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674A ASP 2.9 15.6 + - - +
1675A LEU 3.1 10.7 + - - +
1677A GLN* 1.3 77.9 - - - +
1679A SER* 1.3 53.6 + - - +
1682A ALA* 2.7 38.7 + - - +
1687A LEU* 4.3 11.9 - - + +
1746A VAL* 3.5 36.6 - - + -
1749A ALA* 4.9 0.7 - - + -
1762A LEU* 3.8 12.6 - - + -
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Residues in contact with SER1679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1675A LEU 3.1 7.9 + - - -
1676A ASP* 3.9 9.9 - - - -
1677A GLN 3.4 0.2 - - - -
1678A ALA* 1.3 78.5 - - - +
1680A LEU* 1.3 60.6 + - - +
1683A VAL* 3.2 26.0 + - - +
1759A MET* 3.7 16.6 - - - +
1762A LEU* 3.4 22.3 - - - +
1763A ASP* 5.8 5.4 - - - +
1766A LYS* 6.0 2.9 - - - -
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Residues in contact with LEU1680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1676A ASP 3.4 11.4 + - - +
1677A GLN* 3.2 33.8 + - - +
1678A ALA 3.2 0.4 - - - -
1679A SER* 1.3 77.4 - - - +
1681A ALA* 1.3 62.3 + - - +
1683A VAL* 3.0 26.4 - - + +
1684A SER* 3.6 10.0 + - - -
1686A GLN* 4.2 6.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA1681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1677A GLN* 2.7 20.9 + - + +
1678A ALA 3.8 0.2 - - - +
1680A LEU* 1.3 73.7 - - - +
1682A ALA* 1.3 58.5 + - - +
1684A SER 2.9 4.0 + - - -
1685A GLN 2.9 9.2 + - - -
1686A GLN* 2.7 52.0 + - + +
1687A LEU* 3.5 26.5 - - + -
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Residues in contact with ALA1682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1678A ALA 2.7 22.5 + - - +
1681A ALA* 1.3 72.8 - - - +
1683A VAL* 1.3 60.3 + - - +
1684A SER 3.1 1.0 + - - -
1685A GLN* 3.5 12.1 + - - +
1687A LEU* 3.8 14.1 - - + +
1749A ALA* 3.9 33.9 - - + +
1750A SER* 4.4 2.2 - - - +
1758A GLN* 4.4 5.6 + - - +
1759A MET* 3.9 17.2 - - + +
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Residues in contact with VAL1683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1679A SER 3.2 16.1 + - - +
1680A LEU* 3.0 31.4 - - + +
1682A ALA* 1.3 78.5 - - - +
1684A SER* 1.3 59.9 + - - +
1685A GLN* 3.6 2.0 - - - +
1759A MET* 3.6 14.3 - - + +
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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