Contacts of the helix formed by residues 1679 - 1703 (chain B) in PDB entry 5JCZ
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 ASP1679 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1557B SER* 5.7 1.0 - - - +
1560B CYS* 3.7 20.5 - - - +
1561B ARG* 4.4 1.6 + - - -
1564B HIS* 3.0 29.1 + - - -
1677B GLY 3.7 1.8 + - - +
1678B MET* 1.3 75.3 - - - +
1680B PRO* 1.3 66.2 - - - +
1681B GLU* 3.7 11.9 - - - +
1682B LEU* 2.9 30.6 + - + +
1683B ILE* 3.0 10.6 + - - +
1828B PRO* 4.0 12.7 - - + +
1830B ASN* 2.9 21.3 + - - +
130D HIS* 3.6 12.9 - - - +
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Residues in contact with PRO1680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1678B MET 3.3 4.4 - - - +
1679B ASP* 1.3 82.8 - - - +
1681B GLU* 1.3 78.8 + - - +
1683B ILE* 3.4 11.9 + - + +
1684B LYS* 3.0 42.7 + - - +
127D ASP 5.8 3.1 - - - +
129D ARG* 5.3 7.9 - - - +
130D HIS* 3.6 38.4 - - + +
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Residues in contact with GLU1681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1679B ASP* 3.7 0.2 - - - +
1680B PRO* 1.3 86.6 - - - +
1682B LEU* 1.3 60.8 + - - +
1684B LYS* 3.7 9.4 + - + +
1685B GLN* 3.0 34.5 + - - +
1826B THR* 5.1 1.1 - - + +
1828B PRO* 3.3 34.9 - - + +
1830B ASN* 3.1 32.7 + - - +
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Residues in contact with LEU1682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1556B LEU* 4.0 27.1 - - + +
1557B SER* 6.1 0.2 - - - -
1560B CYS* 3.9 27.8 - - - -
1608B TYR* 4.4 6.9 - - + -
1678B MET* 3.8 15.7 - - + -
1679B ASP* 2.9 19.7 + - + +
1681B GLU* 1.3 77.8 - - - +
1683B ILE* 1.3 65.1 + - - +
1685B GLN* 3.2 21.9 + - - +
1686B VAL* 2.9 29.2 + - - +
1825B VAL* 3.8 16.6 - - + -
1826B THR 4.0 4.3 - - - +
1827B PHE* 4.0 17.3 - - + -
1828B PRO* 4.1 8.5 - - + -
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Residues in contact with ILE1683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1670B HIS* 3.9 23.1 - - + +
1673B MET* 3.9 42.8 - - + +
1674B CYS* 4.1 6.1 - - - -
1678B MET* 3.7 32.3 - - + +
1679B ASP 3.0 11.1 + - - +
1680B PRO* 3.7 9.6 - - + +
1682B LEU* 1.3 76.1 - - - +
1684B LYS* 1.3 57.9 + - - +
1686B VAL* 3.2 7.8 + - - +
1687B VAL* 2.9 36.7 + - + +
1733B LEU* 4.8 5.4 - - + -
129D ARG* 4.0 22.2 - - - +
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Residues in contact with LYS1684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680B PRO* 3.0 33.7 + - - +
1681B GLU* 3.9 8.7 - - + +
1683B ILE* 1.3 77.4 - - + +
1685B GLN* 1.3 58.6 + - + +
1687B VAL* 3.5 3.9 + - - +
1688B LYS* 3.0 28.1 + - - +
1732B ASN 4.9 7.8 + - - -
1733B LEU* 4.0 24.5 - - + +
1735B ASN* 4.6 18.1 + - - +
1736B SER* 3.7 34.5 - - - +
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Residues in contact with GLN1685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1608B TYR* 3.4 18.9 + - + +
1681B GLU* 3.0 22.7 + - - +
1682B LEU* 3.2 13.7 + - - +
1684B LYS* 1.3 75.0 - - + +
