Contacts of the helix formed by residues 1744 - 1766 (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 GLN1744 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1742B GLY* 3.3 4.6 - - - -
1743B GLY* 1.3 78.5 - - - +
1745B PRO* 1.3 91.4 - - - +
1746B GLU* 3.0 31.1 + - - +
1747B ILE* 2.9 57.8 - - + +
1748B LYS* 3.3 7.7 + - - +
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Residues in contact with PRO1745 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1743B GLY 3.3 10.5 - - - +
1744B GLN* 1.3 95.0 - - - +
1746B GLU* 1.3 64.3 + - + +
1748B LYS* 3.6 6.1 + - + +
1749B LYS* 3.0 26.8 + - - +
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Residues in contact with GLU1746 (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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1744B GLN* 3.0 21.5 + - + +
1745B PRO* 1.3 80.0 - - + +
1747B ILE* 1.3 63.1 + - + +
1749B LYS* 3.6 10.1 + - + +
1750B ALA* 3.2 21.8 + - - +
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Residues in contact with ILE1747 (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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1659B HIS* 4.9 7.5 + - + -
1737B ALA 4.8 5.2 - - - +
1740B SER 4.7 3.8 - - - +
1741B ASP* 2.6 33.2 - - - +
1742B GLY 4.0 16.6 - - - +
1744B GLN* 2.9 36.8 + - + +
1746B GLU* 1.3 76.4 - - + +
1748B LYS* 1.3 65.1 + - - +
1750B ALA* 3.1 6.6 + - - +
1751B ASN* 2.6 41.7 + - - +
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Residues in contact with LYS1748 (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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1741B ASP* 3.2 39.5 - - - +
1742B GLY 4.6 7.1 + - - -
1743B GLY* 4.8 12.2 + - - +
1744B GLN 3.3 13.3 + - - +
1745B PRO* 4.0 6.3 - - + +
1747B ILE* 1.3 82.2 - - - +
1749B LYS* 1.3 55.3 + - - +
1751B ASN* 2.9 7.7 - - + +
1752B SER* 2.6 41.4 + - - +
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Residues in contact with LYS1749 (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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1745B PRO 3.0 19.3 + - - +
1746B GLU* 3.7 10.3 - - + +
1748B LYS* 1.3 77.3 - - - +
1750B ALA* 1.3 57.3 + - - +
1752B SER* 3.9 4.0 - - - -
1753B MET* 2.9 60.4 + - + +
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Residues in contact with ALA1750 (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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1655B ARG 5.7 1.1 - - - +
1656B THR* 3.6 12.2 - - - +
1658B SER* 6.1 0.2 - - - +
1659B HIS* 3.7 22.2 - - + +
1746B GLU 3.2 10.1 + - - +
1747B ILE* 3.1 9.7 + - - +
1749B LYS* 1.3 76.2 - - - +
1751B ASN* 1.3 63.9 + - - +
1753B MET* 3.4 12.8 + - - +
1754B VAL* 3.1 23.4 + - - +
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Residues in contact with ASN1751 (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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1659B HIS* 4.2 9.2 + - - -
1734B ILE 4.9 0.2 - - - -
1737B ALA* 3.3 38.2 + - - +
1738B ILE* 2.6 42.3 - - - +
1741B ASP* 4.5 7.4 + - - -
1747B ILE* 2.6 24.5 + - - +
1748B LYS* 2.9 13.2 - - + +
1750B ALA* 1.3 70.7 - - - +
1752B SER* 1.3 57.9 + - - +
1754B VAL* 2.7 39.8 + - - +
1755B LYS* 3.0 4.9 + - - +
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Residues in contact with SER1752 (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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1738B ILE* 6.0 1.3 - - - -
