Contacts of the strand formed by residues 194 - 200 (chain F) in PDB entry 2VIG
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 194 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F TYR* 3.2 30.1 - - + +
139F TRP* 3.6 19.1 - - + -
143F PHE* 3.4 15.7 - - + -
150F GLY* 3.1 6.1 - - - -
151F CYS 3.0 21.5 + - - -
192F ALA* 3.5 6.2 - - - +
193F SER* 1.3 79.4 - - - +
195F ALA* 1.3 59.6 + - - +
215F VAL 3.3 7.9 - - - -
217F MET* 4.0 4.9 - - - +
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Residues in contact with ALA 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F TYR* 4.3 4.7 - - - -
139F TRP* 4.8 0.5 - - - -
151F CYS* 3.3 25.4 - - - +
153F ALA* 5.1 1.1 - - + -
194F ALA* 1.3 73.2 - - - +
196F VAL* 1.3 64.3 + - - +
197F VAL* 3.7 20.6 + - + -
213F PHE 3.4 1.9 - - - +
214F LEU* 3.6 3.3 - - - -
215F VAL* 2.9 36.9 + - + +
217F MET* 4.0 9.9 - - + -
222F LEU* 6.0 0.4 - - + -
241F LEU* 4.3 7.6 - - + -
243F PHE* 5.9 0.2 - - + -
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F LEU 4.2 2.7 - - - +
123F TYR* 3.8 35.9 - - + +
126F PRO* 4.2 14.6 - - + -
127F ILE* 4.3 1.6 - - + -
151F CYS 2.9 9.4 + - - +
152F PHE* 3.7 7.5 - - + -
153F ALA* 2.9 26.5 + - - +
195F ALA* 1.3 72.1 - - - +
197F VAL* 1.3 62.6 + - - +
198F PHE* 4.0 26.9 - - + -
212F ALA* 4.5 4.9 - - + -
213F PHE 3.3 7.9 - - - +
214F LEU* 4.3 13.7 - - + -
254F LEU* 4.2 19.1 - - + -
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ALA* 3.6 12.8 - - + +
168F THR* 5.4 1.6 - - + -
179F LEU* 4.6 9.9 - - + -
183F LYS* 4.4 7.0 - - + -
195F ALA* 3.7 19.7 - - + -
196F VAL* 1.3 78.1 - - - +
198F PHE* 1.3 72.5 + - - +
199F ALA* 5.3 3.4 - - + -
211F SER 3.6 1.0 - - - +
212F ALA* 3.4 3.2 - - - -
213F PHE* 2.8 43.2 + - + +
215F VAL* 3.6 26.5 - - + -
243F PHE* 3.8 33.4 - - + -
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Residues in contact with PHE 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F PRO* 6.0 0.2 - - + -
152F PHE* 3.4 40.6 - + - -
153F ALA 3.1 18.8 + - - +
154F LEU* 3.8 26.5 - - + -
166F ALA* 5.2 1.1 - - - -
168F THR* 4.3 0.2 - - - -
183F LYS* 2.7 33.9 + - - +
196F VAL* 4.0 20.9 - - + -
197F VAL* 1.3 74.0 - - - +
199F ALA* 1.3 60.6 + - - +
210F ILE* 4.1 9.4 - - + -
211F SER 3.3 8.5 - - - +
212F ALA* 3.8 21.1 - - + -
260F GLY 3.4 29.6 - - - -
263F ILE* 3.9 8.3 - - + -
264F ALA* 3.6 21.3 - - + -
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Residues in contact with ALA 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ALA* 5.1 2.5 - - - -
168F THR* 3.3 22.4 - - + +
169F THR 3.9 6.7 - - - +
170F ALA* 3.8 24.9 - - + -
179F LEU* 4.8 5.2 - - + -
197F VAL* 4.2 2.4 + - + -
198F PHE* 1.3 74.8 - - - +
200F SER* 1.3 62.1 + - - +
201F THR 3.4 0.3 + - - -
210F ILE* 3.5 6.7 - - - +
211F SER* 3.0 32.2 + - - +
213F PHE* 4.0 9.7 - - + -
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Residues in contact with SER 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F ALA* 3.6 21.0 + - - +
167F SER* 5.2 0.4 - - - -
168F THR 2.6 17.8 + - - -
169F THR* 3.3 15.1 - - - +
170F ALA 2.9 25.2 + - - +
199F ALA* 1.3 69.4 - - - +
201F THR* 1.3 59.5 + - - +
202F ASP* 3.4 21.3 + - - -
209F SER* 3.5 10.6 + - - -
210F ILE* 4.5 6.3 - - - +
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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