Contacts of the helix formed by residues 1562 - 1590 (chain B) in PDB entry 2YIN
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493B SER* 5.4 2.4 + - - -
1495B LEU* 3.5 20.1 - - + +
1555B TYR* 2.3 39.7 + - + +
1559B HIS* 3.7 20.7 + - + +
1560B PRO 3.2 1.0 - - - -
1561B GLU* 1.3 92.7 - - - +
1563B GLN* 1.3 52.2 + - - +
1564B ASP 3.1 3.4 - - - -
1565B LYS* 2.8 20.1 + - - +
1566B LEU* 2.6 38.3 + - + +
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Residues in contact with GLN1563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1556B VAL* 5.6 7.2 - - + -
1559B HIS 4.9 1.2 + - - -
1560B PRO* 3.4 19.9 + - + +
1561B GLU 3.1 1.4 - - - -
1562B ASP* 1.3 79.0 - - - +
1564B ASP* 1.3 63.2 + - - +
1565B LYS 3.4 0.2 + - - -
1566B LEU* 3.4 21.2 + - + +
1567B THR* 3.4 19.8 + - - +
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Residues in contact with ASP1564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1561B GLU 3.8 9.7 + - - +
1562B ASP 3.1 0.8 - - - -
1563B GLN* 1.3 78.4 - - - +
1565B LYS* 1.3 62.5 + - + +
1567B THR* 2.5 25.4 + - - -
1568B HIS* 3.5 7.6 + - - +
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Residues in contact with LYS1565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493B SER* 5.7 0.4 - - - +
1495B LEU* 3.7 25.8 - - + -
1496B GLU* 4.1 33.9 - - + -
1499B ILE* 3.7 17.4 - - + +
1561B GLU* 5.0 5.9 + - - -
1562B ASP* 2.8 22.9 + - + +
1564B ASP* 1.3 81.0 - - + +
1566B LEU* 1.3 65.3 + - - +
1567B THR 3.2 0.4 - - - -
1568B HIS* 3.0 10.5 + - + +
1569B LEU* 2.9 19.2 + - - +
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Residues in contact with LEU1566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495B LEU* 4.1 18.6 - - + -
1550B PHE* 4.1 6.5 - - + +
1551B PHE* 4.0 28.0 - - + -
1555B TYR* 4.0 24.2 - - + -
1556B VAL* 3.9 34.1 - - + -
1559B HIS 5.7 0.4 - - - +
1562B ASP* 2.6 25.0 + - + +
1563B GLN* 3.4 15.4 + - - +
1565B LYS* 1.3 72.8 - - - +
1567B THR* 1.3 64.2 + - + +
1569B LEU* 3.2 6.9 + - - +
1570B LYS* 2.9 22.7 + - - +
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Residues in contact with THR1567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563B GLN 3.4 11.4 + - - +
1564B ASP* 2.5 31.5 + - - -
1566B LEU* 1.3 76.7 - - + +
1568B HIS* 1.3 56.1 + - - +
1570B LYS* 3.1 9.3 + - - +
1571B ASP* 2.9 38.1 + - - +
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Residues in contact with HIS1568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499B ILE* 3.6 34.3 - - + +
1503B SER* 5.3 1.6 - - - -
1564B ASP 3.9 8.7 - - - +
1565B LYS* 3.0 12.4 + - - +
1567B THR* 1.3 83.1 + - - +
1569B LEU* 1.3 61.9 + - - +
1571B ASP* 3.2 21.0 + - + +
1572B LEU* 3.3 27.4 + - + +
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Residues in contact with LEU1569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495B LEU* 3.9 23.1 - - + -
1498B ALA* 4.5 9.4 - - + -
1499B ILE* 4.2 17.9 - - + +
1502B MET* 4.9 11.9 - - + -
1546B TYR* 4.5 16.2 - - + -
1550B PHE* 4.2 13.7 - - + -
1551B PHE* 4.0 20.0 - - + -
1565B LYS 2.9 12.0 + - - +
1566B LEU* 3.5 9.9 - - - +
