Contacts of the helix formed by residues 1640 - 1667 (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 SER1640 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A TYR* 5.5 1.2 - - - -
1636A ALA 3.4 7.6 + - - -
1637A LEU* 3.5 10.7 + - - +
1638A MET 3.3 0.4 - - - -
1639A MET* 1.3 76.4 - - - +
1641A LEU* 1.3 64.5 + - - +
1642A PRO* 3.3 3.4 - - - -
1643A ALA* 3.3 6.2 + - - +
1644A LEU* 2.9 45.4 + - - +
1757A ALA 4.5 6.5 - - - -
1758A VAL* 4.7 7.6 - - - +
1761A GLU* 3.4 32.5 - - - -
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Residues in contact with LEU1641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485A MET* 5.9 0.2 - - + -
1637A LEU* 3.5 32.9 + - + +
1638A MET* 3.3 21.2 + - + +
1640A SER* 1.3 77.8 - - - +
1642A PRO* 1.4 67.3 - - + +
1644A LEU* 3.8 13.3 - - + +
1645A PHE* 2.9 26.2 + - - +
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Residues in contact with PRO1642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474A MET* 3.1 20.9 - - + -
1478A GLN* 3.2 42.3 + - + +
1481A TYR* 6.1 1.8 - - + -
1482A TYR* 5.1 3.1 - - + -
1485A MET* 3.5 25.6 - - + -
1638A MET 3.9 3.4 - - - +
1639A MET 3.0 19.1 - - - +
1640A SER 3.5 1.1 - - - -
1641A LEU* 1.4 91.3 - - + +
1643A ALA* 1.3 60.6 + - - +
1645A PHE* 3.3 9.7 + - + +
1646A ASN* 3.5 5.6 + - - -
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Residues in contact with ALA1643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1471A ASP* 5.2 2.2 - - - +
1473A PHE* 3.9 32.5 - - + +
1474A MET* 3.6 16.2 - - + +
1640A SER* 3.3 8.6 + - - +
1642A PRO* 1.3 75.5 - - - +
1644A LEU* 1.3 65.9 + - - +
1646A ASN* 3.4 12.3 + - - +
1647A ILE* 3.4 18.8 + - - +
1757A ALA* 4.4 15.9 - - + -
1761A GLU* 4.6 9.0 - - - +
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Residues in contact with LEU1644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A TYR* 5.7 0.4 - - + -
1637A LEU* 4.7 8.7 - - + -
1640A SER* 2.9 37.7 + - - +
1641A LEU* 3.8 19.1 - - + +
1643A ALA* 1.3 77.3 - - - +
1645A PHE* 1.3 57.3 + - - +
1647A ILE* 3.4 8.9 + - + +
1648A GLY* 2.9 26.0 + - - -
1754A MET* 4.1 40.8 - - + -
1757A ALA* 3.9 26.0 - - + -
1758A VAL* 4.7 2.2 - - + -
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Residues in contact with PHE1645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1478A GLN* 4.5 6.5 - - - -
1641A LEU 2.9 17.2 + - - +
1642A PRO* 3.5 7.0 - - + +
1643A ALA 3.2 0.2 - - - -
1644A LEU* 1.3 77.0 - - - +
1646A ASN* 1.3 70.4 + - - +
1648A GLY* 3.1 2.5 + - - +
1649A LEU* 2.8 56.3 + - + +
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Residues in contact with ASN1646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306A GLY* 3.8 25.1 - - - +
1307A MET* 5.0 1.6 - - - -
1309A VAL* 4.4 1.8 - - - +
1310A VAL* 3.6 20.7 - - + +
1473A PHE 2.5 28.1 + - - -
1474A MET* 3.6 6.7 - - - +
1475A THR 4.4 1.4 - - - +
1478A GLN* 2.8 36.2 + - - +
1642A PRO 3.5 5.3 + - - -
1643A ALA* 3.4 4.8 + - - +
1644A LEU 3.3 0.4 - - - -
1645A PHE* 1.3 83.8 - - - +
1647A ILE* 1.3 63.1 + - - +
1649A LEU* 3.2 7.1 + - - +
1650A LEU* 3.1 22.5 + - - +
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Residues in contact with ILE1647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1310A VAL* 4.1 23.3 - - + -
