Contacts of the helix formed by residues 1523 - 1546 (chain A) in PDB entry 5JCY
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 ASP1523 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518A ALA 3.1 11.7 + - - +
1521A LEU* 4.1 15.1 - - + +
1522A ASN* 1.3 75.4 - - - +
1524A ASP* 1.3 60.9 + - - +
1525A GLN* 3.3 10.6 + - - +
1526A LYS* 3.0 45.9 + - + +
1527A VAL* 3.2 16.6 + - - +
1591A PHE* 3.7 2.8 - - - -
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Residues in contact with ASP1524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1522A ASN 4.3 5.5 - - - +
1523A ASP* 1.3 72.2 - - - +
1525A GLN* 1.3 87.0 + - - +
1527A VAL* 3.4 5.9 + - - +
1528A ARG* 3.0 27.7 + - - +
1591A PHE* 3.5 25.8 - - + -
409B LEU* 3.7 27.4 - - + +
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Residues in contact with GLN1525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1523A ASP* 3.2 8.2 + - - +
1524A ASP* 1.3 103.0 + - - +
1526A LYS* 1.3 58.0 + - - +
1528A ARG* 3.4 33.9 + - - +
1529A SER* 2.9 29.5 + - - -
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Residues in contact with LYS1526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1476A GLU* 5.2 1.6 + - - +
1477A TYR* 2.7 65.0 + - - +
1478A LYS* 4.8 0.2 - - - +
1479A LYS* 4.2 24.3 - - + +
1482A GLU* 4.2 2.8 - - - +
1517A HIS* 5.2 3.4 + - - -
1518A ALA* 4.1 19.3 - - + +
1521A LEU* 4.2 20.5 - - + +
1523A ASP* 3.0 34.1 + - + +
1525A GLN* 1.3 74.5 - - - +
1527A VAL* 1.3 59.2 + - - +
1529A SER* 3.3 5.4 + - - -
1530A LEU* 2.9 32.4 + - - +
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Residues in contact with VAL1527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515A VAL* 4.6 11.0 - - + +
1518A ALA* 3.6 22.9 - - + +
1519A ASP* 4.2 3.1 - - + +
1523A ASP 3.2 14.7 + - - +
1524A ASP* 3.6 8.1 - - - +
1525A GLN 3.4 0.2 - - - -
1526A LYS* 1.3 77.8 - - - +
1528A ARG* 1.3 63.0 + - - +
1530A LEU* 3.8 4.5 - - - +
1531A LEU* 3.0 51.1 + - + +
1591A PHE* 4.0 21.3 - - + -
1593A LEU* 3.9 26.5 - - + -
1596A TYR* 4.9 0.9 - - + -
409B LEU* 4.1 5.2 - - + -
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Residues in contact with ARG1528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524A ASP 3.0 17.3 + - - +
1525A GLN* 3.6 32.1 + - - +
1527A VAL* 1.3 77.7 - - - +
1529A SER* 1.3 56.9 + - - +
1531A LEU* 3.8 1.0 - - - +
1532A THR* 2.8 44.8 + - - +
1596A TYR* 3.2 28.9 + - - +
410B LYS 4.8 5.9 + - - -
412B PRO* 3.7 25.2 - - + +
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Residues in contact with SER1529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1482A GLU* 2.5 28.9 + - - -
1525A GLN 2.9 18.4 + - - -
1526A LYS* 3.7 4.9 - - - -
1527A VAL 3.3 0.2 - - - -
1528A ARG* 1.3 77.3 - - - +
1530A LEU* 1.3 57.9 + - - +
1532A THR* 3.8 4.8 - - - -
1533A SER* 2.9 35.3 + - - -
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Residues in contact with LEU1530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477A TYR* 3.5 20.6 - - + +
1482A GLU* 3.5 11.8 + - + -
1485A LEU* 3.9 24.7 - - + -
1486A VAL* 5.0 4.3 - - + -
1511A LEU* 4.2 10.1 - - + +
1514A CYS* 3.7 29.2 - - + +
1515A VAL* 3.7 29.2 - - + +
1518A ALA* 5.4 3.8 - - + -
1526A LYS 2.9 18.1 + - - +
1527A VAL* 3.8 4.3 - - - +
1529A SER* 1.3 77.2 - - - +
1531A LEU* 1.3 57.0 + - + +
1533A SER* 3.4 1.3 + - - -
1534A THR* 2.7 43.2 + - - +
