Contacts of the strand formed by residues 195 - 199 (chain B) in PDB entry 2FV7
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 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B LYS* 4.8 2.7 - - + -
174B THR 2.9 9.8 + - - +
175B LEU* 3.4 24.9 - - + +
176B PHE* 2.9 26.7 + - - +
193B SER* 4.2 3.5 - - - -
194B ASP* 1.3 83.6 - - + +
196B PHE* 1.3 60.8 + - - +
197B CYS* 4.0 0.4 - - + -
231B VAL* 3.7 16.2 - - + -
233B ILE* 3.7 29.8 - - + -
275B LEU* 4.2 5.2 - - + -
279B LEU* 4.2 25.1 - - + -
287B LEU* 5.3 4.0 - - + -
504B UNX 4.1 14.6 - - - -
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Residues in contact with PHE 196 (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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176B PHE* 3.4 36.8 - + - -
178B PRO* 3.3 27.1 - - + -
185B LEU* 4.4 2.9 - - + -
190B TYR* 3.5 32.5 - + - -
193B SER* 3.8 9.6 - - - -
194B ASP 4.2 0.2 - - - -
195B VAL* 1.3 73.3 - - - +
197B CYS* 1.3 62.8 + - - +
198B CYS* 4.5 4.5 - - - -
206B LEU* 3.9 10.1 - - + -
224B LEU* 3.8 30.3 - - + -
229B CYS* 3.4 31.9 - - + -
231B VAL 2.9 10.5 + - - +
232B VAL* 3.4 5.7 - - + -
233B ILE* 2.9 26.5 + - - +
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Residues in contact with CYS 197 (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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175B LEU* 4.3 18.4 - - + -
176B PHE 2.9 12.7 + - - +
177B ASN* 2.7 37.9 + - - -
178B PRO* 3.4 2.0 - - - +
196B PHE* 1.3 75.4 - - - +
198B CYS* 1.3 57.9 + - - +
233B ILE* 3.4 21.5 - - + -
235B THR* 4.4 7.6 - - - -
271B PHE* 4.0 29.2 - - - -
272B VAL* 4.1 20.2 - - + -
275B LEU* 4.8 1.8 - - - -
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Residues in contact with CYS 198 (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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177B ASN* 4.0 2.2 - - - +
178B PRO* 3.8 18.2 - - + -
196B PHE* 4.5 3.1 - - - -
197B CYS* 1.3 77.0 - - - +
199B ASN* 1.3 65.5 + - - +
202B GLU* 3.4 17.9 - - + +
203B ALA* 3.9 22.4 - - - -
206B LEU* 4.4 5.6 - - - -
224B LEU* 4.3 17.3 - - - -
233B ILE 3.1 7.4 + - - +
234B ILE* 3.2 12.8 - - - -
235B THR* 2.7 34.4 + - - +
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Residues in contact with ASN 199 (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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198B CYS* 1.3 75.2 - - - +
200B GLU* 1.3 65.0 + - - +
201B SER* 3.1 12.0 + - - -
202B GLU* 2.9 48.9 + - - +
203B ALA* 3.0 23.6 + - - +
234B ILE* 4.0 3.4 - - - -
235B THR* 3.3 22.9 - - - +
402B ADP 3.0 40.3 + - - +
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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