Contacts of the helix formed by residues 1630 - 1652 (chain B) in PDB entry 3LQJ
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 ALA1630 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1620B THR* 3.5 15.7 - - - +
1625B THR* 3.7 22.9 - - + +
1627B ARG 5.0 0.4 - - - -
1628B HIS* 3.9 9.1 + - + +
1629B PRO* 1.3 75.3 - - - +
1631B GLU* 1.3 66.2 + - - +
1632B TRP* 3.4 31.0 - - + +
1633B ARG* 3.1 24.4 + - + +
1634B LEU* 4.2 1.6 + - - +
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Residues in contact with GLU1631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1616B SER 4.2 5.4 - - - +
1617B VAL* 4.1 28.6 - - - +
1618B ALA 4.2 9.7 + - - +
1620B THR* 5.1 5.6 + - + +
1629B PRO 3.3 4.2 + - - -
1630B ALA* 1.3 71.8 - - - +
1632B TRP* 1.3 66.6 + - + +
1633B ARG 3.2 0.9 + - - -
1634B LEU* 3.4 9.1 + - - +
1635B ALA* 3.3 20.8 + - - +
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Residues in contact with TRP1632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1600B GLU* 4.0 9.6 + - + -
1602B LEU* 3.9 24.7 - - + -
1610B LEU* 4.1 23.6 - - + -
1613B LEU* 4.5 1.4 - - - +
1617B VAL* 4.5 5.8 - - + -
1618B ALA 3.5 17.7 - - - +
1619B TYR* 3.5 26.6 - + - -
1620B THR* 3.3 36.9 + - - -
1630B ALA* 3.2 22.0 - - + +
1631B GLU* 1.3 83.7 - - - +
1633B ARG* 1.3 105.5 + - + +
1635B ALA* 3.6 8.0 - - - +
1636B LEU* 2.9 55.2 + - + +
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Residues in contact with ARG1633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1600B GLU* 3.0 48.3 + - - +
1601B ASN* 4.8 6.3 + - - +
1602B LEU* 4.4 7.5 - - - +
1629B PRO* 4.6 20.4 - - + -
1630B ALA* 3.1 16.4 + - + +
1632B TRP* 1.3 116.5 - - + +
1634B LEU* 1.3 62.8 + - - +
1636B LEU* 3.4 4.5 + - - +
1637B GLU* 3.1 22.5 + - - +
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Residues in contact with LEU1634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1629B PRO* 5.8 7.3 - - + +
1630B ALA 4.2 1.2 + - - +
1631B GLU* 3.4 10.7 + - - +
1633B ARG* 1.3 77.5 - - - +
1635B ALA* 1.3 62.9 + - - +
1637B GLU* 3.3 13.6 + - + +
1638B LYS* 3.0 61.0 + - + +
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Residues in contact with ALA1635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1613B LEU* 4.0 10.1 - - + +
1617B VAL* 3.7 28.5 - - + -
1631B GLU* 3.3 12.5 + - - +
1632B TRP 3.6 7.9 - - - +
1633B ARG 3.2 0.2 - - - -
1634B LEU* 1.3 81.9 - - - +
1636B LEU* 1.3 55.1 + - - +
1638B LYS* 3.9 7.4 - - - +
1639B GLU* 2.9 31.5 + - - +
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Residues in contact with LEU1636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1602B LEU* 3.9 20.4 - - + -
1606B MET* 3.8 30.5 - - + +
1609B ILE* 3.7 26.2 - - + +
1610B LEU* 3.8 22.9 - - + +
1613B LEU* 4.5 6.9 - - + +
1632B TRP* 2.9 43.2 + - + +
1633B ARG* 3.7 5.6 - - - +
1635B ALA* 1.3 75.5 - - - +
1637B GLU* 1.3 64.8 + - - +
1639B GLU* 3.4 3.5 + - - +
1640B LEU* 3.3 20.8 + - - +
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Residues in contact with GLU1637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1606B MET* 5.9 1.8 - - - -
1633B ARG 3.1 13.8 + - - +
1634B LEU* 3.6 18.7 - - + +
1636B LEU* 1.3 79.1 - - - +
1638B LYS* 1.3 79.7 + - - +
1640B LEU* 3.4 12.4 + - - +
1641B GLN* 3.3 31.2 + - - +
