Contacts of the helix formed by residues 1648 - 1670 (chain D) in PDB entry 3SUA
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 LYS1648 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1611D ASN* 3.4 48.0 + - - +
1645D LEU* 3.6 13.0 + - + +
1647D GLY* 1.3 70.9 - - - +
1649D LEU* 1.4 53.2 + - - +
1650D GLU* 3.3 13.5 - - - +
1651D TYR* 3.2 33.1 + - + -
1652D PHE* 2.6 34.5 + - - +
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Residues in contact with LEU1649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1645D LEU 4.3 3.8 - - - +
1646D HIS* 3.6 20.4 - - - +
1647D GLY 2.9 9.1 + - - -
1648D LYS* 1.4 68.8 - - - +
1650D GLU* 1.3 56.3 + - - +
1652D PHE* 3.4 26.8 - - + +
1653D THR* 2.7 40.6 + - - -
1690D TRP* 5.1 2.7 - - + -
1693D ILE* 4.0 30.7 - - + -
2071D LEU* 3.4 37.4 - - + +
2074D LEU* 3.7 25.8 - - + +
2075D SER* 3.3 17.5 - - - +
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Residues in contact with GLU1650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1647D GLY 3.5 10.5 - - - +
1648D LYS* 4.5 10.4 - - - +
1649D LEU* 1.3 93.0 + - - +
1651D TYR* 1.3 57.7 + - - +
1653D THR* 3.7 1.1 - - - -
1654D ASP* 3.4 2.9 + - - +
1657D ARG* 2.8 31.0 + - - -
2068D ASN* 3.2 45.2 + - + +
2071D LEU* 3.8 9.3 - - + +
2072D ALA* 3.8 17.3 - - + +
2075D SER* 3.9 0.3 + - - -
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Residues in contact with TYR1651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1610D LEU 2.5 28.2 + - - -
1611D ASN* 3.2 22.4 - - - -
1612D SER 3.3 1.2 + - - -
1613D LYS* 3.2 32.4 + - + -
1616D LEU* 3.8 0.2 - - - +
1645D LEU* 3.6 22.4 - - + -
1648D LYS* 3.4 43.7 - - + +
1650D GLU* 1.3 76.4 - - + +
1652D PHE* 1.3 53.4 + - - +
1653D THR 3.1 1.6 - - - -
1654D ASP* 2.9 15.9 + - - +
1655D ILE* 2.7 63.3 + - + +
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Residues in contact with PHE1652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641D LEU* 4.2 3.8 - - + -
1642D THR* 3.7 25.8 - - + -
1645D LEU* 3.7 35.2 - - + +
1648D LYS 2.6 20.4 + - - +
1649D LEU* 3.1 21.7 + - + +
1651D TYR* 1.3 71.5 - - - +
1653D THR* 1.3 60.3 + - - +
1655D ILE* 3.4 9.1 + - + +
1656D LEU* 2.8 47.3 + - + +
1686D LEU* 3.6 38.1 - - + -
1690D TRP* 3.9 37.7 - + + -
1693D ILE* 4.6 6.7 - - + -
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Residues in contact with THR1653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1649D LEU 2.7 15.7 + - - -
1650D GLU 3.7 6.7 - - - -
1652D PHE* 1.3 76.4 - - - +
1654D ASP* 1.4 50.0 + - - +
1656D LEU* 2.9 11.9 + - + +
1657D ARG* 2.6 57.1 + - + +
1690D TRP* 3.4 24.0 + - + +
1953D TYR* 4.0 21.1 - - + +
1957D LEU* 6.0 1.6 - - + -
2071D LEU* 3.3 25.5 - - + +
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Residues in contact with ASP1654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1613D LYS* 3.3 25.9 + - - +
1650D GLU 3.4 2.9 + - - +
1651D TYR* 2.9 18.7 + - + +
1653D THR* 1.4 74.3 - - - +
1655D ILE* 1.3 60.5 + - - +
1657D ARG* 3.2 35.7 + - - +
1658D THR* 2.7 41.6 + - - -
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Residues in contact with ILE1655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1613D LYS* 3.7 22.0 - - + +
1616D LEU* 3.8 31.6 - - + -
1617D THR* 4.9 6.4 - - + +
1620D ILE* 5.7 1.8 - - + -
1645D LEU* 4.4 8.1 - - + -
1651D TYR* 2.7 57.2 + - + +
1652D PHE* 3.5 14.1 - - + +
1654D ASP* 1.3 73.1 - - - +
1656D LEU* 1.4 63.7 + - + +
