Contacts of the helix formed by residues 1710 - 1731 (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 SER1710 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1707B ASP 5.6 1.3 + - - -
1708B MET 3.6 2.9 + - - -
1709B CYS* 1.3 77.6 + - - +
1711B TRP* 1.3 67.1 + - - +
1712B SER* 3.7 8.6 + - - -
1713B LYS* 3.3 22.5 + - - +
1714B GLY 3.0 17.8 + - - -
1752B LEU* 3.4 8.7 - - - +
1784B TYR* 3.7 12.1 - - - -
1785B THR 3.9 13.2 - - - -
1786B PRO* 5.0 2.5 - - - -
1787B VAL* 4.0 19.7 - - - +
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Residues in contact with TRP1711 (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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73A TYR* 5.9 1.6 - + - -
75A ALA* 3.6 40.8 - - + -
76A ILE* 3.7 32.6 - - + +
79A ALA* 3.9 15.9 - - + -
1710B SER* 1.3 76.6 - - - +
1712B SER* 1.3 92.0 + - - +
1714B GLY* 3.3 1.0 + - - -
1715B MET* 3.1 53.1 + - - +
1752B LEU 3.3 23.1 + - - +
1753B GLN* 3.8 13.1 - - + +
1784B TYR* 3.6 15.2 + - - +
1786B PRO* 6.2 0.7 - - + -
1787B VAL 6.2 0.2 - - - -
1788B ASN* 5.3 0.4 - - - +
1791B GLU* 3.1 33.1 + - - -
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Residues in contact with SER1712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1633B ILE* 4.2 15.8 - - - +
1710B SER* 3.2 8.6 + - - -
1711B TRP* 1.3 107.6 - - - +
1713B LYS* 1.3 63.9 + - - +
1715B MET* 3.4 6.5 + - - +
1716B GLN* 3.1 21.3 + - - +
1787B VAL* 6.0 2.7 - - - -
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Residues in contact with LYS1713 (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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1628B LEU* 3.2 30.1 - - + +
1629B GLU* 5.0 1.1 - - - +
1631B GLU* 4.4 24.7 - - + +
1707B ASP 4.9 5.2 - - - +
1708B MET* 3.3 53.2 - - - +
1710B SER* 3.3 17.0 + - - +
1712B SER* 1.3 78.9 - - - +
1714B GLY* 1.3 60.6 + - - +
1716B GLN* 3.5 10.2 - - + +
1717B ILE* 2.8 43.5 + - + +
1752B LEU* 4.7 0.4 - - + -
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Residues in contact with GLY1714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1710B SER 3.0 11.2 + - - -
1711B TRP 3.3 4.2 + - - -
1712B SER 3.3 0.2 - - - -
1713B LYS* 1.3 77.3 - - - +
1715B MET* 1.3 54.9 - - - +
1717B ILE* 3.5 0.6 + - - -
1718B ARG* 3.0 28.9 + - - +
1749B ALA* 3.5 25.4 - - - +
1752B LEU* 3.8 16.5 - - - +
1753B GLN* 3.5 9.8 + - - -
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Residues in contact with MET1715 (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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46A VAL* 4.2 22.7 - - + -
48A PHE* 3.5 13.2 - - + -
65A TRP* 3.5 35.0 - - + -
76A ILE* 4.5 8.3 - - - +
79A ALA* 4.5 13.5 - - + -
80A TYR 5.1 0.9 - - - +
1633B ILE* 4.1 13.5 - - + -
1711B TRP* 3.1 45.2 + - - +
1712B SER* 3.6 7.6 - - - +
1713B LYS 3.2 0.2 - - - -
1714B GLY* 1.3 73.5 - - - +
1716B GLN* 1.3 65.1 + - - +
1718B ARG* 3.3 2.7 + - - -
1719B TYR* 3.0 21.1 + - - +
1753B GLN* 3.3 23.8 - - + +
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Residues in contact with GLN1716 (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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1627B MET 4.7 4.0 - - - +
1628B LEU* 4.8 8.3 - - - +
1630B HIS 3.8 13.0 + - - +
1631B GLU* 3.3 8.2 - - + +
1632B THR* 2.7 46.3 + - - -
1633B ILE* 2.9 25.7 + - + +
1712B SER 3.1 13.8 + - - +
1713B LYS* 3.5 17.3 - - + +
1715B MET* 1.3 76.5 - - - +
1717B ILE* 1.3 62.1 + - + +
1719B TYR* 3.3 8.0 + - - +
1720B ASN* 3.0 58.0 + - - +
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Residues in contact with ILE1717 (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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1627B MET* 4.3 6.1 - - + +
