Contacts of the strand formed by residues 229 - 234 (chain B) in PDB entry 3CFV
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 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B GLY* 5.8 0.3 - - - -
180B TYR 5.6 1.4 + - - -
195B ALA* 3.5 21.9 - - + +
196B SER 3.1 28.0 + - - +
197B ASP* 5.1 0.3 - - - +
199B HIS 3.6 16.2 - - - +
200B THR 3.0 28.7 - - - +
201B VAL* 3.7 14.1 - - + -
225B HIS* 4.1 11.4 - - + +
227B ALA 3.0 3.5 + - - +
228B VAL* 1.3 70.4 - - - +
230B GLU* 1.3 60.2 + - - +
231B ASP 3.9 7.4 - - - +
244B SER* 4.6 0.2 - - - -
245B VAL 3.2 18.6 - - - +
246B ALA* 3.4 13.5 - - + -
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Residues in contact with GLU 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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128B ARG* 5.1 0.9 + - - -
180B TYR* 4.2 15.6 + - - +
181B GLY 3.5 16.6 + - - -
195B ALA* 4.3 0.9 - - - -
197B ASP* 5.6 0.2 - - - +
228B VAL* 3.9 13.6 - - - +
229B VAL* 1.3 74.4 - - - +
231B ASP* 1.3 59.6 + - - +
245B VAL 2.6 9.7 + - - +
246B ALA* 4.5 0.4 - - - -
247B ASP* 2.8 35.2 - - - +
274B GLU* 5.2 1.0 - - - +
275B VAL 3.2 24.9 - - - +
276B ASN* 3.3 30.7 - - - +
320B PHE* 5.0 8.8 - - - -
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Residues in contact with ASP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 3.6 14.8 + - - +
181B GLY* 3.5 15.9 - - - -
182B LEU 4.2 1.9 + - - +
195B ALA* 4.2 3.8 - - - +
229B VAL* 3.7 5.0 - - - +
230B GLU* 1.3 80.0 - - - +
232B VAL* 1.3 80.5 + - - +
244B SER* 3.6 1.9 - - - -
245B VAL* 3.1 29.6 + - + +
276B ASN 3.4 15.7 - - - +
277B CYS* 3.6 12.9 - - - +
278B LEU* 3.2 37.5 + - + +
321B GLN* 4.9 4.4 + - - -
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLY* 3.8 21.9 - - - -
182B LEU* 3.8 7.5 - - - +
183B SER* 3.5 8.9 - - - -
193B LEU* 3.8 48.0 - - + +
194B SER 4.0 2.5 - - - +
195B ALA* 4.0 9.4 - - + +
201B VAL* 4.0 16.6 - - + -
231B ASP* 1.3 88.6 + - - +
233B ALA* 1.3 67.1 + - - +
242B PHE* 3.8 9.9 - - + -
243B GLY 3.4 13.9 - - - +
244B SER* 4.7 0.7 - - - -
278B LEU* 4.0 2.5 - - - -
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Residues in contact with ALA 233 (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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183B SER* 3.6 8.3 - - - +
193B LEU* 4.5 1.3 - - - -
231B ASP* 5.4 0.2 - - - +
232B VAL* 1.3 78.4 - - - +
234B TRP* 1.3 61.8 + - - +
242B PHE* 3.1 5.7 - - - +
243B GLY 2.7 37.8 + - - -
278B LEU* 4.0 21.8 - - + +
279B SER* 5.4 0.4 - - - -
280B PHE* 3.5 22.8 - - + +
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Residues in contact with TRP 234 (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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183B SER* 3.0 37.6 + - - +
184B TRP 3.2 23.8 - - - +
185B ASN* 3.2 34.3 - - + -
186B SER* 5.3 1.6 - - - +
188B LEU* 5.8 1.6 - - + -
191B HIS* 3.3 26.3 + + + -
193B LEU* 3.3 27.8 - - + +
203B LEU* 4.2 20.4 - - + -
233B ALA* 1.3 77.3 - - - +
235B HIS* 1.3 67.9 - - - +
236B LEU* 3.7 10.8 + - + +
238B HIS 5.3 0.4 - - - -
239B GLU 3.6 13.5 - - - -
240B SER 4.2 2.9 - - - -
241B LEU 3.5 18.4 - - - -
242B PHE* 3.8 11.7 - + + -
256B THR* 3.8 30.1 - - + -
280B PHE* 3.3 13.1 - - - -
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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