1686B VAL* 1.3 61.8 + - - +
1688B LYS* 3.5 13.0 + - + +
1689B GLN* 3.0 23.2 + - - +
1736B SER 5.3 1.1 - - - +
1823B PHE* 5.8 0.7 - - - +
1824B PRO 4.1 2.9 - - - +
1825B VAL* 3.3 16.7 - - - +
1826B THR* 2.9 59.4 + - - +
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Residues in contact with VAL1686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549B PHE* 5.5 3.4 - - + -
1608B TYR* 3.5 26.0 - - + -
1611B LEU* 3.9 23.6 - - + -
1612B VAL* 5.6 4.7 - - + -
1615B LEU* 5.1 8.7 - - + -
1673B MET* 3.8 28.3 - - + -
1678B MET* 4.8 2.7 - - - -
1682B LEU 2.9 20.9 + - - +
1683B ILE 3.5 7.2 - - - +
1685B GLN* 1.3 73.3 - - - +
1687B VAL* 1.3 59.8 + - - +
1689B GLN* 3.1 6.9 + - + +
1690B MET* 2.9 42.1 + - + +
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Residues in contact with VAL1687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1670B HIS* 4.6 3.8 - - + +
1673B MET* 4.7 4.7 - - + -
1683B ILE* 2.9 30.2 + - + +
1684B LYS* 3.8 6.3 - - - +
1685B GLN 3.4 0.2 - - - -
1686B VAL* 1.3 71.4 - - - +
1688B LYS* 1.3 66.6 + - - +
1690B MET* 3.2 19.7 + - + +
1691B PHE* 3.0 28.8 + - + -
1727B TRP* 3.9 17.7 - - + -
1728B LEU* 3.8 27.8 - - + -
1733B LEU* 3.8 21.3 - - + -
1736B SER* 4.5 2.5 - - - +
1738B ALA* 4.0 4.9 - - + -
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Residues in contact with LYS1688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1684B LYS 3.0 19.4 + - - +
1685B GLN* 3.6 11.9 - - + +
1687B VAL* 1.3 76.4 - - - +
1689B GLN* 1.3 62.6 + - - +
1691B PHE* 3.4 2.3 + - - +
1692B TYR* 3.1 23.4 + - - +
1736B SER 3.7 18.6 - - - +
1737B GLY* 4.1 10.5 - - - +
1738B ALA* 3.7 13.2 - - - +
1741B THR* 3.8 25.6 - - + +
1823B PHE* 4.2 37.0 - - + +
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Residues in contact with GLN1689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1608B TYR* 4.3 6.3 + - - +
1612B VAL* 3.6 36.4 - - + +
1615B LEU* 5.9 1.8 - - + -
1685B GLN 3.0 15.4 + - - +
1686B VAL* 3.1 13.4 + - + +
1688B LYS* 1.3 77.2 - - - +
1690B MET* 1.3 62.2 + - + +
1692B TYR* 3.5 7.3 + - - +
1693B ILE* 3.2 41.2 + - + +
1820B LYS 5.3 0.2 + - - -
1821B HIS 2.9 25.6 + - - -
1822B ILE* 3.5 8.4 - - - +
1823B PHE* 3.1 39.2 + - - +
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Residues in contact with MET1690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615B LEU* 4.3 19.1 - - + -
1619B LEU* 3.9 18.1 - - + +
1666B LEU* 4.2 20.4 - - + +
1669B PHE* 3.4 44.2 - - + -
1670B HIS* 5.6 0.7 - - + +
1673B MET* 5.3 1.8 - - + -
1686B VAL* 2.9 24.1 + - + +
1687B VAL* 3.2 36.1 + - + +
1689B GLN* 1.3 75.7 - - + +
1691B PHE* 1.3 62.5 + - + +
1693B ILE* 3.3 12.3 + - - +
1694B ILE* 3.0 31.0 + - - +
1727B TRP* 4.9 4.0 - - + -
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Residues in contact with PHE1691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1666B LEU* 3.8 26.5 - - + -
1687B VAL* 3.0 25.6 + - + +
1688B LYS 3.8 2.0 - - - +
1690B MET* 1.3 78.2 - - + +
