Contacts of the helix formed by residues 1548 - 1569 (chain C) 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 ASP1548 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1545C ARG* 3.5 14.1 + - + +
1546C GLY 3.3 1.6 - - - -
1547C ASP* 1.3 77.6 - - - +
1549C PHE* 1.3 66.5 + - - +
1550C GLU* 3.6 13.8 + - - +
1551C THR* 2.6 40.6 + - - +
1552C VAL* 3.2 25.2 + - - +
1614C VAL* 4.5 0.2 - - - -
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Residues in contact with PHE1549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547C ASP 3.7 4.8 + - - -
1548C ASP* 1.3 73.2 + - - +
1550C GLU* 1.3 59.4 + - + +
1552C VAL* 3.3 4.1 + - - +
1553C SER* 2.9 36.3 + - - -
1611C LEU* 3.5 30.2 - - + +
1614C VAL* 3.9 21.5 - - + +
1615C LEU* 4.1 18.2 - - + -
1618C ILE* 4.8 5.1 - - + +
1669C PHE* 3.6 62.6 - + + -
1672C VAL* 3.9 23.1 - - + -
1673C MET* 4.0 21.5 - - + -
1686C VAL* 5.3 0.2 - - + -
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Residues in contact with GLU1550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495C PRO* 4.6 8.3 - - + +
1496C ARG* 2.7 53.6 + - - +
1548C ASP* 3.3 12.6 + - - +
1549C PHE* 1.3 78.4 - - + +
1551C THR* 1.3 58.3 + - - +
1554C PHE* 3.0 25.8 + - - +
1672C VAL* 3.9 39.1 - - + +
1676C HIS* 3.1 16.5 + - + -
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Residues in contact with THR1551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495C PRO* 4.7 7.7 - - + +
1541C VAL* 3.7 23.3 - - + +
1542C LEU* 4.5 5.8 - - + -
1545C ARG* 3.1 50.6 + - + +
1548C ASP* 2.6 31.4 + - - +
1550C GLU* 1.3 75.2 - - - +
1552C VAL* 1.3 65.6 + - - +
1554C PHE* 3.4 3.7 + - - +
1555C TRP* 3.2 29.9 + - + +
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Residues in contact with VAL1552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542C LEU* 3.8 12.6 - - + -
1545C ARG 4.7 2.0 - - - +
1546C GLY 3.8 22.4 - - - +
1548C ASP 3.2 15.4 + - - +
1549C PHE* 3.9 2.2 - - - +
1551C THR* 1.3 72.3 - - - +
1553C SER* 1.3 60.9 + - - +
1555C TRP 3.4 0.5 + - - -
1556C LEU* 2.9 28.6 + - - +
1607C ILE* 3.6 32.9 - - + +
1610C GLN* 3.8 18.4 - - + +
1611C LEU* 3.7 28.5 - - + +
1614C VAL* 4.4 5.8 - - + -
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Residues in contact with SER1553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549C PHE* 2.9 23.1 + - - -
1550C GLU 3.9 1.1 - - - -
1552C VAL* 1.3 78.9 - - - +
1554C PHE* 1.3 60.2 + - - +
1556C LEU* 3.4 0.8 + - - -
1557C SER* 2.8 29.8 + - - -
1611C LEU* 3.7 13.2 - - - +
1672C VAL* 3.9 7.6 - - - +
1673C MET* 3.8 11.6 - - - -
1676C HIS* 2.9 19.7 + - - -
1678C MET* 3.3 23.8 - - - +
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Residues in contact with PHE1554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493C LEU* 3.6 32.5 - - + -
1495C PRO* 3.8 34.1 - - + -
1500C VAL* 4.4 18.8 - - + -
1505C GLY 6.0 1.6 - - - -
1507C PRO* 3.9 11.4 - - + -
1550C GLU 3.0 19.4 + - - +
1551C THR 3.7 4.3 - - - +
1552C VAL 3.3 0.2 - - - -
1553C SER* 1.3 77.5 - - - +
1555C TRP* 1.3 84.4 + + - +
1557C SER* 3.5 1.9 + - - -
1558C ASN* 2.9 58.6 + - - -
1676C HIS* 3.2 33.4 + + + -
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Residues in contact with TRP1555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1489C LEU 3.4 19.3 - - - -
1490C ILE* 3.6 45.3 + - + -
1493C LEU* 3.9 12.4 + - + -
1495C PRO* 5.4 2.6 - - + +
1507C PRO* 4.2 10.1 - - + -
1511C LEU* 5.3 4.5 - - + -
1538C ILE* 4.2 34.1 - - + -
1541C VAL* 3.7 28.5 - - + +
1542C LEU* 4.3 12.6 - - + -
1545C ARG* 4.9 2.8 - - - +
1551C THR* 3.2 28.6 + - + +
