Contacts of the helix formed by residues 1737 - 1762 (chain B) in PDB entry 5WBY
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 GLN1737 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734B THR* 4.0 21.2 + - + +
1735B GLU* 3.1 10.2 + - - +
1736B ASP* 1.3 72.4 - - - +
1738B GLN* 1.3 75.3 + - + +
1739B HIS 3.3 1.1 - - - +
1740B LYS* 3.5 12.2 + - + +
1741B GLN* 3.2 22.7 + - - +
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Residues in contact with GLN1738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737B GLN* 1.3 83.9 - - + +
1739B HIS* 1.3 63.0 + - - +
1741B GLN* 3.4 10.7 + - - +
1742B GLU* 3.2 41.0 + - - +
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Residues in contact with HIS1739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1694B PRO* 5.7 5.4 - - + -
1727B GLN* 4.5 11.9 + - - -
1732B ILE* 6.2 2.7 - - + -
1736B ASP* 4.2 26.9 - - + +
1737B GLN 3.3 1.2 - - - +
1738B GLN* 1.3 76.6 - - - +
1740B LYS* 1.3 64.3 + - - +
1742B GLU* 3.6 12.1 + - - +
1743B LEU* 3.0 50.7 + - + +
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Residues in contact with LYS1740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1732B ILE* 3.7 36.5 - - + +
1736B ASP* 4.1 12.2 + - - +
1737B GLN* 3.5 13.7 + - + +
1738B GLN 3.3 0.6 - - - -
1739B HIS* 1.3 79.2 - - - +
1741B GLN* 1.3 56.0 + - - +
1743B LEU* 3.0 7.2 + - - +
1744B HIS* 2.8 70.7 + - + +
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Residues in contact with GLN1741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737B GLN 3.2 13.5 + - - +
1738B GLN* 3.4 11.3 + - - +
1740B LYS* 1.3 82.9 - - + +
1742B GLU* 1.3 59.3 + - + +
1744B HIS* 3.5 5.9 + - - +
1745B LYS* 3.1 64.5 + - - +
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Residues in contact with GLU1742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1695B GLN* 5.4 6.5 + - - +
1738B GLN* 3.2 33.4 + - - +
1739B HIS* 4.0 11.0 + - - +
1741B GLN* 1.3 77.6 - - + +
1743B LEU* 1.3 57.2 + - - +
1745B LYS* 3.5 9.1 + - + +
1746B LEU* 3.1 27.4 + - - +
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Residues in contact with LEU1743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1694B PRO* 4.3 13.7 - - + -
1724B MET* 3.9 45.7 - - + +
1727B GLN* 4.2 23.3 - - + +
1728B ALA* 3.9 22.9 - - + +
1732B ILE* 5.8 1.1 - - + -
1739B HIS* 3.0 38.8 + - + +
1740B LYS* 3.4 7.9 - - - +
1742B GLU* 1.3 75.6 - - - +
1744B HIS* 1.3 65.9 + - + +
1746B LEU* 3.6 7.0 + - + +
1747B MET* 3.2 27.9 + - - +
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Residues in contact with HIS1744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1728B ALA* 4.3 22.6 - - + +
1732B ILE* 4.9 1.0 - - - +
1740B LYS* 2.8 63.1 + - + +
1741B GLN* 3.8 7.9 - - - +
1743B LEU* 1.3 73.4 - - - +
1745B LYS* 1.3 59.4 + - + +
1747B MET* 3.2 10.9 + - - +
1748B ALA 3.1 21.8 + - - -
1782B HIS* 3.4 51.4 + + - +
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Residues in contact with LYS1745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1741B GLN* 3.1 54.5 + - + +
1742B GLU* 3.9 8.5 - - + +
1743B LEU 3.4 0.2 - - - -
1744B HIS* 1.3 73.0 - - + +
1746B LEU* 1.3 62.7 + - - +
1748B ALA* 3.6 7.3 + - - +
1749B ARG* 3.4 30.0 + - - +
1782B HIS 4.3 6.3 - - - +
1783B ASP* 3.8 35.0 - - + +
1785B SER* 5.9 0.9 - - - -
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Residues in contact with LEU1746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1694B PRO* 3.7 39.0 - - + +
1695B GLN* 3.6 32.3 - - - +
1698B TYR* 4.1 26.5 - - + -
1720B PHE* 4.2 12.6 - - + -
1724B MET* 4.6 8.5 - - + -
1742B GLU 3.1 17.4 + - - +