1692B TYR* 1.3 61.1 + - - +
1694B ILE* 3.3 8.9 + - + +
1695B GLY 2.8 23.9 + - - -
1724B LEU* 3.7 33.9 - - + -
1727B TRP* 3.8 20.0 - + - -
1728B LEU* 3.5 34.5 - - + -
1738B ALA* 3.6 28.5 - - + +
1741B THR* 3.6 3.4 - - - +
1742B LEU* 3.3 32.7 - - + +
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Residues in contact with TYR1692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1688B LYS 3.1 17.2 + - - +
1689B GLN* 3.7 7.6 - - - +
1690B MET 3.3 0.2 - - - -
1691B PHE* 1.3 76.2 - - - +
1693B ILE* 1.3 59.4 + - + +
1695B GLY* 3.7 0.8 - - - -
1696B ALA* 2.7 47.5 + - + +
1741B THR* 3.5 22.9 + - - -
1814B GLN* 5.7 1.0 + - - -
1817B MET* 4.2 16.3 - - - +
1818B ASP* 2.6 38.3 + - - +
1819B ALA* 4.5 3.4 - - - -
1821B HIS* 3.8 35.0 - + + +
1823B PHE* 3.6 34.3 - + + -
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Residues in contact with ILE1693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1612B VAL* 4.9 4.0 - - + -
1615B LEU* 5.3 3.8 - - + -
1616B GLU* 3.6 40.8 - - + +
1619B LEU* 4.9 11.7 - - + -
1620B GLN 5.2 1.3 - - - +
1623B ILE* 3.8 15.9 - - + -
1689B GLN* 3.2 39.1 + - + +
1690B MET* 3.4 12.3 - - + +
1691B PHE 3.2 0.2 - - - -
1692B TYR* 1.3 80.7 - - + +
1694B ILE* 1.3 60.0 + - - +
1696B ALA* 4.7 2.5 - - - -
1697B ILE* 3.2 38.0 + - + +
1819B ALA 4.3 16.4 - - - +
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Residues in contact with ILE1694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1619B LEU* 4.6 6.7 - - + -
1623B ILE* 3.6 23.1 - - + +
1627B MET* 4.1 25.8 - - + -
1662B ILE* 4.0 24.9 - - + -
1666B LEU* 4.3 23.3 - - + -
1690B MET 3.0 15.7 + - - +
1691B PHE* 3.6 14.6 - - + +
1693B ILE* 1.3 77.0 - - - +
1695B GLY* 1.3 59.7 + - - +
1698B THR* 2.7 33.1 + - - -
1724B LEU* 4.0 28.0 - - + -
1742B LEU* 4.9 2.0 - - + -
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Residues in contact with GLY1695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1691B PHE 2.8 17.7 + - - -
1692B TYR* 3.7 1.3 - - - -
1694B ILE* 1.3 77.9 - - - +
1696B ALA* 1.3 56.1 + - - +
1698B THR* 3.4 2.1 + - - -
1699B LEU* 2.9 32.4 + - - +
1741B THR 5.0 5.4 - - - -
1742B LEU* 3.8 15.7 - - - +
1745B LEU* 4.3 16.2 - - - +
1817B MET* 5.7 0.7 - - - -
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Residues in contact with ALA1696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1692B TYR* 2.7 39.8 + - + +
1693B ILE 4.2 1.1 - - - +
1695B GLY* 1.3 71.8 - - - +
1697B ILE* 1.3 58.0 + - - +
1699B LEU* 3.4 1.4 + - - +
1700B ASN* 2.9 37.0 + - - +
1817B MET* 4.2 22.9 - - + -
1819B ALA* 4.1 25.1 - - + -
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Residues in contact with ILE1697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1616B GLU* 5.0 2.9 - - - +
1620B GLN* 3.6 35.7 - - + +
1623B ILE* 3.6 36.6 - - + -
1624B VAL* 4.0 11.7 - - + -
1693B ILE* 3.2 23.6 + - + +
1696B ALA* 1.3 75.8 - - - +
1698B THR* 1.3 60.5 + - - +
1700B ASN* 3.8 6.1 - - - +
1701B ASN* 2.7 45.0 + - - +
