Contacts of the helix formed by residues 270 - 279 (chain B) in PDB entry 2VQQ
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 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B VAL* 4.0 26.9 - - + -
248B MET* 4.0 26.7 - - + -
266B ALA 2.9 11.7 + - - +
269B THR* 1.3 93.2 - - - +
271B VAL* 1.3 75.3 + - + +
272B MET 3.6 0.7 - - - -
273B PRO* 3.6 1.2 - - - +
274B ILE* 3.3 36.3 + - + +
373B MET* 4.4 5.2 - - + +
376B VAL* 4.0 16.4 - - + -
377B MET* 3.9 20.6 - - + -
387B LEU* 5.4 1.6 - - + -
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 4.6 16.2 - - + -
216B MET* 3.8 26.5 - - + +
218B LEU* 4.1 23.3 - - + -
248B MET* 5.2 3.8 - - + -
266B ALA 3.1 12.0 + - - +
267B PHE* 4.0 42.0 - - + -
270B VAL* 1.3 84.4 - - + +
272B MET* 1.3 60.2 + - - +
275B ALA* 2.9 35.2 + - + +
316B LEU* 4.6 6.3 - - + -
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Residues in contact with MET 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE* 2.9 35.7 + - + +
268B ARG* 5.2 2.2 - - - -
271B VAL* 1.3 73.7 - - - +
273B PRO* 1.4 60.8 - - + +
275B ALA* 4.4 1.1 - - - -
276B SER* 2.7 41.4 + - - +
315B GLN* 3.3 52.7 - - + +
316B LEU* 4.0 26.2 - - - -
318B GLY 5.7 0.4 - - - -
319B LEU* 3.9 28.9 - - + -
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Residues in contact with PRO 273 (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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267B PHE 3.5 3.8 - - - +
268B ARG 3.3 27.4 - - - +
269B THR* 3.5 15.3 - - - +
270B VAL 3.6 10.1 - - - +
272B MET* 1.4 91.9 - - + +
274B ILE* 1.3 62.2 + - + +
276B SER* 3.8 3.8 - - - -
277B GLU* 3.1 24.4 + - - +
386B CYS* 3.7 27.1 - - + +
387B LEU* 5.3 2.2 - - + -
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Residues in contact with ILE 274 (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* 3.9 9.4 - - + -
216B MET* 3.7 21.8 - - + -
246B VAL* 4.2 17.5 - - + -
270B VAL* 3.3 23.5 + - + +
273B PRO* 1.3 78.3 - - + +
275B ALA* 1.3 59.0 + - - +
277B GLU* 3.2 4.9 + - - +
278B PHE* 3.0 26.9 + - - +
380B HIS* 4.3 4.5 - - + -
384B TRP* 3.6 50.9 - - + +
386B CYS* 4.1 8.5 - - - -
387B LEU* 3.9 26.2 - - + -
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Residues in contact with ALA 275 (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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191B LEU* 3.6 28.0 - - + -
214B LEU* 4.2 12.6 - - - -
216B MET* 4.3 4.9 - - - -
271B VAL* 2.9 28.8 + - + +
272B MET* 4.0 2.9 - - - +
274B ILE* 1.3 72.7 - - - +
276B SER* 1.3 58.1 + - - +
278B PHE* 3.4 1.7 + - - +
279B ALA 3.0 22.9 + - - -
280B PRO* 3.3 12.4 - - - +
319B LEU* 3.8 15.3 - - + -
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Residues in contact with SER 276 (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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272B MET* 2.7 31.5 + - - +
273B PRO* 3.8 4.0 - - - -
275B ALA* 1.3 72.7 - - - +
277B GLU* 1.3 66.5 + - - +
279B ALA* 3.3 16.1 + - - +
319B LEU* 3.7 22.5 - - - +
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Residues in contact with GLU 277 (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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273B PRO 3.1 15.7 + - - +
274B ILE* 3.5 4.5 - - - +
276B SER* 1.3 75.7 - - - +
278B PHE* 1.3 65.0 + - - +
279B ALA* 3.4 4.0 + - - +
383B TYR 4.7 1.2 - - - +
384B TRP* 3.6 23.8 - - + -
385B ARG* 2.9 34.3 + - - +
386B CYS* 2.9 37.0 + - + +
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Residues in contact with PHE 278 (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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189B LYS* 3.2 50.1 + - + +
190B ILE 3.6 21.8 - - - -
191B LEU* 4.7 1.6 - - + -
211B PRO 3.7 18.2 - - - -
212B SER 3.8 21.3 - - - -
214B LEU* 3.6 33.4 - - + -
244B PHE* 3.8 26.2 - + - -
274B ILE 3.0 13.3 + - - +
275B ALA 3.5 7.6 - - - +
277B GLU* 1.3 77.7 - - - +
279B ALA* 1.3 64.4 + - - +
280B PRO* 3.9 17.7 - - + -
384B TRP* 4.0 8.7 - + + -
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Residues in contact with ALA 279 (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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189B LYS* 2.8 30.0 + - - +
275B ALA 3.0 11.3 + - - -
276B SER* 3.3 13.7 + - - +
277B GLU 3.3 5.0 - - - +
278B PHE* 1.3 77.7 - - - +
280B PRO* 1.3 69.6 - - - +
281B ASP* 4.8 1.0 - - - +
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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