1568B HIS* 1.3 77.6 - - - +
1570B LYS* 1.3 62.7 + - - +
1572B LEU* 3.3 18.1 + - - +
1573B ILE* 3.4 30.5 + - + +
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Residues in contact with LYS1570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551B PHE* 4.7 7.1 - - + -
1566B LEU 2.9 13.8 + - - +
1567B THR* 3.3 13.0 - - - +
1569B LEU* 1.3 79.0 - - - +
1571B ASP* 1.3 64.2 + - - +
1573B ILE* 3.2 11.2 + - - +
1574B ALA* 3.2 20.0 + - - +
1617B TYR* 4.3 28.6 - - + +
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Residues in contact with ASP1571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1567B THR* 2.9 23.9 + - - +
1568B HIS* 3.2 17.9 + - + +
1570B LYS* 1.3 79.2 - - - +
1572B LEU* 1.3 57.1 + - + +
1574B ALA* 3.3 7.2 + - - +
1575B TRP* 2.8 30.4 + - - +
1620B ARG* 5.7 0.3 - - - +
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Residues in contact with LEU1572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499B ILE* 3.6 30.7 - - + +
1502B MET* 3.3 38.8 - - + -
1503B SER* 3.8 16.4 - - - +
1506B ASN* 3.3 17.3 - - + +
1568B HIS* 3.3 27.6 + - + +
1569B LEU* 3.6 8.7 - - - +
1570B LYS 3.2 0.6 - - - -
1571B ASP* 1.3 78.9 - - + +
1573B ILE* 1.3 57.5 + - - +
1575B TRP* 3.1 17.1 - - + +
1576B GLN* 2.7 27.2 + - - +
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Residues in contact with ILE1573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1502B MET* 4.1 16.4 - - + -
1543B PHE* 3.5 52.9 - - + +
1546B TYR* 5.9 0.9 - - + -
1547B GLU* 4.8 1.3 - - + -
1551B PHE* 4.5 8.5 - - + -
1569B LEU* 3.4 33.0 - - + +
1570B LYS* 3.2 7.5 + - - +
1572B LEU* 1.3 77.4 - - - +
1574B ALA* 1.3 63.1 + - - +
1576B GLN* 3.1 15.3 + - - +
1577B ILE* 3.4 9.9 - - + +
1613B VAL* 4.2 5.6 - - + -
1617B TYR* 3.9 34.5 - - + +
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Residues in contact with ALA1574 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1570B LYS 3.2 9.1 + - - +
1571B ASP* 3.6 10.3 - - - +
1573B ILE* 1.3 78.9 - - - +
1575B TRP* 1.3 57.9 + - - +
1576B GLN 3.3 0.2 + - - -
1577B ILE* 3.5 4.0 + - - +
1578B PRO* 3.0 25.8 - - - +
1613B VAL* 4.2 11.4 - - - +
1617B TYR* 4.2 12.1 - - + -
1618B GLY 3.9 22.0 - - - +
1620B ARG* 4.2 16.6 + - + +
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Residues in contact with TRP1575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506B ASN* 4.0 15.3 - - + +
1571B ASP 2.8 20.3 + - - +
1572B LEU* 3.1 21.5 - - + +
1574B ALA* 1.3 78.6 - - - +
1576B GLN* 1.3 60.2 + - - +
1578B PRO* 3.2 11.0 - - + +
1579B PHE* 3.0 66.3 - + - -
1620B ARG* 4.4 26.4 - - + +
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Residues in contact with GLN1576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1502B MET* 2.3 33.8 - - - +
1505B ALA* 3.9 12.9 - - - +
1506B ASN* 2.9 31.0 - - - +
1509B ILE* 3.8 8.4 - - + +
1534B ILE* 3.6 24.8 - - - +
1543B PHE* 4.2 10.1 - - + -
1572B LEU 2.7 14.6 + - - +
1573B ILE* 3.1 13.6 + - + +
1575B TRP* 1.3 74.0 - - - +
1577B ILE* 1.3 63.0 + - + +
1579B PHE* 3.2 6.8 + - - +
1580B LEU* 2.8 45.3 + - + +
37D PHE* 4.2 4.5 - - - -