1819B ALA* 3.8 21.8 - - + -
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Residues in contact with THR1698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623B ILE* 3.3 15.8 - - - +
1624B VAL* 6.0 0.7 - - - +
1627B MET* 3.6 19.3 - - + +
1628B LEU* 3.8 35.3 - - + +
1694B ILE 2.7 23.8 + - - -
1695B GLY 3.7 3.1 - - - -
1697B ILE* 1.3 78.0 - - - +
1699B LEU* 1.3 61.3 + - - +
1701B ASN* 3.3 5.4 + - - +
1702B LEU* 3.2 19.6 + - - +
1717B ILE* 4.9 2.7 - - + -
1745B LEU* 3.7 28.7 - - + -
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Residues in contact with LEU1699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1695B GLY 2.9 18.2 + - - +
1696B ALA* 3.9 3.4 - - - +
1698B THR* 1.3 73.9 - - - +
1700B ASN* 1.3 67.4 + - - +
1702B LEU* 3.2 12.5 + - + +
1703B LEU* 3.1 40.4 + - + +
1744B PRO* 3.8 20.2 - - + +
1745B LEU* 4.2 11.4 - - + +
1748B ALA* 3.7 29.2 - - + -
1772B LEU* 4.2 11.2 - - + -
1776B GLN* 4.6 5.6 - - - +
1780B VAL* 5.7 0.4 - - + -
1817B MET* 3.7 35.4 - - + -
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Residues in contact with ASN1700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1696B ALA 2.9 26.8 + - - +
1697B ILE* 3.8 6.4 - - - +
1699B LEU* 1.3 78.2 - - - +
1701B ASN* 1.3 62.7 + - - +
1703B LEU* 3.3 5.4 + - - +
1704B LEU* 3.2 34.9 + - + +
1816B LEU* 3.5 20.5 - - + +
1817B MET* 2.8 50.0 + - - +
1819B ALA* 4.3 11.3 - - - +
----------------------------------------------------------
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Residues in contact with ASN1701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1624B VAL* 3.4 36.2 - - - +
1628B LEU* 3.6 23.8 - - + -
1697B ILE* 2.7 28.5 + - - +
1698B THR 3.6 1.8 - - - +
1699B LEU 3.2 0.2 - - - -
1700B ASN* 1.3 77.7 - - - +
1702B LEU* 1.3 61.4 + - - +
1704B LEU* 4.4 6.9 - - - +
1705B ARG* 2.9 51.5 + - - +
1708B MET* 5.3 0.9 - - - -
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Residues in contact with LEU1702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1628B LEU* 4.7 4.2 - - + +
1698B THR 3.2 12.3 + - - +
1699B LEU* 3.2 14.6 + - + +
1701B ASN* 1.3 75.0 - - - +
1703B LEU* 1.3 62.7 + - + +
1704B LEU 3.1 0.2 - - - -
1705B ARG 3.3 18.8 - - - +
1708B MET* 3.2 38.6 - - + +
1709B CYS* 3.4 14.0 - - - -
1717B ILE* 3.7 27.4 - - + -
1745B LEU* 4.1 14.1 - - + -
1748B ALA* 4.0 27.1 - - + -
1752B LEU* 4.0 16.8 - - + -
1780B VAL* 5.6 4.9 - - + -
1783B LEU* 3.4 7.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU1703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1699B LEU* 3.1 34.7 + - + +
1700B ASN* 3.7 6.5 - - - +
1701B ASN 3.2 0.4 - - - -
1702B LEU* 1.3 76.0 - - - +
1704B LEU* 1.3 62.6 + - - +
1776B GLN* 3.7 28.3 - - + +
1779B LYS* 3.5 28.8 - - + -
1780B VAL* 3.7 28.7 - - + -
1783B LEU* 3.3 17.0 - - - +
1815B LEU* 3.4 29.6 - - + +
1816B LEU* 3.8 18.1 - - + +
1817B MET 5.5 0.2 - - - +
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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