Contacts of the strand formed by residues 355 - 363 (chain A) in PDB entry 2OK5
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 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A SER* 3.3 29.0 + - - +
245A ASN* 3.8 22.4 - - - +
283A ARG* 5.3 3.3 + - - +
351A GLY 3.4 13.5 + - - -
352A TRP* 3.7 9.5 + - - +
353A ASN 3.5 0.4 - - - -
354A ARG* 1.3 77.9 - - - +
356A ARG* 1.3 72.3 + - - +
357A HIS* 3.5 35.3 + - - +
384A LEU* 5.4 0.5 - - - +
394A ARG* 5.0 1.4 + - - -
397A TYR* 3.3 15.3 - - - +
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Residues in contact with ARG 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A SER 5.0 1.8 + - - -
213A LEU* 3.4 39.2 + - - +
236A ILE* 3.8 17.8 - - - +
237A VAL* 3.5 23.3 + - - +
238A LEU* 3.9 15.5 - - + +
239A ASP* 5.7 2.0 - - - +
243A SER 3.1 11.6 + - - +
244A MET* 3.3 25.0 - - + +
245A ASN 2.9 25.5 + - - +
354A ARG 3.7 2.0 + - - -
355A THR* 1.3 74.7 - - - +
357A HIS* 1.3 59.8 + - - +
358A VAL* 4.3 11.6 - - + +
396A ASP 3.9 23.9 + - - +
397A TYR* 3.6 12.6 - - + +
399A ASP* 3.9 18.6 + - - -
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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
----------------------------------------------------------
245A ASN* 3.5 15.8 + - + -
247A TYR* 3.0 38.1 + + + -
341A MET* 4.1 19.1 - - + +
343A TRP* 5.8 3.3 - + - -
352A TRP 4.8 3.6 - - - -
355A THR* 3.5 36.9 + - + +
356A ARG* 1.3 72.4 - - - +
358A VAL* 1.3 62.4 + - - +
359A ILE 4.1 0.2 - - - -
384A LEU* 3.2 40.8 - - + +
397A TYR* 2.8 12.9 + - - +
398A LEU* 3.2 11.9 - - + +
399A ASP* 3.0 24.8 + - - +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 4.4 17.7 - - + -
244A MET* 4.3 22.4 - - + -
245A ASN 2.9 12.0 + - - +
246A ILE* 3.4 11.1 - - + +
247A TYR* 2.9 28.2 + - - +
356A ARG* 4.3 14.4 - - - +
357A HIS* 1.3 77.1 - - - +
359A ILE* 1.3 62.0 + - - +
360A ILE* 3.8 19.9 + - + -
399A ASP* 3.3 11.7 - - + -
401A TYR* 3.8 30.1 - - + -
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Residues in contact with ILE 359 (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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247A TYR* 3.7 23.1 - - + +
249A VAL* 4.2 17.9 - - + -
334A LEU* 4.6 15.0 - - + -
337A VAL* 4.0 19.7 - - + -
341A MET* 4.5 2.5 - - + -
358A VAL* 1.3 74.3 - - - +
360A ILE* 1.3 65.2 + - - +
361A LEU* 4.7 4.0 - - + +
377A ILE* 4.6 8.3 - - + -
380A ILE* 4.2 17.3 - - + -
398A LEU* 4.4 15.3 - - + -
399A ASP 2.8 10.2 + - - +
400A VAL* 3.4 30.0 - - + -
401A TYR* 2.7 33.5 + - - +
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Residues in contact with ILE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 4.5 12.3 - - + -
213A LEU* 6.1 0.2 - - + -
246A ILE* 3.7 30.1 - - + -
247A TYR 2.9 12.4 + - - +
248A LEU* 3.8 10.7 - - + -
249A VAL* 2.9 29.1 + - - +
268A LEU* 5.2 5.4 - - + -
271A LEU* 3.8 24.7 - - + -
358A VAL* 3.8 18.4 - - + -
359A ILE* 1.3 78.1 - - - +
361A LEU* 1.3 63.2 + - - +
362A MET* 4.2 8.0 + - + -
401A TYR* 3.5 13.9 - - + -
403A PHE* 3.8 26.2 - - + -
440A PHE* 5.9 1.1 - - + -
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Residues in contact with LEU 361 (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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249A VAL* 3.4 34.8 - - + +
251A ASP* 4.5 1.6 - - + +
289A TYR* 3.9 18.2 - - + +
330A THR* 4.4 6.7 - - + -
334A LEU* 5.3 8.3 - - + -
359A ILE* 4.1 6.7 - - + -
360A ILE* 1.3 74.3 - - - +
362A MET* 1.3 68.4 + - - +
363A THR* 4.7 2.5 - - + -
366A LEU* 4.0 14.1 - - + -
400A VAL* 5.7 2.7 - - + -
401A TYR 2.8 14.4 + - - +
402A VAL* 3.4 18.4 - - + +
403A PHE* 2.8 33.4 + - - +
417A LEU* 3.7 30.3 - - + -
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Residues in contact with MET 362 (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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249A VAL 3.1 7.7 + - - -
250A LEU* 3.8 20.9 - - + -
251A ASP* 3.1 25.8 + - - +
256A ILE* 3.7 12.7 - - + +
264A ALA* 3.5 38.1 - - + +
267A CYS* 4.5 8.1 - - + -
268A LEU* 3.9 21.8 - - - -
360A ILE* 4.2 6.9 - - + +
361A LEU* 1.3 75.3 - - - +
363A THR* 1.3 62.6 + - - +
403A PHE* 3.4 24.9 - - + +
433A MET* 4.8 2.9 - - + -
436A LEU* 3.6 26.7 - - + -
440A PHE* 5.3 5.2 - - - -
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Residues in contact with THR 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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251A ASP* 2.5 31.1 + - - -
256A ILE* 3.5 11.2 - - - +
361A LEU* 4.7 3.1 - - + -
362A MET* 1.3 75.3 - - - +
364A ASP* 1.3 60.9 + - - +
366A LEU* 3.2 28.0 + - + +
402A VAL* 4.1 10.8 - - + -
403A PHE 3.0 13.3 + - - +
404A GLY* 3.2 7.8 - - - -
405A VAL* 2.8 23.8 + - - +
409A VAL* 3.9 2.8 - - + +
414A ILE* 3.9 28.5 - - + -
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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