Contacts of the strand formed by residues 373 - 383 (chain A) in PDB entry 2OM5
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 THR 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ARG* 5.4 4.0 - - - +
94A GLU* 4.1 18.1 + - - +
366A VAL* 3.5 32.1 - - + -
367A ALA 3.3 6.7 - - - +
368A GLU* 3.4 22.4 + - + +
369A ASN 5.3 0.5 + - - -
372A GLY* 1.3 74.9 - - - -
374A ILE* 1.3 65.5 + - - +
375A TYR* 3.8 25.0 - - + +
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Residues in contact with ILE 374 (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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296A GLN* 5.5 4.5 - - - +
297A PRO* 3.4 45.3 - - + +
298A GLU* 3.7 1.8 - - - -
299A TRP* 3.5 52.7 - - + +
320A ALA* 4.4 0.4 - - + -
366A VAL* 3.6 7.4 - - - +
367A ALA* 3.0 32.1 + - + +
373A THR* 1.3 78.4 - - - +
375A TYR* 1.3 67.3 + - - +
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Residues in contact with TYR 375 (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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12A GLN* 5.9 2.2 - - - +
80A GLN* 3.5 17.7 + - - -
91A VAL* 3.9 37.9 - - + +
92A SER 4.2 0.2 - - - -
93A ARG* 4.0 31.0 - - + +
94A GLU* 4.0 18.3 + - + +
299A TRP* 3.1 15.7 + - - -
331A LEU* 4.3 3.6 - - + -
364A GLN* 4.8 9.0 - - - +
365A CYS 3.7 3.1 - - - -
366A VAL* 3.7 31.1 - - + +
373A THR* 3.8 35.3 - - + +
374A ILE* 1.3 77.8 - - - +
376A ALA* 1.3 58.3 + - - +
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Residues in contact with ALA 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TRP* 3.5 18.6 - - + +
302A VAL* 3.5 30.7 - - + -
303A ILE* 4.0 4.8 - - + +
364A GLN* 3.2 4.5 - - - +
365A CYS* 3.0 42.5 + - - -
375A TYR* 1.3 77.0 - - - +
377A SER* 1.3 61.0 + - - +
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Residues in contact with SER 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO 5.6 0.9 + - - -
9A PHE* 5.4 5.0 - - - -
90A VAL* 3.8 14.1 - - - +
303A ILE* 4.2 8.8 - - - +
305A ASP* 4.9 1.9 - - - +
362A MET* 5.2 1.6 - - - +
363A TYR 3.4 6.1 - - - -
364A GLN* 3.1 33.6 + - - -
376A ALA* 1.3 71.9 - - - +
378A ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 3.8 19.5 - - + -
304A SER* 3.4 35.4 - - - +
305A ASP* 3.6 6.3 - - - +
316A TRP* 4.2 5.6 - - + -
362A MET* 3.7 10.9 - - - +
363A TYR* 3.1 32.9 + - - +
377A SER* 1.3 77.4 - - - +
379A GLU* 1.3 61.5 + - - +
380A LEU 4.1 0.5 + - - -
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Residues in contact with GLU 379 (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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4A THR 4.8 2.1 - - - +
5A PHE* 3.5 14.7 - - - +
6A GLY* 2.6 35.8 + - - +
87A VAL* 3.7 16.9 - - + +
305A ASP* 3.4 23.6 + - + +
306A THR 3.1 27.2 + - - +
316A TRP* 4.4 2.8 - - - -
361A GLY 3.8 3.8 - - - +
362A MET* 3.6 18.5 - - + +
378A ALA* 1.3 74.8 - - - +
380A LEU* 1.3 70.0 + - - +
381A ALA* 4.4 14.7 - - + +
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Residues in contact with LEU 380 (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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87A VAL* 5.5 0.5 - - - +
306A THR* 3.7 10.3 - - - +
308A ALA* 4.3 13.9 - - + -
314A LEU* 3.8 23.6 - - + -
316A TRP* 3.8 9.2 - - + -
352A PHE* 3.8 25.6 - - + -
355A LEU* 4.1 16.2 - - + -
359A ASP* 3.5 19.7 - - + +
360A SER* 3.3 5.6 - - - -
361A GLY 2.9 32.4 + - - +
363A TYR* 3.8 17.0 - - + -
378A ALA 4.1 0.8 + - - -
379A GLU* 1.3 81.1 - - - +
381A ALA* 1.3 67.9 + - - +
382A VAL* 4.1 11.2 - - + -
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Residues in contact with ALA 381 (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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306A THR 3.3 13.1 + - - +
307A GLU* 3.9 7.2 - - + +
308A ALA 3.2 23.0 + - - +
360A SER* 4.4 3.4 - - - -
379A GLU* 4.4 13.5 - - + +
380A LEU* 1.3 75.9 - - - +
382A VAL* 1.3 64.5 + - - +
383A GLN* 3.5 20.7 + - + +
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Residues in contact with VAL 382 (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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308A ALA 3.4 3.8 - - - +
309A ASP 4.2 4.3 - - - +
310A ILE* 3.7 35.0 - - + +
355A LEU* 4.3 14.1 - - + -
356A SER 3.2 28.5 - - - +
357A LEU* 3.5 22.3 - - + +
359A ASP* 4.0 8.1 - - + -
360A SER* 3.1 29.6 + - - +
380A LEU* 4.2 13.0 - - + -
381A ALA* 1.3 73.0 - - - +
383A GLN* 1.3 63.4 + - - +
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Residues in contact with GLN 383 (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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307A GLU* 3.4 42.8 + - - +
308A ALA 2.9 13.9 + - - +
309A ASP* 3.4 10.8 - - - +
310A ILE* 2.7 33.4 + - - +
357A LEU* 5.6 0.9 - - - -
381A ALA* 3.6 16.1 + - + +
382A VAL* 1.3 80.2 - - - +
384A ALA* 1.3 62.0 + - - +
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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