Contacts of the helix formed by residues 1593 - 1628 (chain E) 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 LEU1593 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1813C PRO* 3.7 33.2 - - + -
1515E VAL* 4.1 13.2 - - + -
1527E VAL* 4.0 9.6 - - + -
1531E LEU* 4.0 16.4 - - + -
1566E LEU* 3.9 21.3 - - + -
1588E LEU* 3.7 26.2 - - + -
1591E PHE* 3.7 19.4 + - + +
1592E ASP* 1.3 74.5 + - - +
1594E ALA* 1.3 65.1 + - - +
1595E GLU 3.2 2.9 - - - -
1596E TYR* 3.1 15.4 + - + +
1597E ARG* 3.0 35.5 + - + +
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Residues in contact with ALA1594 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1572E GLU* 4.7 1.1 - - - +
1592E ASP* 3.2 23.6 + - - +
1593E LEU* 1.3 77.3 - - - +
1595E GLU* 1.3 65.6 + - + +
1597E ARG* 3.2 39.2 + - - +
1598E GLN* 3.2 12.5 + - - +
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Residues in contact with GLU1595 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1812C SER* 3.3 29.2 + - - -
1814C GLN* 4.1 22.1 + - - +
1592E ASP 5.1 0.8 + - - +
1593E LEU 3.2 0.4 - - - -
1594E ALA* 1.3 79.1 - - + +
1596E TYR* 1.3 69.3 + - + +
1598E GLN* 3.4 9.1 + - - +
1599E VAL* 3.3 23.7 + - - +
----------------------------------------------------------
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Residues in contact with TYR1596 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1812C SER* 4.4 7.4 - - - -
1813C PRO* 3.7 28.0 - - + +
1814C GLN* 4.3 10.3 - - + +
1528E ARG* 3.7 28.6 - - + +
1531E LEU* 3.8 38.6 - - + -
1532E THR* 5.0 8.9 + - - -
1535E ILE* 5.0 11.3 - - + +
1566E LEU* 5.6 4.5 - - + -
1592E ASP 5.1 0.2 - - - -
1593E LEU* 3.1 28.5 + - + +
1595E GLU* 1.3 80.0 - - + +
1597E ARG* 1.3 59.9 + - - +
1599E VAL* 3.1 12.1 + - + +
1600E LEU* 3.0 34.7 + - + +
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Residues in contact with ARG1597 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563E LEU* 3.4 18.9 - - + +
1566E LEU* 3.8 31.7 + - + -
1567E LYS* 3.7 31.5 - - - +
1570E SER* 3.7 17.6 - - - -
1572E GLU* 3.0 34.7 + - - -
1575E PHE* 4.0 13.6 - - - -
1592E ASP* 4.6 1.6 + - - -
1593E LEU* 3.0 25.6 + - + +
1594E ALA* 3.2 36.3 + - - +
1596E TYR* 1.3 75.6 - - - +
1598E GLN* 1.3 58.0 + - - +
1600E LEU* 3.5 4.0 + - - -
1601E SER* 3.0 27.4 + - - -
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Residues in contact with GLN1598 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1821C HIS* 6.5 1.3 - - + -
1594E ALA 3.2 8.6 + - - +
1595E GLU* 3.6 11.0 - - - +
1596E TYR 3.2 0.4 - - - -
1597E ARG* 1.3 78.2 - - - +
1599E VAL* 1.3 60.5 + - + +
1601E SER* 3.3 11.2 + - - -
1602E ASP* 3.0 61.4 + - - +
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Residues in contact with VAL1599 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1535E ILE* 3.7 30.7 - - + -
1539E LYS* 5.7 4.9 - - - +
1595E GLU 3.3 15.9 - - - +
1596E TYR* 3.1 14.8 + - + +
1598E GLN* 1.3 79.5 - - + +
1600E LEU* 1.3 57.5 + - - +
1602E ASP* 3.3 8.4 + - - +
1603E LEU* 2.9 26.8 + - + +
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Residues in contact with LEU1600 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1531E LEU* 5.8 1.6 - - + -
1534E THR* 5.6 0.2 - - + -
1535E ILE* 3.9 28.0 - - + -
1538E ILE* 5.1 6.1 - - + -
1559E THR* 3.9 23.5 - - + +
1562E PHE* 3.5 35.7 - - + -
1563E LEU* 4.5 18.6 - - + +
1566E LEU* 3.5 23.3 - - + -
1596E TYR* 3.0 19.5 + - + +
1597E ARG* 3.8 5.6 - - - +
1599E VAL* 1.3 73.7 - - - +
1601E SER* 1.3 61.4 + - - +
1603E LEU* 3.2 12.9 + - + +
1604E ALA* 2.8 28.6 + - - +
----------------------------------------------------------
