Contacts of the strand formed by residues 4347 - 4350 (chain A) in PDB entry 4O2W
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 GLN4347 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4030A GLN* 3.2 29.3 + - - +
4031A GLN* 4.3 11.2 - - - +
4295A ASP* 5.8 2.0 - - - -
4306A LEU* 4.3 2.9 - - - -
4345A VAL* 3.5 2.9 - - - +
4346A ARG* 1.3 84.5 - - + +
4348A ILE* 1.3 66.0 + - - +
4357A ALA* 3.3 4.2 - - - -
4358A TRP* 3.0 62.4 + - + +
4360A ALA 3.0 24.8 + - - +
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Residues in contact with ILE4348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4295A ASP* 3.9 23.5 + - + +
4296A VAL 4.1 0.7 - - - -
4297A ALA* 3.8 20.7 - - + +
4304A LEU* 3.6 39.3 - - + +
4305A ALA 4.0 0.2 - - - -
4306A LEU* 3.8 26.9 - - + +
4312A VAL* 4.2 24.9 - - + -
4345A VAL* 4.3 2.5 - - + -
4347A GLN* 1.3 80.4 - - - +
4349A SER* 1.3 63.0 + - - +
4356A ALA 3.4 7.6 - - - +
4357A ALA* 4.0 16.2 - - + -
4358A TRP* 3.5 9.1 - - - -
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Residues in contact with SER4349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4032A VAL 3.4 22.8 + - - -
4033A ILE* 3.7 4.3 - - - +
4034A CYS* 3.0 34.4 + - - +
4297A ALA* 3.9 6.7 - - - -
4304A LEU* 3.7 5.1 - - - +
4348A ILE* 1.3 75.7 - - - +
4350A ALA* 1.3 62.4 + - - +
4355A SER* 3.5 2.3 - - - -
4356A ALA 2.9 31.8 + - - +
4358A TRP* 3.9 5.2 - - - -
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Residues in contact with ALA4350 (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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4034A CYS* 3.6 11.0 - - - +
4088A CYS* 3.8 4.5 - - - -
4297A ALA* 3.9 17.5 - - + +
4298A VAL 3.5 18.3 + - - +
4299A GLY* 3.5 22.6 - - - +
4302A HIS* 3.6 20.4 - - + +
4304A LEU* 4.3 6.1 - - + -
4349A SER* 1.3 77.8 + - - +
4351A GLY* 1.3 59.0 + - - +
4354A HIS 3.9 3.8 - - - -
4355A SER* 4.5 0.2 - - - +
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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
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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