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Residues in contact with LYS1638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634B LEU* 3.0 56.0 + - + +
1635B ALA* 3.9 6.3 - - - +
1637B GLU* 1.3 85.7 + - - +
1639B GLU* 1.3 60.7 + - - +
1641B GLN* 3.3 5.8 + - - +
1642B ILE* 2.8 47.4 + - + +
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Residues in contact with GLU1639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1609B ILE* 3.7 20.2 - - + +
1612B ASN* 5.4 5.9 - - + +
1613B LEU* 3.6 29.7 - - + +
1614B PRO* 5.1 5.7 - - - +
1635B ALA 2.9 18.0 + - - +
1636B LEU 3.6 5.6 - - - +
1637B GLU 3.3 0.2 - - - -
1638B LYS* 1.3 76.5 - - - +
1640B LEU* 1.3 62.0 + - - +
1642B ILE* 3.6 17.8 - - - +
1643B SER* 2.9 41.7 + - - +
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Residues in contact with LEU1640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1605B GLU* 5.2 0.2 - - - +
1606B MET* 3.5 24.0 - - + -
1609B ILE* 3.7 29.7 - - + +
1636B LEU 3.3 9.4 + - - +
1637B GLU* 3.7 9.6 - - - +
1638B LYS 3.2 0.4 - - - -
1639B GLU* 1.3 80.0 - - - +
1641B GLN* 1.3 76.7 + - - +
1643B SER* 3.6 3.2 - - - -
1644B LEU* 2.9 41.6 + - + +
1720B TYR 4.6 0.4 - - - +
1721B THR* 3.6 25.8 - - - +
1722B SER* 4.2 1.1 - - - +
1723B VAL* 3.7 26.2 - - + +
1766B PHE* 4.7 1.8 - - + -
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Residues in contact with GLN1641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1637B GLU* 3.3 30.1 + - - +
1638B LYS* 3.3 8.1 + - - +
1640B LEU* 1.3 86.3 - - - +
1642B ILE* 1.3 58.1 + - + +
1644B LEU* 3.7 12.3 - - - +
1645B LYS* 2.8 38.3 + - + +
1715B MET* 4.5 16.8 + - - +
1718B GLY* 4.6 17.1 - - - +
1720B TYR* 3.0 27.5 + - - +
1721B THR* 4.9 0.3 - - - -
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Residues in contact with ILE1642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1638B LYS* 2.8 44.1 + - + +
1639B GLU* 3.6 19.3 - - - +
1641B GLN* 1.3 74.7 - - + +
1643B SER* 1.3 60.5 + - - +
1645B LYS* 3.2 7.0 + - - +
1646B GLN* 2.8 36.7 + - + +
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Residues in contact with SER1643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1609B ILE* 5.8 1.0 - - - +
1639B GLU* 2.9 32.2 + - - +
1640B LEU* 3.6 2.0 - - - -
1642B ILE* 1.3 75.8 - - - +
1644B LEU* 1.3 67.4 + - - +
1646B GLN* 3.1 17.1 + - - +
1647B VAL* 3.2 17.2 + - - +
1765B VAL* 3.4 26.2 + - - +
1766B PHE* 3.4 19.3 - - - -
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Residues in contact with LEU1644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1640B LEU* 2.9 40.9 + - + +
1641B GLN* 3.7 14.4 - - - +
1643B SER* 1.3 71.8 - - - +
1645B LYS* 1.3 64.8 + - - +
1647B VAL* 3.1 6.6 + - - +
1648B LEU 3.0 18.9 + - - -
1715B MET* 3.6 21.5 - - + +
1720B TYR* 3.8 33.0 - - + +
1722B SER 4.3 4.7 - - - +
1723B VAL* 4.2 12.1 - - - -
1726B PHE* 3.8 30.9 - - + -
1766B PHE* 3.8 20.9 - - + -
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Residues in contact with LYS1645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641B GLN* 2.8 23.3 + - + +
1642B ILE* 3.5 7.2 - - - +
1644B LEU* 1.3 77.3 - - - +
1646B GLN* 1.3 51.9 + - - +
1648B LEU* 4.5 2.9 - - + -
1649B THR* 2.5 67.8 + - + +
1712B LYS* 5.9 2.4 - - - +
1715B MET* 3.6 23.8 - - + -
1716B ASP* 4.5 15.1 + - - +