1473A PHE* 4.3 13.0 - - + -
1643A ALA 3.4 14.6 + - - +
1644A LEU* 3.4 11.1 + - + +
1645A PHE 3.3 0.2 - - - -
1646A ASN* 1.3 76.6 - - - +
1648A GLY* 1.3 57.5 + - - +
1650A LEU* 3.3 4.4 + - - +
1651A LEU* 2.8 29.2 + - + +
1750A VAL* 3.2 32.9 - - + +
1753A ASN* 3.5 38.8 - - + +
1754A MET* 4.3 9.6 - - + +
1757A ALA* 4.8 6.3 - - + -
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Residues in contact with GLY1648 (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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387A PHE* 6.1 4.3 - - - -
1644A LEU 2.9 15.4 + - - -
1645A PHE* 3.1 5.5 + - - -
1647A ILE* 1.3 79.1 - - - +
1649A LEU* 1.3 56.4 + - - +
1651A LEU* 3.3 10.4 + - - +
1652A PHE* 2.9 29.6 + - - +
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Residues in contact with LEU1649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1304A PHE* 4.9 12.6 - - + -
1306A GLY* 6.4 0.7 - - - -
1307A MET* 3.8 36.1 - - + +
1645A PHE* 2.8 42.7 + - + +
1646A ASN* 3.5 11.0 - - - +
1648A GLY* 1.3 77.7 - - - +
1650A LEU* 1.3 61.6 + - - +
1652A PHE* 3.3 16.9 + - + +
1653A LEU* 3.1 22.0 + - - +
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Residues in contact with LEU1650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1301A LEU* 3.3 34.5 - - + -
1307A MET* 3.6 17.4 - - + +
1310A VAL* 4.2 23.6 - - + -
1311A VAL* 3.7 13.2 - - + -
1314A LEU* 5.7 4.9 - - + -
1646A ASN 3.1 12.9 + - - +
1647A ILE 3.7 7.6 - - - +
1649A LEU* 1.3 76.9 - - - +
1651A LEU* 1.3 65.0 + - - +
1653A LEU* 3.4 4.6 + - + +
1654A VAL* 3.2 34.3 + - + +
1750A VAL* 4.4 19.5 - - + -
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Residues in contact with LEU1651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 3.9 29.8 - - + -
1647A ILE* 2.8 20.6 + - + +
1648A GLY* 3.6 8.5 - - - +
1650A LEU* 1.3 82.7 - - - +
1652A PHE* 1.3 60.8 + - - +
1654A VAL* 3.5 9.4 + - + +
1655A MET* 3.1 38.9 + - + +
1695A THR* 4.7 18.8 - - + -
1743A TYR* 4.9 7.0 - - + +
1747A SER* 5.0 11.2 - - - +
1750A VAL* 4.5 25.8 - - + -
1751A VAL* 5.9 4.9 - - + -
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Residues in contact with PHE1652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1648A GLY 2.9 17.2 + - - +
1649A LEU* 3.5 18.4 - - + +
1651A LEU* 1.3 76.4 - - - +
1653A LEU* 1.3 64.2 + - + +
1655A MET* 3.3 13.7 + - + +
1656A PHE* 2.9 42.6 + + + +
1684A PHE* 6.0 0.7 - + - -
1688A MET* 3.7 28.3 - - + -
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Residues in contact with LEU1653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1297A PRO* 3.6 27.4 - - + +
1298A LEU* 4.5 1.3 - - + -
1300A ALA* 3.8 16.8 - - + -
1301A LEU* 3.8 35.9 - - + +
1307A MET* 4.3 16.2 - - + -
1649A LEU 3.1 12.7 + - - +
1650A LEU* 3.8 8.5 - - + +
1651A LEU 3.3 0.2 - - - -
1652A PHE* 1.3 80.9 - - + +
1654A VAL* 1.3 71.1 + - + +
1656A PHE* 3.1 8.6 + - - +
1657A ILE* 3.0 41.1 + - + +
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Residues in contact with VAL1654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1650A LEU* 3.2 33.2 + - + +
1651A LEU* 3.8 9.6 - - + +