1628B LEU* 3.6 32.5 - - + -
1698B THR* 4.9 2.2 - - + -
1702B LEU* 3.7 30.7 - - + -
1713B LYS* 2.8 28.1 + - + +
1714B GLY* 3.8 5.2 - - - +
1716B GLN* 1.3 76.3 - - + +
1718B ARG* 1.3 59.0 + - - +
1720B ASN* 3.2 9.6 + - - +
1721B VAL* 2.9 30.4 + - + +
1745B LEU* 3.8 33.9 - - + -
1749B ALA* 3.8 13.0 - - + -
1752B LEU* 4.4 5.6 - - + -
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Residues in contact with ARG1718 (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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44A ILE 6.1 0.4 - - - +
46A VAL 3.6 19.3 - - - +
47A GLU* 3.2 30.8 + - - +
48A PHE* 4.0 8.3 - - + -
1714B GLY 3.0 17.2 + - - +
1715B MET 3.7 4.5 - - - +
1717B ILE* 1.3 76.6 - - - +
1719B TYR* 1.3 57.3 + - - +
1721B VAL* 3.4 14.0 + - - +
1722B SER* 3.0 22.0 + - - +
1725B GLU* 3.1 32.5 + - - -
1746B ILE* 3.9 38.8 - - - +
1749B ALA* 4.2 5.6 - - + +
1750B GLN* 5.0 6.1 - - - +
1753B GLN* 4.1 11.7 - - - +
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Residues in contact with TYR1719 (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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48A PHE* 3.5 44.3 - + + -
50A THR* 5.0 4.2 - - + +
61A LYS* 5.3 4.2 + - - -
63A GLN* 3.7 34.8 + - + -
65A TRP* 6.0 1.1 - + - -
1632B THR* 4.4 11.4 - - - -
1633B ILE* 5.1 6.5 - - + -
1659B LEU* 4.4 5.4 - - + -
1715B MET 3.0 16.3 + - - +
1716B GLN* 3.6 14.1 - - - +
1718B ARG* 1.3 74.5 - - - +
1720B ASN* 1.3 78.6 + - - +
1722B SER* 2.5 21.6 + - - -
1723B GLN* 3.1 45.1 + - + +
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Residues in contact with ASN1720 (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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1626B GLY 3.9 7.2 + - - -
1627B MET* 2.8 53.7 + - + +
1630B HIS 5.1 1.0 + - - -
1632B THR* 4.6 1.0 + - - -
1659B LEU* 3.5 27.3 - - + +
1716B GLN* 3.0 43.5 + - - +
1717B ILE* 3.5 7.6 - - - +
1719B TYR* 1.3 79.6 - - - +
1721B VAL* 1.3 62.6 + - - +
1723B GLN* 3.2 6.4 + - - +
1724B LEU* 3.2 24.4 + - - +
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Residues in contact with VAL1721 (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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1627B MET* 4.3 5.8 - - + -
1717B ILE* 2.9 25.7 + - + +
1718B ARG* 3.6 20.2 - - - +
1720B ASN* 1.3 72.4 - - - +
1722B SER* 1.3 61.0 + - - +
1724B LEU* 3.0 10.0 + - - +
1725B GLU* 2.8 34.1 + - + +
1742B LEU* 4.0 21.5 - - + -
1745B LEU* 3.9 29.8 - - + -
1746B ILE* 3.7 26.5 - - + -
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Residues in contact with SER1722 (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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48A PHE* 3.7 33.7 + - - +
1718B ARG* 3.0 21.8 + - - +
1719B TYR* 2.5 28.5 + - - -
1721B VAL* 1.3 75.8 - - - +
1723B GLN* 1.3 59.6 + - - +
1725B GLU* 3.4 14.9 + - - +
1726B GLU* 3.0 37.8 + - - +
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Residues in contact with GLN1723 (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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50A THR* 3.8 18.2 + - - +
61A LYS* 4.6 12.0 + - - +
1659B LEU* 3.7 24.3 - - + +
1660B ASP* 5.3 1.7 - - - +
1663B LEU* 4.0 23.5 - - + +
1719B TYR* 3.1 39.1 + - + +
1720B ASN 3.4 9.0 - - - +
1721B VAL 3.1 0.2 - - - -
1722B SER* 1.3 81.6 + - - +
1724B LEU* 1.3 64.3 + - - +
1726B GLU* 3.5 23.0 + - - +
1727B TRP* 3.1 22.0 + - - +
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Residues in contact with LEU1724 (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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1627B MET* 4.1 18.6 - - + -
1659B LEU* 4.5 8.3 - - + -
1662B ILE* 4.7 4.3 - - + -