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Residues in contact with LEU1531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515A VAL* 3.9 14.6 - - + -
1527A VAL* 3.0 40.5 + - + +
1528A ARG 4.1 0.2 - - - +
1530A LEU* 1.3 78.6 - - + +
1532A THR* 1.3 58.0 + - - +
1534A THR* 3.7 3.4 - - - +
1535A ILE* 3.1 39.1 + - + +
1562A PHE* 3.5 37.5 - - + -
1566A LEU* 5.3 3.1 - - + -
1593A LEU* 4.6 7.6 - - + -
1596A TYR* 3.3 49.6 - - + -
1600A LEU* 5.2 6.1 - - + -
417B MET* 4.7 0.7 - - - -
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Residues in contact with THR1532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1528A ARG* 2.8 28.3 + - - +
1529A SER* 3.8 5.2 - - - -
1531A LEU* 1.3 76.8 - - - +
1533A SER* 1.3 59.2 + - - +
1535A ILE* 3.5 0.9 + - - +
1536A ASN* 3.0 46.5 + - - +
1596A TYR* 5.2 0.2 - - - -
412B PRO* 4.2 13.2 - - + +
417B MET* 3.9 32.9 - - + +
420B MET 5.1 6.7 - - - +
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Residues in contact with SER1533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482A GLU* 3.1 12.3 + - - -
1483A GLN* 3.1 29.2 + - - -
1486A VAL* 3.9 17.4 - - - +
1529A SER* 2.9 20.0 + - - -
1530A LEU* 3.9 3.8 - - - -
1532A THR* 1.3 74.0 - - - +
1534A THR* 1.3 58.6 + - - +
1536A ASN* 4.1 5.0 - - - +
1537A SER* 2.7 37.4 + - - -
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Residues in contact with THR1534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486A VAL* 4.3 2.6 - - - +
1490A ILE* 3.8 10.9 - - + +
1511A LEU* 3.6 43.6 - - + +
1530A LEU* 2.7 29.1 + - - +
1531A LEU* 3.7 8.4 - - - +
1533A SER* 1.3 74.9 - - - +
1535A ILE* 1.3 68.8 + - + +
1537A SER* 3.2 3.1 + - - -
1538A ILE* 3.0 39.6 + - + +
1562A PHE* 4.4 17.4 - - + -
1600A LEU* 5.6 0.7 - - + -
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Residues in contact with ILE1535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1531A LEU* 3.1 24.2 + - + +
1534A THR* 1.3 81.4 - - + +
1536A ASN* 1.3 65.6 + - - +
1538A ILE* 3.4 3.3 + - - +
1539A LYS* 3.1 30.5 + - + +
1596A TYR* 5.3 2.9 - - + -
1599A VAL* 3.7 16.4 - - + -
1600A LEU* 3.9 31.0 - - + -
1603A LEU* 4.4 14.3 - - + +
414B LEU* 3.6 26.5 - - + -
417B MET* 3.6 35.0 - - + -
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Residues in contact with ASN1536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532A THR* 3.0 36.8 + - - +
1533A SER* 4.1 4.9 - - - +
1535A ILE* 1.3 76.1 - - - +
1537A SER* 1.3 58.7 + - - +
1539A LYS* 3.5 12.6 + - - +
1540A LYS* 3.0 35.1 + - + +
417B MET* 3.3 38.1 + - - +
418B GLU* 4.3 3.3 + - - -
420B MET* 4.4 10.5 + - - +
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Residues in contact with SER1537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1483A GLN* 5.5 0.3 + - - -
1486A VAL* 3.5 19.6 - - - +
1490A ILE* 3.7 25.4 - - - -
1491A LEU* 3.5 18.8 - - - +
1533A SER 2.7 22.8 + - - -
1534A THR 3.6 3.1 - - - -
1536A ASN* 1.3 73.8 - - - +
1538A ILE* 1.3 61.0 + - - +
1540A LYS* 3.2 5.5 + - - +
1541A VAL* 2.9 32.2 + - - +
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Residues in contact with ILE1538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490A ILE* 3.9 17.9 - - + -
1511A LEU* 5.6 1.1 - - + -
1534A THR* 3.0 38.5 + - + +
1535A ILE* 3.8 4.5 - - + +
1536A ASN 3.3 0.2 - - - -
1537A SER* 1.3 77.4 - - - +
1539A LYS* 1.3 62.8 + - - +
1541A VAL* 3.3 4.7 + - - +
1542A LEU* 3.1 41.7 + - + +
1555A TRP* 4.0 29.4 - - + -
1559A THR* 3.9 18.4 - - + +