1653A LEU* 1.3 82.7 - - + +
1655A MET* 1.3 66.1 + - - +
1657A ILE* 3.4 8.1 + - + +
1658A TYR* 3.2 44.9 + - + -
1743A TYR* 4.4 9.9 - - + -
1746A ILE* 4.3 24.5 - - + -
1750A VAL* 6.2 0.4 - - + -
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Residues in contact with MET1655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 5.9 3.6 - - + -
1651A LEU* 3.1 35.9 + - + +
1652A PHE* 3.4 16.6 - - + +
1654A VAL* 1.3 77.5 - - - +
1656A PHE* 1.3 58.4 + - - +
1658A TYR* 3.4 3.2 + - - +
1659A ALA* 3.0 27.9 + - - +
1688A MET* 4.4 22.4 - - + +
1691A LEU* 3.8 17.9 - - + +
1692A PHE* 4.3 30.5 - - + -
1695A THR* 4.1 14.8 - - + +
1743A TYR* 3.3 23.5 - - - +
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Residues in contact with PHE1656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206A SER* 3.6 31.2 - - - -
1207A GLY* 5.0 2.5 - - - -
1209A LEU* 4.8 0.4 - - + -
1210A ALA* 5.0 7.0 - - + -
1297A PRO* 3.3 37.7 - - + -
1652A PHE* 2.9 32.9 + + + +
1653A LEU* 3.1 12.3 + - + +
1655A MET* 1.3 74.7 - - - +
1657A ILE* 1.3 64.1 + - - +
1659A ALA* 3.3 6.5 + - - +
1660A ILE* 3.2 40.7 + - + +
1684A PHE* 3.6 33.0 - + - -
1688A MET* 4.6 6.7 - - + +
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Residues in contact with ILE1657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1294A ALA* 3.7 18.0 - - - +
1295A LEU* 4.5 7.2 - - + -
1297A PRO* 3.9 19.5 - - + -
1298A LEU* 3.6 42.2 - - + +
1653A LEU* 3.0 31.0 + - + +
1654A VAL* 3.9 8.3 - - + +
1656A PHE* 1.3 77.7 - - - +
1658A TYR* 1.3 67.8 + - + +
1660A ILE* 3.4 6.4 + - - +
1661A PHE* 3.2 40.4 + - + -
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Residues in contact with TYR1658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1654A VAL* 3.2 36.9 + - + +
1655A MET 3.7 4.3 - - - +
1657A ILE* 1.3 86.2 - - + +
1659A ALA* 1.3 59.2 + - - +
1661A PHE* 3.3 9.1 + + + -
1662A GLY 2.9 17.8 + - - -
1691A LEU* 3.8 15.3 - - + -
1738A PHE* 5.7 1.0 - - - -
1739A TYR* 2.8 69.3 + + - +
1742A SER* 3.5 23.9 - - - -
1743A TYR* 3.8 28.4 + + + -
1746A ILE* 3.9 17.2 - - + +
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Residues in contact with ALA1659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655A MET 3.0 17.2 + - - +
1656A PHE 3.6 5.6 - - - +
1658A TYR* 1.3 75.6 - - - +
1660A ILE* 1.3 59.4 + - - +
1662A GLY* 3.3 1.7 + - - -
1663A MET* 2.9 33.1 + - - +
1681A PHE* 5.6 0.4 - - - -
1684A PHE* 4.1 13.7 - - + -
1687A SER* 3.9 21.1 + - - +
1688A MET* 4.0 21.3 - - - -
1691A LEU* 4.7 6.7 - - + +
1739A TYR* 4.7 1.3 - - - -
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Residues in contact with ILE1660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209A LEU* 4.2 44.2 - - + +
1210A ALA* 4.3 1.6 - - - +
1293A ARG* 6.1 1.8 - - - +
1294A ALA* 3.7 26.7 - - + +
1656A PHE* 3.2 29.8 + - + +
1657A ILE* 3.7 8.1 - - - +
1658A TYR 3.2 0.6 - - - -
1659A ALA* 1.3 74.4 - - - +
1661A PHE* 1.3 64.0 + - - +
1663A MET* 3.4 18.0 + - + +
1664A SER* 3.4 15.2 + - - -
1684A PHE* 4.0 28.5 - - + -
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Residues in contact with PHE1661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291A THR* 3.4 32.1 - - + -
