Contacts of the strand formed by residues 4260 - 4264 (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 VAL4260 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4252D VAL* 3.8 27.6 - - + -
4253D ALA 3.4 3.6 - - - +
4254D LEU* 4.1 4.9 - - + -
4258D GLY 4.5 0.4 - - - +
4259D HIS* 1.3 77.8 - - - +
4261D TYR* 1.3 64.5 + - - +
4262D THR* 4.3 0.4 - - + -
4284D GLN* 3.2 7.5 - - - +
4285D ILE* 2.9 53.4 + - + -
4288D LEU* 4.3 14.0 - - + +
4293D ILE* 4.0 37.0 - - + -
4296D VAL* 4.4 9.0 - - + -
4305D ALA* 5.4 0.4 - - + -
4315D TRP* 4.9 4.0 - - + -
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Residues in contact with TYR4261 (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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4235D VAL* 4.3 14.6 - - + -
4236D LEU* 4.1 24.7 - - + -
4239D ILE* 4.2 16.3 - - + +
4252D VAL* 3.4 4.3 - - - +
4253D ALA* 2.8 39.9 + - + +
4255D THR* 3.7 30.5 - - + +
4259D HIS* 4.1 15.0 - + + +
4260D VAL* 1.3 78.2 - - - +
4262D THR* 1.3 64.6 + - - +
4263D PHE* 4.6 2.3 - - + -
4282D PRO* 4.1 8.7 - - + -
4283D GLN* 3.2 15.0 - - - +
4284D GLN* 3.6 37.6 + - + -
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Residues in contact with THR4262 (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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4251D SER 3.4 11.7 - - - +
4252D VAL* 4.3 15.0 - - + -
4260D VAL* 4.3 3.6 - - + -
4261D TYR* 1.3 78.9 - - - +
4263D PHE* 1.3 67.3 + - - +
4269D ILE* 2.7 43.1 + - - +
4271D LEU* 3.7 18.0 - - - +
4279D HIS* 5.9 0.2 - - - -
4281D ARG 3.8 1.9 - - - +
4283D GLN* 3.0 27.5 + - - +
4285D ILE* 3.7 20.1 - - + +
4315D TRP* 4.9 3.4 - - + +
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Residues in contact with PHE4263 (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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4199D LEU* 4.5 8.3 - - + -
4217D GLY 4.3 2.0 - - - +
4218D LYS* 3.2 30.1 - - - -
4219D LEU 3.7 14.1 - - - -
4220D GLY* 3.4 17.9 - - - -
4233D ILE* 4.2 8.3 - - + -
4236D LEU* 4.0 22.7 - - + -
4250D PHE* 3.4 1.6 - - - +
4251D SER* 2.9 52.3 + - - +
4252D VAL 4.7 1.3 - - - -
4253D ALA* 4.9 4.7 - - + -
4261D TYR 4.6 7.2 - - - -
4262D THR* 1.3 85.5 - - - +
4264D GLY* 1.3 59.5 + - - +
4269D ILE* 3.6 9.1 - - - +
4279D HIS 3.4 13.9 - - - +
4281D ARG 3.7 13.9 - - - +
4282D PRO* 3.6 22.7 - - + -
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Residues in contact with GLY4264 (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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4216D TYR 3.1 19.7 - - - -
4217D GLY 4.1 0.8 + - - -
4218D LYS* 3.8 9.0 - - - -
4249D GLN 3.5 9.9 - - - -
4250D PHE* 4.0 0.7 - - - -
4263D PHE* 1.3 74.8 - - - +
4265D GLN* 1.3 69.0 + - - +
4269D ILE* 3.7 2.9 - - - +
4279D HIS* 2.8 33.2 + - - +
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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