Contacts of the strand formed by residues 4349 - 4353 (chain B) in PDB entry 6W4H
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 TYR4349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6881A ALA* 2.5 32.0 + - + -
6884A ARG* 3.0 22.1 - - + +
6885A GLN* 2.9 20.9 + - + -
6904A ASP* 5.4 2.2 - - - -
4297B MET* 3.8 30.5 - - + -
4308B ILE* 3.3 6.1 - - - +
4309B THR 2.8 34.4 + - - +
4310B VAL 3.3 27.1 - - - -
4311B THR* 3.7 9.2 - - - +
4312B PRO* 3.8 30.5 - - + -
4320B SER* 5.0 1.1 - - - -
4321B PHE 3.2 15.9 - - - +
4322B GLY* 3.9 8.3 - - - -
4323B GLY* 5.0 0.4 - - - -
4345B LEU* 5.7 0.2 - - - -
4348B LYS* 1.3 79.0 - - - +
4350B VAL* 1.3 60.1 + - - +
4351B GLN* 3.6 7.7 + - - +
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Residues in contact with VAL4350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4307B ALA 3.3 9.9 - - - +
4308B ILE* 4.5 1.1 - - + +
4319B GLU 3.7 0.9 - - - +
4320B SER* 3.5 1.2 - - - -
4321B PHE* 2.9 38.8 + - + +
4323B GLY* 4.6 4.1 - - - +
4326B CYS* 3.6 38.6 - - + -
4345B LEU* 3.9 19.7 - - + -
4349B TYR* 1.3 73.8 - - - +
4351B GLN* 1.3 64.9 + - - +
4352B ILE* 3.7 23.6 + - + -
4364B THR* 3.8 9.0 - - + -
4376B TRP* 3.8 18.8 - - + -
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Residues in contact with GLN4351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4306B GLN 2.8 33.3 + - - +
4307B ALA* 2.8 17.4 + - - +
4309B THR* 3.0 23.0 + - - +
4312B PRO* 3.7 2.1 - - - +
4313B GLU 2.9 19.0 + - - -
4314B ALA* 3.4 26.9 - - - +
4318B GLN* 3.6 19.1 - - - +
4319B GLU 3.4 3.6 - - - -
4320B SER* 2.6 26.5 + - - +
4349B TYR* 3.6 6.0 + - - +
4350B VAL* 1.3 73.4 - - - +
4352B ILE* 1.3 63.8 + - - +
4353B PRO* 4.6 0.2 - - - -
4376B TRP* 2.8 31.4 + - - -
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Residues in contact with ILE4352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4318B GLN* 3.2 3.2 - - - -
4319B GLU* 2.8 33.0 + - - +
4321B PHE* 3.7 31.0 - - + -
4350B VAL* 3.7 23.6 - - + +
4351B GLN* 1.3 82.4 - - - +
4353B PRO* 1.4 86.7 - - + +
4356B CYS* 3.7 24.2 - - + +
4357B ALA* 3.8 6.1 - - - -
4360B PRO* 4.0 15.5 - - + +
4363B PHE* 3.7 23.3 - - + -
4364B THR* 4.0 10.1 - - + -
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Residues in contact with PRO4353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4317B ASP 3.5 10.8 - - - +
4318B GLN* 4.2 8.7 - - + +
4351B GLN 4.3 2.5 - - - +
4352B ILE* 1.4 87.9 - - + +
4354B THR* 1.3 61.8 + - - +
4355B THR* 4.0 14.1 - - - +
4356B CYS* 2.8 23.8 + - - -
4357B ALA 3.1 9.2 + - - -
4363B PHE* 3.4 28.3 - - + -
4376B TRP* 4.9 3.1 - - + -
4379B TYR* 3.6 38.6 - - + +
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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