1562A PHE* 6.2 1.1 - - + -
1600A LEU* 5.7 2.5 - - + -
1603A LEU* 4.1 16.4 - - + -
1607A ILE* 4.0 16.2 - - + -
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Residues in contact with LYS1539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1535A ILE* 3.1 22.9 + - + +
1536A ASN* 3.7 15.0 - - - +
1537A SER 3.3 0.2 - - - -
1538A ILE* 1.3 76.9 - - - +
1540A LYS* 1.3 62.1 + - + +
1542A LEU* 3.3 7.0 + - - +
1543A LYS* 2.9 25.1 + - - +
1603A LEU* 4.0 14.3 - - + +
1606A GLN* 2.9 28.4 + - - +
414B LEU* 3.5 39.1 - - - +
418B GLU* 5.4 13.0 - - + +
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Residues in contact with LYS1540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491A LEU* 4.1 13.5 - - + -
1536A ASN* 3.0 28.1 + - + +
1537A SER* 3.2 8.9 + - - +
1539A LYS* 1.3 76.4 - - + +
1541A VAL* 1.3 62.6 + - - +
1543A LYS* 3.2 17.4 + - - +
1544A LYS* 3.2 25.4 + - - +
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Residues in contact with VAL1541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490A ILE* 3.5 28.9 - - + +
1491A LEU* 3.8 21.8 - - + +
1537A SER 2.9 16.9 + - - +
1538A ILE* 3.7 8.3 - - - +
1539A LYS 3.3 0.2 - - - -
1540A LYS* 1.3 75.4 - - - +
1542A LEU* 1.3 57.8 + - - +
1544A LYS* 3.2 6.2 + - - +
1545A ARG* 2.8 44.8 + - - +
1551A THR* 3.5 28.0 - - + -
1555A TRP* 3.9 15.0 - - + +
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Residues in contact with LEU1542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1538A ILE* 3.1 26.0 + - + +
1539A LYS* 3.9 6.5 - - - +
1541A VAL* 1.3 75.5 - - + +
1543A LYS* 1.3 60.1 + - - +
1546A GLY* 2.9 27.9 + - - +
1551A THR* 4.2 16.8 - - + +
1552A VAL* 4.0 37.7 - - + -
1555A TRP* 4.5 7.9 - - + -
1603A LEU* 5.5 1.6 - - + -
1607A ILE* 3.6 42.2 - - + -
1610A GLN* 5.6 6.9 - - + +
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Residues in contact with LYS1543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539A LYS 2.9 17.3 + - - +
1540A LYS* 3.2 9.8 + - - +
1542A LEU* 1.3 78.5 - - - +
1544A LYS* 1.3 62.3 + - - +
1546A GLY 4.6 1.0 + - - -
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Residues in contact with LYS1544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491A LEU* 6.1 1.6 - - - +
1540A LYS* 3.2 22.0 + - - +
1541A VAL* 3.9 4.6 - - - +
1543A LYS* 1.3 84.7 - - + +
1545A ARG* 1.3 70.7 + - + +
1546A GLY 3.7 0.7 - - - -
1547A ASP* 4.6 5.6 - - - +
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Residues in contact with ARG1545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490A ILE 4.5 1.8 + - - -
1491A LEU 3.8 18.0 + - - -
1492A GLU* 5.2 0.8 - - - +
1493A LEU 3.5 18.5 + - - -
1494A LYS* 5.3 6.1 - - - +
1495A PRO* 3.7 18.2 - - - +
1541A VAL* 2.8 35.5 + - - +
1542A LEU* 4.6 0.4 - - - -
1544A LYS* 1.3 95.1 - - + +
1546A GLY* 1.3 57.1 + - - +
1547A ASP* 3.0 17.3 + - - -
1548A ASP* 3.0 26.5 + - + +
1551A THR* 2.8 45.3 + - + +
1555A TRP* 5.0 2.0 - - - +
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Residues in contact with GLY1546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542A LEU* 2.9 28.9 + - - -
1543A LYS 4.4 1.4 + - - -
1544A LYS 3.7 1.4 - - - -
1545A ARG* 1.3 77.0 - - - +
1547A ASP* 1.3 56.7 + - - +
1548A ASP 3.3 0.7 - - - -
1552A VAL* 3.4 18.4 - - - +
1610A GLN* 3.0 29.0 + - - -
1614A VAL* 3.3 9.4 - - - +
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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