1552C VAL 4.3 2.0 - - - +
1554C PHE* 1.3 97.5 - + - +
1556C LEU* 1.3 60.1 + - - +
1558C ASN* 3.8 24.2 - - + +
1559C THR* 2.6 36.3 + - - -
1607C ILE* 3.9 3.2 - - - +
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Residues in contact with LEU1556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1552C VAL* 2.9 19.4 + - + +
1553C SER 3.8 5.2 - - - +
1555C TRP* 1.3 77.7 - - - +
1557C SER* 1.3 62.9 + - - +
1559C THR* 3.5 1.1 + - - -
1560C CYS* 3.1 43.7 + - - -
1604C ALA* 3.6 27.4 - - - +
1607C ILE* 3.6 18.1 - - + +
1608C TYR* 4.0 23.6 - - + +
1611C LEU* 4.0 19.3 - - + -
1678C MET* 3.9 24.0 - - + -
1682C LEU* 4.4 11.2 - - + -
1827C PHE* 4.2 6.1 - - + -
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Residues in contact with SER1557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505C GLY* 5.8 1.8 - - - -
1553C SER 2.8 20.6 + - - -
1554C PHE 3.6 4.9 - - - -
1556C LEU* 1.3 79.9 - - - +
1558C ASN* 1.3 58.5 + - - +
1560C CYS* 3.5 5.6 + - - +
1561C ARG* 3.0 27.4 + - - +
1676C HIS* 3.7 26.9 - - - +
1677C GLY 4.6 1.9 - - - +
1678C MET* 3.3 37.2 - - - +
1679C ASP 5.7 0.7 - - - +
1682C LEU* 6.1 0.7 - - - -
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Residues in contact with ASN1558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505C GLY* 3.2 30.2 - - - +
1507C PRO* 3.2 19.0 - - - +
1508C ALA* 3.3 15.8 + - + +
1554C PHE* 2.9 56.6 + - - +
1555C TRP* 3.8 20.6 - - + -
1557C SER* 1.3 78.0 - - - +
1559C THR* 1.3 61.2 + - - +
1560C CYS 3.2 0.2 - - - -
1561C ARG* 4.4 2.0 - - - +
1562C PHE* 2.9 30.0 + - - +
1676C HIS 5.4 1.4 + - - -
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Residues in contact with THR1559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1538C ILE* 3.7 21.9 - - + +
1555C TRP* 2.6 24.8 + - - -
1556C LEU* 3.9 3.6 - - - -
1558C ASN* 1.3 75.0 - - - +
1560C CYS* 1.3 57.8 + - - +
1562C PHE* 3.4 7.7 + - - +
1563C LEU* 3.0 26.4 + - + +
1600C LEU* 4.0 38.4 - - + +
1603C LEU* 4.4 4.9 - - + -
1604C ALA* 4.3 12.6 - - + -
1607C ILE* 3.5 19.3 - - + +
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Residues in contact with CYS1560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1556C LEU* 3.1 27.9 + - - +
1557C SER* 3.6 6.1 - - - +
1559C THR* 1.3 76.0 - - - +
1561C ARG* 1.3 59.9 + - - +
1563C LEU* 3.2 9.8 + - - +
1564C HIS* 2.8 37.5 + - + +
1604C ALA* 4.4 6.5 - - - -
1679C ASP* 3.8 17.9 - - - +
1682C LEU* 3.7 26.9 - - + -
1827C PHE* 3.8 24.2 - - - -
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Residues in contact with ARG1561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A HIS* 3.4 27.1 + - - +
131A LEU* 3.6 10.7 - - - +
1504C PRO 5.2 0.4 + - - +
1505C GLY* 4.1 9.9 - - - +
1508C ALA* 3.8 18.4 - - + -
1509C TYR* 3.5 44.8 + - + -
1557C SER 3.0 18.3 + - - +
1558C ASN* 3.5 2.0 + - - +
1560C CYS* 1.3 73.0 - - - +
1562C PHE* 1.3 60.9 + - - +
1564C HIS* 3.2 28.2 + - + +
1565C CYS* 2.9 31.8 + - - -
1568C GLN* 4.5 2.8 + - - -
1679C ASP* 4.6 1.6 + - - -
1830C ASN* 2.8 32.4 + - - +
1831C PRO* 4.1 0.8 - - - +
1832C SER* 3.8 13.1 + - - +
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Residues in contact with PHE1562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508C ALA* 3.5 24.5 - - + +
1511C LEU* 3.8 15.9 - - + -
1512C PHE* 3.7 30.1 - - + -
1515C VAL* 4.2 7.0 - - + -
1530C LEU* 6.4 0.4 - - + -
1531C LEU* 3.9 25.4 - - + -
1534C THR* 4.2 24.0 - - + -
1535C ILE* 6.2 0.4 - - + -
1558C ASN 2.9 20.0 + - - +
1559C THR* 3.5 7.0 - - - +
1561C ARG* 1.3 77.9 - - - +
1563C LEU* 1.3 55.7 + - - +
