Contacts of the strand formed by residues 257 - 262 (chain A) in PDB entry 2WSK
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 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PRO* 3.8 18.6 - - + -
145A ARG* 3.5 9.5 + - - -
146A THR* 3.1 28.9 + - - +
151A THR* 4.6 1.4 + - - -
194A THR* 2.8 15.2 + - - +
195A ALA* 4.2 15.2 - - + +
196A LEU* 2.9 24.3 + - - +
252A HIS* 4.4 0.2 - - - -
256A ILE* 1.3 79.8 - - - +
258A VAL* 1.3 64.5 + - - +
259A ILE* 5.4 1.5 - - + +
331A ASP* 3.3 29.1 - - + +
367A LYS* 2.9 40.4 + - - +
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Residues in contact with VAL 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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196A LEU* 3.5 7.4 - - + +
198A LEU* 3.9 27.4 - - + -
244A PHE* 4.5 9.4 - - + -
248A ILE* 4.4 21.3 - - + -
251A LEU* 4.1 30.1 - - + -
252A HIS* 4.6 2.0 - - + -
257A GLU* 1.3 77.9 - - - +
259A ILE* 1.3 64.1 + - - +
260A LEU* 4.1 13.9 - - + -
330A VAL* 3.7 11.1 - - + +
331A ASP* 2.6 46.2 + - - +
332A GLY 3.6 0.5 + - - -
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Residues in contact with ILE 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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153A ILE* 4.5 10.1 - - + -
195A ALA* 3.8 28.3 - - + -
196A LEU 2.9 6.9 + - - +
197A GLU* 3.2 28.6 - - + +
198A LEU* 2.9 27.9 + - - +
257A GLU* 5.4 0.7 - - + -
258A VAL* 1.3 77.2 - - - +
260A LEU* 1.3 64.0 + - - +
331A ASP* 5.0 3.8 - - + -
332A GLY* 3.4 21.8 - - - +
333A PHE 3.8 20.9 - - - +
334A ARG* 4.0 2.5 - - + +
367A LYS* 4.8 15.9 - - + +
369A ILE* 4.2 20.0 - - + -
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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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198A LEU* 4.0 8.5 - - + -
201A VAL* 4.0 27.8 - - + -
244A PHE* 4.0 15.7 - - + -
258A VAL* 4.1 6.5 - - + -
259A ILE* 1.3 78.4 - - - +
261A ASP* 1.3 67.2 + - - +
262A ILE* 3.4 4.1 + - + -
324A TRP* 3.9 33.7 - - + -
330A VAL* 3.4 36.3 - - + -
332A GLY 3.2 6.7 + - - -
333A PHE* 3.5 20.5 - - + -
334A ARG 3.0 21.9 + - - -
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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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155A GLU* 4.2 5.2 - - - +
197A GLU* 4.3 4.5 - - + +
198A LEU 2.8 23.4 + - - +
199A LEU* 3.8 11.3 - - + +
200A PRO* 3.3 21.4 - - - +
201A VAL 4.4 1.4 + - - -
221A TYR* 2.7 37.1 + - - -
259A ILE 3.9 0.6 + - - -
260A LEU* 1.3 76.0 - - - +
262A ILE* 1.3 68.3 + - - +
334A ARG* 2.7 51.5 + - + +
336A ASP* 4.2 4.5 - - - +
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Residues in contact with ILE 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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200A PRO* 5.2 1.3 - - - -
202A ALA* 5.5 8.5 - - + -
226A MET* 5.8 1.6 - - + +
260A LEU* 4.0 4.9 - - + +
261A ASP* 1.3 76.0 + - - +
263A VAL* 1.3 76.4 + - - +
264A LEU* 3.9 14.2 + - + -
320A CYS* 4.5 13.9 - - - -
321A LEU* 3.8 22.4 - - + -
324A TRP* 4.8 6.7 - - + +
333A PHE* 3.9 29.6 - - + -
334A ARG 2.8 16.0 + - - +
335A PHE* 3.6 24.4 - - + +
336A ASP* 3.0 23.5 + - - -
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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
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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