1663B LEU* 3.6 24.7 - - + -
1666B LEU* 4.1 18.6 - - + -
1691B PHE* 3.7 17.9 - - + -
1694B ILE* 4.0 33.9 - - + -
1720B ASN 3.2 10.5 + - - +
1721B VAL* 3.0 9.5 + - - +
1723B GLN* 1.3 74.6 - - - +
1725B GLU* 1.3 66.2 + - - +
1727B TRP* 3.3 7.2 + - + +
1728B LEU* 3.1 24.6 + - - +
1742B LEU* 4.1 18.4 - - + -
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Residues in contact with GLU1725 (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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1718B ARG* 3.1 37.9 + - - -
1721B VAL* 2.8 22.0 + - + +
1722B SER* 3.5 15.0 - - - +
1723B GLN 3.3 0.2 - - - -
1724B LEU* 1.3 77.4 - - - +
1726B GLU* 1.3 59.2 + - + +
1728B LEU* 3.1 14.4 + - + +
1729B ARG* 3.0 26.1 + - - +
1734B MET* 5.6 2.4 - - - +
1739B LYS* 3.3 39.9 - - + +
1742B LEU* 5.3 3.6 - - + -
1746B ILE* 4.7 0.4 - - - -
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Residues in contact with GLU1726 (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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48A PHE 4.4 2.4 - - - +
49A ALA* 3.3 13.7 - - - +
50A THR* 2.7 51.0 + - - +
1722B SER* 3.0 23.5 + - - +
1723B GLN* 3.8 18.2 + - - +
1725B GLU* 1.3 74.5 - - + +
1727B TRP* 1.3 60.8 + - - +
1729B ARG* 3.7 12.0 - - - +
1730B ASP* 3.0 41.0 + - - +
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Residues in contact with TRP1727 (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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1663B LEU* 4.2 22.8 + - + -
1666B LEU* 3.7 36.8 - - + -
1667B ASN* 2.6 35.7 + - - +
1670B HIS* 4.0 15.5 - - + -
1687B VAL* 3.9 9.6 - - + -
1690B MET* 4.9 2.2 - - + -
1691B PHE* 3.8 31.4 - + - -
1723B GLN 3.1 13.8 + - - +
1724B LEU* 3.4 10.8 - - - +
1725B GLU 3.2 0.2 - - - -
1726B GLU* 1.3 73.9 - - - +
1728B LEU* 1.3 71.2 + - + +
1730B ASP* 3.4 7.0 + - + +
1731B LYS* 3.1 47.3 + - + +
1733B LEU* 3.9 28.0 - - + -
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Residues in contact with LEU1728 (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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1687B VAL* 3.8 22.4 - - + -
1691B PHE* 3.5 34.1 - - + -
1724B LEU 3.1 15.5 + - - +
1725B GLU* 3.1 14.7 + - + +
1727B TRP* 1.3 84.8 - - + +
1729B ARG* 1.3 60.1 + - - +
1731B LYS 3.3 1.8 + - - +
1732B ASN 3.1 3.8 + - - -
1733B LEU* 2.8 51.7 + - + +
1734B MET* 4.4 7.0 - - + +
1738B ALA* 3.9 6.5 - - + -
1739B LYS* 3.7 36.8 - - + +
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Residues in contact with ARG1729 (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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32A THR 5.3 2.7 - - - -
33A ARG* 3.3 47.2 + - - +
35A GLU* 2.8 35.0 + - - -
1725B GLU 3.0 12.7 + - - +
1726B GLU* 3.7 14.0 - - - +
1727B TRP 3.3 0.4 - - - -
1728B LEU* 1.3 76.5 - - - +
1730B ASP* 1.3 69.0 + - - +
1732B ASN* 3.1 17.8 + - - +
1734B MET* 3.3 45.9 - - + +
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Residues in contact with ASP1730 (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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1726B GLU* 3.0 27.6 + - - +
1727B TRP* 3.8 8.0 - - + +
1728B LEU 3.3 0.2 - - - -
1729B ARG* 1.3 82.1 - - - +
1731B LYS* 1.3 69.5 + - + +
1732B ASN* 3.3 9.9 + - - -
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Residues in contact with LYS1731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1667B ASN* 3.3 28.5 + - - +
1670B HIS* 4.0 30.6 + - + +
1727B TRP* 3.1 39.0 + - + +
1728B LEU 3.3 0.6 + - - +
1729B ARG 3.2 0.2 - - - -
1730B ASP* 1.3 84.4 - - - +
1732B ASN* 1.3 76.5 + - - +
1733B LEU* 3.3 27.0 + - + +
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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