Contacts of the helix formed by residues 1639 - 1665 (chain A) in PDB entry 5XJY
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 THR1639 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A MET* 3.8 14.8 - - - +
527A LEU* 5.3 9.8 - - + +
528A ASP* 3.7 23.3 + - - +
1638A LEU* 1.3 79.5 - - - +
1640A LYS* 1.3 81.9 + - - +
1641A GLN* 3.5 24.6 + - + +
1642A GLN* 3.6 23.7 - - + +
1643A LEU* 3.2 24.0 + - - +
1837A GLU* 5.6 0.4 - - - -
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Residues in contact with LYS1640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A MET* 6.6 0.2 - - - -
528A ASP* 6.0 1.3 - - - +
1639A THR* 1.3 87.4 + - - +
1641A GLN* 1.3 71.6 + - - +
1643A LEU* 3.9 3.0 - - - +
1644A SER* 2.9 31.9 + - - -
1834A ARG* 4.3 18.4 - - + +
1837A GLU* 2.7 29.6 + - - -
1838A ASN* 3.3 21.0 - - - +
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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
----------------------------------------------------------
528A ASP* 5.5 2.0 + - - -
1639A THR* 3.4 18.2 + - + +
1640A LYS* 1.3 92.3 - - - +
1642A GLN* 1.3 69.1 + - - +
1644A SER* 3.7 6.0 - - - -
1645A GLU* 2.9 28.1 + - - +
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Residues in contact with GLN1642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A ILE* 5.3 13.2 - - + +
561A ASP* 5.4 9.3 + - - +
565A ARG* 5.7 2.8 + - - -
1374A TYR* 5.4 5.0 - - - -
1638A LEU* 3.6 29.7 - - + +
1639A THR* 3.6 19.1 - - + +
1640A LYS 3.3 0.2 - - - -
1641A GLN* 1.3 84.5 + - - +
1643A LEU* 1.3 60.5 + - - +
1645A GLU* 3.3 9.0 + - - +
1646A VAL* 3.0 35.0 + - - +
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Residues in contact with LEU1643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372A GLY* 6.6 0.2 - - - -
1638A LEU* 3.9 27.1 - - + +
1639A THR 3.2 22.2 + - - +
1640A LYS* 4.1 4.0 - - - +
1642A GLN* 1.3 75.6 - - - +
1644A SER* 1.3 57.9 + - - +
1646A VAL* 3.3 14.3 - - + +
1647A ALA* 3.0 28.4 + - - +
1833A GLU* 3.3 41.4 - - + +
1837A GLU* 4.1 31.4 - - + +
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Residues in contact with SER1644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1640A LYS 2.9 20.5 + - - -
1641A GLN* 3.7 8.5 - - - -
1643A LEU* 1.3 77.0 - - - +
1645A GLU* 1.3 57.9 + - - +
1647A ALA* 3.2 7.0 + - - +
1648A LEU* 3.0 38.9 + - - +
1830A ASP* 5.0 7.5 + - - -
1833A GLU* 4.9 4.7 + - - -
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Residues in contact with GLU1645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1641A GLN 2.9 18.4 + - - +
1642A GLN* 3.3 12.7 + - - +
1644A SER* 1.3 77.1 - - - +
1646A VAL* 1.3 60.6 + - + +
1648A LEU* 3.1 17.8 + - - +
1649A MET* 3.0 53.6 + - + +
----------------------------------------------------------
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Residues in contact with VAL1646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1371A PHE* 3.5 32.5 - - + +
1372A GLY* 4.9 7.4 - - - -
1374A TYR* 4.8 12.6 - - + +
1638A LEU* 4.3 16.2 - - + -
1642A GLN* 3.0 16.6 + - - +
1643A LEU* 3.3 26.5 - - + +
1645A GLU* 1.3 75.1 - - + +
1647A ALA* 1.3 61.9 + - - +
1649A MET* 3.9 9.0 - - + +
1650A THR* 2.8 35.7 + - - +
1833A GLU* 6.5 0.2 - - + -
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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
----------------------------------------------------------
1643A LEU 3.0 16.0 + - - +
1644A SER* 3.2 13.0 + - - +
1646A VAL* 1.3 78.3 - - - +
1648A LEU* 1.3 56.2 + - + +
1650A THR* 3.6 4.1 + - - -
1651A THR* 2.7 38.4 + - - +
1826A GLN* 5.7 2.7 - - + +
1829A ALA* 5.2 7.4 - - + +
1830A ASP* 4.5 26.5 - - + +
1833A GLU* 4.6 9.4 - - + +
----------------------------------------------------------
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Residues in contact with LEU1648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1644A SER* 3.0 31.7 + - - +
1645A GLU* 3.1 24.4 + - - +
1647A ALA* 1.3 80.0 - - + +
1649A MET* 1.3 64.4 + - + +
1651A THR* 3.3 9.6 - - + +
