Contacts of the strand formed by residues 213 - 220 (chain B) in PDB entry 2VQO
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 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLN* 3.3 29.4 - - - +
190B ILE* 3.3 22.9 - - + +
192B ILE* 3.9 23.1 - - + -
207B PHE* 3.6 43.5 - - + -
210B ASP* 3.3 9.0 + - - +
211B PRO 3.2 2.2 - - - -
212B SER* 1.3 81.3 - - - +
214B LEU* 1.3 64.8 + - - +
215B TYR* 4.7 2.0 - - + +
244B PHE* 3.7 3.3 - - - +
278B PHE* 4.5 0.9 - - - -
1408B K 2.9 24.6 - - - -
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE 2.8 9.5 + - - +
191B LEU* 3.4 25.0 - - + +
192B ILE* 2.8 31.9 + - - +
213B VAL* 1.3 72.1 - - - +
215B TYR* 1.3 53.9 + - - +
216B MET* 3.9 9.4 - - + -
244B PHE* 3.5 30.3 - - + +
246B VAL* 4.2 16.4 - - + -
274B ILE* 4.0 16.8 - - + +
275B ALA* 4.3 2.9 - - - -
278B PHE* 3.6 49.8 - - + -
384B TRP* 4.1 13.9 - - + -
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Residues in contact with TYR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 3.5 22.9 - - + -
194B ASP* 3.2 35.5 + - + -
199B HIS* 4.2 5.2 - - - -
200B GLY* 3.2 26.6 + - - -
203B THR* 3.8 27.1 - - + +
204B GLN* 3.8 23.8 - - + -
207B PHE* 5.6 4.7 - - + -
213B VAL* 3.7 7.7 + - + +
214B LEU* 1.3 72.1 - - - +
216B MET* 1.3 64.0 + - - +
217B SER* 3.5 24.9 - - - -
244B PHE 3.3 8.4 + - - +
245B ASN* 3.3 30.8 - - - +
246B VAL* 2.9 26.3 + - - -
247B ASN* 4.4 1.3 - - - -
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Residues in contact with MET 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 3.7 27.1 - - + -
192B ILE 2.8 10.9 + - - +
193B VAL* 3.3 12.5 - - + +
194B ASP* 2.9 26.2 + - - +
214B LEU* 3.9 17.3 - - + -
215B TYR* 1.3 79.4 - - - +
217B SER* 1.3 59.9 + - - +
218B LEU* 4.3 1.6 - - + -
246B VAL* 3.4 31.9 - - + +
270B VAL* 4.0 3.8 - - + +
271B VAL* 3.7 50.9 - - + +
274B ILE* 3.9 18.8 - - + -
275B ALA* 4.3 3.1 - - - -
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Residues in contact with SER 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ASP* 3.4 4.7 - - - -
199B HIS* 3.8 5.5 - - - -
200B GLY 4.1 0.3 + - - -
215B TYR* 3.5 27.4 + - - -
216B MET* 1.3 73.2 - - - +
218B LEU* 1.3 61.0 + - - +
219B HIS* 3.1 18.9 + - - -
246B VAL 3.0 6.7 + - - -
247B ASN* 3.8 13.0 - - - -
248B MET* 2.8 31.1 + - - +
1407B K 2.8 23.9 - - - -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 4.4 13.9 - - + -
194B ASP 3.1 11.1 + - - +
195B TRP* 4.2 9.4 - - + +
196B ASP 3.0 9.2 - - - +
216B MET* 4.8 2.2 - - + +
217B SER* 1.3 75.1 - - - +
219B HIS* 1.3 61.0 + - - +
248B MET* 3.5 19.3 - - + +
250B PHE* 4.6 3.6 - - + -
263B TYR* 3.9 39.3 + - + -
266B ALA* 4.1 20.6 - - + -
267B PHE* 4.0 28.7 - - + -
271B VAL* 3.9 19.3 - - + -
1407B K 2.9 15.1 - - - -
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Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 3.2 16.4 - - - +
198B HIS 3.8 2.2 - - - -
199B HIS* 3.5 45.3 - + + +
217B SER* 3.1 21.9 + - - -
218B LEU* 1.3 73.9 - - - +
220B ARG* 1.3 74.0 + - - +
221B TYR* 3.9 9.4 - - + -
230B SER 4.3 2.7 - - - -
231B GLY* 2.7 34.0 + - - -
247B ASN* 3.6 16.6 - - + -
248B MET 3.3 4.4 + - - -
249B ALA* 3.6 9.1 - - + +
250B PHE* 2.8 35.5 + - - +
263B TYR* 4.8 1.8 - - - -
1407B K 3.9 0.4 - - - -
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Residues in contact with ARG 220 (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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197B VAL* 3.0 14.9 + - + +
199B HIS 5.2 0.9 + - - -
219B HIS* 1.3 80.5 - - - +
221B TYR* 1.3 60.0 + - - +
222B ASP* 3.1 28.7 + - - +
226B PHE* 3.4 57.2 - - + +
227B PHE 4.9 1.6 - - - +
250B PHE 4.0 0.4 - - - -
253B GLY* 4.8 3.4 - - - +
254B LEU* 3.5 33.4 - - - +
297B THR 2.9 27.4 + - - -
300B GLY 3.0 18.9 + - - -
301B GLY* 3.9 0.2 - - - -
302B TYR* 3.3 40.7 + - + +
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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
------------------------------------------------------------
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