Contacts of the helix formed by residues 1748 - 1766 (chain A) 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 LYS1748 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1741A ASP* 2.6 46.6 + - - +
1742A GLY* 4.2 1.2 - - - -
1743A GLY* 3.5 12.6 - - - +
1744A GLN 2.7 38.4 + - - +
1745A PRO* 3.7 5.8 - - + -
1747A ILE 1.3 83.2 - - - +
1749A LYS* 1.3 63.1 + - - +
1750A ALA 3.5 0.2 - - - -
1751A ASN* 3.7 2.8 + - - +
1752A SER* 3.3 21.7 + - - -
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Residues in contact with LYS1749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1745A PRO* 3.9 9.8 - - + +
1746A GLU* 3.1 33.0 - - - +
1748A LYS* 1.3 78.1 - - - +
1750A ALA* 1.3 67.7 + - - +
1752A SER* 3.1 7.9 + - - -
1753A MET* 3.1 46.4 + - - +
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Residues in contact with ALA1750 (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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1656A THR* 3.8 14.8 - - - +
1659A HIS* 3.7 14.6 - - + +
1746A GLU* 2.7 37.0 - - + +
1749A LYS* 1.3 80.2 - - - +
1751A ASN* 1.3 57.3 + - - +
1753A MET* 2.9 15.1 + - + +
1754A VAL* 2.6 36.0 + - - +
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Residues in contact with ASN1751 (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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1659A HIS* 2.5 34.7 + - - -
1660A LEU* 4.4 2.7 - - - +
1734A ILE* 4.2 5.1 - - + +
1737A ALA* 2.9 44.0 + - - +
1738A ILE* 3.3 15.1 - - + +
1741A ASP* 3.0 8.1 + - - +
1747A ILE* 2.5 29.2 + - - +
1748A LYS 3.7 7.1 + - - +
1749A LYS 3.2 0.6 - - - -
1750A ALA* 1.3 78.0 - - - +
1752A SER* 1.3 57.5 + - - +
1754A VAL* 3.5 9.9 + - - +
1755A LYS* 3.0 26.9 + - - +
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Residues in contact with SER1752 (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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1738A ILE* 5.9 1.8 - - - -
1748A LYS 3.3 9.5 + - - -
1749A LYS* 3.1 9.7 + - - -
1750A ALA 3.1 0.8 - - - -
1751A ASN* 1.3 79.6 - - - +
1753A MET* 1.3 59.1 + - - +
1755A LYS* 3.6 10.9 - - - +
1756A SER* 2.8 29.5 + - - -
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Residues in contact with MET1753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656A THR* 3.7 29.6 + - + +
1749A LYS* 3.1 45.5 + - - +
1750A ALA* 2.9 19.9 + - - +
1752A SER* 1.3 75.1 - - - +
1754A VAL* 1.3 54.0 + - - +
1755A LYS 3.3 0.2 - - - -
1756A SER* 3.4 10.5 + - - +
1757A PHE* 2.6 32.9 + - - +
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Residues in contact with VAL1754 (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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1651A LEU* 4.3 5.2 - - + +
1656A THR* 3.3 30.1 - - - +
1657A THR* 4.0 16.8 - - + -
1659A HIS* 4.2 6.5 - - + -
1660A LEU* 3.8 20.6 - - + -
1734A ILE* 3.9 19.5 - - + -
1750A ALA 2.6 29.2 - - - +
1751A ASN* 3.7 9.0 - - - +
1753A MET* 1.3 76.8 - - - +
1755A LYS* 1.3 60.6 + - - +
1757A PHE* 3.4 7.1 - - - +
1758A PHE* 2.6 34.0 + - - +
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Residues in contact with LYS1755 (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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1734A ILE* 4.0 14.6 - - + -
1735A GLN* 5.3 0.8 + - - -
1738A ILE* 4.2 15.8 - - + +
1751A ASN 3.0 18.1 + - - +
1752A SER* 3.6 11.0 - - - +
1754A VAL* 1.3 77.9 - - - +
1756A SER* 1.3 67.1 + - - +
1758A PHE* 3.0 2.3 + - - +
1759A ILE* 2.8 43.7 + - + +
1777A TRP* 3.7 47.9 - - + +
1778A GLU 5.5 3.8 + - - -
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Residues in contact with SER1756 (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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1752A SER* 2.8 21.9 + - - -
1753A MET* 3.4 13.0 + - - +
1755A LYS* 1.3 74.9 - - - +
1757A PHE* 1.3 66.7 + - - +
1759A ILE* 3.4 7.2 + - - +
1760A ARG* 2.9 69.5 + - - +
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Residues in contact with PHE1757 (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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1650A ALA* 3.6 31.6 - - + -
1651A LEU* 4.0 20.4 - - + -
1654A SER* 3.5 32.1 - - - -
1656A THR* 4.3 6.1 - - - -
1657A THR* 4.6 0.7 - - + -
1753A MET 2.6 20.4 + - - +
1754A VAL* 3.4 6.1 - - - +
1756A SER* 1.3 82.2 + - - +
1758A PHE* 1.3 55.9 + - - +
1760A ARG* 4.0 5.6 - - + +
