Contacts of the strand formed by residues 4260 - 4264 (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 VAL4260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4252C VAL* 3.8 26.9 - - + -
4253C ALA 3.4 4.0 - - - +
4254C LEU* 4.2 4.7 - - + -
4259C HIS* 1.3 76.2 - - - +
4261C TYR* 1.3 65.7 + - - +
4262C THR* 4.4 0.7 - - + -
4284C GLN* 3.3 5.7 - - - +
4285C ILE* 3.0 52.0 + - + +
4288C LEU* 4.4 14.0 - - + +
4293C ILE* 3.8 37.7 - - + -
4296C VAL* 4.4 7.6 - - + -
4305C ALA* 5.3 0.9 - - + -
4315C TRP* 4.9 4.3 - - + -
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Residues in contact with TYR4261 (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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4235C VAL* 4.0 17.7 - - + -
4236C LEU* 3.9 25.6 - - + -
4239C ILE* 4.1 15.4 - - + +
4252C VAL* 3.5 4.0 - - - +
4253C ALA* 2.8 46.3 + - + +
4255C THR* 3.7 31.4 - - + -
4259C HIS* 4.3 4.3 - - + -
4260C VAL* 1.3 76.4 - - - +
4262C THR* 1.3 62.3 + - - +
4263C PHE* 4.6 1.6 - - + -
4282C PRO* 3.9 10.1 - - + -
4283C GLN* 3.2 23.8 - - - -
4284C GLN* 3.2 42.2 + - + -
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Residues in contact with THR4262 (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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4250C PHE* 5.8 0.4 - - + -
4251C SER 3.4 12.1 - - - +
4252C VAL* 4.1 14.6 - - + -
4260C VAL* 4.4 3.1 - - + -
4261C TYR* 1.3 79.0 - - - +
4263C PHE* 1.3 66.0 + - - +
4269C ILE* 2.6 44.8 + - - +
4271C LEU* 3.8 18.0 - - - +
4279C HIS* 5.9 0.2 - - - -
4281C ARG 3.9 2.1 - - - +
4282C PRO* 3.6 0.2 - - - +
4283C GLN* 2.9 27.4 + - - +
4285C ILE* 3.6 20.2 - - + +
4315C TRP* 4.9 3.4 - - + +
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Residues in contact with PHE4263 (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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4199C LEU* 4.7 8.7 - - + -
4208C VAL* 6.2 0.2 - - + -
4217C GLY 4.1 2.2 - - - +
4218C LYS* 3.2 30.4 - - - -
4219C LEU 3.7 13.2 - - - -
4220C GLY* 3.4 17.3 - - - -
4233C ILE* 4.1 9.0 - - + -
4236C LEU* 4.0 20.0 - - + -
4250C PHE* 3.4 2.4 - - - +
4251C SER* 2.9 54.3 + - - +
4252C VAL 4.8 1.3 - - - -
4253C ALA* 4.8 4.7 - - + -
4261C TYR 4.6 6.7 - - - -
4262C THR* 1.3 83.3 - - - +
4264C GLY* 1.3 59.2 + - - +
4269C ILE* 3.6 8.1 - - - -
4279C HIS 3.5 13.0 - - - +
4281C ARG 3.9 15.0 - - - -
4282C PRO* 3.6 24.2 - - + -
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Residues in contact with GLY4264 (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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4216C TYR 3.1 19.1 - - - -
4217C GLY 3.9 1.0 + - - -
4218C LYS* 3.8 8.7 - - - -
4249C GLN 3.4 10.8 - - - -
4263C PHE* 1.3 74.9 - - - +
4265C GLN* 1.3 65.3 + - - -
4269C ILE* 3.6 4.8 - - - +
4279C HIS* 2.7 34.7 + - - +
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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