1565C CYS* 3.3 5.7 + - - +
1566C LEU* 3.1 40.7 + - + +
1600C LEU* 3.6 39.3 - - + -
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Residues in contact with LEU1563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1559C THR 3.0 13.9 + - - +
1560C CYS* 3.2 12.3 + - - +
1562C PHE* 1.3 74.4 - - - +
1564C HIS* 1.3 69.6 + - + +
1566C LEU* 3.3 6.1 + - + +
1567C LYS* 3.0 52.9 + - - +
1597C ARG* 3.7 41.3 - - + +
1600C LEU* 4.4 11.0 - - + +
1601C SER* 4.1 31.2 - - - +
1604C ALA* 5.6 4.7 - - + -
1827C PHE* 6.4 2.9 - - + -
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Residues in contact with HIS1564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1560C CYS* 2.8 29.3 + - + -
1561C ARG* 3.2 52.7 + - + +
1563C LEU* 1.3 76.9 - - + +
1565C CYS* 1.3 52.2 + - - +
1567C LYS* 3.4 3.6 + - - +
1568C GLN* 2.8 38.4 + - - +
1679C ASP* 2.9 30.5 + - - -
1828C PRO 3.1 28.5 - - - -
1829C PHE* 3.6 17.5 - - + -
1830C ASN 3.4 23.0 + - - +
1831C PRO* 5.2 0.4 - - + -
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Residues in contact with CYS1565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508C ALA 4.7 1.6 - - - -
1509C TYR* 3.6 41.3 - - - -
1512C PHE* 3.7 33.8 - - + -
1561C ARG* 2.9 24.1 + - - +
1562C PHE* 3.5 9.2 - - - +
1564C HIS* 1.3 74.5 - - - +
1566C LEU* 1.3 59.6 + - - +
1568C GLN* 4.4 3.1 - - - -
1569C TYR* 2.9 46.8 + - + +
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Residues in contact with LEU1566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1512C PHE* 3.7 28.5 - - + -
1515C VAL* 4.6 4.5 - - + -
1531C LEU* 5.0 4.7 - - + -
1562C PHE* 3.1 36.9 + - + +
1563C LEU* 3.8 6.5 - - - +
1565C CYS* 1.3 75.0 - - - +
1567C LYS* 1.3 58.1 + - - +
1569C TYR 4.0 0.3 - - - -
1570C SER* 3.1 26.3 + - - -
1588C LEU* 4.7 3.9 - - + +
1593C LEU* 3.8 29.9 - - + +
1596C TYR* 5.6 1.6 - - + -
1597C ARG* 3.9 28.5 + - + +
1600C LEU* 3.5 32.3 - - + -
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Residues in contact with LYS1567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563C LEU* 3.0 48.3 + - + +
1564C HIS* 4.9 2.2 + - - +
1566C LEU* 1.3 76.0 - - - +
1568C GLN* 1.3 64.9 + - - +
1569C TYR 3.1 1.8 - - - -
1570C SER* 2.8 26.3 + - - -
1571C GLY 4.7 0.2 + - - -
1575C PHE* 3.1 43.9 - - + +
1597C ARG* 3.9 17.0 - - - +
1827C PHE* 5.9 0.8 + - - +
1828C PRO 5.1 4.2 + - - -
1829C PHE* 3.6 39.9 - - + +
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Residues in contact with GLN1568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509C TYR* 5.9 0.5 - - - -
1561C ARG* 4.5 4.0 + - - -
1564C HIS 2.8 22.6 + - - +
1565C CYS* 4.0 3.9 - - - +
1567C LYS* 1.3 72.4 - - - +
1569C TYR* 1.3 77.7 - - + +
1575C PHE 3.9 10.5 - - - -
1576C MET* 3.8 9.2 - - - +
1578C HIS 5.2 1.4 + - - -
1579C ASN* 2.9 52.2 + - - +
1583C GLN* 3.4 13.9 + - - +
1587C CYS* 4.1 0.2 - - - -
1829C PHE* 4.0 7.6 - - + -
1831C PRO* 3.4 16.0 - - + +
1832C SER* 2.9 46.8 + - - +
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Residues in contact with TYR1569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509C TYR* 5.6 2.9 - + - -
1512C PHE* 3.3 31.6 - + + -
1565C CYS* 2.9 31.2 + - - -
1566C LEU 4.0 3.1 - - - -
1568C GLN* 1.3 102.9 + - + +
1570C SER* 1.3 58.9 + - - +
1571C GLY 3.3 2.0 - - - -
1583C GLN* 3.2 61.8 + - + +
1586C HIS* 3.8 26.6 + - + +
1587C CYS* 3.7 6.1 - - - -
1588C LEU* 2.9 30.9 + - - +
1832C SER* 5.5 0.5 + - - -
1834C LEU 3.4 13.0 + - - -
1836C LEU* 4.0 22.2 + - + +
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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