1292A LEU* 4.2 11.0 - - + -
1294A ALA* 3.8 15.5 - - + -
1295A LEU* 3.9 27.8 - - + -
1657A ILE* 3.2 30.2 + - + +
1658A TYR* 3.6 14.8 - + - +
1660A ILE* 1.3 78.0 - - - +
1662A GLY* 1.3 60.2 + - - +
1664A SER* 3.0 17.4 + - - -
1665A ASN* 3.1 34.0 + - - +
1739A TYR* 4.0 17.5 - + + -
----------------------------------------------------------
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Residues in contact with GLY1662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658A TYR 2.9 14.6 + - - -
1659A ALA 3.6 3.6 - - - -
1661A PHE* 1.3 77.2 - - - +
1663A MET* 1.3 59.9 + - - +
1666A PHE* 2.8 47.1 + - - +
1681A PHE* 3.9 14.1 - - - +
1739A TYR* 3.9 11.6 + - - -
----------------------------------------------------------
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Residues in contact with MET1663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209A LEU 4.6 4.7 - - - +
1210A ALA 4.1 5.4 - - - +
1212A GLU* 2.1 39.9 - - + +
1213A ASP* 3.4 16.2 - - + -
1659A ALA 2.9 17.8 + - - +
1660A ILE* 3.4 15.9 + - + +
1662A GLY* 1.3 76.9 - - - +
1664A SER* 1.3 63.2 + - - +
1667A ALA* 3.3 24.6 - - - +
1681A PHE 3.7 15.0 - - - +
1682A GLU 5.5 0.4 - - - +
1683A THR* 4.2 0.9 - - - -
1684A PHE* 3.8 42.4 - - - +
1687A SER* 3.9 13.1 + - - +
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Residues in contact with SER1664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291A THR* 3.5 23.4 + - - -
1660A ILE* 3.4 9.6 + - - -
1661A PHE* 3.0 13.2 + - - -
1663A MET* 1.3 82.4 - - - +
1665A ASN* 1.3 66.5 + - - +
1667A ALA* 4.5 5.4 + - - +
1668A TYR* 5.3 4.9 - - - -
----------------------------------------------------------
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Residues in contact with ASN1665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291A THR* 4.3 13.8 + - - +
1661A PHE* 3.1 36.7 + - - +
1664A SER* 1.3 85.5 + - - +
1666A PHE* 1.3 84.9 + - + +
1667A ALA 3.7 3.5 - - - +
1669A VAL* 4.9 2.9 - - - +
1735A VAL* 4.6 22.9 - - + +
1739A TYR* 5.7 2.6 - - - -
----------------------------------------------------------
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Residues in contact with PHE1666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1662A GLY* 2.8 30.7 + - - +
1665A ASN* 1.3 91.6 - - + +
1667A ALA* 1.3 64.9 + - - +
1668A TYR 3.5 0.2 + - - -
1669A VAL* 3.1 33.3 - - + +
1681A PHE* 3.9 32.8 - + + +
1707A ILE* 3.7 30.1 - - + -
1731A GLY* 5.7 0.4 - - - -
1732A ASN 5.4 3.1 - - - -
1735A VAL* 4.5 12.1 - - + -
1736A GLY* 4.0 20.9 - - - -
1739A TYR* 3.5 48.2 - + + -
1740A PHE* 4.3 5.4 - + - -
----------------------------------------------------------
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Residues in contact with ALA1667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213A ASP* 6.5 0.2 - - - -
1214A ILE* 3.9 25.6 - - + -
1662A GLY 3.9 1.4 + - - -
1663A MET 3.3 21.3 + - - +
1664A SER 4.7 1.9 - - - +
1665A ASN 3.7 6.0 - - - +
1666A PHE* 1.3 81.2 - - - +
1668A TYR* 1.3 81.2 + - + +
1669A VAL* 3.5 0.7 + - - +
1681A PHE* 3.9 19.2 - - - +
1682A GLU* 4.3 5.8 - - - +
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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