1743B LEU* 3.7 8.5 - - + +
1744B HIS 3.3 0.2 - - - -
1745B LYS* 1.3 75.2 - - - +
1747B MET* 1.3 60.3 + - - +
1749B ARG* 3.2 18.3 + - - +
1750B CYS* 3.0 34.7 + - - -
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Residues in contact with MET1747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1721B VAL* 4.6 6.7 - - + -
1724B MET* 3.8 26.2 - - + +
1725B GLN* 3.7 43.7 - - + +
1728B ALA* 5.1 2.7 - - - -
1743B LEU* 3.2 15.2 + - - +
1744B HIS* 3.2 20.9 + - - +
1746B LEU* 1.3 74.4 - - - +
1748B ALA* 1.3 54.1 + - - +
1750B CYS* 3.1 9.4 + - - +
1751B PHE* 2.7 56.6 + - + -
1782B HIS* 3.5 32.8 - - + +
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Residues in contact with ALA1748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1744B HIS 3.1 7.1 + - - +
1745B LYS 3.7 9.2 - - - +
1746B LEU 3.3 0.2 - - - -
1747B MET* 1.3 75.3 - - - +
1749B ARG* 1.3 57.7 + - - +
1751B PHE* 4.3 0.2 - - - -
1752B LEU* 3.0 26.7 + - - +
1779B ALA* 3.4 40.4 - - - +
1782B HIS* 3.9 6.2 - - + +
1783B ASP* 3.8 24.5 - - + +
1786B TRP* 3.6 11.1 - - + -
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Residues in contact with ARG1749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1695B GLN* 3.1 26.7 + - - +
1698B TYR* 3.3 44.8 + - + +
1702B LYS* 5.8 2.2 - - - +
1745B LYS* 3.4 19.7 + - - +
1746B LEU* 3.2 17.0 + - - +
1748B ALA* 1.3 77.6 - - - +
1750B CYS* 1.3 59.0 + - - +
1752B LEU* 3.7 2.6 + - - +
1753B LYS* 3.3 18.9 + - - +
1786B TRP* 3.6 30.7 - - + -
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Residues in contact with CYS1750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1698B TYR* 3.5 29.2 - - - -
1717B MET* 3.7 8.2 - - - +
1720B PHE* 3.7 29.8 - - - -
1721B VAL* 3.4 23.1 - - + -
1746B LEU* 3.0 24.8 + - - -
1747B MET* 3.4 8.1 - - - +
1749B ARG* 1.3 74.3 - - - +
1751B PHE* 1.3 59.2 + - - +
1752B LEU 3.2 0.2 - - - -
1753B LYS* 3.1 5.1 + - - +
1754B LEU* 3.0 30.7 + - - +
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Residues in contact with PHE1751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1721B VAL* 3.5 29.4 - - + -
1725B GLN* 4.4 9.2 - - - -
1747B MET* 2.7 32.7 + - + +
1748B ALA 3.7 4.9 - - - +
1750B CYS* 1.3 73.0 - - - +
1752B LEU* 1.3 61.9 + - - +
1754B LEU* 3.6 9.4 + - + +
1755B GLY* 3.4 15.4 + - - -
1774B GLN* 5.3 2.9 - - + -
1775B TYR* 3.6 52.9 - + - +
1776B TYR* 4.5 0.3 + - - -
1778B ALA* 3.5 24.2 - - + -
1779B ALA 3.8 6.5 - - - +
1782B HIS* 3.5 36.8 - + - -
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Residues in contact with LEU1752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1748B ALA 3.0 15.2 + - - +
1749B ARG 3.8 6.3 - - - +
1750B CYS 3.2 0.2 - - - -
1751B PHE* 1.3 75.0 - - - +
1753B LYS* 1.3 64.4 + - + +
1755B GLY 3.4 1.0 + - - -
1756B GLU* 3.1 34.7 + - - +
1776B TYR* 3.6 27.5 - - + -
1779B ALA* 4.1 9.8 - - + +
1786B TRP* 3.8 21.5 - - + -
1788B LYS* 4.0 25.4 - - + +
1789B ALA* 3.7 29.2 - - + +
1792B ALA* 3.9 9.4 - - + -
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Residues in contact with LYS1753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1698B TYR* 3.5 23.6 - - + +
1702B LYS* 4.7 23.3 - - + +
1706B LYS* 6.3 1.2 - - - +
1717B MET* 4.2 8.3 - - + -
1749B ARG 3.3 13.2 + - - +
1750B CYS 3.1 9.2 + - - +
1752B LEU* 1.3 77.1 - - + +
1754B LEU* 1.3 57.1 + - - +
1756B GLU* 3.7 27.7 + - - +
1757B TRP* 2.7 77.3 + - + +
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Residues in contact with LEU1754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1714B PHE* 3.5 21.8 - - + +
1717B MET* 3.7 16.4 - - + +
1718B GLN* 3.6 41.7 - - + +