1658D THR* 3.6 3.8 + - - -
1659D LEU* 3.0 47.7 + - + +
1686D LEU* 5.5 2.7 - - + -
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Residues in contact with LEU1656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1652D PHE* 2.8 50.6 + - + +
1653D THR* 2.9 10.6 + - + +
1655D ILE* 1.4 78.8 - - + +
1657D ARG* 1.4 55.6 + - - +
1658D THR 3.1 2.0 - - - -
1659D LEU* 2.8 6.7 + - - -
1660D LEU* 2.6 39.8 + - + +
1683D VAL* 4.7 9.5 - - + +
1686D LEU* 3.9 28.5 - - + +
1687D LEU* 4.0 10.1 - - + +
1690D TRP* 3.7 39.7 - - + -
1954D PHE* 6.2 0.9 - - + -
1957D LEU* 5.7 2.7 - - + -
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Residues in contact with ARG1657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1650D GLU 2.8 29.1 + - - -
1653D THR* 2.6 31.3 + - + +
1654D ASP* 3.2 40.1 + - - +
1656D LEU* 1.4 70.4 - - - +
1658D THR* 1.3 59.4 + - - +
1660D LEU* 3.5 7.1 - - - +
1661D SER* 3.2 23.7 + - - -
1953D TYR* 2.7 39.8 + - - +
1957D LEU* 3.9 25.4 - - + +
1961D GLN* 4.8 1.6 + - - -
2064D ASP* 3.6 13.1 + - - -
2067D MET* 5.4 1.0 - - - +
2068D ASN* 3.7 21.7 + - - +
2071D LEU* 5.0 0.8 - - - +
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Residues in contact with THR1658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1613D LYS* 3.5 36.6 + - - +
1617D THR* 4.4 15.3 - - + -
1654D ASP* 2.7 23.6 + - - -
1655D ILE* 3.8 3.8 - - - -
1657D ARG* 1.3 73.8 - - - +
1659D LEU* 1.3 62.0 + - - +
1660D LEU 3.4 0.5 + - - -
1661D SER* 3.5 8.3 + - - -
1662D ASP* 3.1 30.9 + - - +
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Residues in contact with LEU1659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1617D THR* 5.1 11.9 - - + +
1620D ILE* 4.6 31.4 - - + -
1621D HIS* 4.4 17.3 - - + +
1624D GLU* 5.8 3.1 - - - +
1655D ILE* 3.0 39.9 + - + +
1656D LEU* 2.8 9.9 + - - +
1658D THR* 1.3 68.9 - - - +
1660D LEU* 1.3 63.8 + - - +
1662D ASP* 3.4 17.3 + - + +
1663D LEU* 3.2 20.4 + - - +
1683D VAL* 3.9 23.8 - - + +
1686D LEU* 4.3 21.5 - - + -
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Residues in contact with LEU1660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1656D LEU* 2.6 21.3 + - + +
1657D ARG* 3.5 7.2 - - - +
1658D THR 3.3 0.2 - - - -
1659D LEU* 1.3 71.2 - - - +
1661D SER* 1.3 54.2 + - - +
1663D LEU* 2.9 33.1 + - + +
1664D VAL* 3.0 21.8 + - + +
1675D MET* 6.3 2.5 - - + -
1676D LEU* 5.6 4.9 - - + -
1683D VAL* 4.5 7.1 - - + +
1687D LEU* 4.7 14.6 - - + -
1954D PHE* 4.5 24.2 - - + -
1957D LEU* 3.8 31.2 - - + +
1958D LEU* 4.8 16.8 - - + -
1961D GLN* 3.8 26.9 - - + +
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Residues in contact with SER1661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1657D ARG 3.2 11.7 + - - -
1658D THR* 3.7 10.8 - - - -
1659D LEU 3.5 0.2 - - - -
1660D LEU* 1.3 76.0 - - - +
1662D ASP* 1.4 61.3 + - - +
1664D VAL* 3.7 3.5 + - - +
1665D ALA* 3.5 20.3 + - - +
1961D GLN* 2.7 41.6 + - - +
1964D GLN* 4.9 3.3 + - - -
1965D HIS* 4.5 5.8 + - - -
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Residues in contact with ASP1662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1617D THR* 5.2 2.1 - - - +
1621D HIS* 3.6 29.3 - - - +
1658D THR* 3.1 24.7 - - - +
1659D LEU* 3.4 18.0 - - + +
1660D LEU 3.1 0.6 - - - -
1661D SER* 1.4 76.1 - - - +
1663D LEU* 1.4 61.7 + - - +
1664D VAL 3.4 0.5 + - - -
1665D ALA* 3.5 13.0 + - - +
1666D GLN* 2.8 33.6 + - - +
