Contacts of the helix formed by residues 1681 - 1702 (chain X) in PDB entry 3HM6
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 THR1681 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X UNX 3.6 8.1 - - - -
1624X GLU* 3.5 15.7 - - - +
1634X ARG* 4.0 8.7 - - - +
1663X LEU* 5.8 1.7 - - + +
1680X GLU* 1.3 85.7 + - + +
1682X VAL* 1.3 65.0 + - - +
1683X VAL* 3.6 7.0 - - + +
1684X GLU* 3.2 34.3 + - - +
1685X LYS* 3.1 22.3 + - - +
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Residues in contact with VAL1682 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X UNX 3.9 0.7 - - - -
1620X ILE* 3.9 28.3 - - + +
1623X LEU* 6.2 0.7 - - + -
1624X GLU* 3.2 32.2 + - + +
1629X PHE* 4.3 7.0 - - + -
1634X ARG* 3.5 31.6 - - + +
1637X VAL* 5.0 4.0 - - + -
1638X ALA* 3.7 14.1 - - + +
1641X LEU* 4.8 3.6 - - + -
1659X LEU* 4.9 0.2 - - + -
1681X THR* 1.3 73.3 - - - +
1683X VAL* 1.3 52.7 + - - +
1685X LYS 3.1 2.3 + - - -
1686X LEU* 2.7 60.1 + - + +
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Residues in contact with VAL1683 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X UNX 3.2 18.3 - - - -
1656X LEU* 4.2 12.7 - - + +
1659X LEU* 3.6 39.7 - - + +
1660X LEU* 4.1 8.3 - - + +
1663X LEU* 3.9 34.3 - - + -
1676X LEU* 5.1 2.5 - - + -
1681X THR* 3.6 8.5 - - - +
1682X VAL* 1.3 76.4 - - - +
1684X GLU* 1.3 67.0 + - + +
1686X LEU* 3.4 9.1 + - - +
1687X LEU* 3.1 23.4 + - + +
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Residues in contact with GLU1684 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1663X LEU* 5.5 2.0 - - + -
1667X TYR* 5.4 3.1 + - - -
1676X LEU* 3.5 38.3 + - + -
1677X ARG 3.7 1.6 + - - -
1678X ARG* 2.9 42.2 + - - +
1679X THR* 4.0 3.6 - - - -
1680X GLU* 2.9 24.4 + - - +
1681X THR* 3.2 26.8 + - - +
1682X VAL 3.3 0.2 - - - -
1683X VAL* 1.3 83.3 - - + +
1685X LYS* 1.3 60.3 + - - +
1687X LEU* 3.5 2.8 + - - +
1688X THR 3.2 13.2 + - - -
1984X ARG* 3.1 21.5 + - - +
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Residues in contact with LYS1685 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1575X ILE 2.8 26.9 + - - -
1576X PHE 3.5 6.9 + - - -
1578X PRO* 4.0 11.8 - - - +
1635X ALA* 3.3 35.2 - - + +
1638X ALA* 3.5 17.0 - - + -
1639X SER* 3.3 22.0 - - - +
1679X THR* 3.9 22.2 - - + +
1681X THR 3.1 13.8 + - - +
1682X VAL 3.7 1.8 - - - +
1684X GLU* 1.3 75.0 - - - +
1686X LEU* 1.3 63.9 + - - +
1688X THR* 3.4 14.2 + - - +
1689X ASN* 3.1 34.1 + - - +
1988X ASN* 6.1 0.2 - - - +
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Residues in contact with LEU1686 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1620X ILE* 4.7 3.4 - - + -
1638X ALA* 3.4 33.0 - - - +
1641X LEU* 4.6 8.3 - - + -
1642X THR* 4.0 0.2 - - - +
1652X PHE* 3.7 32.0 - - + -
1655X ILE* 4.7 10.3 - - + -
1656X LEU* 4.1 14.6 - - + -
1659X LEU* 3.4 33.7 - - + -
1682X VAL* 2.7 36.1 + - + +
1683X VAL* 3.4 4.9 + - - +
1685X LYS* 1.3 71.4 - - - +
1687X LEU* 1.3 57.3 + - - +
1689X ASN* 3.3 5.6 + - - +
1690X TRP* 2.8 29.9 + - - +
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Residues in contact with LEU1687 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656X LEU* 3.9 16.9 - - + +
1660X LEU* 5.6 1.1 - - + -
1676X LEU* 3.8 27.8 - - + -
1683X VAL* 3.1 13.3 + - + +
1684X GLU* 3.5 9.6 - - - +
1686X LEU* 1.3 73.1 - - - +
1688X THR* 1.3 59.7 + - - +
1690X TRP* 3.2 5.1 + - + +
1691X MET* 2.9 47.1 + - + +
1954X PHE* 3.4 38.1 - - + -
1980X SER* 3.8 33.0 - - - +
1984X ARG* 3.8 9.6 - - - -