1652A SER* 3.1 20.4 + - - -
1788A LEU* 4.7 19.5 - - + -
1826A GLN* 4.5 25.1 - - + +
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Residues in contact with MET1649 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1371A PHE* 4.7 26.2 - - + -
1645A GLU* 3.0 44.8 + - + +
1646A VAL* 3.9 8.7 - - + +
1647A ALA 3.4 0.2 - - - -
1648A LEU* 1.3 76.8 - - + +
1650A THR* 1.3 60.2 + - - +
1652A SER* 2.4 31.0 + - - -
1653A VAL* 3.0 12.7 + - + +
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Residues in contact with THR1650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1370A PRO* 3.6 21.7 + - + +
1371A PHE* 4.3 6.8 - - + +
1646A VAL* 2.8 18.3 + - - +
1647A ALA* 4.0 5.2 - - - -
1649A MET* 1.3 74.3 - - - +
1651A THR* 1.3 63.0 + - - +
1653A VAL* 3.4 11.1 + - + +
1654A ASP* 3.0 23.1 + - + +
1829A ALA* 5.7 9.2 - - + -
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Residues in contact with THR1651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1647A ALA* 2.7 22.5 + - - +
1648A LEU* 3.3 12.3 - - + +
1649A MET 3.2 0.2 - - - -
1650A THR* 1.3 76.1 - - - +
1652A SER* 1.3 57.9 + - - +
1654A ASP* 3.0 10.3 + - - +
1655A VAL* 2.9 35.0 + - + +
1822A MET* 4.0 12.1 - - + +
1825A ASN* 4.9 2.4 + - + -
1826A GLN* 3.6 52.9 + - + +
1829A ALA* 5.0 3.7 - - - +
----------------------------------------------------------
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Residues in contact with SER1652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1648A LEU 3.1 10.1 + - - -
1649A MET* 2.4 35.6 + - - -
1651A THR* 1.3 75.8 - - - +
1653A VAL* 1.3 61.4 + - - +
1655A VAL* 2.8 34.3 + - - +
1656A LEU* 3.3 5.2 + - - +
1786A PHE* 4.8 14.2 - - - -
----------------------------------------------------------
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Residues in contact with VAL1653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1365A SER* 5.1 3.3 + - - +
1368A VAL* 4.0 36.1 - - + -
1369A PRO 5.7 0.4 - - - +
1371A PHE* 3.7 28.9 - - + -
1649A MET* 3.0 14.3 + - + +
1650A THR* 3.7 11.2 - - + +
1651A THR 3.4 0.2 - - - -
1652A SER* 1.3 77.7 - - - +
1654A ASP* 1.3 56.2 + - - +
1656A LEU* 3.3 26.5 - - + +
1657A VAL* 4.1 4.7 + - - +
----------------------------------------------------------
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Residues in contact with ASP1654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1365A SER* 5.8 0.3 - - - -
1650A THR* 3.0 14.0 + - + +
1651A THR* 3.0 11.2 + - - +
1653A VAL* 1.3 75.7 - - - +
1655A VAL* 1.3 57.6 + - - +
1656A LEU 3.1 1.8 - - - -
1657A VAL* 2.8 37.6 + - - +
1658A SER 3.0 8.7 + - - -
1727A LYS* 4.1 12.0 + - - +
1822A MET* 3.2 28.6 - - - +
1825A ASN* 2.8 36.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL1655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651A THR* 2.9 23.3 + - + +
1652A SER* 2.8 23.7 + - - +
1654A ASP* 1.3 67.7 - - - +
1656A LEU* 1.3 64.7 + - - +
1658A SER* 3.1 8.8 + - - +
1659A ILE* 3.0 22.6 + - + +
1782A SER* 4.8 16.4 - - - -
1785A THR* 5.8 4.0 - - - +
1786A PHE* 4.0 30.3 - - + -
1819A LEU* 5.6 4.9 - - + -
1822A MET* 3.6 26.5 - - + -
----------------------------------------------------------
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Residues in contact with LEU1656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361A ALA* 5.5 4.5 - - + +
1364A PHE* 3.5 39.3 - - + -
1365A SER* 5.1 6.7 - - - +
1368A VAL* 6.1 0.4 - - + -
1652A SER 3.3 6.4 + - - +
1653A VAL* 3.3 19.5 - - + +
1654A ASP 3.1 0.2 - - - -
1655A VAL* 1.3 75.7 - - - +
1657A VAL* 1.3 63.2 + - + +
1659A ILE* 3.1 20.1 + - + +
1660A CYS* 3.0 23.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL1657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361A ALA* 4.9 7.6 - - + +
1362A LEU* 4.2 21.8 - - + -
1365A SER* 3.3 28.0 - - - +
1653A VAL 4.4 2.7 - - - +
1654A ASP* 2.8 39.5 + - - +
1656A LEU* 1.3 73.7 - - + +
1658A SER* 1.3 62.4 + - - +
1660A CYS* 4.4 4.3 - - - +
1661A VAL* 3.0 39.0 + - + +
1721A PHE* 6.0 1.6 - - + -
