Contacts of the strand formed by residues 352 - 357 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351B ALA* 1.3 82.5 - - - +
353B THR* 1.3 65.7 + - - +
365B LYS* 3.6 5.5 - - - +
366B THR* 3.2 44.8 + - + +
368B PRO* 3.6 45.6 - - + +
414B TRP* 5.0 2.7 - + - -
417B VAL* 4.2 26.0 - - + -
420B TYR* 3.3 47.3 - + - -
422B LEU 6.0 0.4 - - - -
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Residues in contact with THR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ALA* 4.8 5.4 - - + +
352B TYR* 1.3 80.3 - - - +
354B LEU* 1.3 59.5 - - - +
363B VAL* 3.8 24.4 - - + +
364B MSE 3.4 10.5 - - - +
365B LYS* 4.4 7.0 - - + -
366B THR* 3.7 7.3 - - - +
414B TRP* 5.9 0.2 - - - -
420B TYR 2.9 7.0 + - - -
421B CYS* 3.2 24.2 - - - +
422B LEU* 3.0 25.3 + - - +
305K LEU* 4.5 14.4 - - + -
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B THR* 1.3 73.0 - - - +
355B LYS* 1.3 61.3 + - - +
356B VAL* 4.1 4.9 + - + -
362B VAL 3.9 0.2 - - - +
363B VAL* 3.3 6.3 - - - +
364B MSE 2.9 55.9 + - + +
366B THR* 3.7 10.7 - - + +
375B VAL* 4.0 16.6 - - + -
378B MSE 4.6 11.4 - - - -
379B VAL* 3.9 28.7 - - + -
414B TRP* 4.5 11.0 - - + -
422B LEU* 3.4 37.7 - - + +
424B LEU* 4.1 13.5 - - + -
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Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B THR 4.1 0.4 - - - -
354B LEU* 1.3 73.1 - - - +
356B VAL* 1.3 63.2 + - - +
357B HIS* 4.1 11.2 - - + +
361B THR* 3.9 23.1 - - + -
362B VAL 3.4 4.7 - - - +
363B VAL* 3.8 17.3 - - + +
421B CYS* 3.8 20.6 - - - -
422B LEU 2.9 8.8 + - - +
423B THR* 3.3 14.3 - - + +
424B LEU* 2.8 27.5 + - - +
289K ASP* 2.5 32.5 + - - +
291K GLU* 3.1 23.1 + - - +
293K ASP* 2.8 29.5 + - + +
295K VAL* 5.0 0.2 - - + -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 4.4 9.0 - - + -
355B LYS* 1.3 77.1 - - - +
357B HIS* 1.3 65.7 + - - +
358B TYR* 3.5 2.5 + - - +
360B TYR 3.8 0.7 - - - +
361B THR* 3.3 3.4 - - - -
362B VAL* 2.9 42.6 + - + +
364B MSE 3.6 26.9 - - + -
379B VAL* 4.0 27.4 - - + -
383B LEU* 4.3 7.2 - - + -
392B LEU* 4.5 4.7 - - + -
424B LEU* 3.4 13.2 - - + +
426B CYS* 3.9 28.5 - - + +
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Residues in contact with HIS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B LYS* 4.1 7.6 - - + +
356B VAL* 1.3 69.7 - - - +
358B TYR* 1.3 62.0 + - - +
360B TYR 4.1 2.7 - - - -
361B THR* 3.0 38.4 + - + +
423B THR* 3.7 22.0 - - + +
424B LEU 2.9 8.8 + - - -
425B TRP* 3.4 48.3 - + + +
426B CYS 2.9 27.2 + - - +
293K ASP* 3.8 20.0 + - + -
336K ASN* 3.4 22.5 + - - -
337K THR* 3.7 17.6 - - - +
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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