Contacts of the helix formed by residues 1540 - 1570 (chain A) in PDB entry 6J8H
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 SER1540 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1538A GLY 3.5 4.5 - - - -
1539A GLN* 1.3 90.1 + - - +
1541A GLN* 1.3 66.1 + - - +
1542A HIS* 4.4 3.1 + - - +
1543A MET* 3.4 12.1 + - - +
1544A THR* 2.6 37.0 + - - -
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Residues in contact with GLN1541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1540A SER* 1.3 78.0 - - - +
1542A HIS* 1.3 61.8 + - - +
1543A MET 3.1 1.6 - - - -
1544A THR* 3.5 7.1 - - - -
1545A GLU* 2.7 37.5 + - + +
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Residues in contact with HIS1542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1540A SER* 3.6 4.0 + - - +
1541A GLN* 1.3 78.7 - - - +
1543A MET* 1.3 63.9 + - - +
1545A GLU* 3.4 5.9 + - - +
1546A VAL* 3.3 42.3 + - + +
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Residues in contact with MET1543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1534A VAL* 4.9 19.1 - - + +
1539A GLN* 3.4 32.8 - - + +
1540A SER* 3.4 22.0 + - - +
1541A GLN 3.1 0.4 - - - -
1542A HIS* 1.3 84.5 - - - +
1544A THR* 1.3 59.3 + - - +
1546A VAL* 3.6 6.7 + - - +
1547A LEU* 3.4 34.9 + - + +
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Residues in contact with THR1544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1539A GLN* 3.6 27.9 + - - +
1540A SER 2.6 27.8 + - - -
1541A GLN* 3.0 8.8 + - - -
1543A MET* 1.3 77.9 - - - +
1545A GLU* 1.3 65.5 + - - +
1547A LEU* 3.5 5.2 + - + +
1548A TYR* 3.2 21.3 + - + +
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Residues in contact with GLU1545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1541A GLN* 2.7 23.3 + - + +
1542A HIS* 3.8 8.7 - - - +
1544A THR* 1.3 75.7 - - - +
1546A VAL* 1.3 66.4 + - + +
1548A TYR* 3.2 16.0 + - - +
1549A TRP* 3.0 44.0 + - + +
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Residues in contact with VAL1546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542A HIS* 3.3 38.2 + - + +
1543A MET* 4.0 8.7 - - - +
1544A THR 3.4 0.2 - - - -
1545A GLU* 1.3 76.5 - - + +
1547A LEU* 1.3 66.2 + - + +
1549A TRP* 3.2 7.4 + - + +
1550A ILE* 2.9 43.6 + - + +
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Residues in contact with LEU1547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1531A THR* 3.5 27.6 - - + +
1534A VAL* 3.9 19.3 - - + -
1535A GLU* 3.3 38.8 - - + +
1539A GLN* 4.1 18.2 - - - +
1543A MET* 3.4 23.1 + - + +
1544A THR* 3.8 8.7 - - - +
1545A GLU 3.3 0.4 - - - -
1546A VAL* 1.3 80.6 - - + +
1548A TYR* 1.3 63.9 + - - +
1550A ILE* 3.4 11.2 + - + +
1551A ASN* 3.1 29.9 + - - +
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Residues in contact with TYR1548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A THR* 3.2 12.2 + - + +
1545A GLU* 3.2 18.5 + - - +
1547A LEU* 1.3 80.4 - - - +
1549A TRP* 1.3 94.7 + + - +
1551A ASN* 3.3 10.0 + - + +
1552A VAL* 3.2 42.4 + - + +
1593A MET* 4.5 15.2 - - + +
1597A ASP* 3.7 29.8 + - - -
1600A GLU* 6.1 0.7 - - - -
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Residues in contact with TRP1549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1545A GLU* 3.0 42.9 + - + +
1546A VAL* 3.2 6.0 + - - +
1548A TYR* 1.3 101.1 - + - +
1550A ILE* 1.3 66.4 + - + +
1552A VAL* 3.2 33.8 + - + +
1553A VAL* 3.3 16.4 + - - +
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Residues in contact with ILE1550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1531A THR* 4.3 11.9 - - + +
1546A VAL* 2.9 37.5 + - + +
1547A LEU* 3.9 17.0 - - + +
1549A TRP* 1.3 76.5 - - + +
1551A ASN* 1.3 63.5 + - - +
1553A VAL* 3.2 10.9 + - + +
1554A PHE* 3.2 43.5 + - + -
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Residues in contact with ASN1551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1528A ASN* 4.8 3.2 - - - +
1531A THR* 3.6 25.9 - - - +
1532A MET* 6.0 0.2 - - - +
1535A GLU* 5.7 0.7 - - - +
1547A LEU* 3.1 18.7 + - - +
1548A TYR* 3.3 13.0 - - + +
1549A TRP 3.1 0.2 - - - -
