Contacts of the helix formed by residues 1562 - 1591 (chain A) 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 ASP1562 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493A SER* 5.3 2.6 + - - -
1495A LEU* 4.1 9.9 - - + +
1555A TYR* 3.0 26.0 + - + +
1559A HIS* 3.1 33.4 - - + +
1560A PRO 2.8 2.0 + - - -
1561A GLU* 1.3 86.2 - - - +
1563A GLN* 1.3 66.4 + - - +
1564A ASP 3.3 1.8 - - - -
1565A LYS* 3.0 34.6 + - - +
1566A LEU* 2.9 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1556A VAL* 3.4 28.6 - - - +
1559A HIS 4.4 0.6 + - - -
1560A PRO* 3.0 16.5 + - - +
1561A GLU 3.4 2.0 - - - -
1562A ASP* 1.3 76.8 - - - +
1564A ASP* 1.3 68.5 + - - +
1566A LEU* 3.0 16.0 + - - +
1567A THR* 2.9 33.8 + - - +
1570A LYS* 5.7 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1561A GLU 5.2 1.5 + - - +
1562A ASP 3.3 0.8 - - - -
1563A GLN* 1.3 79.1 - - - +
1565A LYS* 1.3 53.9 + - + +
1567A THR* 3.0 12.3 + - - -
1568A HIS* 2.7 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495A LEU* 3.7 15.5 - - + -
1496A GLU* 3.4 39.3 + - + +
1499A ILE* 3.7 24.0 - - + +
1561A GLU 5.1 3.5 + - - +
1562A ASP* 3.0 31.9 + - - +
1564A ASP* 1.3 77.7 - - + +
1566A LEU* 1.3 66.2 + - - +
1568A HIS* 2.9 8.2 + - - +
1569A LEU* 2.8 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495A LEU* 4.0 13.0 - - + +
1550A PHE* 3.3 35.0 - - + +
1551A PHE* 3.7 21.6 - - + -
1555A TYR* 3.8 15.3 - - + -
1556A VAL* 3.8 33.0 - - + -
1559A HIS 4.8 0.7 - - - +
1562A ASP* 2.9 24.6 + - + +
1563A GLN* 3.3 18.6 - - - +
1565A LYS* 1.3 74.3 - - - +
1567A THR* 1.3 63.9 + - - +
1569A LEU* 3.0 15.1 + - - +
1570A LYS* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563A GLN* 2.9 26.9 + - - +
1564A ASP* 3.2 12.7 + - - -
1566A LEU* 1.3 75.4 - - - +
1568A HIS* 1.3 64.3 + - - +
1570A LYS* 3.0 18.0 + - + +
1571A ASP* 2.8 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499A ILE* 3.6 30.8 - - + +
1503A SER* 5.0 3.0 + - - -
1564A ASP 2.7 15.8 + - - +
1565A LYS* 2.9 13.7 + - + +
1567A THR* 1.3 70.6 - - - +
1569A LEU* 1.3 64.5 + - - +
1571A ASP* 3.0 19.5 + - - +
1572A LEU* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495A LEU* 3.8 23.6 - - + -
1498A ALA* 4.3 5.2 - - + -
1499A ILE* 4.2 25.0 - - + +
1502A MET* 3.8 29.2 - - + -
1546A TYR* 4.1 15.3 - - + -
1550A PHE* 4.0 16.8 - - + -
1551A PHE* 4.1 15.0 - - + -
1565A LYS 2.8 15.0 + - - +
1566A LEU* 3.3 10.1 - - - +
1568A HIS* 1.3 72.2 - - - +
1570A LYS* 1.3 63.8 + - - +
1572A LEU* 2.9 19.2 + - + +
1573A ILE* 3.0 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551A PHE* 3.4 38.7 + - + +
1563A GLN* 5.7 4.4 - - - +
1566A LEU* 3.0 22.6 + - - +
1567A THR* 3.0 13.9 + - + +
1569A LEU* 1.3 73.5 - - - +
1571A ASP* 1.3 60.5 + - - +
1573A ILE* 3.0 11.2 + - - +
1574A ALA* 2.8 29.9 + - - +
1617A TYR* 3.5 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1567A THR* 2.8 17.7 + - + +
1568A HIS* 3.2 23.6 + - - +
1570A LYS* 1.3 72.0 - - - +
1572A LEU* 1.3 51.6 + - - +
1574A ALA* 3.0 2.4 + - - +
1575A TRP* 2.7 58.5 + - - +
1620A ARG* 2.2 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499A ILE* 3.4 47.6 - - + +
1502A MET* 3.9 19.7 - - + +
1503A SER* 3.8 21.3 - - - +
1506A ASN* 3.3 27.0 + - + +
1568A HIS* 2.8 35.2 + - + +
1569A LEU* 2.9 9.8 + - - +