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Residues in contact with ILE1577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1543B PHE* 5.3 2.5 - - + -
1573B ILE* 3.4 18.4 - - + +
1574B ALA 3.5 4.2 + - - +
1576B GLN* 1.3 81.4 - - + +
1578B PRO* 1.3 66.9 - - + +
1580B LEU* 3.0 7.3 + - + +
1581B GLY 2.8 31.5 + - - -
1606B PHE* 3.4 16.7 - - + -
1609B LEU* 4.2 12.3 - - + -
1610B LYS* 3.8 51.6 - - + +
1613B VAL* 3.8 28.5 - - + -
1614B GLU* 5.0 5.2 - - + +
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Residues in contact with PRO1578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1574B ALA 3.0 18.6 - - - +
1575B TRP* 3.2 15.5 - - + +
1577B ILE* 1.3 97.5 - - + +
1579B PHE* 1.3 62.5 + - + +
1581B GLY* 3.3 1.0 + - - -
1582B ALA* 2.8 36.4 + - - +
1620B ARG 3.9 25.8 - - - +
----------------------------------------------------------
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Residues in contact with PHE1579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506B ASN* 3.7 35.2 - - + -
1509B ILE* 3.8 22.2 - - + +
1510B LEU* 3.8 38.8 - - + -
1513B ILE* 4.3 6.3 - - + +
1575B TRP* 3.0 72.2 - + - -
1576B GLN* 3.2 8.0 + - - +
1578B PRO* 1.3 81.1 - - + +
1580B LEU* 1.3 59.3 + - - +
1582B ALA* 3.3 8.0 + - - +
1583B GLY* 2.8 27.4 + - - -
----------------------------------------------------------
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Residues in contact with LEU1580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509B ILE* 4.0 13.9 - - + -
1531B LEU* 4.2 18.8 - - + +
1534B ILE* 3.9 25.8 - - + +
1535B VAL* 3.7 31.6 - - + -
1576B GLN* 2.8 37.0 + - + +
1577B ILE* 3.0 13.9 + - + +
1579B PHE* 1.3 76.9 - - - +
1581B GLY* 1.3 57.7 + - - +
1583B GLY* 3.1 4.2 + - - -
1584B ILE* 2.8 33.2 + - - +
1606B PHE* 3.6 16.8 - - + -
1609B LEU* 5.3 7.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY1581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1577B ILE 2.8 15.6 + - - -
1578B PRO* 3.8 1.3 - - - -
1580B LEU* 1.3 69.4 - - - +
1582B ALA* 1.3 55.6 + - - +
1584B ILE* 2.8 7.2 + - - +
1585B LYS* 2.7 36.2 + - - +
1606B PHE* 3.4 26.8 - - - -
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Residues in contact with ALA1582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513B ILE* 4.4 18.6 - - + -
1578B PRO 2.8 22.1 + - - +
1579B PHE* 3.3 9.2 - - - +
1581B GLY* 1.3 72.7 - - - +
1583B GLY* 1.3 60.9 - - - +
1585B LYS* 3.4 8.8 - - - +
1586B ILE* 3.3 23.5 + - - +
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Residues in contact with GLY1583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513B ILE* 3.9 17.4 - - - +
1527B LEU* 4.4 5.0 - - - +
1531B LEU* 3.6 20.3 - - - +
1579B PHE 2.8 17.6 + - - -
1580B LEU 3.5 4.0 - - - -
1582B ALA* 1.3 71.7 - - - +
1584B ILE* 1.3 59.1 + - - +
1586B ILE* 3.5 9.7 + - - +
1587B HIS* 3.0 25.8 + - - +
----------------------------------------------------------
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Residues in contact with ILE1584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1531B LEU* 4.5 11.7 - - + -
1535B VAL* 4.2 13.7 - - + -
1580B LEU* 2.8 22.8 + - + +
