Contacts of the strand formed by residues 253 - 258 (chain D) in PDB entry 6WNX
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 VAL 253 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211D LEU* 3.6 12.5 - - - +
223D CYS* 3.1 40.8 - - + -
224D SER 3.2 14.0 + - - +
227D ARG 3.5 32.5 - - - +
228D SER 4.0 5.6 - - - +
229D ILE* 3.9 11.7 - - + -
249D HIS* 3.7 22.4 - - + -
252D ALA* 1.3 70.4 - - - +
254D ASN* 1.3 57.7 + - - +
255D VAL 3.8 7.2 - - - +
265D SER* 4.1 9.2 - - - -
266D ALA 3.6 14.6 - - - +
267D SER* 4.2 0.7 - - - +
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Residues in contact with ASN 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LEU* 3.4 22.9 - - - +
212D HIS* 3.5 15.1 + - - +
223D CYS* 4.1 2.0 - - - -
252D ALA* 3.7 5.1 + - - +
253D VAL* 1.3 72.1 - - - +
255D VAL* 1.3 63.1 + - + +
266D ALA 3.0 6.5 + - - +
268D GLY* 3.4 12.9 - - - +
292D GLY 5.5 0.2 - - - -
293D ILE 2.9 29.6 + - - +
294D ALA* 4.3 6.4 - - - +
34F GLY 4.5 3.0 - - - +
35F ILE* 3.2 26.1 - - + +
36F HIS 3.0 44.4 + - - +
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D HIS* 3.6 24.5 - - + +
223D CYS* 3.7 2.0 - - - -
253D VAL* 3.4 5.2 + - - +
254D ASN* 1.3 82.7 - - + +
256D VAL* 1.3 76.2 + - - +
257D ASP* 5.6 0.4 - - + -
265D SER* 3.5 1.4 - - - -
266D ALA* 3.0 52.0 + - + +
293D ILE* 4.8 0.2 - - + -
294D ALA 4.3 2.7 - - - +
295D CYS* 4.1 20.2 - - - +
296D LEU* 3.9 38.1 - - + +
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Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D HIS* 3.3 17.1 + - - -
213D LEU* 4.2 15.5 - - - +
214D ARG* 4.5 6.4 - - + +
221D VAL* 3.5 48.2 - - + +
223D CYS* 3.9 20.9 - - + -
229D ILE* 4.2 9.4 - - + -
255D VAL* 1.3 81.3 - - - +
257D ASP* 1.3 61.1 + - - +
258D PHE* 6.1 0.2 - - + -
263D ILE* 3.9 12.3 - - + -
264D VAL 3.2 16.2 - - - +
265D SER* 4.4 6.5 - - - -
296D LEU* 5.8 0.2 - - - -
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Residues in contact with ASP 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ARG* 3.0 30.2 + - - +
256D VAL* 1.3 73.5 - - - +
258D PHE* 1.3 80.2 + - - +
263D ILE* 3.5 3.3 - - - +
264D VAL 2.7 34.1 + - - +
296D LEU* 4.1 21.8 - - + +
297D GLN* 3.8 11.7 - - - +
298D TYR* 3.1 39.3 + - + +
337D ARG* 4.6 5.4 + - - -
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Residues in contact with PHE 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ARG* 3.3 61.6 + - + -
215D PHE 4.1 1.1 - - - -
216D SER* 3.8 28.5 - - - -
219D LEU* 3.6 37.2 - - + -
221D VAL* 3.6 26.0 - - + -
256D VAL 5.8 0.2 - - - -
257D ASP* 1.3 87.8 + - - +
259D ASP* 1.3 77.5 - - - +
262D TYR 3.1 15.9 - - - +
263D ILE* 3.6 14.1 - - + -
277D THR* 4.5 6.3 - - + -
298D TYR* 3.9 9.4 - - - +
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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