1761A GLN* 2.9 57.0 + - + +
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Residues in contact with PHE1758 (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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1647A VAL* 4.0 12.1 - - + -
1651A LEU* 3.7 25.1 - - + -
1726A PHE* 4.2 2.2 - + - -
1727A SER* 4.0 23.1 - - - -
1730A ILE* 3.5 42.0 - - + -
1731A VAL* 4.2 3.8 - - + -
1734A ILE* 3.9 15.3 - - + -
1754A VAL 2.6 22.1 + - - +
1755A LYS 3.0 3.3 + - - +
1757A PHE* 1.3 73.1 - - - +
1759A ILE* 1.3 65.6 + - - +
1761A GLN* 3.2 3.6 + - - +
1762A MET* 2.9 55.6 + - + +
1771A VAL* 3.8 26.0 - - + -
1777A TRP* 4.9 4.9 - + - -
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Residues in contact with ILE1759 (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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1755A LYS* 2.8 50.2 + - + +
1756A SER* 3.8 7.2 - - - +
1758A PHE* 1.3 73.0 - - + +
1760A ARG* 1.3 62.8 + - + +
1762A MET* 3.5 2.6 + - - +
1763A GLU* 2.9 28.7 + - + +
1771A VAL* 3.8 30.2 - - + +
1772A LYS* 3.4 44.4 - - + +
1777A TRP* 4.4 10.1 - - + +
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Residues in contact with ARG1760 (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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1756A SER* 2.9 48.9 + - - +
1757A PHE* 4.0 4.9 - - + +
1759A ILE* 1.3 74.8 - - + +
1761A GLN* 1.3 66.1 + - - +
1763A GLU* 3.2 12.9 + - - +
1764A ARG* 3.1 22.2 + - - +
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Residues in contact with GLN1761 (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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1646A GLN* 4.9 10.3 + - - +
1647A VAL* 4.1 28.2 - - + +
1650A ALA* 4.1 19.5 - - + +
1651A LEU* 6.1 2.0 - - + -
1757A PHE* 2.9 44.3 + - + +
1758A PHE* 3.6 4.9 - - - +
1760A ARG* 1.3 75.3 - - - +
1762A MET* 1.3 62.2 + - - +
1764A ARG* 2.9 51.1 + - - +
1765A VAL* 3.0 31.6 - - - +
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Residues in contact with MET1762 (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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1647A VAL* 3.9 21.1 - - + -
1723A VAL* 4.0 22.0 - - + -
1726A PHE* 4.0 12.3 - - + -
1727A SER* 3.7 30.7 - - - -
1758A PHE* 2.9 41.8 + - + +
1759A ILE 3.6 1.1 - - - +
1761A GLN* 1.3 75.6 - - - +
1763A GLU* 1.3 60.6 + - - +
1765A VAL* 4.6 2.7 - - - +
1766A PHE* 2.8 50.3 + - + +
1769A PHE* 4.0 5.6 - - + -
1771A VAL* 3.5 25.8 - - + -
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Residues in contact with GLU1763 (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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1759A ILE* 2.9 19.1 + - + +
1760A ARG* 3.2 12.8 + - - +
1762A MET* 1.3 76.9 - - - +
1764A ARG* 1.3 61.4 + - - +
1766A PHE 4.3 5.4 - - - -
1767A PRO* 3.3 29.4 - - + +
1769A PHE 5.4 4.0 - - - +
1772A LYS* 4.1 18.4 + - - -
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Residues in contact with ARG1764 (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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1646A GLN* 5.2 8.0 - - - +
1760A ARG 3.1 11.6 + - - +
1761A GLN* 2.9 47.4 + - - +
1762A MET 3.1 0.4 - - - -
1763A GLU* 1.3 80.3 - - - +
1765A VAL* 1.3 64.1 + - + +
1767A PRO* 3.8 10.1 - - - +
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Residues in contact with VAL1765 (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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1612A ASN* 4.4 7.1 + - - -
1643A SER* 3.4 41.8 + - - +
1646A GLN* 4.1 27.1 - - + +
1647A VAL* 3.5 22.7 - - + -
1761A GLN* 3.0 24.3 + - - +
1764A ARG* 1.3 79.2 - - + +
1766A PHE* 1.3 72.0 + - + +
1767A PRO* 3.4 8.5 - - - +
1768A TRP* 4.9 0.5 + - - -
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Residues in contact with PHE1766 (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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1609A ILE* 4.6 9.4 - - + -
1640A LEU* 4.5 7.6 - - + -
1643A SER* 3.4 35.0 - - - -
1644A LEU* 3.9 28.5 - - + -
1647A VAL* 4.4 5.8 - - + -
1723A VAL* 3.8 23.8 - - + -
1762A MET* 2.8 46.2 + - - +
1763A GLU* 4.2 1.2 - - - +
1765A VAL* 1.3 87.4 - - + +
1767A PRO* 1.3 59.2 - - - +
1768A TRP* 3.1 26.5 - + - +
1769A PHE* 2.9 40.1 + - + +
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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