1727A LYS* 4.8 17.9 - - + +
1821A ASP* 5.7 0.4 - - - -
1822A MET* 4.9 0.4 - - + -
----------------------------------------------------------
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Residues in contact with SER1658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1654A ASP 3.0 6.1 + - - -
1655A VAL* 3.2 13.9 - - - +
1657A VAL* 1.3 77.2 - - - +
1659A ILE* 1.3 58.7 + - - +
1661A VAL* 4.3 1.5 - - - -
1662A ILE* 2.9 33.1 + - - +
1818A GLY* 3.3 30.1 + - - -
1819A LEU* 5.1 2.9 - - - +
1821A ASP* 4.9 4.5 - - - -
1822A MET* 3.6 33.6 - - - +
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Residues in contact with ILE1659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655A VAL* 3.0 12.6 + - + +
1656A LEU* 3.1 30.0 + - + +
1658A SER* 1.3 78.5 + - - +
1660A CYS* 1.3 60.9 + - + +
1662A ILE* 3.3 14.6 - - + +
1663A PHE* 3.0 23.7 + - - +
1775A LEU* 4.9 7.7 - - + +
1778A GLY* 3.5 35.2 - - - +
1779A ILE* 3.7 20.9 - - + +
1782A SER* 4.9 9.0 - - - -
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Residues in contact with CYS1660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357A PHE* 3.3 36.6 - - - -
1358A VAL* 5.3 0.6 - - - +
1360A ILE* 4.8 4.7 - - - -
1361A ALA* 3.6 23.1 - - + -
1656A LEU* 3.0 17.4 + - + +
1657A VAL 4.2 0.9 - - - +
1658A SER 3.2 0.2 - - - -
1659A ILE* 1.3 80.3 - - + +
1661A VAL* 1.3 61.3 + - - +
1663A PHE* 3.0 24.0 + - - +
1664A ALA* 3.0 13.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL1661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1358A VAL* 3.9 29.4 - - + -
1361A ALA* 5.2 0.9 - - + -
1362A LEU* 5.0 2.7 - - + -
1657A VAL* 3.0 32.4 + - + +
1658A SER* 4.6 1.1 - - - +
1660A CYS* 1.3 75.5 - - + +
1662A ILE* 1.3 60.7 + - - +
1664A ALA* 3.1 4.7 + - - +
1665A MET* 2.9 30.5 + - + -
1717A VAL* 4.8 8.5 - - + -
1721A PHE* 4.8 15.5 - - + -
1727A LYS* 6.2 1.1 - - - +
1742A LEU* 5.2 1.8 - - + -
1817A ARG* 2.8 36.0 + - - +
----------------------------------------------------------
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Residues in contact with ILE1662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658A SER* 2.9 20.9 + - - +
1659A ILE* 3.3 36.3 - - + +
1661A VAL* 1.3 79.4 - - - +
1663A PHE* 1.3 48.0 + - - +
1666A SER* 2.5 37.4 + - - -
1745A TYR* 3.3 26.7 - - + +
1774A ASN 5.7 2.9 - - - +
1775A LEU* 5.3 4.5 - - + -
1778A GLY* 4.3 16.2 - - - -
1814A CYS* 3.7 21.8 - - - +
1817A ARG* 3.3 21.6 - - + +
1818A GLY* 4.3 15.9 - - - +
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Residues in contact with PHE1663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1353A LEU* 4.4 8.7 - - + -
1357A PHE* 3.5 39.5 - + + -
1659A ILE 3.0 15.6 + - - +
1660A CYS* 3.0 16.8 + - - +
1662A ILE* 1.3 78.0 - - - +
1664A ALA* 1.3 61.8 + - - +
1666A SER* 3.3 5.9 - - - -
1667A PHE* 2.9 37.8 + + + +
1771A THR* 3.6 28.7 - - + +
1775A LEU* 3.5 38.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA1664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1353A LEU* 6.1 0.7 - - - -
1354A PRO* 3.6 42.5 - - + +
1357A PHE* 5.1 3.8 - - + -
1358A VAL* 4.1 15.3 - - + +
1660A CYS 3.0 12.2 + - - +
1661A VAL 3.1 5.3 + - - +
1663A PHE* 1.3 79.3 - - - +
1665A MET* 1.3 62.5 + - + +
1667A PHE* 2.6 27.2 + - - +
1668A VAL 3.0 10.4 + - - -
----------------------------------------------------------
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Residues in contact with MET1665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354A PRO* 3.7 30.1 - - + -
1661A VAL* 2.9 12.3 + - + +
1664A ALA* 1.3 73.8 - - + +
1666A SER* 1.3 61.5 + - - +
1667A PHE 3.2 0.2 - - - -
1668A VAL* 3.3 18.7 - - + +
1669A PRO* 3.8 0.2 - - - +
1710A TYR* 3.5 33.7 - - - +
1713A PRO* 4.6 9.4 - - + +
1714A ALA* 4.3 12.3 - - - +
1717A VAL* 4.0 22.9 - - + -
1742A LEU* 4.2 12.8 - - + -
1745A TYR* 3.6 15.4 - - + -
1749A ILE* 3.3 21.3 - - - +
1817A ARG* 3.5 22.9 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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