Contacts of the strand formed by residues 241 - 247 (chain F) in PDB entry 2VLR
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 PHE 241 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F ASP* 3.8 38.6 - - + -
207F SER 3.2 23.2 + - - -
208F PHE* 3.1 43.4 + - + +
209F TYR* 3.9 8.7 - + - -
211F ALA* 3.9 24.5 - - + -
233F THR* 3.7 10.3 - - + -
234F ARG* 3.4 15.7 - - - -
235F PRO* 3.8 24.9 - - + -
236F ALA 4.4 0.2 - - - +
239F GLY 3.8 17.3 - - - -
240F THR* 1.3 77.9 + - - +
242F GLN* 1.3 63.9 + - - +
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Residues in contact with GLN 242 (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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204F TRP* 4.7 2.0 - - + -
205F ALA 3.4 5.2 - - - -
206F LEU* 3.8 30.5 - - + +
207F SER 5.2 0.9 - - - +
208F PHE* 3.7 2.9 - - - -
232F GLU 4.1 0.7 - - - +
233F THR* 3.4 3.8 - - - +
234F ARG* 2.8 79.3 + - + +
236F ALA* 3.6 17.3 - - + +
241F PHE* 1.3 79.2 - - - +
243F LYS* 1.3 63.4 + - - +
10G TYR* 3.5 11.9 - - - -
11G SER 3.4 11.4 + - - +
12G ARG 3.3 22.2 - - - +
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Residues in contact with LYS 243 (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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204F TRP* 3.9 3.4 - - - -
205F ALA* 2.8 34.2 + - + +
208F PHE* 3.8 12.8 - - + -
213F ILE* 3.7 28.4 + - + -
215F LEU* 4.2 27.8 - - + +
230F LEU* 4.7 20.8 - - - +
231F VAL* 3.3 26.5 + - - +
232F GLU* 4.6 3.9 - - - +
233F THR* 3.8 20.5 + - - +
234F ARG* 5.9 0.7 - - - +
242F GLN* 1.3 75.9 - - - +
244F TRP* 1.3 72.1 + - - +
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Residues in contact with TRP 244 (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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202F ARG* 3.2 35.5 - - - +
203F CYS 3.4 11.9 - - - +
204F TRP* 3.4 34.3 - + + -
215F LEU* 4.2 5.8 - - - +
229F GLU* 3.2 46.9 - - + -
230F LEU* 3.8 10.2 - - - +
231F VAL* 3.3 60.6 + - + +
234F ARG* 3.7 19.0 - - - +
242F GLN 6.2 0.2 - - - -
243F LYS* 1.3 83.8 - - - +
245F ALA* 1.3 65.4 + - - +
8G GLN* 5.3 0.9 - - - -
99G MET* 3.7 26.1 - - + +
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Residues in contact with ALA 245 (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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202F ARG* 4.0 2.0 - - - -
203F CYS* 2.8 37.7 + - + +
215F LEU* 4.3 21.0 - - + +
217F TRP* 3.4 7.6 + - + -
228F THR* 4.2 12.3 - - + -
229F GLU 3.0 19.7 - - - +
230F LEU* 5.0 4.0 - - + -
243F LYS* 6.5 0.2 - - - -
244F TRP* 1.3 75.9 - - - +
246F ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 246 (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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200F THR* 5.1 5.4 - - + -
201F LEU 4.0 1.1 - - - +
202F ARG* 3.0 42.4 - - + +
217F TRP* 4.1 0.7 - - - -
227F ASP 3.5 1.2 - - - +
228F THR* 2.9 23.5 - - - -
229F GLU* 3.1 30.8 + - + +
245F ALA* 1.3 73.0 - - - +
247F VAL* 1.3 64.7 + - - +
248F VAL* 3.9 3.5 + - + +
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Residues in contact with VAL 247 (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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199F ALA 4.8 0.5 - - - +
200F THR* 3.3 12.2 - - - +
201F LEU* 2.9 41.2 + - + +
217F TRP* 3.6 52.4 - - + +
224F GLN* 4.9 9.0 - - + -
227F ASP 3.4 3.1 - - - +
228F THR* 3.4 22.0 - - - +
246F ALA* 1.3 71.5 - - - +
248F VAL* 1.3 61.1 + - - +
249F VAL* 3.6 25.4 + - + -
257F TYR* 5.3 5.2 - - + -
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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