Contacts of the strand formed by residues 201 - 205 (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 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LEU* 3.9 25.6 - - + -
194B SER 3.2 12.3 - - - +
195B ALA* 4.2 5.6 - - + -
200B THR* 1.3 81.1 - - - +
202B CYS* 1.3 59.3 + - - +
221B ILE* 4.6 0.4 - - - -
222B PHE* 3.1 45.5 + - + +
225B HIS* 5.3 2.9 - - - +
229B VAL* 3.7 25.1 - - + -
232B VAL* 4.0 14.1 - - + -
242B PHE* 4.1 10.8 - - + -
244B SER* 4.4 13.7 - - - -
254B TRP* 5.9 1.8 - - + +
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Residues in contact with CYS 202 (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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174B GLY* 3.5 37.0 - - - -
175B HIS* 3.4 22.4 + - + -
193B LEU* 3.5 9.5 - - - +
194B SER 3.0 29.5 + - - -
200B THR* 4.3 4.3 - - - -
201B VAL* 1.3 75.3 - - - +
203B LEU* 1.3 59.1 - - - +
204B TRP* 3.2 29.4 - - + -
218B ALA* 4.2 2.0 - - + -
220B ALA 3.4 5.6 - - - +
221B ILE* 4.1 14.8 - - - +
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Residues in contact with LEU 203 (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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191B HIS* 4.5 10.5 - - + -
192B LEU 3.5 11.0 - - - +
193B LEU* 3.9 13.9 - - + -
202B CYS* 1.3 74.9 - - - +
204B TRP* 1.3 83.6 + - - +
218B ALA* 3.2 4.7 - - - -
219B LYS* 2.6 53.2 + - + +
220B ALA* 2.9 32.4 + - + +
222B PHE* 4.2 9.6 - - + -
234B TRP* 4.2 16.8 - - + -
256B THR* 4.0 26.0 - - + -
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Residues in contact with TRP 204 (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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148B VAL* 3.8 15.0 - - + -
172B LEU* 3.3 43.6 - - + +
173B ARG 3.0 33.2 + - - +
174B GLY 4.4 0.2 - - - -
175B HIS* 3.6 16.4 - + - -
190B GLY 3.5 0.8 - - - +
191B HIS* 3.3 7.0 - - - +
192B LEU* 3.1 42.2 + - + +
193B LEU 4.5 0.4 - - - -
194B SER* 3.3 26.2 - - - -
202B CYS* 3.2 32.3 - - + -
203B LEU* 1.3 84.3 - - - +
205B ASP* 1.3 62.6 + - - +
206B ILE* 4.0 4.3 - - + -
216B VAL* 3.4 20.2 - - + -
217B ASP 3.4 23.8 - - - -
218B ALA* 3.4 4.6 - - - +
219B LYS* 4.4 5.2 - - - +
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Residues in contact with ASP 205 (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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190B GLY 3.7 3.6 - - - -
191B HIS* 3.3 34.3 + - + +
204B TRP* 1.3 74.6 - - - +
206B ILE* 1.3 59.3 + - - +
207B ASN* 2.8 32.6 + - - +
208B ALA* 3.3 29.6 + - + +
209B GLY 4.5 0.7 + - - -
216B VAL* 5.1 7.5 - - - +
217B ASP 5.4 2.0 + - - -
219B LYS* 4.5 19.1 - - + +
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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