1550A ILE* 1.3 78.5 - - - +
1552A VAL* 1.3 61.5 + - + +
1554A PHE* 3.1 14.2 + - - +
1555A ILE* 3.0 30.9 + - + +
1613A ARG* 5.1 3.8 + - - -
1616A ARG* 3.6 28.2 + - - +
1619A ARG* 4.4 14.3 + - - +
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Residues in contact with VAL1552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1548A TYR* 3.5 41.5 - - + +
1549A TRP* 3.2 25.4 + - + +
1551A ASN* 1.3 73.9 - - + +
1553A VAL* 1.3 69.0 + - + +
1555A ILE* 3.1 10.5 + - + +
1556A ILE* 3.0 38.0 + - + +
1593A MET* 4.4 19.3 - - + -
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Residues in contact with VAL1553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549A TRP 3.3 12.5 + - - +
1550A ILE* 3.2 11.7 + - + +
1552A VAL* 1.3 79.8 - - + +
1554A PHE* 1.3 64.5 + - + +
1556A ILE* 3.2 10.3 + - + +
1557A LEU* 2.9 46.1 + - + +
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Residues in contact with PHE1554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524A LEU* 3.8 35.9 - - + -
1527A LEU* 3.9 12.8 - - + -
1528A ASN* 3.5 56.1 - - + +
1531A THR* 3.6 16.2 - - - -
1550A ILE* 3.2 29.2 + - + -
1551A ASN* 3.1 13.2 + - - +
1553A VAL* 1.3 83.3 - - + +
1555A ILE* 1.3 61.6 + - - +
1557A LEU* 3.4 9.8 + - + +
1558A PHE* 3.0 37.7 + + + +
1619A ARG* 5.0 2.9 - - - +
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Residues in contact with ILE1555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551A ASN* 3.0 21.9 + - + +
1552A VAL* 3.1 9.2 + - + +
1554A PHE* 1.3 75.4 - - - +
1556A ILE* 1.3 58.3 + - + +
1558A PHE* 3.9 4.7 - - + +
1559A THR* 2.9 36.3 + - - +
1586A VAL* 5.4 0.9 - - + +
1589A SER* 3.7 20.4 - - - +
1590A ILE* 4.1 25.8 - - + +
1593A MET* 3.1 44.2 - - + -
1619A ARG* 3.7 22.0 - - - +
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Residues in contact with ILE1556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1552A VAL* 3.0 32.9 + - + +
1553A VAL* 3.6 10.8 - - + +
1555A ILE* 1.3 78.6 - - + +
1557A LEU* 1.3 65.6 + - + +
1559A THR* 3.4 5.5 + - - +
1560A GLY* 2.8 26.3 + - - -
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Residues in contact with LEU1557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1521A ILE* 5.6 1.0 - - - +
1524A LEU* 4.2 29.6 - - + -
1553A VAL* 2.9 42.9 + - + +
1554A PHE* 3.9 11.0 - - + +
1556A ILE* 1.3 84.6 - - + +
1558A PHE* 1.3 61.2 + - + +
1560A GLY* 3.0 2.2 + - - -
1561A GLU* 2.8 28.4 + - - +
----------------------------------------------------------
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Residues in contact with PHE1558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1521A ILE* 4.3 11.2 - - + -
1524A LEU* 4.1 28.7 - - + -
1525A ILE* 3.4 44.2 - - + -
1528A ASN* 3.6 22.4 - - + -
1554A PHE* 3.0 26.9 + + - +
1555A ILE* 4.0 4.0 - - + +
1557A LEU* 1.3 75.9 - - - +
1559A THR* 1.3 63.2 + - - +
1561A GLU* 2.8 31.2 - - + +
1562A CYS* 3.2 6.1 + - - +
1586A VAL* 4.2 12.0 - - + +
1619A ARG* 4.0 26.9 - - + -
1622A ARG* 4.1 19.9 + - - +
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Residues in contact with THR1559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1555A ILE* 2.9 20.9 + - - +
1556A ILE* 3.8 6.5 - - - +
1558A PHE* 1.3 76.7 - - - +
1560A GLY* 1.3 64.3 + - - +
1562A CYS* 3.3 5.0 + - + +
1563A VAL* 3.1 31.7 + - + +
1586A VAL* 3.1 31.9 - - + +
1590A ILE* 3.6 20.2 - - + +
----------------------------------------------------------
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Residues in contact with GLY1560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1556A ILE 2.8 15.5 + - - -
1557A LEU* 3.0 6.0 + - - -
1559A THR* 1.3 79.9 - - - +
1561A GLU* 1.3 60.5 + - - +
1563A VAL* 3.3 7.7 + - - +
1564A LEU* 3.1 24.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU1561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517A PHE* 4.7 11.6 - - + -
1521A ILE* 3.7 36.5 - - + +
1557A LEU 2.8 11.1 + - - +
1558A PHE* 2.8 28.7 - - + +
1560A GLY* 1.3 75.5 - - - +
1562A CYS* 1.3 62.6 + - + +
1564A LEU* 3.2 8.4 + - - +
1565A LYS* 3.0 57.9 + - - +
1582A ASP* 3.5 9.4 - - - +
1622A ARG* 2.6 34.9 + - - +