1571A ASP* 1.3 71.9 - - - +
1573A ILE* 1.3 57.2 + - - +
1575A TRP* 3.0 6.3 + - + -
1576A GLN* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1502A MET* 3.7 22.2 - - + -
1543A PHE* 3.5 54.7 - - + +
1546A TYR* 5.5 0.7 - - + -
1547A GLU* 5.0 2.0 - - + -
1551A PHE* 4.3 14.6 - - + -
1569A LEU* 3.0 37.9 + - + +
1570A LYS* 3.4 9.9 - - - +
1572A LEU* 1.3 71.4 - - - +
1574A ALA* 1.3 68.2 + - - +
1576A GLN* 3.0 16.4 + - - +
1577A ILE* 3.8 9.0 + - - +
1613A VAL* 4.0 5.2 - - + -
1617A TYR* 4.0 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1570A LYS 2.8 15.1 + - - +
1571A ASP* 3.3 8.7 - - - +
1573A ILE* 1.3 73.7 - - - +
1575A TRP* 1.3 61.9 + - - +
1576A GLN 3.4 0.2 + - - -
1577A ILE* 3.6 6.2 + - - +
1578A PRO* 3.4 15.4 - - - +
1613A VAL* 4.2 11.9 - - - +
1617A TYR* 4.1 11.0 - - + +
1618A GLY 4.4 7.1 - - - +
1620A ARG* 3.3 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506A ASN* 4.0 11.4 - - - +
1571A ASP* 2.7 51.9 + - - +
1572A LEU* 3.0 8.9 + - + +
1574A ALA* 1.3 73.1 - - - +
1576A GLN* 1.3 61.8 + - - +
1577A ILE 3.3 0.4 - - - -
1578A PRO* 3.2 15.1 - - + +
1579A PHE* 3.2 48.0 - + + -
1620A ARG* 3.7 31.2 - - + +
1621A GLU 3.5 26.0 - - - -
1622A MET* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1502A MET* 3.5 13.9 - - - +
1505A ALA* 3.7 23.6 - - - +
1506A ASN* 2.7 31.6 + - - +
1509A ILE* 4.0 6.2 - - + +
1534A ILE* 3.8 15.5 - - - +
1543A PHE* 3.7 15.1 - - + -
1572A LEU 2.9 8.0 + - - +
1573A ILE* 3.0 14.2 + - - +
1575A TRP* 1.3 79.8 - - - +
1577A ILE* 1.3 58.6 + - + +
1579A PHE* 3.5 4.2 - - - +
1580A LEU* 3.1 45.0 + - + +
37B PHE* 3.4 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1543A PHE* 5.5 1.3 - - + -
1573A ILE 3.8 6.1 - - - +
1574A ALA 3.8 4.5 - - - +
1576A GLN* 1.3 75.2 - - + +
1578A PRO* 1.4 69.2 - - + +
1580A LEU* 3.3 2.1 + - - -
1581A GLY 2.9 24.1 + - - -
1606A PHE* 3.2 23.6 - - + -
1609A LEU* 3.9 30.1 - - + +
1610A LYS* 3.6 35.9 - - + +
1613A VAL* 3.5 44.9 - - + -
1614A GLU* 4.7 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1574A ALA 3.4 9.0 - - - +
1575A TRP* 3.2 33.2 - - + +
1577A ILE* 1.4 98.8 - - + +
1579A PHE* 1.3 59.1 + - + +
1581A GLY* 3.4 2.4 + - - +
1582A ALA* 2.9 30.0 + - - +
1606A PHE* 5.3 0.9 - - + -
1620A ARG* 3.3 28.7 - - + +
1621A GLU* 4.3 2.2 - - + -
1622A MET* 4.2 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506A ASN* 3.9 39.5 - - + -
1509A ILE* 3.9 17.8 - - + +
1510A LEU* 3.3 39.0 - - + -
1513A ILE* 3.5 7.5 - - - +
1575A TRP* 3.2 48.5 - + + -
1576A GLN* 3.5 7.0 - - - +
1578A PRO* 1.3 73.0 - - + +
1580A LEU* 1.3 66.9 + - - +
1582A ALA* 3.1 13.2 + - - +
1583A GLY 3.1 10.2 + - - -
1622A MET* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509A ILE* 3.7 24.8 - - + +
1531A LEU* 3.8 17.9 - - + +
1534A ILE* 3.8 19.5 - - + -
1535A VAL* 3.6 28.3 - - + -
1576A GLN* 3.1 33.1 + - + +
1577A ILE* 3.5 7.9 - - - +
1579A PHE* 1.3 78.6 - - - +
1581A GLY* 1.3 58.1 + - - +
1583A GLY* 3.3 2.6 + - - -
1584A ILE* 2.8 34.9 + - - +
1606A PHE* 3.6 13.2 - - + -
1609A LEU* 4.5 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1577A ILE 2.9 10.3 + - - -
1578A PRO* 3.7 4.5 - - - -
1579A PHE 3.2 0.2 - - - -
1580A LEU* 1.3 73.4 - - - +
1582A ALA* 1.3 64.5 + - - +
1584A ILE* 3.3 4.9 + - - +
1585A LYS* 3.0 24.4 + - - +