1581B GLY* 2.8 10.6 + - - +
1583B GLY* 1.3 75.9 - - - +
1585B LYS* 1.3 54.7 + - - +
1587B HIS* 2.9 7.1 + - + +
1588B GLU* 2.7 33.5 + - + +
1599B HIS* 3.8 18.8 - - + +
1602B MET* 4.4 15.9 - - - +
1603B GLU* 3.8 24.5 - - + +
1606B PHE* 3.5 44.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS1585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1581B GLY 2.7 13.9 + - - +
1582B ALA* 3.4 13.7 - - - +
1584B ILE* 1.3 73.6 - - - +
1586B ILE* 1.3 64.8 + - + +
1588B GLU* 3.1 20.6 + - - +
1589B LYS* 3.2 20.4 + - + +
----------------------------------------------------------
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Residues in contact with ILE1586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513B ILE* 3.6 42.8 - - + +
1516B TYR* 4.0 13.7 - - + -
1517B GLN* 4.0 16.8 - - + +
1527B LEU* 4.1 11.9 - - + -
1582B ALA* 3.3 12.5 + - + +
1583B GLY* 3.6 7.9 - - - +
1584B ILE 3.3 0.4 - - - -
1585B LYS* 1.3 76.4 - - + +
1587B HIS* 1.3 63.6 + - - +
1589B LYS* 3.3 9.5 + - - +
1590B ARG* 3.1 52.5 + - - +
----------------------------------------------------------
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Residues in contact with HIS1587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524B ILE* 4.9 7.0 - - + +
1527B LEU* 4.2 11.9 - - + +
1528B SER* 2.7 53.6 + - - -
1531B LEU* 4.0 15.4 - - + +
1583B GLY 3.0 13.5 + - - +
1584B ILE* 2.9 10.2 + - - +
1586B ILE* 1.3 75.4 - - - +
1588B GLU* 1.3 62.8 + - - +
1590B ARG* 3.1 13.8 + - - +
1591B VAL* 3.2 39.0 + - + +
1595B LEU* 6.0 0.2 - - - +
1598B PHE* 4.0 6.9 - - - -
1599B HIS* 2.9 34.2 - + + +
1602B MET* 4.0 13.6 - - + +
----------------------------------------------------------
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Residues in contact with GLU1588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584B ILE* 2.7 9.6 + - + +
1585B LYS* 3.3 15.2 - - - +
1587B HIS* 1.3 77.5 - - - +
1589B LYS* 1.3 81.2 + - + +
1591B VAL* 3.5 13.2 - - - +
1596B ARG* 3.6 27.4 + - - +
1599B HIS* 3.3 30.0 + - + +
1603B GLU* 4.6 9.5 - - - +
----------------------------------------------------------
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Residues in contact with LYS1589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1585B LYS* 3.2 15.6 + - + +
1586B ILE* 3.7 7.6 - - + +
1588B GLU* 1.3 97.4 - - + +
1590B ARG* 1.3 64.9 + - + +
1591B VAL 3.7 1.0 + - - -
----------------------------------------------------------
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Residues in contact with ARG1590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1516B TYR* 3.0 35.9 + - + -
1517B GLN* 4.8 2.4 + - - +
1519B ASP 3.2 23.0 + - - -
1520B GLU* 3.5 35.6 + - - +
1522B LEU 4.9 3.9 + - - -
1524B ILE* 3.3 35.2 - - + +
1527B LEU* 5.9 0.7 - - + -
1586B ILE* 3.1 36.7 + - + +
1587B HIS* 3.1 7.7 + - - +
1589B LYS* 1.3 84.5 - - + +
1591B VAL* 1.3 59.1 + - - +
1592B SER 3.9 1.4 + - - -
----------------------------------------------------------
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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