Contacts of the helix formed by residues 1493 - 1519 (chain C) in PDB entry 3B13
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 SER1493 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1462C MET 4.4 0.4 - - - -
1463C TRP* 3.3 25.5 - - - -
1491C THR 4.0 0.6 + - - -
1492C ILE* 1.3 74.1 - - - +
1494C PRO* 1.3 77.5 - - - +
1495C LEU* 3.9 7.5 + - - +
1496C GLU* 3.0 35.1 + - - +
1497C ASN* 2.9 20.3 + - - +
1555C TYR* 5.9 1.1 - - - -
1562C ASP* 5.3 4.2 + - - -
1565C LYS* 4.4 4.2 + - - -
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Residues in contact with PRO1494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459C PHE 3.5 22.2 - - - +
1460C ALA 3.4 20.2 - - - +
1461C SER 4.2 0.2 - - - -
1462C MET 3.4 27.8 - - - +
1463C TRP* 3.4 33.0 - - + +
1493C SER* 1.3 85.6 - - - +
1495C LEU* 1.3 56.8 + - - +
1497C ASN* 3.2 4.9 + - + +
1498C ALA* 2.9 28.4 + - - +
1546C TYR* 5.4 0.5 - - - -
1550C PHE* 3.7 12.1 - - + -
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Residues in contact with LEU1495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493C SER* 3.1 7.2 + - - +
1494C PRO* 1.3 78.2 - - - +
1496C GLU* 1.3 64.8 + - + +
1498C ALA* 3.0 6.1 + - - +
1499C ILE* 2.9 33.3 + - + +
1550C PHE* 3.7 23.6 - - + -
1555C TYR* 3.6 26.5 - - + +
1562C ASP* 4.0 15.5 - - + +
1565C LYS* 3.9 27.6 - - + +
1566C LEU* 3.7 24.0 - - + -
1569C LEU* 3.7 28.9 - - + -
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Residues in contact with GLU1496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491C THR 3.9 4.4 - - - +
1492C ILE* 3.3 28.7 - - + +
1493C SER* 3.0 35.3 + - - +
1495C LEU* 1.3 80.4 - - - +
1497C ASN* 1.3 56.2 + - - +
1499C ILE* 3.1 13.4 - - - +
1500C GLU* 3.0 32.1 + - - +
1565C LYS* 2.8 36.6 + - + +
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Residues in contact with ASN1497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459C PHE* 5.8 1.2 - - - -
1462C MET* 3.4 32.7 + - - +
1464C ILE* 3.6 26.8 - - + +
1466C ARG* 5.1 1.6 + - - -
1492C ILE* 3.7 10.5 - - + +
1493C SER 2.9 11.9 + - - +
1494C PRO* 3.4 12.1 - - + +
1495C LEU 3.1 0.2 - - - -
1496C GLU* 1.3 73.3 - - - +
1498C ALA* 1.3 62.1 + - - +
1500C GLU* 3.0 15.9 + - - +
1501C THR* 2.9 40.1 + - - -
1546C TYR* 5.5 2.2 + - - -
33D ILE* 4.7 5.9 - - - +
34D PRO 5.2 1.6 + - - -
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Residues in contact with ALA1498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1494C PRO 2.9 12.7 + - - +
1495C LEU 3.0 9.6 + - - +
1497C ASN* 1.3 76.6 - - - +
1499C ILE* 1.3 62.8 + - - +
1501C THR* 3.2 1.9 + - - -
1502C MET* 2.9 30.1 + - - +
1546C TYR* 3.4 48.1 - - + -
1550C PHE* 3.7 11.0 - - + -
1569C LEU* 4.3 7.2 - - + -
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Residues in contact with ILE1499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495C LEU* 2.9 24.6 + - + +
1496C GLU* 3.1 15.0 - - - +
1498C ALA* 1.3 76.0 - - - +
1500C GLU* 1.3 66.1 + - + +
1502C MET* 3.3 2.7 + - - +
1503C SER* 2.9 26.6 + - - -
1565C LYS* 3.6 32.3 - - + +
1568C HIS* 3.6 30.7 - - + +
1569C LEU* 3.7 26.0 - - + +
1572C LEU* 3.6 13.2 - - + +
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Residues in contact with GLU1500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1466C ARG* 2.7 45.5 + - - -
1492C ILE* 4.2 15.8 - - - +
1496C GLU* 3.0 18.9 + - - +
1497C ASN* 3.0 12.9 + - - +
1499C ILE* 1.3 77.1 - - + +
1501C THR* 1.3 57.5 + - - +
1503C SER* 3.3 6.9 + - - -
1504C THR* 2.9 35.2 + - - +
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Residues in contact with THR1501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497C ASN* 2.9 25.5 + - - -
1498C ALA 3.5 4.0 - - - -
1500C GLU* 1.3 73.1 - - - +
1502C MET* 1.3 66.9 + - - +