1721B VAL* 3.9 28.0 - - + -
1750B CYS 3.0 14.6 + - - +
1751B PHE* 3.8 16.4 - - + +
1752B LEU 3.4 0.2 - - - -
1753B LYS* 1.3 76.1 - - - +
1755B GLY* 1.3 56.3 + - - +
1757B TRP* 4.7 0.9 - - - -
1758B GLN* 2.9 31.9 + - - +
1775B TYR* 3.6 34.8 - - + +
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Residues in contact with GLY1755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1751B PHE 3.4 7.9 + - - -
1752B LEU 3.9 2.7 - - - -
1753B LYS 3.3 0.2 - - - -
1754B LEU* 1.3 75.3 - - - +
1756B GLU* 1.3 64.0 + - - +
1759B LEU* 3.2 29.5 + - - +
1772B VAL* 3.4 18.1 - - - +
1775B TYR* 3.8 12.5 - - - -
1776B TYR* 3.6 19.1 - - - -
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Residues in contact with GLU1756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1705B TRP* 5.2 2.9 + - - -
1752B LEU* 3.1 23.7 + - - +
1753B LYS* 3.5 34.5 + - - +
1755B GLY* 1.3 75.7 - - - +
1757B TRP* 1.3 71.8 + - + +
1759B LEU* 3.4 7.9 + - - +
1760B ASN* 3.2 25.4 + - + +
1776B TYR* 3.5 12.5 + - + +
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Residues in contact with TRP1757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1701B MET 3.9 17.7 - - - -
1702B LYS* 4.1 11.2 - - + -
1705B TRP* 3.3 71.6 - + + +
1713B ALA* 3.6 23.6 - - + -
1714B PHE* 3.8 24.5 - + + -
1717B MET* 3.5 34.5 - - + -
1753B LYS* 2.7 51.9 + - + +
1754B LEU 5.0 0.2 - - - -
1756B GLU* 1.3 85.7 + - + +
1758B GLN* 1.3 60.3 + - - +
1760B ASN* 3.3 1.2 + - - +
1761B LEU* 3.0 35.9 + - - +
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Residues in contact with GLN1758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1714B PHE* 3.5 30.3 - - + -
1754B LEU 2.9 21.2 + - - +
1756B GLU 3.4 0.2 - - - -
1757B TRP* 1.3 75.9 - - - +
1759B LEU* 1.3 56.9 + - - +
1761B LEU* 4.0 2.4 - - - +
1762B GLN* 3.0 59.4 + - - +
1763B GLY 4.7 0.2 - - - +
1768B THR* 4.2 13.1 - - + +
1771B LYS* 3.8 30.4 + - + +
1772B VAL* 3.5 26.5 - - + -
1775B TYR* 4.0 14.4 + - + -
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Residues in contact with LEU1759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1755B GLY 3.2 16.9 + - - +
1756B GLU* 3.6 7.9 - - - +
1757B TRP 3.2 0.4 - - - -
1758B GLN* 1.3 75.2 - - - +
1760B ASN* 1.3 61.1 + - - +
1763B GLY* 2.9 37.6 + - - +
1764B ILE* 3.8 22.7 - - + -
1768B THR* 5.0 2.0 - - - +
1769B ILE* 6.1 0.4 - - + +
1772B VAL* 3.9 14.8 - - + -
1776B TYR* 3.5 20.4 - - + +
1796B MET* 3.4 35.9 - - + -
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Residues in contact with ASN1760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1705B TRP* 3.8 20.1 + - + -
1710B LYS* 3.3 30.0 + - - +
1756B GLU* 3.2 11.7 + - + +
1757B TRP 3.3 8.0 + - - +
1759B LEU* 1.3 81.0 - - - +
1761B LEU* 1.3 62.2 + - - +
1762B GLN 5.2 0.2 - - - -
1763B GLY 5.0 0.2 + - - -
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Residues in contact with LEU1761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1705B TRP* 4.1 9.2 - - + -
1710B LYS* 4.2 22.4 - - + +
1711B ILE* 4.0 27.4 - - + -
1714B PHE* 3.6 45.3 - - + -
1757B TRP 3.0 20.4 + - - +
1758B GLN* 4.0 3.4 - - - +
1760B ASN* 1.3 79.6 - - - +
1762B GLN* 1.3 74.8 + - + +
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Residues in contact with GLN1762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1714B PHE* 6.4 0.4 - - - -
1758B GLN* 3.0 30.5 + - - +
1760B ASN 5.2 0.2 - - - -
1761B LEU* 1.3 90.8 - - + +
1763B GLY* 1.3 58.6 + - - +
1765B ASN* 4.0 11.0 + - - +
1768B THR* 3.6 19.1 - - + -
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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