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Residues in contact with GLN1646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1642B ILE* 2.8 23.3 + - + +
1643B SER* 3.3 12.9 - - - +
1644B LEU 3.1 0.2 - - - -
1645B LYS* 1.3 77.8 - - - +
1647B VAL* 1.3 59.7 + - - +
1649B THR* 3.0 17.3 + - - -
1650B ALA* 3.3 14.8 + - + +
1764B ARG* 6.1 2.0 - - - +
1765B VAL* 3.5 26.8 - - + +
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Residues in contact with VAL1647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1643B SER 3.2 7.6 + - - +
1644B LEU 3.1 7.2 + - - +
1646B GLN* 1.3 75.2 - - - +
1648B LEU* 1.3 65.1 + - - +
1650B ALA* 3.3 6.0 + - - +
1651B LEU* 3.0 27.3 + - + +
1726B PHE* 3.7 23.6 - - + -
1758B PHE* 4.1 12.8 - - + -
1761B GLN* 3.8 19.6 - - + +
1762B MET* 3.8 23.6 - - + -
1765B VAL* 3.6 32.3 - - + -
1766B PHE* 4.2 3.1 - - + -
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Residues in contact with LEU1648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1644B LEU 3.0 6.3 + - - +
1645B LYS* 3.9 5.4 - - + +
1647B VAL* 1.3 78.1 - - - +
1649B THR* 1.3 59.3 + - + +
1651B LEU* 3.2 14.2 + - + +
1652B LEU* 3.0 56.7 + - + +
1708B LEU* 4.6 6.7 - - + +
1711B VAL* 4.0 20.6 - - + -
1712B LYS* 3.6 36.8 - - + +
1715B MET* 3.5 39.0 - - + -
1716B ASP* 6.0 0.7 - - - +
1726B PHE* 4.1 6.5 - - + -
1730B ILE* 5.1 0.7 - - + -
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Residues in contact with THR1649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1645B LYS* 2.5 58.8 + - + +
1646B GLN* 3.0 16.3 + - - -
1648B LEU* 1.3 75.3 - - + +
1650B ALA* 1.3 58.0 + - - +
1652B LEU* 3.9 9.8 + - + +
1653B ASN* 2.8 34.2 + - - +
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Residues in contact with ALA1650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1646B GLN* 3.3 15.1 + - + +
1647B VAL 3.7 4.0 - - - +
1648B LEU 3.1 0.6 - - - -
1649B THR* 1.3 79.0 + - - +
1651B LEU* 1.3 67.5 + - - +
1653B ASN* 3.0 16.6 + - - +
1654B SER 3.2 8.7 + - - -
1757B PHE* 4.0 9.4 - - + -
1761B GLN* 3.5 27.1 - - + +
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Residues in contact with LEU1651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1647B VAL* 3.0 24.6 + - + +
1648B LEU* 3.6 15.3 - - + +
1650B ALA* 1.3 76.0 - - - +
1652B LEU* 1.3 53.7 + - - +
1653B ASN 2.8 11.1 + - - -
1654B SER 3.0 9.9 + - - -
1657B THR* 2.9 33.3 + - + +
1708B LEU* 4.4 10.5 - - + -
1726B PHE* 5.0 0.4 - - + -
1730B ILE* 4.3 22.2 - - + -
1734B ILE* 6.1 0.7 - - + -
1754B VAL* 5.6 1.6 - - + +
1757B PHE* 3.8 28.5 - - + -
1758B PHE* 3.9 46.4 - - + -
1761B GLN* 4.7 4.5 - - + -
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Residues in contact with LEU1652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1648B LEU* 3.0 39.0 + - + +
1649B THR* 4.1 11.2 - - + +
1651B LEU* 1.3 75.6 - - - +
1653B ASN* 1.3 64.7 + - - +
1654B SER 4.6 1.0 - - - +
1657B THR* 4.0 7.3 + - - -
1661B LEU* 3.5 34.4 - - + +
1708B LEU* 3.6 29.6 - - + +
1709B GLU* 5.8 0.4 - - - -
1712B LYS* 4.4 24.2 - - + -
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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) + - + + + + + -
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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