----------------------------------------------------------
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Residues in contact with CYS1562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1558A PHE 3.2 8.2 + - - +
1559A THR* 3.6 10.1 - - - +
1561A GLU* 1.3 90.7 - - + +
1563A VAL* 1.3 68.8 + - - +
1565A LYS* 3.4 7.2 + - - +
1566A LEU* 3.1 28.1 + - - +
1573A TYR* 4.7 10.4 - - - +
1582A ASP* 5.4 4.3 - - - +
1583A PHE* 4.1 31.0 - - - -
1586A VAL* 4.4 21.3 - - + -
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Residues in contact with VAL1563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1559A THR* 3.1 23.9 + - + +
1560A GLY* 3.8 8.5 - - - +
1561A GLU 3.3 0.2 - - - -
1562A CYS* 1.3 81.5 - - - +
1564A LEU* 1.3 59.5 + - + +
1566A LEU* 3.2 8.9 + - + +
1567A ILE* 2.9 43.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU1564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508A ILE* 2.9 44.0 - - + -
1511A LEU* 4.7 20.2 - - + -
1512A VAL* 3.9 11.6 - - + +
1517A PHE* 4.9 9.0 - - + -
1560A GLY 3.1 14.1 + - - +
1561A GLU* 3.2 11.0 + - - +
1563A VAL* 1.3 77.5 - - + +
1565A LYS* 1.3 65.0 + - - +
1567A ILE* 3.3 16.7 + - + +
1568A SER* 3.4 15.8 + - - -
----------------------------------------------------------
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Residues in contact with LYS1565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1512A VAL* 3.3 30.5 - - + -
1517A PHE* 5.1 9.9 - - + -
1561A GLU* 3.0 41.6 + - - +
1562A CYS* 3.9 3.9 - - - +
1564A LEU* 1.3 76.2 - - - +
1566A LEU* 1.3 57.1 + - - +
1569A LEU* 2.8 46.4 + - + +
1573A TYR* 3.8 26.4 - - + -
1579A ASN* 3.8 24.5 + - - +
1582A ASP* 3.1 19.6 + - - +
1622A ARG* 5.0 0.6 - - - +
1625A LYS* 5.1 8.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU1566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1562A CYS* 3.1 16.2 + - - +
1563A VAL* 3.4 11.9 - - + +
1564A LEU 3.1 0.2 - - - -
1565A LYS* 1.3 76.6 - - - +
1567A ILE* 1.3 67.5 + - + +
1570A ARG* 3.1 29.7 + - - +
1573A TYR* 3.1 49.6 - - + -
1574A PHE* 4.7 16.2 - - + -
1583A PHE* 4.9 17.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE1567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505A GLN* 2.8 45.3 + - + +
1508A ILE* 4.4 22.2 - - + -
1563A VAL* 2.9 36.6 + - + +
1564A LEU* 3.3 13.6 + - + +
1566A LEU* 1.3 76.9 - - + +
1568A SER* 1.3 65.0 + - - +
1570A ARG* 3.9 3.6 - - - +
----------------------------------------------------------
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Residues in contact with SER1568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497A ILE* 5.5 0.5 - - - +
1498A PRO 5.2 0.3 - - - +
1500A PRO* 3.7 13.0 - - - +
1505A GLN* 3.4 8.3 + - - -
1508A ILE* 2.9 18.0 + - - +
1509A PHE* 2.4 58.5 + - - -
1512A VAL* 4.7 3.6 - - - -
1564A LEU 3.4 7.7 + - - -
1565A LYS 4.2 1.1 - - - -
1566A LEU 3.3 0.2 - - - -
1567A ILE* 1.3 78.7 - - - +
1569A LEU* 1.3 61.7 + - - +
1570A ARG* 3.2 19.2 - - - -
----------------------------------------------------------
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Residues in contact with LEU1569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497A ILE* 4.6 18.8 - - + -
1509A PHE* 3.7 28.7 - - + -
1512A VAL* 5.2 7.4 - - + -
1513A THR* 5.2 3.6 - - - +
1565A LYS* 2.8 37.4 + - + +
1568A SER* 1.3 69.8 - - - +
1570A ARG* 1.3 72.6 + - - +
1572A TYR* 3.1 31.2 + - - +
1573A TYR* 3.4 39.7 - - + +
1579A ASN* 4.5 8.7 - - - +
----------------------------------------------------------
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Residues in contact with ARG1570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1498A PRO* 3.9 16.3 + - - +
1500A PRO* 4.1 26.8 - - - +
1505A GLN* 4.5 6.2 - - - +
1566A LEU* 3.1 22.3 + - - +
1567A ILE 3.9 11.9 - - - +
1568A SER 3.2 22.2 - - - +
1569A LEU* 1.3 73.6 - - - +
1571A HIS* 1.3 90.8 + - + +
1572A TYR* 3.6 28.0 + - - -
1573A TYR* 3.1 17.0 + - - +
1574A PHE* 4.1 5.1 + - - -
----------------------------------------------------------
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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