Contacts of the strand formed by residues 262 - 267 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A PHE* 3.1 4.0 - - - -
259A ASP* 2.9 27.8 + - - -
261A LYS* 1.3 106.4 - - + +
263A ILE* 1.3 59.1 + - - +
264A VAL* 4.5 2.0 - - + -
274A VAL* 3.4 29.6 - - + -
275A TRP 3.2 11.4 - - - +
276A SER* 4.7 1.6 - - - -
277A THR* 2.8 7.7 + - - -
283A VAL* 4.2 17.8 - - + +
284A ARG* 3.6 15.6 + - - -
298A TYR* 3.4 30.0 - + + +
317A ILE* 4.0 14.6 - - + -
318A GLU* 2.7 41.1 + - - -
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Residues in contact with ILE 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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219A LEU* 5.3 0.4 - - + -
221A VAL* 4.4 14.8 - - + -
229A ILE* 5.0 1.1 - - + -
231A VAL* 4.1 31.0 - - + -
246A LEU* 4.6 12.3 - - + -
256A VAL* 4.1 19.3 - - + -
257A ASP 3.6 10.3 - - - +
258A PHE* 3.7 15.7 - - + -
262A TYR* 1.3 74.9 - - - +
264A VAL* 1.3 65.4 + - - +
265A SER* 5.5 0.2 - - - -
274A VAL* 3.4 3.3 - - - -
275A TRP* 2.8 51.6 + - + +
276A SER 4.2 6.5 - - - +
277A THR* 3.3 28.2 + - + +
280A CYS* 4.7 2.0 - - - -
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Residues in contact with VAL 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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256A VAL* 3.2 5.4 - - - +
257A ASP 2.7 39.5 + - - +
262A TYR* 4.5 5.8 - - + -
263A ILE* 1.3 81.0 - - - +
265A SER* 1.3 59.1 + - - +
272A ILE* 3.6 19.1 - - + -
273A LYS 3.5 4.3 - - - +
274A VAL* 5.0 3.4 - - + -
296A LEU* 3.6 32.4 - - + +
298A TYR* 3.5 41.1 - - + -
303A VAL* 4.4 7.9 - - + -
317A ILE* 4.5 10.8 - - + -
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Residues in contact with SER 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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229A ILE* 3.3 29.3 - - - +
249A HIS* 2.8 24.1 + - - -
253A VAL* 4.1 6.7 - - - -
255A VAL 3.6 6.1 - - - -
256A VAL* 4.5 3.1 - - - -
264A VAL* 1.3 73.9 - - - +
266A ALA* 1.3 59.1 - - - +
272A ILE* 3.2 7.8 - - - +
273A LYS* 2.9 32.0 + - - +
275A TRP* 2.9 19.5 + - - +
296A LEU* 4.8 0.4 - - - -
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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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253A VAL* 3.6 4.5 - - - +
254A ASN* 3.0 21.8 + - - -
255A VAL* 3.0 27.2 + - + +
265A SER* 1.3 75.0 - - - +
267A SER* 1.3 61.8 + - - +
271A THR 3.5 7.2 - - - -
272A ILE* 4.1 5.6 - - + -
293A ILE* 3.5 29.2 - - + -
296A LEU* 3.8 15.5 - - + -
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Residues in contact with SER 267 (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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249A HIS* 3.0 32.5 + - - -
251A ALA 3.1 11.4 + - - -
252A ALA 2.8 20.7 + - - -
254A ASN* 3.8 8.3 - - - +
266A ALA* 1.3 75.0 - - - +
268A GLY* 1.3 60.2 + - - +
269A ASP* 3.0 22.3 + - - -
270A ARG* 3.2 8.8 + - - -
271A THR 3.3 4.0 + - - -
293A ILE* 3.2 21.4 + - - +
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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