Contacts of the strand formed by residues 352 - 357 (chain A) in PDB entry 1OEY
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 TYR 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A SER* 3.6 23.7 + - - -
350A MSE 3.9 7.8 + - + -
351A ALA* 1.3 79.0 - - - +
353A THR* 1.3 67.4 + - - +
365A LYS* 3.6 5.2 - - - +
366A THR* 2.9 45.4 + - + +
368A PRO* 3.6 44.1 - - + +
414A TRP* 5.2 2.0 - + - -
417A VAL* 3.9 30.1 - - + -
420A TYR* 3.2 44.2 - + - +
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Residues in contact with THR 353 (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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351A ALA* 5.4 3.4 - - + +
352A TYR* 1.3 79.9 - - - +
354A LEU* 1.3 59.8 + - - +
363A VAL* 3.9 24.4 - - + +
364A MSE 3.2 15.5 - - - +
365A LYS* 4.5 5.8 - - + +
366A THR* 3.7 10.7 - - - +
414A TRP* 5.4 0.3 - - - -
420A TYR 3.0 5.4 + - - +
421A CYS* 3.4 23.9 - - - +
422A LEU* 3.0 24.6 + - - +
305J LEU* 4.8 11.7 - - + -
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Residues in contact with LEU 354 (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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353A THR* 1.3 75.2 - - - +
355A LYS* 1.3 60.9 + - - +
356A VAL* 4.1 6.0 + - + -
362A VAL 4.0 0.5 - - - +
363A VAL* 3.4 2.9 - - - -
364A MSE 2.9 45.8 + - + +
366A THR* 3.8 6.4 - - + +
375A VAL* 3.9 17.9 - - + -
378A MSE 4.2 19.5 - - + -
379A VAL* 3.8 28.7 - - + -
414A TRP* 4.2 13.7 - - + -
422A LEU* 3.4 39.5 - - + +
424A LEU* 4.3 13.2 - - + -
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Residues in contact with LYS 355 (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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354A LEU* 1.3 74.0 - - - +
356A VAL* 1.3 57.2 + - - +
357A HIS* 4.1 13.2 - - + +
361A THR* 3.8 24.0 - - + -
362A VAL 3.4 6.5 - - - +
363A VAL* 4.0 14.6 - - + -
421A CYS* 3.7 19.9 - - - -
422A LEU 2.8 7.7 + - - +
423A THR* 3.2 15.8 - - + +
424A LEU* 2.8 32.6 + - - +
289J ASP* 2.6 29.4 + - - +
291J GLU* 3.0 26.4 + - - +
293J ASP* 2.9 28.2 + - + +
295J VAL* 5.0 0.2 - - + -
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Residues in contact with VAL 356 (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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354A LEU* 4.3 10.3 - - + -
355A LYS* 1.3 77.3 - - - +
357A HIS* 1.3 65.5 + - - +
358A TYR* 3.6 1.7 + - + +
360A TYR 3.8 0.5 - - - +
361A THR* 3.3 4.3 - - - -
362A VAL* 2.9 41.3 + - + +
364A MSE 3.8 24.2 - - + -
379A VAL* 3.8 28.9 - - + -
383A LEU* 4.4 5.8 - - + -
392A LEU* 4.6 2.9 - - + -
424A LEU* 3.3 13.9 - - + +
426A CYS* 3.9 27.4 - - + +
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Residues in contact with HIS 357 (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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355A LYS* 4.1 5.2 - - + +
356A VAL* 1.3 70.5 - - - +
358A TYR* 1.3 62.7 + - - +
360A TYR 4.0 2.7 - - - -
361A THR* 2.7 40.0 + - + +
423A THR* 3.6 29.7 - - + +
424A LEU 2.8 9.3 + - - -
425A TRP* 3.4 40.1 - + + +
426A CYS 2.9 26.2 + - - +
293J ASP* 3.8 20.7 + - - -
336J ASN* 3.0 24.6 + - - -
337J THR* 3.8 14.8 - - - -
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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