Contacts of the strand formed by residues 4354 - 4358 (chain D) 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 HIS4354 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4001D LEU* 5.8 0.9 - - + -
4002D TRP 3.2 14.4 - - - +
4003D GLY* 4.2 1.6 - - - -
4004D ALA 3.5 19.1 - - - +
4009D GLN* 3.9 9.6 + - + +
4010D LEU* 3.8 15.7 - - + -
4034D CYS* 3.5 26.4 - - + +
4035D GLY 3.4 22.3 + - - -
4037D ASN* 4.0 5.8 + - - -
4038D CYS 3.1 29.3 + - - -
4039D THR* 2.9 26.3 + - - -
4302D HIS* 3.8 2.6 + - - -
4322D GLN* 4.2 1.7 - - - +
4351D GLY 2.8 25.5 + - - -
4353D CYS* 1.3 81.7 + - - +
4355D SER* 1.3 68.8 + - - +
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Residues in contact with SER4355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4001D LEU* 3.5 5.5 - - - +
4002D TRP* 2.9 60.5 + - - +
4034D CYS* 3.8 5.5 - - - -
4302D HIS* 2.9 22.5 + - - -
4304D LEU* 3.9 4.4 - - - +
4322D GLN 2.9 18.7 + - - -
4349D SER 3.5 11.7 - - - -
4354D HIS* 1.3 75.4 - - - +
4356D ALA* 1.3 63.7 + - - +
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Residues in contact with ALA4356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3999D VAL* 5.0 1.1 - - + -
4000D TYR 3.2 6.3 - - - +
4001D LEU* 3.3 24.9 - - + -
4002D TRP* 4.0 5.8 - - - -
4032D VAL* 3.9 14.4 - - + -
4034D CYS* 3.7 15.0 - - - -
4304D LEU* 4.4 0.7 - - - +
4348D ILE* 3.3 5.7 - - - +
4349D SER* 2.9 32.1 + - - +
4355D SER* 1.3 75.9 - - - +
4357D ALA* 1.3 61.8 + - - +
4358D TRP* 4.0 9.2 - - + -
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Residues in contact with ALA4357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3999D VAL* 4.2 0.3 - - - +
4000D TYR* 2.7 38.4 + - - +
4002D TRP* 3.8 20.6 - - + -
4340D LEU* 3.9 15.7 - - + -
4345D VAL* 3.8 22.4 - - + -
4347D GLN 3.3 6.3 - - - +
4348D ILE* 4.2 5.4 - - + -
4356D ALA* 1.3 77.0 - - - +
4358D TRP* 1.3 60.8 + - - +
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Residues in contact with TRP4358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3997D CYS* 4.3 5.8 - - - -
3998D ASP 3.1 14.4 - - - +
3999D VAL* 3.6 14.8 - - + -
4000D TYR* 5.1 1.1 - - - -
4029D ALA 4.6 0.2 - - - -
4030D GLN 3.1 22.5 + - - -
4031D GLN* 3.9 3.8 - - + +
4032D VAL* 3.2 56.8 - - + -
4345D VAL* 4.1 2.8 - - - +
4346D ARG 3.0 20.9 + - - -
4347D GLN* 3.0 55.5 + - + +
4348D ILE* 3.5 34.8 - - - -
4349D SER* 3.7 6.1 - - - -
4356D ALA* 3.9 3.6 - - + -
4357D ALA* 1.3 83.4 - - - +
4359D THR* 1.3 63.2 + - - +
4360D ALA* 3.7 23.0 + - + -
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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