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Residues in contact with SER1601 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563E LEU* 4.1 20.4 - - - +
1567E LYS* 6.1 0.7 - - - -
1597E ARG 3.0 19.4 + - - -
1598E GLN* 3.5 18.3 + - - -
1599E VAL 3.3 0.2 - - - -
1600E LEU* 1.3 77.6 - - - +
1602E ASP* 1.3 62.2 + - - +
1604E ALA* 3.3 7.0 + - - +
1605E ILE* 3.1 29.6 + - - +
----------------------------------------------------------
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Residues in contact with ASP1602 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1598E GLN* 3.0 44.8 + - - +
1599E VAL* 3.7 8.0 - - - +
1601E SER* 1.3 73.5 + - - +
1603E LEU* 1.3 65.2 + - - +
1605E ILE* 3.4 20.2 + - + +
1606E GLN* 3.2 25.7 + - - +
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Residues in contact with LEU1603 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1535E ILE* 4.4 18.4 - - + +
1538E ILE* 4.1 27.1 - - + -
1539E LYS* 3.8 33.7 - - + -
1542E LEU* 5.2 1.6 - - + -
1559E THR* 4.3 6.5 - - + -
1599E VAL* 2.9 13.8 + - + +
1600E LEU* 3.2 28.9 + - + +
1602E ASP* 1.3 75.0 - - - +
1604E ALA* 1.3 59.1 + - - +
1606E GLN* 3.0 14.2 + - + +
1607E ILE* 2.9 47.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA1604 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1556E LEU* 3.6 8.9 - - + +
1559E THR* 4.2 10.5 - - + +
1560E CYS* 4.5 21.1 - - - +
1563E LEU* 5.5 4.9 - - + -
1600E LEU 2.8 13.8 + - - +
1601E SER* 3.3 13.0 + - - +
1603E LEU* 1.3 76.0 - - - +
1605E ILE* 1.3 55.9 + - - +
1607E ILE* 3.4 11.1 + - - -
1608E TYR* 2.9 30.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE1605 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1601E SER* 3.1 19.9 + - - +
1602E ASP* 3.4 22.9 - - - +
1603E LEU 3.2 0.2 - - - -
1604E ALA* 1.3 76.0 - - - +
1606E GLN* 1.3 70.0 + - - +
1608E TYR* 3.3 8.1 + - + +
1609E GLN* 3.0 44.5 + - + +
----------------------------------------------------------
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Residues in contact with GLN1606 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1602E ASP 3.2 12.7 + - - +
1603E LEU* 3.0 17.6 + - + +
1605E ILE* 1.3 83.4 - - - +
1607E ILE* 1.3 62.5 + - + +
1609E GLN* 3.4 30.9 + - - +
1610E GLN* 3.1 21.8 + - - +
1613E ARG* 4.6 6.1 + - - -
----------------------------------------------------------
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Residues in contact with ILE1607 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1538E ILE* 4.1 2.7 - - + -
1542E LEU* 3.5 33.7 - - + -
1552E VAL* 3.6 21.3 - - + +
1555E TRP 3.8 6.5 - - - +
1556E LEU* 3.7 27.4 - - + +
1559E THR* 3.5 30.3 - - + +
1603E LEU* 2.9 35.6 + - + +
1604E ALA* 3.7 7.0 - - - +
1606E GLN* 1.3 73.4 - - + +
1608E TYR* 1.3 61.2 + - - +
1610E GLN* 3.1 7.5 + - - +
1611E LEU* 2.9 24.1 + - - +
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Residues in contact with TYR1608 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1556E LEU* 4.1 24.6 - - + +
1604E ALA 2.9 17.8 + - - +
1605E ILE* 3.5 8.5 - - + +
1607E ILE* 1.3 77.2 - - - +
1609E GLN* 1.3 64.6 + - + +
1611E LEU* 3.1 15.8 + - + +
1612E VAL* 3.0 51.0 + - + +
----------------------------------------------------------
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Residues in contact with GLN1609 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1605E ILE* 3.0 33.9 + - + +
1606E GLN* 3.4 32.5 + - - +
1607E ILE 3.3 0.2 - - - -
1608E TYR* 1.3 83.0 - - + +
1610E GLN* 1.3 61.4 + - - +
1612E VAL* 3.5 6.4 + - - +
1613E ARG* 3.1 44.4 + - - +
----------------------------------------------------------