1748B LYS* 2.6 22.4 + - - +
1749B LYS* 4.1 4.0 - - - -
1751B ASN* 1.3 68.3 + - - +
1753B MET* 1.3 61.9 + - - +
1754B VAL 2.9 6.8 + - - -
1755B LYS* 3.3 7.9 + - - +
1756B SER* 3.0 31.7 + - - -
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Residues in contact with MET1753 (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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1655B ARG* 6.5 0.2 - - + -
1656B THR* 3.7 29.3 - - + +
1749B LYS* 2.9 57.2 + - + +
1750B ALA* 3.5 11.7 - - - +
1751B ASN 3.1 0.2 - - - -
1752B SER* 1.3 76.1 - - - +
1754B VAL* 1.3 56.9 + - - +
1756B SER* 4.7 3.1 - - - -
1757B PHE* 2.9 26.9 + - - +
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Residues in contact with VAL1754 (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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1651B LEU* 5.7 1.6 - - + -
1656B THR* 3.1 33.0 - - - +
1657B THR* 3.7 15.0 - - + -
1659B HIS* 4.7 1.8 - - + +
1660B LEU* 4.0 17.3 - - + -
1734B ILE* 3.5 31.9 - - + -
1737B ALA* 6.5 0.4 - - + -
1750B ALA 3.1 9.7 + - - +
1751B ASN* 2.7 25.4 + - - +
1753B MET* 1.3 78.8 - - - +
1755B LYS* 1.3 58.8 + - - +
1756B SER 3.1 1.8 - - - -
1757B PHE* 4.2 2.2 - - + -
1758B PHE* 2.9 32.9 + - - +
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Residues in contact with LYS1755 (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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1734B ILE* 4.2 17.0 - - + -
1735B GLN* 5.3 1.0 + - - -
1738B ILE* 4.3 14.6 - - + +
1751B ASN 3.0 6.7 + - - +
1752B SER* 3.3 8.7 + - - +
1754B VAL* 1.3 82.6 - - - +
1756B SER* 1.3 60.3 + - - +
1758B PHE* 4.3 0.7 - - - +
1759B ILE* 3.1 43.9 + - + +
1777B TRP* 3.7 53.6 - - + +
1778B GLU* 5.4 4.4 - - - +
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Residues in contact with SER1756 (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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1752B SER* 3.0 19.2 + - - -
1753B MET* 4.7 3.6 - - - -
1755B LYS* 1.3 77.7 - - - +
1757B PHE* 1.3 60.4 + - - +
1758B PHE 3.2 1.3 - - - -
1759B ILE* 3.5 4.6 + - - +
1760B ARG* 2.8 59.7 + - - +
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Residues in contact with PHE1757 (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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1650B ALA* 4.1 8.3 - - + -
1651B LEU* 3.8 29.2 - - + -
1654B SER* 3.3 37.7 - - - -
1656B THR* 3.7 11.4 - - + +
1657B THR* 4.9 0.4 - - + -
1753B MET 2.9 23.4 + - - +
1754B VAL* 3.4 2.9 + - + +
1756B SER* 1.3 79.6 - - - +
1758B PHE* 1.3 57.4 + - - +
1760B ARG* 3.9 9.5 - - + +
1761B GLN* 3.0 71.1 + - + +
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Residues in contact with PHE1758 (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* 4.1 5.6 - - + -
1651B LEU* 3.9 30.3 - - + -
1726B PHE* 4.4 0.9 - + - -
1727B SER* 4.1 16.6 - - - -
1730B ILE* 3.4 48.5 - - + -
1731B VAL* 4.2 4.7 - - + -
1734B ILE* 3.8 15.0 - - + -
1754B VAL 2.9 17.7 + - - +
1755B LYS 4.3 2.0 - - - +
1757B PHE* 1.3 76.6 - - - +
1759B ILE* 1.3 61.6 + - + +
1761B GLN* 2.9 2.1 + - + -
1762B MET* 2.8 59.7 + - + +
1771B VAL* 3.7 27.8 - - + -
1777B TRP* 4.9 2.9 - + - -
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Residues in contact with ILE1759 (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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1755B LYS* 3.1 41.1 + - + +
