Contacts of the helix formed by residues 279 - 289 (chain A) in PDB entry 2WOK
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 GLN 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A VAL* 3.6 47.4 - - + +
258A ASP* 3.3 21.1 - - - +
261A ASP* 2.8 17.6 + - - +
276A ARG* 4.2 23.4 + - - +
277A GLY 4.0 13.3 + - - +
278A LEU* 1.3 74.1 - - - +
280A HIS* 1.3 69.1 + - - +
281A ALA 3.3 0.9 - - - -
282A ALA 3.1 4.3 + - - -
283A GLN* 2.8 22.7 + - - +
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Residues in contact with HIS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLN* 1.3 75.6 + - - +
281A ALA* 1.3 63.1 + - - +
283A GLN* 3.2 27.2 + - - +
284A ARG* 3.0 51.9 + - - +
339A GLY* 5.4 9.9 - - - -
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ASP* 4.3 17.2 + - + +
279A GLN 3.2 1.0 + - - -
280A HIS* 1.3 79.0 - - - +
282A ALA* 1.3 62.8 + - - +
284A ARG* 3.3 22.9 + - - +
285A ARG* 3.1 21.0 + - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ASP* 5.2 0.6 + - - -
261A ASP* 3.5 37.9 + - + +
265A ILE* 3.9 11.8 - - + +
278A LEU* 3.8 16.2 - - + -
279A GLN 3.1 2.9 + - - +
281A ALA* 1.3 76.2 - - - +
283A GLN* 1.3 60.3 + - - +
285A ARG* 3.6 9.3 - - - +
286A ALA* 2.8 34.3 + - - +
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 2.9 31.0 + - + +
279A GLN* 2.8 22.2 + - - +
280A HIS* 3.2 32.0 + - - +
282A ALA* 1.3 76.0 - - - +
284A ARG* 1.3 54.0 + - + +
287A THR* 2.6 42.5 + - - +
343A ASN* 4.0 26.8 - - - +
532A LEU* 3.7 27.6 - - + +
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Residues in contact with ARG 284 (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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280A HIS* 3.0 35.7 + - - +
281A ALA* 3.3 29.1 - - - +
282A ALA 3.2 0.2 - - - -
283A GLN* 1.3 75.4 - - + +
285A ARG* 1.3 67.0 + - - +
287A THR* 3.4 4.6 + - - -
288A ALA* 3.3 26.5 + - - +
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Residues in contact with ARG 285 (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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10A PRO* 4.2 15.8 - - - +
262A ALA* 5.0 12.1 + - - +
265A ILE* 3.9 40.1 - - + +
266A ALA* 5.8 1.0 - - - +
281A ALA 3.1 10.5 + - - +
282A ALA* 3.6 9.9 - - - +
284A ARG* 1.3 82.3 - - - +
286A ALA* 1.3 63.1 + - - +
288A ALA* 4.1 1.8 - - - +
289A ASP* 3.3 24.0 + - + +
292A LEU* 3.7 18.2 - - + +
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Residues in contact with ALA 286 (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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17A TRP* 5.7 0.4 - - - -
265A ILE* 5.1 3.1 - - + -
278A LEU* 3.7 21.5 - - + -
282A ALA 2.8 21.7 + - - +
283A GLN 4.3 0.9 - - - +
285A ARG* 1.3 75.8 - - + +
287A THR* 1.3 61.1 + - + +
288A ALA 3.4 0.7 + - - -
289A ASP 3.4 4.3 - - - +
292A LEU* 3.8 17.5 - - + -
293A ARG* 3.3 27.5 + - - +
296A THR* 4.0 16.4 - - + +
534A PHE* 4.8 5.4 - - + -
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Residues in contact with THR 287 (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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17A TRP* 4.2 18.2 - - + -
283A GLN* 2.6 26.7 + - - +
284A ARG* 3.4 6.8 + - - -
286A ALA* 1.3 76.3 - - + +
288A ALA* 1.3 59.0 + - - +
289A ASP 3.6 0.2 - - - -
293A ARG* 2.8 39.4 + - - +
296A THR* 5.7 0.2 - - + -
343A ASN* 4.7 13.6 + - - +
532A LEU* 3.7 26.2 - - + -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ARG 3.3 16.9 + - - +
285A ARG* 4.3 2.0 - - - +
286A ALA 3.2 0.4 - - - -
287A THR* 1.3 82.1 + - - +
289A ASP* 1.3 58.4 + - - +
290A GLU 4.0 1.2 + - - -
293A ARG* 5.1 1.6 - - - -
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Residues in contact with ASP 289 (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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10A PRO 5.1 1.0 - - - +
285A ARG* 3.3 17.3 + - + +
286A ALA 3.4 0.4 + - - +
288A ALA* 1.3 77.7 - - - +
290A GLU* 1.3 60.9 + - - +
291A VAL* 3.0 18.2 + - - +
292A LEU* 2.8 42.7 + - + +
293A ARG* 2.9 33.6 + - - +
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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