Contacts of the strand formed by residues 361 - 366 (chain A) in PDB entry 2OKC
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 GLU 361 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ASN* 4.2 3.0 + - - +
330A LEU 3.7 3.6 - - - +
331A HIS* 3.8 11.6 - - - +
359A THR* 3.7 7.3 - - - +
360A LYS* 1.3 91.1 - - + +
362A ILE* 1.3 66.9 + - - +
363A TRP* 4.2 14.5 + - - +
411A LYS* 2.9 45.1 + - + +
412A TYR 3.3 11.7 - - - +
413A PRO* 4.6 7.0 - - + -
414A VAL 4.3 1.6 - - - +
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Residues in contact with ILE 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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325A LEU* 3.7 23.3 - - + -
330A LEU* 3.3 26.7 - - + +
331A HIS 3.8 2.0 - - - -
333A ILE* 4.2 14.6 - - + -
359A THR* 3.5 7.9 - - + -
361A GLU* 1.3 76.1 - - - +
363A TRP* 1.3 69.1 + - - +
364A PHE* 3.6 30.8 - - + -
411A LYS* 3.7 0.2 - - - -
412A TYR 2.8 37.3 + - - +
414A VAL* 5.2 3.1 - - + -
417A ILE* 3.4 28.0 - - + -
425A LEU* 3.7 18.6 - - + -
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Residues in contact with TRP 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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331A HIS* 2.9 24.2 + - + +
332A THR* 3.2 4.5 - - - +
333A ILE 2.8 31.4 + - - +
361A GLU* 4.2 17.3 + - + -
362A ILE* 1.3 76.9 - - - +
364A PHE* 1.3 56.3 + - - +
395A ARG* 3.2 55.4 - - + +
396A VAL 3.7 0.7 - - - -
397A GLU* 3.6 31.2 - - + -
409A TRP* 3.4 51.8 - + + -
410A ARG 3.4 5.4 - - - -
411A LYS* 3.4 43.2 - - + +
501A GOL 5.8 0.8 + - - -
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Residues in contact with PHE 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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333A ILE* 3.2 32.3 - - + -
335A ARG* 3.9 21.3 - - - -
362A ILE* 3.6 24.9 - - + -
363A TRP* 1.3 73.0 - - - +
365A TYR* 1.3 59.6 + - - +
366A ASP 4.0 0.2 - - - -
408A ARG 3.1 5.0 - - - +
409A TRP* 3.3 6.0 - - - -
410A ARG 2.8 33.2 + - - +
412A TYR* 3.6 28.5 - + - -
417A ILE* 4.2 3.1 - - + -
425A LEU* 3.3 31.9 - - + -
427A ILE* 3.9 29.4 - - + -
429A TRP* 3.6 22.7 - + + -
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Residues in contact with TYR 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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333A ILE 2.8 10.0 + - - +
334A LEU* 3.4 19.1 - - + +
335A ARG* 2.7 34.6 + - - +
364A PHE* 1.3 72.1 - - - +
366A ASP* 1.3 66.5 + - - +
367A TYR* 3.5 28.8 + + + -
384A HIS 5.4 2.0 + - - -
387A ASP* 2.5 38.1 + - - +
388A PHE* 3.6 48.8 + + + -
391A CYS* 3.9 9.2 - - - -
398A ILE* 5.1 0.2 - - + -
408A ARG* 3.1 28.3 - - + -
409A TRP* 3.6 26.1 - + + -
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Residues in contact with ASP 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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335A ARG* 4.1 13.7 - - + +
364A PHE 4.0 0.8 - - - -
365A TYR* 1.3 72.9 - - - +
367A TYR* 1.3 57.4 + - - +
368A ARG* 2.9 28.2 + - - +
369A THR* 2.7 33.9 + - - -
408A ARG* 2.9 42.0 + - - +
428A THR* 4.2 18.3 - - - +
429A TRP* 4.3 12.5 + - + -
430A ILE* 3.7 25.0 + - + +
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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