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Residues in contact with LEU1663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1659D LEU 3.2 9.1 + - - +
1660D LEU* 2.9 15.8 + - + +
1662D ASP* 1.4 76.5 - - - +
1664D VAL* 1.3 63.6 + - + +
1666D GLN* 3.2 23.8 + - + +
1667D TYR* 3.3 28.6 + - + -
1675D MET* 3.9 30.7 - - + -
1676D LEU* 4.3 20.6 - - + -
1681D THR* 3.3 40.2 - - + +
1683D VAL* 3.8 17.9 - - + -
1684D GLU* 5.0 3.6 - - + +
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Residues in contact with VAL1664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660D LEU* 3.0 25.9 + - + +
1661D SER 3.7 8.5 - - - +
1662D ASP 3.3 0.2 - - - -
1663D LEU* 1.3 74.6 - - + +
1665D ALA* 1.3 62.2 + - - +
1667D TYR* 3.3 14.2 + - - +
1668D VAL* 3.4 14.6 + - + +
1675D MET* 4.2 24.2 - - + +
1958D LEU* 6.0 1.8 - - + -
1961D GLN* 3.9 31.0 - - + +
1965D HIS* 3.5 34.5 - - + +
1967D ILE* 5.5 0.7 - - + -
1976D TRP* 4.9 16.7 - - + -
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Residues in contact with ALA1665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1661D SER 3.5 9.6 + - - +
1662D ASP* 3.5 9.5 + - - +
1663D LEU 3.5 0.6 - - - -
1664D VAL* 1.3 77.6 - - - +
1666D GLN* 1.3 61.3 + - + +
1668D VAL* 3.6 23.3 + - - +
1669D ALA* 4.5 3.1 + - - +
1965D HIS* 4.2 15.9 + - + +
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Residues in contact with GLN1666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1621D HIS* 4.9 8.9 + - - -
1624D GLU* 5.4 3.8 - - - +
1662D ASP* 2.8 36.5 + - - +
1663D LEU* 3.2 17.5 + - + +
1665D ALA* 1.3 77.2 - - + +
1667D TYR* 1.3 63.7 + - + +
1668D VAL 3.7 0.3 + - - -
1669D ALA* 4.1 9.5 + - - +
1670D LYS* 3.9 23.9 + - - +
1681D THR* 5.1 6.8 - - - +
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Residues in contact with TYR1667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1663D LEU* 3.3 34.8 + - + -
1664D VAL 3.3 6.0 + - - +
1666D GLN* 1.3 78.8 - - + +
1668D VAL* 1.3 63.3 + - - +
1669D ALA 3.4 1.3 + - - -
1670D LYS* 4.3 4.5 - - + +
1671D ASN 3.3 30.5 + - - +
1672D PRO* 3.2 29.8 - - + -
1674D LEU* 3.6 19.1 + - + -
1675D MET* 3.6 59.7 - - + -
1676D LEU 4.5 0.9 - - - -
1677D ARG* 5.0 0.9 + - - +
1678D ARG 5.3 1.2 + - - -
1680D GLU* 6.1 0.7 - - - +
1681D THR* 5.8 3.4 - - + +
1684D GLU* 4.0 13.7 + - - -
1976D TRP* 6.0 0.4 - - + -
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Residues in contact with VAL1668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1664D VAL* 3.4 19.1 - - + +
1665D ALA* 3.6 17.5 - - - +
1666D GLN 3.4 0.8 - - - -
1667D TYR* 1.3 77.7 - - - +
1669D ALA* 1.3 62.2 + - - +
1670D LYS 4.6 0.7 - - - +
1672D PRO* 4.2 19.5 - - + +
1965D HIS* 4.6 25.4 - - + +
1967D ILE* 5.6 4.9 - - + -
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Residues in contact with ALA1669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1665D ALA 4.5 2.5 + - - +
1666D GLN 4.1 9.3 + - - +
1667D TYR 3.4 0.4 - - - -
1668D VAL* 1.3 78.0 - - - +
1670D LYS* 1.3 74.4 + - + +
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Residues in contact with LYS1670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1666D GLN* 3.9 22.3 + - - +
1667D TYR* 3.9 7.3 + - + +
1668D VAL 4.6 0.7 - - - +
1669D ALA* 1.3 88.7 - - + +
1671D ASN* 1.4 65.0 + - + +
1672D PRO* 4.5 2.4 - - - +
1674D LEU* 6.1 2.2 - - + -
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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