Contacts of the strand formed by residues 262 - 267 (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 TYR 262 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D PHE* 3.1 3.8 - - - -
259D ASP* 2.9 27.8 + - - -
261D LYS* 1.3 105.8 + - + +
263D ILE* 1.3 59.3 + - - +
274D VAL* 3.4 24.9 - - + -
275D TRP 3.2 11.0 - - - +
276D SER* 4.7 1.6 - - - -
277D THR* 2.8 7.6 + - - -
283D VAL* 4.2 18.6 - - + +
284D ARG* 3.6 15.7 + - - -
298D TYR* 3.4 28.7 - + + +
317D ILE* 3.9 22.7 - - + -
318D GLU* 2.7 41.1 + - - -
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Residues in contact with ILE 263 (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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219D LEU* 5.7 0.2 - - + -
221D VAL* 4.3 16.2 - - + -
229D ILE* 5.0 4.0 - - + -
231D VAL* 4.2 30.3 - - + -
246D LEU* 4.5 9.6 - - + -
256D VAL* 3.9 20.4 - - + -
257D ASP 3.5 10.5 - - - +
258D PHE* 3.6 13.7 - - + -
262D TYR* 1.3 74.5 - - - +
264D VAL* 1.3 65.5 + - - +
274D VAL* 3.4 4.0 - - - +
275D TRP* 2.8 51.2 + - + +
276D SER 4.2 7.0 - - - +
277D THR* 3.3 26.6 + - + +
280D CYS* 4.9 2.2 - - - -
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Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D VAL 4.7 0.2 - - - -
256D VAL* 3.2 5.0 - - - +
257D ASP 2.7 37.8 + - - +
262D TYR* 4.5 0.9 - - + -
263D ILE* 1.3 80.3 - - - +
265D SER* 1.3 60.6 + - - +
272D ILE* 3.6 28.3 - - + -
273D LYS 3.5 4.5 - - - +
274D VAL* 5.0 0.9 - - + -
296D LEU* 3.6 24.5 - - + +
298D TYR* 3.5 28.9 - - + -
303D VAL* 4.4 8.1 - - + -
317D ILE* 3.5 30.1 - - + -
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Residues in contact with SER 265 (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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229D ILE* 3.3 28.9 - - - -
249D HIS* 2.7 25.7 + - - -
253D VAL* 4.1 6.5 - - - -
255D VAL 3.5 5.4 - - - -
256D VAL* 4.4 2.9 - - - -
264D VAL* 1.3 73.9 - - - +
266D ALA* 1.3 59.4 - - - +
272D ILE* 3.3 8.0 - - - +
273D LYS* 2.8 32.4 + - - +
275D TRP* 2.9 19.0 + - - +
296D LEU* 4.8 0.4 - - - -
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Residues in contact with ALA 266 (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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249D HIS* 4.5 0.2 - - - -
253D VAL* 3.6 4.3 - - - -
254D ASN 3.0 21.1 + - - -
255D VAL* 3.0 27.6 + - + +
265D SER* 1.3 74.1 - - - +
267D SER* 1.3 61.3 + - - +
271D THR 3.5 7.0 - - - -
272D ILE* 4.1 5.8 - - + -
293D ILE* 3.5 29.6 - - + -
296D LEU* 3.8 15.5 - - + -
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Residues in contact with SER 267 (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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249D HIS* 3.0 32.4 + - - -
251D ALA 3.1 11.6 + - - -
252D ALA 2.8 21.2 + - - -
253D VAL* 4.2 0.7 - - - +
254D ASN* 3.8 7.2 - - - +
266D ALA* 1.3 74.6 - - - +
268D GLY* 1.3 61.1 + - - +
269D ASP* 3.0 23.5 + - - +
270D ARG* 3.2 8.8 + - - -
271D THR 3.3 4.0 + - - -
293D ILE* 3.1 22.1 + - - +
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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