1504C THR* 3.1 8.2 + - - -
1505C ALA* 2.9 22.4 + - + +
1546C TYR* 3.4 29.2 + - + +
35D THR* 3.6 31.3 - - + +
36D VAL 5.0 0.7 - - - +
37D PHE* 4.9 12.3 - - + -
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Residues in contact with MET1502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1498C ALA 2.9 19.0 + - - +
1499C ILE 3.6 4.0 - - - +
1501C THR* 1.3 75.2 - - - +
1503C SER* 1.3 63.5 + - - +
1505C ALA* 3.2 2.8 + - - +
1506C ASN* 2.9 30.8 + - - +
1543C PHE* 4.1 20.9 - - + -
1546C TYR* 3.9 21.5 - - + -
1569C LEU* 3.7 20.0 - - + -
1572C LEU* 3.9 18.6 - - + -
1573C ILE* 4.4 13.0 - - - -
1576C GLN* 3.9 15.5 - - - +
37D PHE* 3.0 46.4 - - + -
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Residues in contact with SER1503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499C ILE* 2.9 19.6 + - - -
1500C GLU* 3.4 9.2 - - - -
1502C MET* 1.3 77.5 - - - +
1504C THR* 1.3 58.0 + - - +
1506C ASN* 3.5 4.3 + - - +
1507C GLU* 2.9 32.5 + - - +
1568C HIS* 5.8 1.2 + - - -
1572C LEU* 4.3 19.6 - - - +
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Residues in contact with THR1504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1500C GLU* 2.9 15.3 + - - +
1501C THR* 3.4 11.6 - - - -
1503C SER* 1.3 75.5 - - - +
1505C ALA* 1.3 61.0 + - - +
1507C GLU* 3.3 10.3 + - + +
1508C LYS* 2.9 51.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA1505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1501C THR* 2.9 13.5 + - + +
1502C MET 3.7 6.7 - - - +
1504C THR* 1.3 72.7 - - - +
1506C ASN* 1.3 68.4 + - - +
1508C LYS* 3.1 11.0 + - - +
1509C ILE* 3.0 28.7 + - - +
1534C ILE* 4.2 13.0 - - + +
1576C GLN* 4.0 7.9 - - - +
37D PHE* 3.8 30.7 - - + -
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Residues in contact with ASN1506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1502C MET* 2.9 17.2 + - - +
1503C SER* 3.6 6.3 - - - +
1505C ALA* 1.3 75.2 - - - +
1507C GLU* 1.3 58.8 + - - +
1509C ILE* 3.4 6.4 + - - +
1510C LEU* 2.9 29.1 + - - +
1572C LEU* 3.4 39.2 + - - +
1575C TRP* 4.1 4.2 - - - +
1576C GLN* 2.9 38.4 + - - +
1579C PHE* 3.7 35.0 - - + -
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Residues in contact with GLU1507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1435C LYS* 3.7 22.2 + - - -
1503C SER* 2.9 19.6 + - - +
1504C THR* 3.5 9.4 - - - +
1505C ALA 3.2 0.2 - - - -
1506C ASN* 1.3 78.9 - - - +
1508C LYS* 1.3 55.9 + - - +
1510C LEU* 3.4 11.1 + - + +
1511C MET* 3.0 42.8 + - + +
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Residues in contact with LYS1508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1504C THR* 2.9 35.2 + - + +
1505C ALA* 3.1 11.9 + - - +
1507C GLU* 1.3 72.2 - - - +
1509C ILE* 1.3 66.7 - - - +
1511C MET* 3.2 11.7 + - + +
1512C MET* 2.9 27.1 + - + +
1530C LEU* 4.2 28.5 - - + +
1534C ILE* 6.0 0.4 - - + -
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Residues in contact with ILE1509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505C ALA 3.0 23.3 + - - +
1506C ASN* 3.6 10.3 - - - +
1508C LYS* 1.3 75.9 - - - +
1510C LEU* 1.3 65.0 + - - +
1512C MET* 3.3 2.8 + - - +
1513C ILE* 2.9 34.5 + - + +
1530C LEU* 4.0 13.4 - - + +
1531C LEU* 4.4 10.3 - - + -
1534C ILE* 3.7 26.0 - - + -
1576C GLN* 4.3 9.2 - - + +
1579C PHE* 3.7 31.6 - - + +
1580C LEU* 3.5 33.9 - - + +
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Residues in contact with LEU1510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506C ASN 2.9 14.7 + - - +
1507C GLU* 3.5 10.3 - - + +
1508C LYS 3.2 0.2 - - - -
1509C ILE* 1.3 76.2 - - - +
1511C MET* 1.3 65.5 + - + +
1513C ILE* 3.0 20.9 + - + +
1514C ASN* 3.0 34.7 + - - +
1579C PHE* 3.5 52.3 - - + -
1622C MET* 4.3 9.0 - - + -
