Contacts of the strand formed by residues 362 - 368 (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 MET 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A GLY* 4.1 7.0 - - - +
7A PRO* 3.5 40.2 - - + +
8A VAL* 5.8 2.0 - - + -
87A VAL* 4.3 1.6 - - + -
88A GLY* 3.8 21.8 - - - +
89A THR 3.1 26.5 - - - +
90A VAL* 3.7 16.6 - - + -
305A ASP* 5.9 0.2 - - - +
332A ARG* 3.6 4.9 - - - +
333A ASN* 3.1 33.0 + - - +
361A GLY* 1.3 71.2 - - - -
363A TYR* 1.3 64.1 + - - +
377A SER* 5.2 1.3 - - - +
378A ALA* 3.7 21.8 - - - +
379A GLU* 3.6 30.1 - - + -
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Residues in contact with TYR 363 (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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303A ILE* 3.7 6.4 - - + +
316A TRP* 3.7 29.2 - + + -
330A TRP* 4.8 2.5 - + + -
331A LEU 3.3 8.1 - - - +
332A ARG* 3.5 42.0 + - + -
337A LEU* 4.3 11.2 - - + -
343A VAL* 5.5 1.8 - - + +
350A LEU* 3.9 16.2 - - + -
352A PHE* 3.7 25.0 - + - -
359A ASP* 3.0 41.4 + - - +
361A GLY* 3.4 18.4 - - - -
362A MET* 1.3 73.4 - - - +
364A GLN* 1.3 67.8 + - - +
377A SER* 3.4 0.9 - - - -
378A ALA 3.1 31.6 + - - +
380A LEU* 3.8 11.2 - - + -
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Residues in contact with GLN 364 (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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9A PHE* 4.8 2.2 - - - -
89A THR 4.9 0.2 - - - +
90A VAL* 3.6 15.3 - - + +
91A VAL* 3.2 57.7 + - - +
303A ILE* 4.4 0.9 - - - -
330A TRP* 3.3 12.0 - - - -
331A LEU* 2.7 54.0 + - + +
334A GLY 4.7 4.0 + - - -
363A TYR* 1.3 74.2 - - - +
365A CYS* 1.3 62.8 + - - +
366A VAL* 4.9 1.1 - - + -
375A TYR* 4.8 9.8 - - + +
376A ALA 3.2 8.1 - - - +
377A SER* 3.1 35.2 + - - -
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Residues in contact with CYS 365 (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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299A TRP* 3.5 15.8 - - - -
303A ILE* 4.6 1.8 - - - +
318A CYS* 2.0 53.6 - - + -
328A VAL* 4.2 4.0 - - + -
329A ARG 3.6 10.3 - - - +
330A TRP* 4.1 14.1 - - + -
364A GLN* 1.3 72.7 - - - +
366A VAL* 1.3 65.1 + - - +
375A TYR* 3.7 1.2 - - - -
376A ALA* 3.0 45.5 + - - -
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Residues in contact with VAL 366 (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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299A TRP* 4.5 0.2 - - - -
327A THR 3.0 4.7 - - - +
328A VAL* 4.1 1.7 - - - +
329A ARG* 2.6 65.1 + - + +
331A LEU* 3.7 36.1 - - + -
364A GLN* 4.7 1.1 - - + +
365A CYS* 1.3 81.5 - - - +
367A ALA* 1.3 57.7 + - - +
368A GLU* 4.0 0.6 + - + -
373A THR* 3.5 30.1 - - + -
374A ILE 3.6 3.1 - - - +
375A TYR* 3.7 20.4 - - + +
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Residues in contact with ALA 367 (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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297A PRO* 4.2 2.5 - - + +
299A TRP* 3.6 23.6 - - + -
320A ALA* 3.6 25.6 - - + -
326A PRO* 4.3 7.2 - - + -
327A THR 3.2 6.7 - - - +
328A VAL* 4.2 8.1 - - + +
366A VAL* 1.3 72.0 - - - +
368A GLU* 1.3 63.2 + - - +
372A GLY 3.9 0.5 - - - +
373A THR* 3.3 1.4 - - - +
374A ILE* 3.0 39.4 + - + +
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Residues in contact with GLU 368 (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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297A PRO* 4.3 0.4 - - - -
326A PRO* 3.4 9.5 - - - +
327A THR* 2.8 49.5 + - - +
329A ARG* 3.2 36.0 + - - +
367A ALA* 1.3 76.3 - - - +
369A ASN* 1.3 63.9 + - - +
372A GLY 3.2 6.1 - - - +
373A THR* 3.4 31.3 + - + +
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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