Contacts of the strand formed by residues 260 - 266 (chain B) in PDB entry 1WZ2
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 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B LYS* 3.3 31.5 - - + +
254B VAL 3.9 2.5 - - - -
255B ARG* 4.1 27.4 + - + +
258B ASP 3.3 6.6 + - - +
259B LYS* 1.3 77.8 - - - +
261B GLU* 1.3 77.6 + - - +
262B THR* 5.9 0.2 - - - +
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Residues in contact with GLU 261 (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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213B LYS* 2.8 37.1 + - - +
224B TYR* 3.6 30.1 + - + +
253B LYS* 3.3 7.3 - - - +
254B VAL 2.8 28.9 + - - +
259B LYS* 3.0 38.0 + - + -
260B GLU* 1.3 81.7 - - - +
262B THR* 1.3 65.8 + - - +
263B TRP* 3.3 22.3 + - + +
438B GLU* 6.0 0.9 - - - -
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Residues in contact with THR 262 (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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222B VAL 5.1 3.5 + - - -
223B ILE* 3.4 14.6 - - + +
224B TYR* 3.1 27.2 + - - -
251B LYS* 3.9 32.8 - - + -
252B ALA* 3.2 19.7 - - - +
253B LYS* 4.5 9.5 - - + +
260B GLU* 5.9 0.2 - - - +
261B GLU* 1.3 78.1 + - - +
263B TRP* 1.3 62.6 + - - +
283B ILE* 6.1 1.3 - - + -
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Residues in contact with TRP 263 (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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211B ILE* 3.3 27.6 - - + -
213B LYS* 3.8 10.8 - - - -
223B ILE* 4.8 0.2 - - - -
224B TYR* 3.5 10.5 - + + +
226B PRO* 3.4 23.6 - - + -
250B VAL* 3.4 1.6 - - - +
251B LYS* 3.2 4.3 - - - +
252B ALA* 2.7 34.9 + - - +
254B VAL* 3.3 43.7 + - + +
261B GLU* 3.3 28.5 + - + +
262B THR* 1.3 86.0 - - - +
264B ILE* 1.3 65.9 + - - +
265B VAL* 4.0 8.9 - - + +
273B LEU* 4.3 24.2 - - + -
278B ARG* 3.5 16.4 - - - -
319B THR* 5.5 0.4 - - + -
438B GLU* 3.3 27.1 - - - -
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Residues in contact with ILE 264 (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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216B LEU* 4.7 10.8 - - + -
223B ILE* 3.1 35.9 - - + -
224B TYR 3.0 10.7 + - - +
225B LEU* 3.1 39.4 - - + +
249B TYR* 4.8 1.1 - - + -
250B VAL 2.9 4.0 - - - +
251B LYS* 3.9 4.5 - - + -
263B TRP* 1.3 74.6 - - - +
265B VAL* 1.3 67.4 + - - +
286B PHE* 3.4 44.0 - - + -
291B LEU* 3.5 24.7 - - + -
321B VAL* 4.3 1.0 - - - +
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Residues in contact with VAL 265 (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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226B PRO* 3.4 32.1 - - + +
249B TYR* 3.2 10.7 - - - +
250B VAL* 2.8 36.9 + - + +
263B TRP* 4.5 11.0 - - + -
264B ILE* 1.3 81.3 - - - +
266B SER* 1.3 68.4 + - - +
269B ALA* 4.1 6.7 - - + -
270B ALA* 4.5 6.1 - - + +
273B LEU* 4.3 16.4 - - + -
319B THR* 3.7 27.6 - - + +
321B VAL* 4.6 2.5 - - + -
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Residues in contact with SER 266 (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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248B THR 4.1 3.3 + - - -
249B TYR* 3.4 15.7 - - - +
265B VAL* 1.3 75.2 - - - +
267B LYS* 1.3 52.2 + - - +
268B GLU* 2.5 39.8 + - - +
269B ALA* 2.7 16.4 + - - +
270B ALA* 2.7 34.5 + - - +
315B PRO* 3.5 15.3 + - - +
319B THR 2.9 18.6 + - - -
320B GLY* 4.5 2.0 - - - -
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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
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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