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Residues in contact with THR1688 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1575X ILE* 4.4 7.0 - - + -
1679X THR* 4.2 7.9 + - + +
1684X GLU 3.2 3.3 + - - -
1685X LYS* 3.4 29.1 + - + +
1687X LEU* 1.3 77.6 - - - +
1689X ASN* 1.3 57.5 + - - +
1691X MET* 3.8 3.0 - - - +
1692X SER* 2.6 43.7 + - - +
1984X ARG* 3.1 55.2 + - - +
1985X PHE* 4.9 1.4 - - - -
1988X ASN* 4.6 7.0 - - - +
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Residues in contact with ASN1689 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1575X ILE* 4.3 1.9 - - - +
1576X PHE* 3.2 32.7 - - + -
1638X ALA 4.1 1.4 + - - -
1639X SER* 3.0 30.7 + - - +
1642X THR* 3.1 29.5 + - + +
1652X PHE* 4.9 0.4 - - + -
1685X LYS* 3.1 37.1 + - - +
1686X LEU 3.6 4.3 - - - +
1687X LEU 3.2 0.2 - - - -
1688X THR* 1.3 78.8 - - - +
1690X TRP* 1.3 59.9 + - - +
1692X SER* 3.3 3.8 + - - -
1693X ILE* 2.9 36.6 + - - +
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Residues in contact with TRP1690 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1649X LEU* 5.7 1.3 - - + -
1652X PHE* 3.7 27.1 - + + -
1653X THR* 3.0 32.3 + - + +
1656X LEU* 3.6 25.8 - - + -
1686X LEU 2.8 17.7 + - - +
1687X LEU* 3.5 6.3 - - + +
1689X ASN* 1.3 73.8 - - - +
1691X MET* 1.3 89.9 + - + +
1693X ILE* 3.4 10.5 + - + +
1694X CYS* 3.0 44.9 + - - -
1950X ALA* 3.5 40.6 - - + -
1953X TYR* 4.0 22.4 - + - -
1954X PHE* 3.9 13.9 - + + -
2067X MET* 5.3 1.6 - - - -
2071X LEU* 4.2 8.5 - - + +
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Residues in contact with MET1691 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1687X LEU* 2.9 27.0 + - + +
1688X THR* 3.8 6.1 - - - +
1690X TRP* 1.3 87.4 - - + +
1692X SER* 1.3 57.8 + - - +
1694X CYS* 3.3 2.5 + - - -
1695X LEU* 2.9 43.7 + - + +
1950X ALA* 5.4 0.7 - - - +
1951X VAL* 5.0 7.2 - - - -
1954X PHE* 3.7 40.2 - - + -
1955X PHE* 4.7 4.7 - - + -
1980X SER* 3.4 31.9 - - - +
1981X LEU* 4.0 24.9 - - + -
1984X ARG* 5.3 0.4 - - + -
1985X PHE* 4.2 17.7 - - + -
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Residues in contact with SER1692 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1571X TYR* 2.6 32.3 + - - -
1575X ILE* 3.4 40.7 - - - +
1576X PHE* 4.9 4.7 - - - -
1688X THR* 2.6 25.1 + - - +
1689X ASN* 3.6 5.8 - - - -
1690X TRP 3.3 0.4 - - - -
1691X MET* 1.3 73.2 - - - +
1693X ILE* 1.3 64.5 + - - +
1696X TYR 3.2 8.7 + - - -
1985X PHE* 3.5 17.6 - - - -
1988X ASN* 5.3 0.2 + - - -
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Residues in contact with ILE1693 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1568X TYR* 3.2 31.0 - - + +
1576X PHE* 4.0 8.1 - - + -
1642X THR* 3.9 26.2 - - + -
1646X HIS* 3.8 9.4 - - + +
1649X LEU* 3.8 38.6 - - + -
1652X PHE* 4.7 3.1 - - + -
1689X ASN 2.9 23.9 + - - +
1690X TRP* 3.6 10.5 - - + +
1692X SER* 1.3 77.8 - - - +
1694X CYS* 1.3 66.6 + - - +
1695X LEU 3.4 0.2 + - - -
1696X TYR* 3.5 14.2 + - - +
2074X LEU* 3.8 25.7 - - + +
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Residues in contact with CYS1694 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1690X TRP* 3.0 48.5 + - + +
1691X MET* 4.0 4.3 - - - +
1693X ILE* 1.3 83.0 - - - +
1695X LEU* 1.3 66.0 + - + +
1696X TYR 3.4 0.8 + - - -
1697X THR* 4.8 7.6 + - - -
1698X PHE* 5.2 1.2 + - - +
1948X PRO* 5.6 1.9 - - - +
1950X ALA* 3.5 29.7 - - + +
2070X VAL* 6.0 0.9 - - + -
2071X LEU* 4.2 6.7 - - - -
2074X LEU* 3.9 30.4 - - + +
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Residues in contact with LEU1695 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1571X TYR* 4.1 2.2 - - - -
1691X MET* 2.9 25.3 + - - +
