Contacts of the strand formed by residues 294 - 300 (chain A) in PDB entry 2OHM
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 GLN 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A TRP* 3.7 26.4 - - + -
190A TYR 5.6 0.2 + - - -
289A GLY* 2.8 32.0 + - - -
290A GLU* 2.7 31.1 + - - +
291A VAL* 3.1 32.2 + - + +
292A THR 3.9 2.9 - - - +
293A ASN* 1.3 76.9 - - - +
295A SER* 1.3 85.9 + - - +
296A PHE* 4.1 0.8 - - - +
373A PRO* 4.1 17.9 - - + -
374A PHE 3.4 3.6 - - - +
375A VAL* 5.6 0.4 - - - -
379A MET* 3.2 9.2 - - - +
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 4.1 8.7 - - - -
286A TYR* 3.7 8.0 - - - -
287A LEU 3.5 16.4 - - - -
289A GLY 3.9 0.7 - - - +
293A ASN 4.2 0.2 + - - -
294A GLN* 1.3 86.0 + - - +
296A PHE* 1.3 62.3 + - - +
373A PRO* 3.6 1.2 - - - +
374A PHE* 2.7 44.3 + - - +
376A THR* 2.7 27.3 + - - -
379A MET* 4.0 9.4 - - - -
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Residues in contact with PHE 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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189A TRP* 3.3 58.6 - + + -
190A TYR 3.4 29.2 - - - -
191A THR* 3.8 5.2 - - - -
285A LEU 4.0 0.2 - - - +
286A TYR* 3.3 3.2 - - - -
287A LEU* 2.9 52.7 + - + +
288A MET 3.9 9.9 - - - -
289A GLY* 4.3 5.6 - - - -
295A SER* 1.3 76.8 - - - +
297A ARG* 1.3 59.5 + - - +
298A ILE* 3.9 22.2 - - + -
354A PHE* 4.1 6.5 - + + -
370A VAL* 3.7 14.8 - - + -
371A GLU 3.2 17.0 - - - +
372A GLY* 4.2 0.2 - - - -
374A PHE* 4.1 4.9 - - - -
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Residues in contact with ARG 297 (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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207A GLU* 4.2 5.9 + - - -
284A SER* 3.5 14.3 + - - -
285A LEU 3.4 10.1 - - - +
286A TYR* 2.9 43.7 + - + -
296A PHE* 1.3 75.2 - - - +
298A ILE* 1.3 63.9 + - - +
299A THR* 3.4 23.6 + - - +
369A ALA 3.5 1.4 - - - +
370A VAL* 3.3 5.2 - - - +
371A GLU* 2.9 61.2 + - + +
374A PHE* 3.4 33.3 - - + -
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Residues in contact with ILE 298 (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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283A ILE 3.8 0.9 - - - +
284A SER* 3.2 3.6 - - - -
285A LEU* 3.0 52.7 + - + +
287A LEU* 4.2 9.2 - - + -
296A PHE* 3.9 23.1 - - + -
297A ARG* 1.3 78.7 - - - +
299A THR* 1.3 61.4 + - - +
300A ILE* 4.2 0.6 - - - +
333A MET* 3.7 30.1 - - + -
337A ILE* 4.0 12.8 - - + -
341A PHE* 3.5 13.0 - - + -
354A PHE* 3.9 29.8 - - + -
369A ALA 3.3 3.4 - - - -
370A VAL* 4.0 11.0 - - + -
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Residues in contact with THR 299 (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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282A VAL* 3.8 24.9 - - + -
283A ILE 3.2 8.3 - - - +
284A SER* 2.9 23.9 + - - +
297A ARG* 3.4 17.5 + - - +
298A ILE* 1.3 73.9 - - - +
300A ILE* 1.3 64.1 + - - +
301A LEU* 5.8 0.4 - - + -
341A PHE* 3.7 2.4 - - - -
367A THR 5.1 4.9 - - - +
368A ALA* 3.1 28.2 - - - +
369A ALA* 2.9 27.2 + - - +
371A GLU* 4.7 0.2 + - - -
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Residues in contact with ILE 300 (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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234A LEU* 4.6 8.5 - - + -
282A VAL* 3.5 10.9 - - - +
283A ILE* 2.9 52.0 + - + +
285A LEU* 6.2 0.4 - - + -
298A ILE 5.4 1.6 - - - -
299A THR* 1.3 80.2 - - - +
301A LEU* 1.3 72.0 + - - +
304A GLN* 4.1 13.9 - - + -
305A TYR* 4.1 10.8 - - + -
336A VAL* 4.0 24.9 - - + +
337A ILE* 3.4 41.1 - - + +
340A GLY* 5.5 0.4 - - - -
341A PHE* 3.8 17.5 - - + -
368A ALA* 4.8 0.4 - - - -
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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