Contacts of the strand formed by residues 4349 - 4353 (chain D) in PDB entry 6W75
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6881C ALA* 2.5 32.3 + - + -
6884C ARG* 3.2 21.3 - - + +
6885C GLN* 2.9 19.7 + - + -
6904C ASP* 5.4 2.2 - - - +
4297D MET* 3.8 30.3 - - + -
4308D ILE* 3.3 5.4 - - - -
4309D THR 2.8 34.1 + - - +
4310D VAL 3.5 26.9 - - - -
4311D THR* 3.6 13.5 - - - +
4312D PRO* 3.8 27.6 - - + -
4320D SER* 4.9 1.1 - - - -
4321D PHE 3.3 14.4 - - - +
4322D GLY* 3.9 8.3 - - - -
4323D GLY* 5.0 0.2 - - - -
4347D GLY 4.8 0.4 - - - -
4348D LYS* 1.3 82.2 - - - +
4350D VAL* 1.3 60.3 + - - +
4351D GLN* 3.5 7.6 + - - +
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Residues in contact with VAL4350 (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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4307D ALA 3.3 11.0 - - - +
4308D ILE* 4.3 0.9 - - + -
4319D GLU 3.7 1.0 - - - +
4320D SER* 3.5 1.4 - - - -
4321D PHE* 2.9 38.9 + - + +
4323D GLY* 4.5 3.9 - - - +
4326D CYS* 3.7 37.7 - - + -
4345D LEU* 3.8 21.1 - - + -
4348D LYS 4.4 0.2 + - - -
4349D TYR* 1.3 73.2 - - - +
4351D GLN* 1.3 65.5 + - - +
4352D ILE* 3.8 18.5 + - + -
4364D THR* 3.8 7.4 - - + -
4376D TRP* 3.7 25.4 - - + -
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Residues in contact with GLN4351 (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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4306D GLN 2.8 31.8 + - - +
4307D ALA 2.8 16.5 + - - +
4309D THR* 3.1 21.9 + - - +
4312D PRO* 3.7 2.3 - - - +
4313D GLU 2.9 20.8 + - - -
4314D ALA* 3.4 26.2 - - + +
4318D GLN* 3.6 20.8 + - - +
4319D GLU 3.4 4.0 - - - +
4320D SER* 2.6 25.4 + - - +
4349D TYR* 3.5 6.3 + - - +
4350D VAL* 1.3 73.2 - - - +
4352D ILE* 1.3 62.7 + - - +
4376D TRP* 2.8 32.7 + - - -
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Residues in contact with ILE4352 (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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4318D GLN* 3.3 4.0 - - - -
4319D GLU* 2.9 29.2 + - - +
4321D PHE* 3.8 29.4 - - + -
4350D VAL* 3.8 27.6 - - + +
4351D GLN* 1.3 74.5 - - - +
4353D PRO* 1.4 83.8 - - + +
4354D THR* 4.1 0.3 - - - -
4356D CYS* 3.7 25.8 - - + +
4357D ALA* 3.8 6.3 - - - +
4360D PRO* 4.1 17.0 - - + +
4363D PHE* 3.7 25.8 - - + -
4364D THR* 4.0 10.5 - - + -
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Residues in contact with PRO4353 (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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4317D ASP 3.5 11.9 - - - +
4318D GLN* 4.3 7.1 - - + +
4351D GLN 4.2 2.2 - - - +
4352D ILE* 1.4 85.4 - - + +
4354D THR* 1.3 57.3 + - - +
4355D THR* 3.1 13.5 - - - +
4356D CYS* 2.8 28.7 + - - -
4357D ALA 3.1 7.4 + - - -
4363D PHE* 3.3 41.1 - - + -
4376D TRP* 4.9 3.4 - - + -
4379D TYR* 3.7 28.3 - - + +
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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