Contacts of the strand formed by residues 4347 - 4350 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4030C GLN* 3.2 29.6 + - - +
4031C GLN* 4.4 10.6 - - - +
4295C ASP* 5.8 1.3 - - - -
4306C LEU* 4.3 3.4 - - - -
4345C VAL* 3.7 2.9 - - - +
4346C ARG* 1.3 82.2 - - + +
4348C ILE* 1.3 65.8 + - - +
4357C ALA* 3.3 4.3 - - - -
4358C TRP* 3.1 62.7 + - + +
4360C ALA* 3.0 25.5 + - - +
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Residues in contact with ILE4348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4002C TRP* 5.6 0.2 - - + -
4295C ASP* 3.9 22.1 + - - +
4296C VAL 4.1 1.6 - - - -
4297C ALA* 3.8 18.0 - - + +
4304C LEU* 3.5 45.1 - - + +
4305C ALA 4.0 0.2 - - - +
4306C LEU* 3.8 26.9 - - + +
4312C VAL* 4.3 25.8 - - + -
4345C VAL* 4.4 2.5 - - + -
4347C GLN* 1.3 79.4 - - - +
4349C SER* 1.3 61.9 + - - +
4356C ALA 3.3 11.9 - - - +
4357C ALA* 4.2 11.4 - - + -
4358C TRP* 3.6 7.7 - - - -
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Residues in contact with SER4349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4032C VAL 3.3 24.3 + - - -
4033C ILE* 3.6 4.3 - - - +
4034C CYS* 2.9 34.1 + - - -
4297C ALA* 4.0 6.1 - - - -
4304C LEU* 3.7 4.2 - - - +
4348C ILE* 1.3 76.4 - - - +
4350C ALA* 1.3 62.6 + - - +
4355C SER* 3.4 2.3 - - - -
4356C ALA* 2.8 33.7 + - - +
4358C TRP* 3.7 5.1 - - - -
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Residues in contact with ALA4350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4034C CYS* 3.7 8.1 - - - +
4088C CYS* 3.7 6.6 - - - -
4297C ALA* 3.9 18.8 - - + +
4298C VAL 3.6 10.7 - - - +
4299C GLY* 3.5 29.5 - - - +
4302C HIS* 3.6 18.2 - - + +
4304C LEU* 4.2 7.0 - - + -
4349C SER* 1.3 77.5 + - - +
4351C GLY* 1.3 60.3 + - - +
4354C HIS 3.8 3.6 - - - -
4355C SER* 4.3 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
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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