Contacts of the helix formed by residues 1687 - 1696 (chain A) in PDB entry 3AU5
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 SER1687 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1590A GLN* 3.5 1.1 - - - +
1685A VAL 3.3 3.7 + - - -
1686A PRO* 1.3 76.5 - - - +
1688A ARG* 1.3 61.7 + - - +
1689A ASP* 3.8 4.8 + - - +
1690A GLU* 3.0 22.4 + - - +
1691A ILE* 2.8 25.9 + - - +
1700A MET* 4.2 7.6 - - - +
1765A LEU* 4.2 7.3 + - - +
1766A ALA* 3.9 22.5 + - - +
1769A GLU* 3.4 27.4 - - - -
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Residues in contact with ARG1688 (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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1584A ASP* 5.2 2.8 + - - -
1586A ILE* 4.0 30.0 - - + +
1587A PRO* 3.6 41.6 + - - +
1590A GLN* 3.4 21.4 + - - +
1687A SER* 1.3 71.2 - - - +
1689A ASP* 1.3 64.4 + - - +
1691A ILE* 3.2 3.0 + - - +
1692A GLU* 2.8 27.7 + - - +
1769A GLU* 2.8 25.0 + - - +
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Residues in contact with ASP1689 (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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1687A SER* 3.3 5.1 + - - +
1688A ARG* 1.3 78.8 - - - +
1690A GLU* 1.3 63.0 + - - +
1692A GLU* 3.5 10.5 + - - +
1693A ALA* 3.1 22.7 + - - +
1700A MET* 3.8 21.5 - - + +
1701A THR 5.0 6.8 - - - +
1769A GLU* 4.6 0.8 + - - -
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Residues in contact with GLU1690 (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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1682A ARG* 2.7 41.4 + - - -
1686A PRO* 3.2 22.0 - - + +
1687A SER* 3.0 18.7 + - - +
1689A ASP* 1.3 77.2 - - - +
1691A ILE* 1.3 65.9 + - - +
1693A ALA* 3.2 5.7 + - + +
1694A LEU* 3.0 31.1 + - + +
1700A MET* 3.5 24.3 - - + +
1717A ASN 5.8 0.2 - - - -
1718A SER* 2.7 29.8 + - - +
1762A ALA* 3.4 17.0 - - + +
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Residues in contact with ILE1691 (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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1586A ILE* 3.9 22.0 - - + +
1589A ILE* 4.1 12.3 - - + -
1590A GLN* 3.7 38.6 - - + +
1593A LEU* 3.9 11.9 - - + -
1634A CYS* 4.0 20.2 - - - -
1686A PRO* 3.5 28.5 - - + +
1687A SER 2.8 18.1 + - - +
1688A ARG 3.7 6.3 - - - +
1690A GLU* 1.3 72.6 - - - +
1692A GLU* 1.3 64.7 + - - +
1694A LEU* 3.2 3.9 + - - +
1695A ILE* 2.9 41.1 + - + +
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Residues in contact with GLU1692 (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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1586A ILE* 3.8 24.3 - - + +
1688A ARG 2.8 17.0 + - - +
1689A ASP* 3.7 11.5 - - - +
1691A ILE* 1.3 77.4 - - - +
1693A ALA* 1.3 61.6 + - - +
1695A ILE* 3.2 14.3 + - + +
1696A HIS* 3.2 39.6 + - + +
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Residues in contact with ALA1693 (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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1689A ASP 3.1 11.6 + - - +
1690A GLU* 3.4 9.0 - - + +
1692A GLU* 1.3 80.0 - - - +
1694A LEU* 1.3 58.8 + - + +
1696A HIS* 3.1 6.0 + - - +
1697A ARG 3.1 6.9 + - - -
1698A GLN* 2.9 45.8 + - - +
1699A GLU 3.8 15.7 - - - +
1700A MET* 3.8 14.4 - - + -
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Residues in contact with LEU1694 (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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1633A THR* 3.8 21.5 - - + +
1634A CYS* 3.9 37.9 - - + +
1637A CYS* 4.0 13.5 - - + -
1668A TYR* 4.0 4.7 - - - -
1671A PHE* 3.7 29.4 - - + -
1686A PRO* 4.8 4.7 - - + -
1690A GLU* 3.0 31.5 + - + +
1691A ILE* 3.7 4.9 - - - +
1693A ALA* 1.3 72.8 - - + +
1695A ILE* 1.3 65.0 + - - +
1696A HIS 3.1 2.0 - - - -
1697A ARG* 3.0 14.4 + - - +
1698A GLN 4.6 4.0 - - - +
1717A ASN* 6.3 1.3 - - + -
1718A SER* 3.5 28.5 - - - +
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Residues in contact with ILE1695 (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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1585A PRO* 4.7 7.6 - - + -
1586A ILE* 4.4 13.9 - - + -
1589A ILE* 3.9 24.5 - - + -
1630A GLN* 3.6 43.1 - - + +
1634A CYS* 4.9 3.6 - - - -
1668A TYR* 2.5 28.6 + - - +
1691A ILE* 2.9 27.2 + - + +
1692A GLU* 3.5 11.2 - - + +
1693A ALA 3.2 0.4 - - - -
1694A LEU* 1.3 78.6 - - - +
1696A HIS* 1.3 73.4 + - + +
1697A ARG* 3.3 0.7 + - - -
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Residues in contact with HIS1696 (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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1692A GLU* 3.2 39.4 + - + +
1693A ALA* 3.1 6.5 + - - +
1694A LEU 3.1 0.4 - - - -
1695A ILE* 1.3 92.3 + - + +
1697A ARG* 1.3 76.1 + - - +
1698A GLN* 2.9 39.0 + - + +
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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