Contacts of the strand formed by residues 293 - 296 (chain A) in PDB entry 3GVJ
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 ARG 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LYS 3.1 7.8 + - - +
277A THR* 2.8 33.8 + - - +
278A TYR* 2.9 27.6 + - - -
292A THR* 1.3 74.8 - - - +
294A PHE* 1.3 71.2 + - - +
305A TYR* 3.4 37.6 - - + -
306A TYR 3.4 13.9 - - - +
311A PHE* 3.6 38.4 - - + -
684A GLU* 2.8 31.9 + - - +
686A VAL* 3.8 24.9 - - + +
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Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 3.8 17.9 - - + -
277A THR* 4.4 1.8 - - - -
278A TYR* 3.3 17.0 - - + +
280A VAL* 4.1 12.6 - - + -
283A LEU* 4.0 17.9 - - + -
284A PRO* 3.5 30.7 - - + -
286A ILE* 4.0 34.1 - - + -
289A PHE* 3.8 22.7 - + + -
292A THR* 3.6 28.9 - - + -
293A ARG* 1.3 74.5 - - - +
295A VAL* 1.3 61.7 - - - +
304A LEU 3.8 0.3 - - - +
305A TYR* 3.2 6.8 - - - +
306A TYR* 2.8 42.8 + - - +
308A SER* 4.9 2.0 - - - -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLY* 3.7 15.5 - - - +
277A THR* 3.8 11.8 - - + +
278A TYR 3.0 7.3 + - - +
279A LYS* 3.4 32.2 - - + +
280A VAL* 3.1 26.4 + - - +
294A PHE* 1.3 72.7 - - - +
296A TYR* 1.3 64.8 + - - +
297A GLU* 5.9 0.9 - - + -
303A PRO* 3.9 17.7 - - + -
304A LEU 3.5 8.3 - - - +
305A TYR* 3.4 38.1 - - + +
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A VAL* 3.9 14.1 - - + -
281A THR 3.3 29.7 + - - -
282A SER* 3.8 12.1 + - - -
283A LEU* 3.8 35.7 - - + -
295A VAL* 1.3 76.5 - - - +
297A GLU* 1.3 72.2 + - - +
298A ARG* 3.5 47.6 + - + +
302A GLN 4.0 0.3 - - - +
303A PRO* 4.3 0.2 - - - -
304A LEU* 3.0 29.3 + - - +
306A TYR* 3.8 26.7 - + + -
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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