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Residues in contact with MET1511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1428C ASP* 3.3 31.0 - - + +
1432C ASN* 3.8 33.0 - - - +
1435C LYS* 4.0 13.2 - - - -
1507C GLU* 3.0 33.5 + - + +
1508C LYS* 3.2 10.1 + - + +
1510C LEU* 1.3 75.5 - - + +
1512C MET* 1.3 59.0 + - - +
1514C ASN* 3.2 5.2 + - - +
1515C GLN* 2.9 30.8 + - - +
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Residues in contact with MET1512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508C LYS* 2.9 16.9 + - + +
1509C ILE 3.6 7.4 - - - +
1511C MET* 1.3 75.8 - - + +
1513C ILE* 1.3 58.1 + - + +
1515C GLN* 3.2 23.0 + - - +
1516C TYR* 2.8 65.1 + - + +
1526C PRO* 3.9 33.7 - - + +
1527C LEU* 4.1 17.5 - - + -
1530C LEU* 3.7 27.8 - - + -
1531C LEU* 6.5 0.2 - - + -
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Residues in contact with ILE1513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509C ILE* 2.9 30.0 + - + +
1510C LEU* 3.0 24.7 + - + +
1512C MET* 1.3 75.5 - - + +
1514C ASN* 1.3 67.1 + - - +
1516C TYR* 3.9 0.4 - - - -
1517C GLN* 2.9 50.2 + - - +
1527C LEU* 6.0 2.2 - - + -
1579C PHE 3.6 23.6 - - - +
1582C ALA* 4.1 13.5 - - + -
1583C GLY* 4.0 22.0 - - - +
1586C ILE* 3.9 13.4 - - + +
1622C MET* 4.2 7.6 - - + -
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Residues in contact with ASN1514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1428C ASP* 2.9 29.4 + - - +
1510C LEU* 3.0 28.3 + - - +
1511C MET* 3.4 5.8 - - - +
1513C ILE* 1.3 80.0 - - - +
1515C GLN* 1.3 57.4 + - - +
1517C GLN* 3.8 12.4 - - - +
1518C SER* 3.0 37.1 + - - +
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Residues in contact with GLN1515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1511C MET* 2.9 16.1 + - - +
1512C MET* 3.2 31.3 + - - +
1514C ASN* 1.3 77.8 - - - +
1516C TYR* 1.3 60.6 + - + +
1518C SER* 3.8 3.9 - - - -
1519C ASP* 3.0 23.6 + - - +
1522C LEU* 3.5 30.2 - - + +
----------------------------------------------------------
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Residues in contact with TYR1516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1512C MET* 2.8 58.1 + - + +
1513C ILE* 4.1 1.8 - - - +
1515C GLN* 1.3 74.0 - - + +
1517C GLN* 1.3 63.5 + - - +
1518C SER 3.1 1.6 - - - -
1519C ASP 3.2 11.4 + - - +
1522C LEU* 3.5 28.4 - - + +
1523C PRO 2.5 31.4 + - - -
1524C ILE* 4.4 6.7 - - + -
1526C PRO* 3.7 19.9 - - - +
1527C LEU* 3.7 30.6 + - + -
1586C ILE* 4.1 14.6 - - + -
1590C ARG* 2.3 54.2 + - - +
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Residues in contact with GLN1517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513C ILE* 2.9 39.2 + - - +
1514C ASN* 3.8 12.5 - - - +
1516C TYR* 1.3 75.5 - - - +
1518C SER* 1.3 63.4 + - - +
1520C GLU* 4.4 12.5 - - - +
1582C ALA* 5.8 3.0 - - - +
1586C ILE* 3.8 17.1 - - + +
1590C ARG* 4.2 3.8 - - - +
1622C MET* 6.1 1.4 - - - +
----------------------------------------------------------
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Residues in contact with SER1518 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1514C ASN* 3.0 20.5 + - - +
1515C GLN* 3.8 5.2 - - - -
1517C GLN* 1.3 79.8 - - - +
1519C ASP* 1.3 59.4 + - - +
1520C GLU* 4.2 1.1 + - - +
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Residues in contact with ASP1519 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1515C GLN 3.0 13.2 + - - +
1516C TYR 3.2 6.6 + - - +
1518C SER* 1.3 77.7 - - - +
1520C GLU* 1.3 60.1 + - - +
1521C THR* 2.8 36.8 + - - +
1522C LEU* 3.3 35.0 - - + +
1590C ARG* 3.1 13.2 + - - -
----------------------------------------------------------
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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