Contacts of the strand formed by residues 266 - 272 (chain B) in PDB entry 2WK6
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 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B LEU* 4.5 2.2 - - + -
230B LEU* 3.2 35.4 - - + +
232B VAL* 4.5 9.6 - - + -
255B LEU* 4.0 7.9 - - + +
256B VAL* 3.3 41.7 - - + +
259B GLY* 4.2 10.8 - - - -
264B LEU* 3.0 28.6 + - + +
265B ARG* 1.3 78.8 - - - +
267B ALA* 1.3 69.5 + - - +
268B ALA* 5.2 0.2 - - + -
316B LEU* 4.1 1.6 - - - -
479B PRO* 3.2 22.9 - - - +
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU 2.8 5.5 + - - +
231B VAL* 3.1 12.8 - - + +
232B VAL 2.8 23.2 + - - -
256B VAL* 4.0 1.3 - - - -
266B VAL* 1.3 75.9 - - - +
268B ALA* 1.3 60.8 + - - +
312B ALA* 5.5 1.3 - - + +
315B TRP* 5.7 0.2 - - + -
316B LEU* 3.3 29.6 - - + +
476B LEU* 4.3 9.9 - - + -
477B VAL 3.6 11.9 - - - +
478B LEU* 4.2 14.8 - - + -
479B PRO* 4.3 0.9 - - + -
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B VAL* 3.1 15.3 - - + +
234B VAL* 4.2 6.7 - - + -
252B ALA* 3.8 28.0 - - + +
255B LEU* 5.0 2.7 - - + -
256B VAL* 3.7 17.0 - - + +
266B VAL* 5.2 0.2 - - + -
267B ALA* 1.3 75.4 - - - +
269B ALA* 1.3 59.3 + - - +
476B LEU* 3.7 3.4 - - - -
477B VAL* 2.7 43.5 + - + +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B VAL* 5.1 0.8 - - + +
232B VAL 2.7 10.5 + - - +
233B ASP* 4.3 3.8 - - - +
234B VAL* 2.5 37.1 + - - +
267B ALA 4.3 0.4 + - - -
268B ALA* 1.3 73.7 - - - +
270B LEU* 1.3 58.7 + - - +
271B THR* 4.0 1.8 - - + -
309B LEU* 3.2 34.5 - - + -
473B PHE* 4.0 14.8 - - + -
475B GLU 3.5 10.3 - - - +
476B LEU* 3.9 8.2 - - + +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B VAL* 3.1 36.3 - - + +
236B PHE* 3.8 15.9 - - + -
245B GLN* 4.6 4.5 - - + +
248B ALA* 3.8 18.8 - - + +
249B ARG* 4.0 28.5 - - + +
252B ALA* 3.9 11.0 - - + -
269B ALA* 1.3 72.2 - - - +
271B THR* 1.3 61.5 + - - +
474B ALA* 2.9 28.6 + - + +
475B GLU* 3.0 47.5 + - + +
477B VAL* 4.8 4.3 - - + -
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Residues in contact with THR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASP* 2.5 38.2 + - - +
234B VAL 3.0 5.1 + - - -
235B LYS* 3.3 15.4 + - - +
236B PHE* 3.1 30.6 + - - +
269B ALA* 4.5 3.1 - - + -
270B LEU* 1.3 81.7 - - - +
272B ALA* 1.3 64.7 + - - +
305B LEU* 4.4 15.3 - - + -
309B LEU* 5.0 0.2 - - + -
472B PRO* 3.6 13.0 - - - -
473B PHE* 3.7 26.2 - - + +
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LYS* 5.3 0.5 + - - -
236B PHE* 3.6 22.6 - - + -
271B THR* 1.3 77.8 + - - +
273B MET* 1.3 68.1 + - - +
274B ASP* 3.7 12.3 - - + +
275B LYS* 4.7 2.9 - - + +
277B LEU* 5.9 1.7 - - - +
305B LEU* 5.8 0.7 - - - +
471B SER 5.6 0.2 - - - +
472B PRO* 3.1 34.0 + - + +
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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
------------------------------------------------------------
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