Contacts of the helix formed by residues 256 - 266 (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 ASP 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A GLY 3.7 2.0 + - - -
255A LEU* 1.3 74.2 - - - +
257A VAL* 1.3 66.1 + - - +
258A ASP* 3.0 31.2 + - - +
259A VAL* 3.0 30.6 + - + +
260A LEU* 2.8 26.2 + - - +
9B ARG* 5.5 5.2 + - - -
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Residues in contact with VAL 257 (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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40A SER* 3.7 16.4 - - - +
255A LEU 3.5 0.4 + - - -
256A ASP* 1.3 78.9 + - - +
258A ASP* 1.3 65.5 + - - +
260A LEU* 3.6 10.2 + - + +
261A ASP* 3.2 31.4 + - - +
274A GLU* 5.1 0.7 - - - +
276A ARG* 3.4 29.4 - - - +
279A GLN* 3.6 37.0 - - + +
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Residues in contact with ASP 258 (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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256A ASP* 3.0 12.9 + - - +
257A VAL* 1.3 81.6 - - - +
259A VAL* 1.3 66.1 + - - +
260A LEU 3.2 0.2 - - - -
261A ASP* 3.3 7.6 + - - +
262A ALA* 3.0 24.4 + - - +
279A GLN* 3.3 23.6 - - - +
281A ALA* 4.3 19.3 + - + +
282A ALA 5.2 0.2 + - - -
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Residues in contact with VAL 259 (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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255A LEU* 4.0 22.9 - - + -
256A ASP* 3.0 33.9 + - + +
258A ASP* 1.3 75.8 - - + +
260A LEU* 1.3 63.1 + - - +
262A ALA* 3.4 6.1 + - - +
263A ARG* 3.1 44.1 + - + +
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Residues in contact with LEU 260 (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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38A VAL* 3.6 31.9 - - + -
39A SER* 3.8 11.2 - - - +
40A SER* 3.7 34.8 - - - +
255A LEU* 4.2 16.2 - - + +
256A ASP 2.8 15.7 + - - +
257A VAL* 3.6 8.3 - - + +
259A VAL* 1.3 76.4 - - - +
261A ASP* 1.3 62.6 + - - +
263A ARG* 3.2 2.1 + - - +
264A LEU* 2.8 42.7 + - + +
269A PHE* 4.9 1.6 - - - -
272A ASN* 3.5 33.7 - - + +
274A GLU* 4.7 1.1 - - - +
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Residues in contact with ASP 261 (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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257A VAL 3.2 11.6 + - - +
258A ASP* 3.3 9.3 + - - +
260A LEU* 1.3 89.6 - - - +
262A ALA* 1.3 58.0 + - - +
264A LEU* 3.6 5.1 - - - +
265A ILE* 2.8 37.1 + - - +
272A ASN* 4.8 2.3 + - - -
277A GLY 4.1 5.5 - - - +
278A LEU* 3.7 24.0 - - + +
279A GLN* 2.8 37.7 + - - +
282A ALA* 3.5 21.6 - - + +
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Residues in contact with ALA 262 (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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258A ASP 3.0 17.1 + - - +
259A VAL* 3.6 8.3 - - - +
261A ASP* 1.3 77.8 - - - +
263A ARG* 1.3 60.2 + - + +
265A ILE* 3.5 4.8 + - - +
266A ALA* 3.0 28.2 + - - +
285A ARG* 5.0 10.9 + - - +
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Residues in contact with ARG 263 (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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252A THR* 5.6 1.2 - - - +
255A LEU* 4.0 16.3 - - - +
259A VAL* 3.1 33.0 + - + +
260A LEU* 4.0 1.1 - - - +
262A ALA* 1.3 76.2 - - + +
264A LEU* 1.3 63.7 + - - +
266A ALA* 3.4 5.6 + - - +
267A GLY 3.2 4.0 + - - -
268A GLU* 2.5 63.2 + - - +
269A PHE* 3.7 42.2 - - + -
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Residues in contact with LEU 264 (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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38A VAL* 4.9 2.9 - - + -
260A LEU* 2.8 24.9 + - + +
261A ASP* 3.6 4.7 - - - +
263A ARG* 1.3 73.2 - - - +
265A ILE* 1.3 67.1 + - - +
267A GLY* 3.0 12.0 + - - -
269A PHE* 3.7 17.1 - - + +
270A ASP 3.5 34.8 - - - +
271A ILE* 3.7 13.5 - - - +
272A ASN* 4.1 22.7 - - + -
278A LEU* 4.9 9.9 - - + -
534A PHE* 4.1 35.4 - - + +
536A ASN* 3.0 21.4 + - - +
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Residues in contact with ILE 265 (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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9A ALA* 4.2 7.8 + - - +
10A PRO* 3.5 19.5 - - + +
261A ASP 2.8 25.0 + - - +
262A ALA* 4.0 3.1 - - - +
264A LEU* 1.3 75.2 - - + +
266A ALA* 1.3 59.8 + - - +
267A GLY 3.4 0.5 + - - -
278A LEU* 4.4 9.2 - - + -
282A ALA* 3.9 30.1 - - + +
285A ARG* 3.9 41.1 - - - +
286A ALA* 5.1 3.6 - - + -
292A LEU* 3.8 26.9 - - + -
534A PHE* 4.0 31.2 - - + -
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Residues in contact with ALA 266 (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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8A PRO* 3.4 23.1 - - - +
10A PRO* 5.2 2.5 - - - -
262A ALA 3.0 17.6 + - - +
263A ARG* 3.8 8.5 - - - +
264A LEU 3.1 0.6 - - - -
265A ILE* 1.3 75.1 - - - +
267A GLY* 1.3 59.7 + - - +
268A GLU* 3.5 15.7 - - - +
285A ARG* 5.8 1.1 - - - +
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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