1756B SER* 3.9 5.2 - - - +
1758B PHE* 1.3 81.1 - - + +
1760B ARG* 1.3 60.9 + - + +
1762B MET* 4.0 6.3 - - - +
1763B GLU* 3.2 25.8 + - + +
1771B VAL* 4.0 26.3 - - + +
1772B LYS* 4.1 42.0 - - + +
1777B TRP* 4.6 7.9 - - + -
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Residues in contact with ARG1760 (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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1756B SER* 2.8 54.9 + - - +
1757B PHE* 4.0 10.2 - - + +
1759B ILE* 1.3 82.1 - - + +
1761B GLN* 1.3 67.1 + - + +
1763B GLU* 3.5 17.1 + - - +
1764B ARG* 3.2 28.7 + - - +
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Residues in contact with GLN1761 (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* 3.8 19.4 - - + +
1650B ALA* 3.5 22.9 - - + +
1651B LEU* 4.7 3.4 - - + -
1757B PHE* 3.0 62.6 + - + +
1758B PHE* 2.9 7.4 + - - +
1760B ARG* 1.3 77.5 - - - +
1762B MET* 1.3 64.2 + - - +
1764B ARG* 3.6 27.5 + - - +
1765B VAL* 3.6 24.4 + - - +
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Residues in contact with MET1762 (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* 3.8 22.9 - - + -
1723B VAL* 3.8 29.6 - - + -
1726B PHE* 3.9 11.4 - - + -
1727B SER* 3.8 22.9 - - - +
1758B PHE* 2.8 42.2 + - + +
1759B ILE 4.0 2.2 - - - +
1761B GLN* 1.3 78.2 - - - +
1763B GLU* 1.3 55.6 + - - +
1765B VAL 3.3 0.2 + - - -
1766B PHE* 2.7 54.8 + - + +
1769B PHE* 4.0 13.0 - - + +
1771B VAL* 3.6 19.1 - - + -
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Residues in contact with GLU1763 (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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1759B ILE* 3.2 19.2 + - + +
1760B ARG* 3.7 19.7 - - - +
1761B GLN 3.3 0.2 - - - -
1762B MET* 1.3 77.6 - - - +
1764B ARG* 1.3 63.6 + - + +
1766B PHE 4.3 5.4 - - - -
1767B PRO* 3.3 31.4 - - + +
1769B PHE 5.5 2.9 - - - -
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Residues in contact with ARG1764 (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* 6.1 2.0 - - - +
1760B ARG* 3.2 16.4 + - - +
1761B GLN* 3.7 33.8 + - - +
1762B MET 3.1 0.2 - - - -
1763B GLU* 1.3 82.5 - - + +
1765B VAL* 1.3 62.5 + - + +
1767B PRO* 4.2 4.5 - - - +
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Residues in contact with VAL1765 (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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1612B ASN* 4.9 6.4 + - - -
1643B SER* 3.4 39.3 + - - +
1646B GLN* 3.5 32.5 - - + +
1647B VAL* 3.6 26.5 - - + -
1761B GLN* 3.6 6.8 + - - +
1762B MET 3.3 1.8 + - - -
1764B ARG* 1.3 80.5 - - + +
1766B PHE* 1.3 74.2 + - + +
1767B PRO* 3.4 9.6 - - - +
1768B TRP* 4.8 1.6 + - - -
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Residues in contact with PHE1766 (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* 4.8 6.3 - - + -
1640B LEU* 4.7 4.9 - - + -
1643B SER* 3.4 32.8 - - - -
1644B LEU* 3.8 22.7 - - + -
1647B VAL* 4.2 6.3 - - + -
1723B VAL* 3.5 26.2 - - + -
1726B PHE* 5.3 0.2 - + - -
1762B MET* 2.7 51.0 + - + +
1763B GLU* 4.2 1.0 - - - +
1765B VAL* 1.3 89.1 - - + +
1767B PRO* 1.3 57.3 - - - +
1768B TRP* 3.1 32.8 - + + +
1769B PHE* 3.0 39.6 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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