1606A PHE* 3.4 27.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513A ILE* 3.6 19.3 - - + -
1517A GLN* 5.9 1.5 + - - +
1578A PRO 2.9 14.6 + - - +
1579A PHE 3.1 8.5 + - - +
1581A GLY* 1.3 76.6 - - - +
1583A GLY* 1.3 61.7 - - - +
1585A LYS* 3.5 9.6 + - - +
1586A ILE* 3.4 22.9 + - - +
1622A MET* 3.8 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513A ILE* 3.7 19.4 - - - +
1527A LEU* 3.9 5.7 - - - +
1531A LEU* 3.5 22.5 - - - +
1579A PHE 3.1 11.2 + - - -
1580A LEU 3.7 2.5 - - - -
1582A ALA* 1.3 74.6 - - - +
1584A ILE* 1.3 59.5 + - - +
1586A ILE* 3.3 11.0 + - - +
1587A HIS 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1531A LEU* 4.0 18.2 - - + -
1535A VAL* 4.2 14.8 - - + -
1580A LEU 2.8 25.7 + - - +
1581A GLY* 3.3 6.0 + - - +
1583A GLY* 1.3 74.3 - - - +
1585A LYS* 1.3 55.1 + - - +
1587A HIS* 3.1 3.9 + - + +
1588A GLU* 2.7 31.0 + - - +
1599A HIS* 3.4 20.1 - - + -
1602A MET* 4.4 15.5 - - - +
1603A GLU* 4.0 22.9 - - + +
1606A PHE* 3.6 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1581A GLY 3.0 13.1 + - - +
1582A ALA* 3.5 13.5 - - - +
1584A ILE* 1.3 76.3 - - - +
1586A ILE* 1.3 60.8 + - + +
1588A GLU* 3.2 12.8 + - + +
1589A LYS* 3.2 50.0 + - - +
1603A GLU* 5.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513A ILE* 3.9 41.3 - - + +
1516A TYR* 4.4 11.9 - - + -
1517A GLN* 4.4 20.4 - - + +
1527A LEU* 4.0 14.8 - - + -
1582A ALA 3.4 10.5 + - - +
1583A GLY* 3.3 11.1 + - - +
1584A ILE 3.2 0.4 - - - -
1585A LYS* 1.3 72.7 - - + +
1587A HIS* 1.3 70.2 + - - +
1589A LYS* 2.9 22.0 + - + +
1590A ARG* 3.0 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524A ILE* 4.5 7.3 - - + +
1527A LEU* 3.9 18.6 - - + -
1528A SER* 2.9 42.2 + - - -
1531A LEU* 4.1 3.6 - - + -
1583A GLY 2.9 13.5 + - - +
1584A ILE* 3.1 13.7 + - - +
1586A ILE* 1.3 76.0 - - - +
1588A GLU* 1.3 64.2 + - - +
1590A ARG* 4.6 2.2 - - - +
1591A VAL* 3.0 57.5 + - + +
1598A PHE* 4.1 7.2 - + - -
1599A HIS* 2.6 30.9 + - + +
1602A MET* 3.4 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584A ILE 2.7 12.6 + - - +
1585A LYS* 3.2 15.5 - - + +
1586A ILE 3.0 0.2 - - - -
1587A HIS* 1.3 74.9 - - - +
1589A LYS* 1.3 76.6 + - - +
1591A VAL* 3.7 4.3 - - - +
1596A ARG* 2.7 47.3 + - - +
1599A HIS* 3.3 29.6 - - + +
1603A GLU* 4.0 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1585A LYS* 3.2 44.2 + - - +
1586A ILE* 2.9 15.3 + - + +
1588A GLU* 1.3 88.9 + - - +
1590A ARG* 1.3 66.6 + - + +
1591A VAL 3.7 1.9 + - - +
1596A ARG* 5.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1516A TYR* 2.3 60.2 + - + +
1517A GLN* 4.2 3.8 + - - +
1519A ASP 3.7 2.4 + - - -
1520A GLU* 3.6 46.8 + - - +
1522A LEU 4.5 6.8 + - - +
1524A ILE* 3.3 30.6 - - + +
1586A ILE* 3.0 31.0 + - + +
1587A HIS* 4.3 1.1 - - - +
1589A LYS* 1.3 82.3 - - + +
1591A VAL* 1.3 63.6 + - - +
1592A SER* 3.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524A ILE* 4.3 11.6 - - + +
1587A HIS* 3.0 41.7 + - + +
1588A GLU* 3.7 5.2 - - - +
1589A LYS 3.5 2.0 - - - +
1590A ARG* 1.3 77.9 - - - +
1592A SER* 1.3 77.1 + - - +
1593A ASP* 3.9 2.3 + - - +
1595A LEU* 3.5 27.6 - - + +
1596A ARG* 3.5 35.6 + - - +
1599A HIS* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
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