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Residues in contact with GLN1610 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542E LEU* 5.4 10.1 - - + +
1546E GLY* 3.0 33.3 + - - +
1547E ASP* 4.0 9.9 + - - -
1552E VAL* 4.4 10.1 - - + -
1606E GLN 3.1 13.3 + - - +
1607E ILE* 3.4 11.0 - - - +
1609E GLN* 1.3 75.7 - - - +
1611E LEU* 1.3 63.4 + - - +
1613E ARG* 2.3 48.9 + - - +
1614E VAL* 3.0 34.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU1611 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549E PHE* 3.5 38.6 - - + -
1552E VAL* 3.7 23.3 - - + +
1553E SER* 3.8 20.2 - - - +
1556E LEU* 3.8 24.2 - - + -
1607E ILE 2.9 13.8 + - - +
1608E TYR* 3.1 19.9 + - + +
1610E GLN* 1.3 77.4 - - - +
1612E VAL* 1.3 60.9 + - + +
1614E VAL* 3.2 5.3 + - + +
1615E LEU* 3.0 32.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL1612 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1608E TYR* 3.0 49.5 + - + +
1609E GLN* 3.7 9.0 - - - +
1610E GLN 3.3 0.2 - - - -
1611E LEU* 1.3 76.5 - - + +
1613E ARG* 1.3 59.6 + - + +
1615E LEU* 3.4 20.0 - - + +
1616E GLU* 2.9 32.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG1613 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1606E GLN* 4.6 6.9 + - - -
1609E GLN* 3.1 38.6 + - - +
1610E GLN* 2.3 52.2 + - - +
1611E LEU 3.3 0.2 - - - -
1612E VAL* 1.3 79.7 - - + +
1614E VAL* 1.3 56.7 - - - +
1616E GLU* 3.5 8.0 + - - +
1617E ASN* 3.0 28.1 + - - +
----------------------------------------------------------
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Residues in contact with VAL1614 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1546E GLY 3.3 25.8 - - - +
1547E ASP* 3.9 22.0 - - - +
1549E PHE* 3.9 34.5 - - + +
1552E VAL* 4.3 7.0 - - + -
1610E GLN* 3.0 25.7 + - - +
1611E LEU* 3.2 8.7 + - + +
1613E ARG* 1.3 76.6 - - - +
1615E LEU* 1.3 64.1 + - - +
1617E ASN* 3.3 7.8 + - - +
1618E ILE* 3.2 30.1 + - + +
----------------------------------------------------------
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Residues in contact with LEU1615 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549E PHE* 4.2 23.6 - - + -
1611E LEU* 3.0 30.9 + - + +
1612E VAL* 3.4 24.9 - - + +
1614E VAL* 1.3 76.4 - - - +
1616E GLU* 1.3 67.7 + - + +
1618E ILE* 3.3 9.3 + - - +
1619E LEU* 2.9 50.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU1616 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1612E VAL* 2.9 23.6 + - + +
1613E ARG* 3.7 8.8 - - - +
1615E LEU* 1.3 84.2 - - + +
1617E ASN* 1.3 62.9 + - - +
1619E LEU* 4.7 3.4 - - - -
1620E GLN* 2.9 58.2 + - + +
----------------------------------------------------------
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Residues in contact with ASN1617 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1613E ARG 3.0 16.4 + - - +
1614E VAL* 3.5 8.4 - - - +
1616E GLU* 1.3 83.2 + - - +
1618E ILE* 1.3 64.8 + - - +
1620E GLN* 4.9 2.2 - - - +
1621E PRO* 3.2 19.8 - - - +
----------------------------------------------------------
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Residues in contact with ILE1618 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547E ASP 5.8 0.4 - - - +
1549E PHE* 4.5 14.8 - - + +
1614E VAL* 3.2 31.9 + - + +
1615E LEU* 3.7 10.5 - - - +
1616E GLU 3.2 0.2 - - - -
1617E ASN* 1.3 82.8 - - - +
1619E LEU* 1.3 67.4 + - + +
1621E PRO* 3.4 9.5 - - - +
1622E MET* 3.5 22.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU1619 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615E LEU* 2.9 37.5 + - + +
1616E GLU* 4.1 3.4 - - - +
1618E ILE* 1.3 82.1 - - + +
1620E GLN* 1.3 55.5 + - - +
1622E MET* 2.8 45.9 + - + +
1623E ILE* 3.3 26.4 - - + +
