Contacts of the strand formed by residues 4312 - 4316 (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 VAL4312 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4002C TRP* 5.4 1.8 - - + -
4304C LEU* 4.6 12.6 - - + -
4305C ALA 3.3 8.1 - - - +
4306C LEU* 4.0 6.1 - - + -
4310C GLY 3.9 9.6 - - - +
4311C ASP* 1.3 79.4 + - - +
4313C TYR* 1.3 67.7 + - - +
4336C LEU* 3.6 6.9 - - - +
4337C VAL* 2.8 46.8 + - + +
4340C LEU* 3.6 35.0 - - + +
4341C GLN* 5.5 0.4 - - - +
4345C VAL* 4.0 18.2 - - + -
4348C ILE* 4.3 17.0 - - + -
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Residues in contact with TYR4313 (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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4287C VAL 6.1 0.2 - - - -
4288C LEU* 4.0 22.7 - - + -
4291C VAL* 4.1 31.3 - - + +
4293C ILE* 4.6 7.0 - - + -
4303C THR 3.9 0.2 - - - +
4304C LEU* 3.4 4.9 - - - -
4305C ALA* 2.9 40.2 + - + +
4307C ALA* 4.3 2.5 - - + -
4311C ASP* 4.3 21.7 + - + -
4312C VAL* 1.3 78.7 - - - +
4314C ALA* 1.3 61.2 + - - +
4315C TRP* 4.1 8.6 - - + -
4334C PRO* 4.2 17.5 - - + -
4335C THR* 3.3 11.2 - - - +
4336C LEU* 3.6 42.5 - - + +
4337C VAL* 4.3 0.2 - - - -
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Residues in contact with ALA4314 (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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4303C THR 3.3 5.2 - - - -
4304C LEU* 3.7 17.3 - - + -
4313C TYR* 1.3 76.2 - - - +
4315C TRP* 1.3 65.3 + - - +
4323C LEU* 3.5 38.8 - - + +
4325C LEU* 4.7 3.1 - - + +
4331C VAL* 4.1 2.6 - - - +
4333C GLU 4.0 0.7 - - - +
4334C PRO 3.8 0.2 - - - -
4335C THR* 2.9 33.9 + - - +
4337C VAL* 3.9 6.7 - - + -
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Residues in contact with TRP4315 (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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4260C VAL* 4.9 7.6 - - + -
4262C THR* 4.9 5.0 - - + +
4268C LEU 3.7 16.1 + - - +
4269C ILE 3.9 2.4 - - - -
4270C GLY* 3.4 32.6 - - - +
4285C ILE* 3.7 19.3 - - + -
4288C LEU* 4.2 11.9 - - + -
4296C VAL* 5.4 0.4 - - + -
4302C HIS* 3.4 4.3 - - - +
4303C THR* 2.9 67.8 + - + -
4305C ALA* 3.8 28.0 - - + -
4313C TYR* 4.1 8.1 - - + -
4314C ALA* 1.3 85.1 - - - +
4316C GLY* 1.3 61.5 + - - +
4323C LEU* 3.6 11.6 - - - +
4331C VAL* 3.7 10.8 - - - +
4332C ARG 3.8 8.3 - - - +
4333C GLU 3.9 1.3 - - - +
4334C PRO* 3.6 35.4 - - + -
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Residues in contact with GLY4316 (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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4267C ARG 4.3 3.4 - - - -
4268C LEU* 4.3 7.9 - - - -
4301C GLU 3.6 7.6 - - - -
4315C TRP* 1.3 78.0 - - - +
4317C SER* 1.3 67.4 + - - -
4318C ASN 3.7 0.3 + - - -
4323C LEU* 3.6 5.2 - - - +
4330C HIS* 3.5 14.6 + - - -
4331C VAL 2.8 37.0 + - - -
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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