1692X SER 4.0 1.1 - - - -
1694X CYS* 1.3 80.6 - - + +
1696X TYR* 1.3 66.0 + - - +
1697X THR 3.3 2.9 - - - -
1698X PHE* 3.2 18.5 + - + +
1699X VAL* 3.1 23.8 + - + +
1948X PRO* 3.8 35.0 - - + -
1950X ALA* 5.6 1.6 - - + -
1951X VAL* 3.9 14.1 - - + +
1981X LEU* 3.5 32.1 - - + -
1985X PHE* 3.6 28.7 - - + -
1986X TRP* 4.4 4.9 - - + -
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Residues in contact with TYR1696 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565X PHE* 6.1 1.6 - + - -
1566X LEU 2.8 25.3 + - - -
1567X ASP* 3.9 0.2 - - - -
1568X TYR* 3.3 41.3 + + + -
1571X TYR* 3.5 50.0 - + + -
1692X SER 3.2 9.8 + - - +
1693X ILE 3.5 13.4 + - - +
1694X CYS 3.4 2.0 - - - -
1695X LEU* 1.3 78.2 - - - +
1697X THR* 1.3 73.0 + - + +
1699X VAL* 3.4 4.9 + - + +
1700X ARG* 2.9 60.6 + - + +
1996X VAL* 6.3 1.3 - - + -
2074X LEU* 6.1 0.9 - - + -
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Residues in contact with THR1697 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1693X ILE 5.2 0.2 + - - -
1694X CYS 4.8 6.7 + - - -
1695X LEU 3.3 0.4 - - - -
1696X TYR* 1.3 90.1 - - + +
1698X PHE* 1.3 58.5 + - - +
1700X ARG* 3.2 11.1 - - + +
1701X ASP* 2.7 48.4 + - - -
2074X LEU* 5.5 11.6 - - + +
2077X ASN* 5.1 12.3 - - - +
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Residues in contact with PHE1698 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1694X CYS 5.3 0.7 - - - +
1695X LEU* 3.2 26.4 + - + +
1697X THR* 1.3 81.1 + - - +
1699X VAL* 1.3 53.5 + - - +
1701X ASP* 4.3 4.5 - - + -
1702X SER* 2.7 59.3 + - - -
1703X VAL* 3.3 20.4 + - + -
1939X VAL 4.3 16.6 - - - -
1940X ILE 5.1 4.5 - - - -
1945X ARG* 5.1 10.8 - - + -
1946X PRO 4.9 7.2 - - - -
1948X PRO* 3.9 30.7 - - + -
1986X TRP* 3.7 29.8 - + - -
2052X TYR* 6.0 1.8 - - - -
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Residues in contact with VAL1699 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1565X PHE* 4.8 0.4 - - + -
1571X TYR* 4.7 7.2 - - + +
1695X LEU 3.1 15.0 + - - +
1696X TYR* 3.5 9.0 - - + +
1698X PHE* 1.3 72.4 - - - +
1700X ARG* 1.3 66.6 + - - +
1701X ASP 3.2 0.5 + - - -
1703X VAL* 3.5 11.5 + - + -
1704X GLY* 2.7 37.2 + - - +
1707X LEU* 5.2 4.0 - - + -
1985X PHE* 3.8 24.7 - - + -
1986X TRP* 4.0 18.8 - - + -
1989X ILE* 5.2 2.9 - - + -
1996X VAL* 3.7 36.3 - - + -
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Residues in contact with ARG1700 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563X ILE 5.6 0.2 + - - -
1565X PHE* 3.5 66.4 + - - +
1566X LEU 3.7 9.7 + - - -
1567X ASP* 4.8 7.3 + - - +
1696X TYR* 2.9 51.4 + - + +
1697X THR* 3.2 17.5 - - + +
1699X VAL* 1.3 79.5 - - - +
1701X ASP* 1.3 63.3 + - - +
1704X GLY 5.1 0.3 + - - -
1705X GLU 5.6 0.3 + - - -
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Residues in contact with ASP1701 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1697X THR* 2.7 33.9 + - - +
1698X PHE* 3.9 5.0 - - + +
1699X VAL 3.2 0.2 - - - -
1700X ARG* 1.3 84.0 - - - +
1702X SER* 1.3 63.3 + - - +
1704X GLY 5.3 0.2 - - - -
1705X GLU* 5.9 2.1 - - - +
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Residues in contact with SER1702 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1698X PHE* 2.7 43.5 + - - -
1699X VAL 3.7 0.2 + - - -
1701X ASP* 1.3 79.4 - - - +
1703X VAL* 1.3 58.7 + - - +
1704X GLY 3.4 1.8 - - - -
1705X GLU* 4.1 3.9 + - - +
1706X PRO* 3.2 23.4 - - - +
1939X VAL* 3.7 16.4 - - - +
1945X ARG* 3.6 28.4 + - - +
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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