Contacts of the strand formed by residues 245 - 250 (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 ASN 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLN* 3.0 38.2 + - - +
207B PHE 5.8 1.2 + - - -
208B TYR* 3.7 16.6 - - + +
215B TYR* 3.3 34.7 - - - +
235B GLU 3.1 25.6 - - - +
236B VAL* 3.2 19.5 + - - +
237B GLY* 3.9 4.5 - - - +
243B GLY 3.4 0.8 - - - -
244B PHE* 1.3 80.0 + - - +
246B VAL* 1.3 61.5 + - - +
247B ASN* 3.6 3.1 - - - +
380B HIS* 3.2 18.0 + - - -
1408B K 4.7 2.9 - - - -
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Residues in contact with VAL 246 (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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214B LEU* 4.2 21.3 - - + -
215B TYR 2.9 12.6 + - - +
216B MET* 3.4 29.7 - - + +
217B SER 3.0 25.6 + - - -
243B GLY 4.5 2.9 - - - +
245B ASN* 1.3 73.4 - - - +
247B ASN* 1.3 62.4 + - - +
248B MET* 3.5 5.4 + - + +
270B VAL* 4.1 18.6 - - + -
274B ILE* 4.3 9.6 - - + -
376B VAL* 4.3 6.1 - - + -
380B HIS* 3.4 37.5 - - + +
384B TRP* 4.6 1.8 - - - +
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Residues in contact with ASN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B HIS* 3.2 28.1 + - - -
204B GLN* 2.9 23.4 + - - +
215B TYR* 4.4 2.4 - - - -
217B SER* 3.8 10.4 - - - -
219B HIS* 3.6 4.7 - - + -
231B GLY* 3.3 28.2 - - - +
232B ALA 3.1 21.5 - - - +
233B PRO* 3.7 11.7 + - + +
235B GLU* 3.7 6.6 + - - +
245B ASN* 3.6 8.6 + - - +
246B VAL* 1.3 73.0 + - - +
248B MET* 1.3 61.7 + - - +
249B ALA 2.8 8.3 + - - -
376B VAL* 3.5 16.3 - - - +
380B HIS* 4.7 3.6 + - - -
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Residues in contact with MET 248 (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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217B SER 2.8 16.6 + - - +
218B LEU* 3.5 22.8 - - + -
219B HIS* 3.3 21.3 + - - -
246B VAL* 3.5 4.9 + - + +
247B ASN* 1.3 67.9 - - - +
249B ALA* 1.3 69.9 + - - +
250B PHE* 3.7 13.9 + - + -
266B ALA* 4.1 15.5 - - + +
270B VAL* 4.0 37.5 - - + -
271B VAL* 5.4 2.5 - - + -
372B SER* 3.7 35.7 - - - +
373B MET* 3.8 16.8 - - + +
376B VAL* 3.8 9.4 - - + -
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Residues in contact with ALA 249 (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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219B HIS* 3.6 8.7 - - - +
221B TYR* 3.4 25.1 - - + -
231B GLY 3.6 19.7 - - - +
233B PRO* 3.7 23.8 - - + +
247B ASN 2.8 7.2 + - - +
248B MET* 1.3 76.1 - - - +
250B PHE* 1.3 61.6 + - - +
251B THR* 3.7 3.0 + - - +
372B SER* 3.4 18.9 + - - +
376B VAL* 4.1 2.6 - - - +
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Residues in contact with PHE 250 (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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218B LEU* 4.6 8.1 - - + -
219B HIS 2.8 22.5 + - - +
220B ARG 3.8 0.2 - - - -
221B TYR* 2.8 28.1 + - - -
222B ASP* 3.0 9.0 + - - +
248B MET* 4.2 21.8 - - + -
249B ALA* 1.3 70.8 - - - +
251B THR* 1.3 60.0 + - - +
258B MET* 3.6 28.5 - - + -
262B GLU* 4.2 7.9 - - + -
263B TYR* 3.4 47.8 - + - -
266B ALA* 4.1 21.1 - - + -
302B TYR* 3.3 21.5 - - - +
369B ALA* 4.3 19.5 - - + -
372B SER* 3.7 10.3 - - - -
373B MET* 5.0 1.3 - - + -
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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