Contacts of the strand formed by residues 225 - 230 (chain B) in PDB entry 2W8B
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 ALA 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B TYR 3.8 0.9 - - - +
217B VAL* 3.4 3.5 - - - -
218B THR* 2.9 42.7 + - + +
221B SER* 5.0 7.6 - - - +
223B ARG 4.6 2.0 - - - +
224B SER* 1.3 75.4 - - - +
226B LEU* 1.3 59.6 + - - +
227B VAL* 4.4 12.6 - - + -
238B GLN* 4.5 9.0 - - - +
240B ALA 3.4 7.2 - - - +
241B SER* 3.6 15.7 - - - +
246B ASN* 4.4 4.3 - - - -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA* 4.6 1.1 - - + -
216B TYR 3.4 17.3 - - - +
217B VAL* 4.3 4.5 - - + +
225B ALA* 1.3 72.0 - - - +
227B VAL* 1.3 69.9 + - - +
238B GLN* 4.2 1.0 + - - -
239B VAL* 2.8 42.8 + - + +
240B ALA* 2.8 21.6 + - + +
246B ASN* 4.1 13.8 - - + +
247B GLY* 4.5 6.3 - - - +
249B PRO* 3.6 35.2 - - + -
258B LEU* 4.1 5.2 - - + -
260B PHE* 3.6 44.6 - - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA* 3.1 6.9 - - - +
216B TYR* 3.0 69.6 + - + +
218B THR* 4.6 9.0 - - + -
225B ALA* 4.3 10.3 - - + +
226B LEU* 1.3 83.8 - - - +
228B ILE* 1.4 64.5 + - - +
236B VAL* 3.9 13.7 - - + -
237B ARG 3.3 11.9 - - - +
238B GLN* 3.6 29.8 - - - +
239B VAL* 4.1 2.7 - - - +
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Residues in contact with ILE 228 (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* 3.7 37.9 - - + -
214B LEU 3.5 4.9 - - - +
215B ALA* 4.0 7.9 - - + -
227B VAL* 1.4 78.2 - - - +
229B GLN* 1.3 62.6 + - - +
230B THR* 4.1 1.0 + - - +
235B ALA 3.7 1.0 - - - +
236B VAL* 3.3 2.4 - - - -
237B ARG* 2.9 49.8 + - + +
239B VAL* 3.7 21.1 - - + -
251B PHE* 3.8 31.2 - - + -
258B LEU* 4.2 5.8 - - + -
275B LEU* 4.0 21.1 - - + -
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Residues in contact with GLN 229 (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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195B VAL* 3.0 47.9 + - + +
196B HIS* 3.9 5.2 + - - +
213B LYS* 3.3 3.1 - - - +
214B LEU* 2.8 34.0 + - + +
216B TYR* 2.8 41.6 + - + -
227B VAL 4.2 0.6 - - - -
228B ILE* 1.3 75.7 - - - +
230B THR* 1.3 69.5 + - - +
231B LEU* 3.7 5.3 + - + +
234B GLY* 3.8 18.3 - - - +
235B ALA 3.2 10.1 - - - +
236B VAL* 4.0 15.6 - - + +
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Residues in contact with THR 230 (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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212B SER* 3.8 14.8 - - - +
213B LYS* 3.3 30.9 - - - +
228B ILE* 4.1 1.5 + - - +
229B GLN* 1.3 70.5 - - - +
231B LEU* 1.3 61.0 + - - +
232B ALA* 4.1 10.8 - - + +
233B ASN* 3.5 23.6 - - - +
234B GLY* 2.7 36.0 + - - -
235B ALA* 2.8 21.7 + - - +
1432B SO4 5.4 1.0 + - - -
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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