Contacts of the strand formed by residues 258 - 263 (chain A) in PDB entry 2OHI
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A ASP* 3.2 26.0 + - - +
257A GLU* 1.3 74.5 - - - +
259A VAL* 1.3 67.7 + - - +
286A VAL* 3.5 0.4 - - - -
287A ASP* 2.9 45.1 + - + +
288A VAL 4.6 0.2 - - - +
289A ARG* 3.9 28.2 - - + +
304A ASP* 4.4 7.2 + - - -
307A GLU* 3.0 43.1 + - - +
308A SER* 3.5 20.0 - - - +
309A GLY 3.1 23.2 + - - -
310A ALA 3.6 1.2 + - - -
402A ILE* 3.4 15.8 - - - +
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Residues in contact with VAL 259 (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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258A ARG* 1.3 79.5 - - - +
260A THR* 1.3 73.8 + - - +
261A VAL* 4.2 13.0 - - + -
277A ILE* 5.7 1.6 - - + -
281A ALA* 4.3 18.8 - - + -
286A VAL* 3.6 6.0 - - + +
287A ASP 3.0 7.9 + - - +
288A VAL* 3.3 7.3 - - + +
289A ARG 3.1 22.9 + - - +
310A ALA* 3.2 25.8 - - + +
311A ILE* 4.6 0.9 - - - -
312A ALA* 4.7 0.4 - - + +
398A LEU* 3.7 22.9 - - + -
399A ALA* 4.2 18.8 - - - -
402A ILE* 3.9 11.0 - - + -
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Residues in contact with THR 260 (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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259A VAL* 1.3 73.1 + - - +
261A VAL* 1.3 63.0 + - - +
262A ILE* 4.0 17.2 + - + +
289A ARG* 3.5 8.3 - - + +
291A TYR* 3.7 33.2 - - + -
301A ILE 4.8 0.9 - - - +
304A ASP* 3.7 16.6 + - + +
305A ILE* 4.7 7.0 - - + -
308A SER* 2.5 25.6 + - - -
310A ALA 3.1 6.7 + - - -
311A ILE* 3.1 17.0 - - - +
312A ALA 2.8 25.5 + - - +
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Residues in contact with VAL 261 (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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259A VAL* 4.3 14.6 - - + -
260A THR* 1.3 74.8 - - - +
262A ILE* 1.3 61.9 + - - +
263A TYR* 4.8 0.2 - - + -
274A ALA* 3.7 37.5 - - + +
277A ILE* 4.3 12.6 - - + -
278A ALA* 4.3 24.5 - - + -
281A ALA* 5.9 0.4 - - + -
288A VAL* 4.4 3.6 - - + -
289A ARG 2.6 18.3 + - - +
290A VAL* 3.2 12.7 - - + -
291A TYR* 2.8 32.6 + - - +
312A ALA* 3.6 5.6 - - + +
349A PHE* 4.3 11.4 - - + -
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Residues in contact with ILE 262 (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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260A THR* 4.0 16.8 - - + -
261A VAL* 1.3 79.0 - - - +
263A TYR* 1.3 67.0 + - - +
291A TYR* 3.4 10.3 - - + +
293A LEU* 3.7 35.4 - - + -
301A ILE* 3.6 30.3 - - + -
305A ILE* 4.2 14.4 - - + -
311A ILE* 4.8 15.3 - - + -
312A ALA 2.8 19.0 + - - +
313A LEU* 3.3 7.6 - - + -
314A GLY 2.9 22.3 + - - -
329A LEU* 4.0 16.2 - - + -
349A PHE* 4.0 1.9 - - - -
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Residues in contact with TYR 263 (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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261A VAL* 4.8 0.4 - - + -
262A ILE* 1.3 80.1 - - - +
264A ASP* 1.3 72.2 + - - +
265A THR* 3.8 12.8 - - + -
270A THR* 4.1 3.1 - - + -
271A ARG* 3.5 41.7 + - + -
274A ALA* 3.5 21.5 - - + -
275A HIS* 4.6 1.6 - + - -
290A VAL* 4.2 10.3 - - + -
291A TYR 3.1 21.1 + - - -
292A CYS* 3.3 20.9 - - + +
293A LEU* 2.9 30.4 + - - -
314A GLY 3.0 15.0 - - - +
349A PHE* 4.0 15.0 - - + -
21D ASP* 2.7 41.0 + - - +
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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