Contacts of the helix formed by residues 308 - 313 (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 ASP 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A PRO* 1.3 72.2 - - - +
309A ASN* 1.3 53.2 + - - +
311A LEU* 2.8 32.9 + - - +
312A PHE* 3.2 26.4 - - + -
335A ARG* 3.1 16.1 + - - -
347A LYS* 3.1 26.0 + - + +
349A ASN* 2.7 30.9 + - - +
368A ARG* 2.8 38.5 + - - -
426A ASP* 3.9 6.3 - - - +
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Residues in contact with ASN 309 (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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283A ASN* 2.8 27.0 + - - +
285A GLN* 5.1 1.7 - - - +
307A PRO* 3.1 12.7 + - + +
308A ASP* 1.3 78.4 - - - +
310A VAL* 1.3 63.0 + - - +
312A PHE* 3.5 24.1 - - + -
313A GLU* 2.7 67.4 + - - +
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Residues in contact with VAL 310 (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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285A GLN* 3.9 32.3 - - + +
286A LEU* 4.3 21.9 - - + +
289A LEU* 3.7 28.3 - - + -
306A LEU* 4.1 17.3 - - + -
307A PRO* 3.1 22.2 + - + +
309A ASN* 1.3 84.5 - - - +
311A LEU* 1.3 63.5 + - + +
321A ARG* 3.1 26.0 + - + +
351A LEU* 5.0 3.6 - - + -
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Residues in contact with LEU 311 (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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307A PRO 4.4 1.6 - - - +
308A ASP* 2.8 20.2 + - - +
310A VAL* 1.3 78.4 - - + +
312A PHE* 1.3 54.7 + - - -
321A ARG* 3.4 17.2 + - - +
333A ILE* 4.4 11.7 - - + -
335A ARG* 3.9 16.4 - - - +
349A ASN* 3.7 32.5 - - - +
351A LEU* 4.1 29.6 - - + -
424A SER* 3.5 1.4 + - - -
425A LEU* 2.9 57.8 + - + +
426A ASP* 3.8 15.5 - - - +
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Residues in contact with PHE 312 (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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308A ASP* 3.2 32.1 - - + -
309A ASN* 3.2 33.1 + - + -
311A LEU* 1.3 78.2 - - - +
313A GLU* 1.3 76.9 + - + +
314A ALA 3.2 2.3 + - - -
321A ARG* 3.6 8.1 + - - +
422A LYS* 4.2 11.8 - - - +
424A SER* 4.2 9.9 - - - +
426A ASP* 3.6 29.4 - - + +
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Residues in contact with GLU 313 (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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281A THR* 5.0 1.9 + - - -
283A ASN* 3.2 25.3 + - - +
286A LEU* 4.0 11.6 - - + +
309A ASN* 2.7 42.9 + - - +
310A VAL* 5.4 0.2 - - - -
312A PHE* 1.3 83.2 - - + +
314A ALA* 1.3 74.9 + - - +
316A ALA* 5.6 1.2 - - - +
317A GLY* 3.5 11.3 - - - -
318A GLU 3.6 0.2 + - - -
321A ARG* 3.0 23.6 + - - +
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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