Contacts of the strand formed by residues 4302 - 4307 (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 HIS4302 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4250D PHE* 4.4 2.2 - - - -
4268D LEU 6.1 0.7 - - - -
4298D VAL* 3.6 3.6 - - - +
4299D GLY* 2.9 29.0 + - - -
4300D ALA 3.8 0.4 - - - -
4301D GLU* 1.3 80.3 - - - +
4303D THR* 1.3 63.9 + - - +
4304D LEU* 4.1 12.3 - - + -
4315D TRP 3.4 12.8 - - - +
4316D GLY* 4.4 0.2 - - - -
4317D SER 3.7 7.6 - - - +
4322D GLN* 3.7 33.7 + - + +
4323D LEU* 3.6 16.6 - - + -
4350D ALA* 3.8 14.1 - - + +
4351D GLY 3.2 27.5 + - - -
4352D ARG 4.3 7.2 + - - -
4354D HIS 3.8 8.7 - - - -
4355D SER* 2.9 25.6 + - - -
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Residues in contact with THR4303 (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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4250D PHE* 3.5 24.4 - - - -
4252D VAL* 4.3 7.1 - - + +
4268D LEU 4.5 1.2 + - - -
4296D VAL* 4.6 7.2 - - + -
4297D ALA 3.4 9.2 - - - +
4298D VAL* 3.8 14.2 - - + +
4302D HIS* 1.3 76.7 + - - +
4304D LEU* 1.3 75.5 + - - +
4314D ALA* 3.4 5.0 - - - -
4315D TRP* 3.0 74.3 + - + +
4323D LEU* 4.7 0.3 - - - +
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Residues in contact with LEU4304 (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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4002D TRP* 4.1 18.2 - - + -
4296D VAL* 3.3 3.6 - - - -
4297D ALA* 2.8 35.8 + - + +
4302D HIS* 4.1 13.9 - - + -
4303D THR* 1.3 85.4 - - - +
4305D ALA* 1.3 61.7 + - - +
4312D VAL* 4.7 7.6 - - + -
4313D TYR 3.3 4.9 - - - +
4314D ALA* 3.7 21.3 - - + -
4315D TRP* 4.6 0.4 - - - -
4322D GLN 4.5 2.9 - - - +
4337D VAL* 5.6 0.2 - - + -
4348D ILE* 3.9 19.7 - - + -
4349D SER 3.6 28.0 - - - +
4350D ALA* 4.4 6.7 - - + -
4355D SER* 3.9 17.0 - - - +
4356D ALA 4.4 6.5 - - - +
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Residues in contact with ALA4305 (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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4260D VAL* 5.4 0.4 - - + -
4288D LEU* 4.7 2.7 - - + -
4293D ILE* 4.0 24.5 - - + -
4295D ASP 3.4 9.6 - - - +
4296D VAL* 4.1 4.9 - - + -
4304D LEU* 1.3 74.6 - - - +
4306D LEU* 1.3 60.6 + - - +
4307D ALA 4.1 0.2 - - - -
4311D ASP 3.7 0.5 - - - +
4312D VAL* 3.3 5.9 - - - +
4313D TYR* 2.9 37.8 + - + +
4315D TRP* 3.9 25.4 - - + -
4348D ILE* 4.2 2.5 - - - -
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Residues in contact with LEU4306 (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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4293D ILE* 3.6 4.3 - - - -
4294D GLU* 2.8 32.5 + - + -
4295D ASP* 2.9 22.7 + - + +
4305D ALA* 1.3 73.1 - - - +
4307D ALA* 1.3 66.3 + - - +
4310D GLY* 3.6 20.9 - - - +
4311D ASP 3.5 13.9 - - - +
4312D VAL* 3.6 13.5 - - + -
4345D VAL* 3.9 14.8 - - + +
4346D ARG* 3.4 36.1 - - - +
4347D GLN* 4.0 6.3 - - - +
4348D ILE* 4.0 15.2 - - + +
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Residues in contact with ALA4307 (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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4291D VAL* 3.5 30.3 - - + -
4292D ILE 3.3 6.5 - - - +
4293D ILE* 3.8 5.5 - - + +
4294D GLU* 4.0 2.7 - - - +
4305D ALA 4.0 0.4 + - - -
4306D LEU* 1.3 79.9 - - - +
4308D SER* 1.3 61.6 + - - +
4309D ASN* 3.1 20.0 - - - +
4310D GLY* 2.9 20.6 + - - -
4311D ASP* 2.7 20.2 + - + +
4313D TYR* 4.4 2.2 - - + -
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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