Contacts of the strand formed by residues 199 - 208 (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 ALA 199 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191F HIS* 3.7 31.2 - - + +
193F ALA* 4.1 9.6 - - + +
198F GLU* 1.3 76.7 - - - +
200F THR* 1.3 62.8 + - - +
201F LEU* 3.8 3.5 + - - +
247F VAL 4.8 1.0 - - - +
248F VAL* 5.9 0.4 - - - -
249F VAL* 4.4 14.5 + - - +
251F SER* 4.2 12.4 - - - +
254F GLU* 4.2 17.7 - - - +
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Residues in contact with THR 200 (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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190F THR 3.4 5.0 - - - +
191F HIS* 3.5 2.4 + - - -
192F HIS* 2.9 49.4 + - - +
194F VAL* 3.7 15.3 - - + +
199F ALA* 1.3 70.5 - - - +
201F LEU* 1.3 65.8 + - - +
202F ARG* 5.2 2.9 - - + +
246F ALA* 5.1 6.3 - - + -
247F VAL 3.3 20.2 - - - +
248F VAL* 3.3 36.7 - - + +
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Residues in contact with LEU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189F MET* 5.0 9.6 - - + -
190F THR 3.4 14.8 - - - +
191F HIS* 3.5 25.4 - - + -
199F ALA 3.8 4.1 + - - +
200F THR* 1.3 73.8 - - - +
202F ARG* 1.3 61.0 + - - +
217F TRP* 4.1 21.8 - - + -
247F VAL* 2.9 38.1 + - + +
254F GLU* 3.3 25.1 - - - +
257F TYR* 4.8 20.6 - - + -
274F TRP* 3.8 34.1 - - + -
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Residues in contact with ARG 202 (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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188F HIS 4.0 12.1 - - - +
189F MET* 4.9 3.5 - - - +
190F THR* 3.4 29.7 + - - +
200F THR* 5.2 4.0 - - + +
201F LEU* 1.3 75.4 - - - +
203F CYS* 1.3 58.8 + - - +
204F TRP* 3.3 48.4 + - + +
217F TRP* 4.2 4.0 - - - -
229F GLU* 3.5 6.6 + - - -
244F TRP* 3.2 52.3 - - - +
245F ALA 4.0 0.2 - - - -
246F ALA* 3.0 42.7 - - + +
98G ASP* 4.4 5.9 + - - +
99G MET* 3.5 25.0 - - - +
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Residues in contact with CYS 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F THR* 5.3 7.2 - - - -
188F HIS 5.4 0.7 - - - -
189F MET* 5.4 6.3 - - + -
202F ARG* 1.3 69.5 - - - +
204F TRP* 1.3 68.9 + - - +
215F LEU* 4.0 15.9 - - - +
217F TRP* 3.2 18.9 - - + +
244F TRP* 3.4 5.5 - - - +
245F ALA* 2.8 44.8 + - + +
259F CYS* 2.0 50.5 - - - -
261F VAL* 5.5 0.7 - - - -
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Residues in contact with TRP 204 (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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186F LYS 4.3 0.2 - - - -
187F THR* 3.2 27.9 - - - +
188F HIS* 3.3 44.5 + + + +
189F MET* 5.9 0.2 - - - +
190F THR* 4.5 2.7 - - - -
202F ARG* 3.3 36.7 + - + +
203F CYS* 1.3 76.1 - - - +
205F ALA* 1.3 58.4 + - - +
206F LEU* 3.8 38.4 - - + -
234F ARG* 3.6 25.8 - - - -
242F GLN* 4.7 1.8 - - + -
243F LYS 3.9 12.1 - - - -
244F TRP* 3.4 28.5 - + + -
98G ASP* 3.5 36.4 + - - -
99G MET* 3.9 14.1 - - - -
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Residues in contact with ALA 205 (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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185F PRO* 4.6 4.9 - - + -
186F LYS 3.8 2.9 - - - -
187F THR* 4.4 4.3 - - + -
203F CYS 3.9 0.2 + - - -
204F TRP* 1.3 74.1 - - - +
206F LEU* 1.3 63.0 + - - +
208F PHE* 3.2 19.4 - - + -
213F ILE* 3.9 14.8 - - + -
215F LEU* 3.9 22.9 - - + -
242F GLN* 3.4 1.7 - - - +
243F LYS* 2.8 46.3 + - + +
261F VAL* 4.9 0.4 - - + -
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Residues in contact with LEU 206 (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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185F PRO* 3.4 3.1 - - - +
186F LYS* 2.8 41.8 + - + +
188F HIS* 3.8 31.9 - - + +
204F TRP* 3.8 34.1 - - + -
205F ALA* 1.3 74.4 - - - +
207F SER* 1.3 68.5 + - - +
208F PHE* 3.3 5.0 + - - -
241F PHE 4.0 3.6 - - - -
242F GLN* 3.8 38.6 - - + +
12G ARG 5.9 0.4 - - - +
14G PRO* 4.9 12.6 - - + -
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Residues in contact with SER 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F ASP* 3.8 15.2 - - - +
184F ALA 4.0 6.0 - - - +
186F LYS* 3.7 38.2 + - - +
206F LEU* 1.3 78.9 - - - +
208F PHE* 1.3 60.3 + - - +
240F THR* 4.0 22.4 + - - +
241F PHE 3.2 8.7 + - - -
242F GLN* 5.2 1.8 - - - +
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Residues in contact with PHE 208 (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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183F ASP 3.2 13.7 - - - +
184F ALA 4.6 0.2 - - - -
185F PRO* 4.1 13.5 - - + -
205F ALA* 3.2 34.5 - - + -
206F LEU 3.7 11.0 - - - -
207F SER* 1.3 78.2 - - - +
209F TYR* 1.3 63.7 + - - +
210F PRO 3.6 14.8 - - - -
211F ALA 3.6 20.0 - - - -
213F ILE* 3.9 22.2 - - + -
233F THR* 4.0 2.7 - - + -
240F THR* 3.6 4.8 - - - -
241F PHE* 3.1 52.1 + - + -
242F GLN 3.7 16.8 - - - -
243F LYS* 3.8 10.3 - - + -
263F HIS* 3.8 13.7 - - + +
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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