1662E ILE* 5.3 8.5 - - - -
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Residues in contact with GLN1620 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1616E GLU* 2.9 38.3 + - + +
1617E ASN* 4.7 1.8 - - - +
1619E LEU* 1.3 77.2 - - - +
1621E PRO* 1.3 82.8 - - + +
1622E MET 3.2 1.0 + - - -
1623E ILE* 3.5 21.2 + - + +
1624E VAL* 4.6 9.3 + - - +
----------------------------------------------------------
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Residues in contact with PRO1621 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1617E ASN 3.2 22.7 - - - +
1618E ILE 3.4 11.7 - - - +
1620E GLN* 1.3 104.2 - - + +
1622E MET* 1.3 57.3 + - + +
1623E ILE 3.5 0.2 - - - -
1624E VAL* 5.1 1.3 + - - +
1625E SER* 4.6 7.3 + - - -
1657E TYR* 3.6 25.0 - - + +
----------------------------------------------------------
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Residues in contact with MET1622 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618E ILE* 3.5 31.6 - - - +
1619E LEU* 2.8 22.4 + - + +
1621E PRO* 1.3 79.6 - - + +
1623E ILE* 1.3 59.2 + - + +
1624E VAL 3.7 0.7 - - - -
1625E SER 3.7 1.9 + - - -
1626E GLY* 2.9 29.3 + - - -
1657E TYR* 3.6 41.0 - - + +
1658E THR 5.0 1.4 - - - +
1661E SER* 3.3 46.4 - - - +
1662E ILE* 3.5 11.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE1623 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1619E LEU* 3.3 36.1 - - + +
1620E GLN* 3.5 12.1 + - - +
1621E PRO 3.5 1.2 - - - -
1622E MET* 1.3 75.8 - - + +
1624E VAL* 1.3 64.4 + - + +
1626E GLY* 5.1 0.2 - - - -
1627E MET* 2.7 56.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL1624 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1620E GLN* 4.6 9.2 + - - +
1621E PRO 5.1 1.7 + - - +
1622E MET 3.7 0.2 - - - -
1623E ILE* 1.3 78.7 - - + +
1625E SER* 1.3 59.2 + - - +
1628E LEU* 3.0 45.8 + - + +
1629E GLU* 3.0 32.5 + - + +
----------------------------------------------------------
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Residues in contact with SER1625 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1621E PRO 4.6 7.3 + - - -
1622E MET 3.7 7.5 + - - -
1623E ILE 3.3 0.2 - - - -
1624E VAL* 1.3 81.5 - - - +
1626E GLY* 1.3 58.9 + - - +
1629E GLU* 3.4 22.5 + - - +
1630E HIS* 2.8 33.6 + - - +
1656E THR* 3.0 18.4 + - - -
1657E TYR* 2.7 32.1 + - - -
----------------------------------------------------------
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Residues in contact with GLY1626 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622E MET 2.9 19.2 + - - -
1625E SER* 1.3 76.9 - - - +
1627E MET* 1.3 62.5 + - - +
1630E HIS* 4.6 8.2 - - - +
1657E TYR 3.6 2.7 + - - -
1658E THR* 3.6 25.8 - - - -
1659E LEU* 3.7 23.6 + - - +
----------------------------------------------------------
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Residues in contact with MET1627 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623E ILE* 2.7 39.7 + - + +
1626E GLY* 1.3 76.3 - - - +
1628E LEU* 1.3 70.4 + - + +
1630E HIS 5.5 1.6 - - - -
1659E LEU* 3.9 26.2 - - - -
----------------------------------------------------------
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Residues in contact with LEU1628 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623E ILE* 6.6 0.2 - - + -
1624E VAL* 3.0 32.5 + - + +
1626E GLY 3.6 0.2 - - - -
1627E MET* 1.3 94.0 - - + +
1629E GLU* 1.3 65.8 + - + +
1630E HIS 3.7 4.9 - - - +
1631E GLU* 5.6 1.9 - - - +
----------------------------------------------------------
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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