Contacts of the strand formed by residues 4312 - 4316 (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 VAL4312 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4002D TRP* 5.3 1.8 - - + -
4304D LEU* 4.7 12.3 - - + -
4305D ALA 3.3 7.0 - - - +
4306D LEU* 3.6 21.3 - - + -
4310D GLY 3.7 4.5 + - - +
4311D ASP* 1.3 77.4 - - - +
4313D TYR* 1.3 73.4 + - - +
4336D LEU* 3.7 6.3 - - - +
4337D VAL* 2.9 41.6 + - + +
4340D LEU* 3.9 31.2 - - + +
4345D VAL* 4.2 11.9 - - + -
4348D ILE* 4.2 17.3 - - + -
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Residues in contact with TYR4313 (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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4287D VAL* 5.4 4.0 - - + -
4288D LEU* 3.9 27.6 - - + -
4291D VAL* 3.9 27.4 - - + +
4293D ILE* 4.6 6.3 - - + -
4304D LEU* 3.3 4.9 - - - -
4305D ALA* 2.9 38.5 + - + +
4307D ALA* 4.4 1.8 - - + -
4311D ASP* 4.0 25.8 + - + -
4312D VAL* 1.3 81.3 - - - +
4314D ALA* 1.3 60.5 + - - +
4315D TRP* 4.2 8.0 - - + -
4334D PRO* 4.1 17.9 - - + -
4335D THR 3.4 10.8 - - - +
4336D LEU* 3.7 38.1 - - + +
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Residues in contact with ALA4314 (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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4303D THR 3.4 5.6 - - - -
4304D LEU* 3.7 16.6 - - + -
4313D TYR* 1.3 75.4 - - - +
4315D TRP* 1.3 65.6 + - - +
4323D LEU* 3.5 37.5 - - + +
4325D LEU* 4.7 2.4 - - + +
4331D VAL* 4.2 2.1 - - - +
4333D GLU 3.9 0.3 - - - +
4335D THR* 2.9 34.2 + - - +
4337D VAL* 3.7 8.3 - - + -
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Residues in contact with TRP4315 (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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4252D VAL* 5.5 0.4 - - + +
4260D VAL* 4.9 7.9 - - + -
4262D THR* 4.9 5.3 - - + +
4268D LEU 3.8 15.3 + - - -
4269D ILE* 3.8 3.2 - - - +
4270D GLY* 3.4 34.6 - - - +
4285D ILE* 3.5 28.7 - - + -
4288D LEU* 4.3 4.9 - - + -
4296D VAL* 5.4 0.7 - - + -
4302D HIS* 3.4 5.0 - - - +
4303D THR* 3.0 73.2 + - + -
4305D ALA* 3.9 27.8 - - + -
4313D TYR* 4.2 5.8 - - + -
4314D ALA* 1.3 83.5 - - - +
4316D GLY* 1.3 62.4 + - - +
4323D LEU* 3.7 10.7 - - - +
4331D VAL* 3.7 10.8 - - - +
4332D ARG 3.9 1.6 - - - +
4333D GLU 3.8 15.0 - - - +
4334D PRO* 3.6 24.7 - - + -
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Residues in contact with GLY4316 (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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4267D ARG 4.4 3.6 - - - -
4268D LEU* 4.3 9.0 - - - -
4301D GLU 3.6 7.0 - - - -
4315D TRP* 1.3 79.1 - - - +
4317D SER* 1.3 67.1 + - - -
4323D LEU* 3.7 3.2 - - - +
4330D HIS* 3.4 14.7 + - - -
4331D VAL 2.8 39.2 + - - -
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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