Contacts of the strand formed by residues 361 - 366 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B ASN* 4.7 1.9 - - - +
330B LEU 3.7 1.7 - - - +
331B HIS* 3.7 20.8 - - - +
359B THR* 3.9 2.7 - - - +
360B LYS* 1.3 91.0 + - - +
362B ILE* 1.3 64.0 + - - +
363B TRP* 3.9 16.8 + - - +
411B LYS* 3.5 42.2 + - + +
412B TYR 3.2 9.9 - - - +
413B PRO* 4.7 4.5 - - + -
414B VAL 4.5 0.7 - - - +
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Residues in contact with ILE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 3.9 21.8 - - + -
330B LEU* 3.4 23.6 - - + +
331B HIS 3.8 3.6 - - - +
333B ILE* 4.0 18.2 - - + -
359B THR* 3.8 7.2 - - + -
361B GLU* 1.3 73.7 - - - +
363B TRP* 1.3 65.1 + - - +
364B PHE* 3.2 34.1 - - + -
410B ARG 3.7 0.9 - - - +
412B TYR* 2.9 29.5 + - - +
414B VAL* 5.3 1.1 - - + -
417B ILE* 3.3 30.3 - - + -
425B LEU* 3.5 20.9 - - + -
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Residues in contact with TRP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B HIS* 2.9 16.4 + - + +
332B THR* 3.4 5.9 - - - +
333B ILE 3.0 26.6 + - - +
361B GLU* 3.9 25.7 + - - +
362B ILE* 1.3 75.4 - - - +
364B PHE* 1.3 62.4 + - - +
395B ARG* 3.1 69.2 - - + +
396B VAL 3.7 1.8 - - - -
397B GLU* 3.6 32.8 - - + -
409B TRP* 3.4 41.3 - + + -
410B ARG 3.3 10.1 - - - -
411B LYS* 3.5 35.0 - - + -
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Residues in contact with PHE 364 (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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333B ILE* 3.3 34.8 - - + -
335B ARG* 4.5 9.2 - - + -
362B ILE* 3.2 38.4 - - + -
363B TRP* 1.3 71.7 - - - +
365B TYR* 1.3 59.9 + - - +
366B ASP 4.0 0.4 - - - -
408B ARG 3.1 5.4 - - - +
409B TRP* 3.5 4.2 - - - -
410B ARG 3.0 30.7 + - - +
412B TYR* 3.9 13.7 - + + -
417B ILE* 4.9 0.4 - - + -
425B LEU* 3.2 34.1 - - + -
427B ILE* 3.6 44.9 - - + -
429B TRP* 3.6 22.3 - + + -
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Residues in contact with TYR 365 (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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333B ILE 3.0 7.9 + - - +
334B LEU* 3.6 15.2 - - + -
335B ARG* 2.9 29.9 + - - +
364B PHE* 1.3 72.7 - - - +
366B ASP* 1.3 75.3 + - - +
367B TYR* 3.5 23.3 + + + -
384B HIS 5.5 1.4 + - - -
385B LEU* 5.8 0.2 - - + -
387B ASP* 2.7 36.8 + - - +
388B PHE* 3.5 51.0 + + + -
391B CYS* 3.9 11.9 - - - -
408B ARG* 3.2 27.3 - - + -
409B TRP* 3.5 24.5 - + + -
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Residues in contact with ASP 366 (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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335B ARG* 4.1 10.0 - - + +
364B PHE 4.0 0.8 - - - -
365B TYR* 1.3 74.0 - - - +
367B TYR* 1.3 54.8 + - - +
368B ARG* 2.7 38.4 + - - +
369B THR* 2.6 33.0 + - - -
408B ARG* 2.8 52.1 + - - +
428B THR* 3.9 17.2 - - + +
429B TRP* 4.3 13.4 + - + -
430B ILE* 3.6 22.5 - - + +
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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
------------------------------------------------------------
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