Contacts of the helix formed by residues 275 - 286 (chain B) in PDB entry 2V5Q
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 275 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLU* 3.6 36.1 + - - +
273B HIS 3.5 10.0 + - - +
274B ILE* 1.3 76.9 - - - +
276B PRO* 1.3 75.3 - - + +
277B VAL* 3.3 3.6 - - + +
278B ALA* 3.2 5.5 + - + +
279B ALA* 3.0 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE 3.7 3.1 - - - +
275B ASN* 1.3 88.7 - - + +
277B VAL* 1.3 59.7 + - + +
279B ALA* 3.3 7.8 + - + +
280B SER* 2.8 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASN* 3.3 2.9 - - + +
276B PRO* 1.3 80.3 - - + +
278B ALA* 1.3 61.9 + - - +
280B SER* 3.5 5.8 + - - -
281B LEU* 3.1 22.0 + - - +
284B LYS* 5.5 0.3 + - - -
302B ASP* 4.5 2.3 - - - +
303B GLU* 3.8 39.0 - - + +
304B PHE* 3.5 36.6 - - + +
307B SER* 4.1 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLU* 3.6 23.2 + - - +
241B MET* 3.5 5.6 - - - +
245B LEU* 3.8 18.4 - - + -
274B ILE* 4.0 7.0 - - + -
275B ASN* 3.2 8.1 + - - +
277B VAL* 1.3 76.2 - - - +
279B ALA* 1.3 65.2 + - - +
281B LEU 3.2 1.7 + - - -
282B ILE* 2.9 28.4 + - - +
304B PHE* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.5 32.0 - - + +
274B ILE* 4.0 10.4 - - + +
275B ASN 3.0 16.8 + - - +
276B PRO* 3.6 8.3 - - + +
278B ALA* 1.3 75.7 - - - +
280B SER* 1.3 63.2 + - - +
282B ILE* 3.2 3.6 + - - -
283B GLN* 3.0 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B PRO 2.8 18.4 + - - -
277B VAL* 3.7 7.2 - - - -
279B ALA* 1.3 78.3 - - - +
281B LEU* 1.3 56.8 + - - +
283B GLN* 3.3 15.8 + - - +
284B LYS* 3.1 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B MET* 3.7 18.2 - - + -
277B VAL 3.1 14.4 + - - +
278B ALA 3.2 4.2 + - - +
280B SER* 1.3 74.0 + - - +
282B ILE* 1.3 67.3 + - - +
284B LYS* 3.1 23.7 + - + +
285B MET* 3.2 24.3 + - + +
294B PRO* 4.6 4.3 - - + -
299B LEU* 3.6 33.0 - - + -
302B ASP* 3.6 35.2 - - + +
304B PHE* 3.7 27.8 - - + -
305B PHE* 4.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLY 4.6 2.0 - - - +
241B MET* 3.8 23.3 - - + -
242B TYR* 4.1 34.5 - - + +
245B LEU* 4.4 11.2 - - + -
246B VAL* 5.2 1.6 - - + -
268B TYR* 4.0 5.2 - - + -
270B ILE* 3.8 23.3 - - + -
274B ILE* 4.7 3.4 - - + -
278B ALA 2.9 24.0 + - - +
279B ALA* 3.2 11.0 + - - +
281B LEU* 1.3 76.5 - - - +
283B GLN* 1.3 56.2 + - - +
285B MET* 3.2 9.4 + - - +
286B LEU* 2.9 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B TYR* 3.3 20.1 + - + +
270B ILE* 3.7 11.9 - - + +
279B ALA* 3.0 36.0 + - - +
280B SER* 3.5 13.3 - - - +
281B LEU 3.2 0.2 - - - -
282B ILE* 1.3 72.7 - - - +
284B LYS* 1.3 64.1 + - - +
285B MET 3.5 0.2 + - - -
286B LEU 3.6 9.2 - - - +
287B GLN* 3.5 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL 5.5 0.4 + - - -
280B SER* 3.1 35.1 + - - +
281B LEU* 3.1 15.2 + - + +
283B GLN* 1.3 77.6 - - - +
285B MET* 1.3 57.0 + - - +
287B GLN* 2.8 32.7 - - - +
292B ALA 5.7 0.2 - - - +
293B ARG* 3.5 2.4 - - - -
294B PRO* 3.4 29.3 - - + +
302B ASP* 2.7 35.3 + - - +
303B GLU* 5.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B VAL* 3.6 22.4 - - + +
235B TRP* 3.8 6.8 - - - -
237B ILE* 4.0 5.4 - - + +
238B GLY* 3.5 36.8 - - - +
241B MET* 3.6 34.3 - - + -
281B LEU* 3.2 29.2 + - + +
282B ILE* 3.7 5.4 - - - +
284B LYS* 1.3 77.7 - - - +
286B LEU* 1.3 58.6 + - - +
287B GLN 3.1 8.2 + - - -
293B ARG* 3.2 24.2 + - - -
294B PRO* 4.1 9.9 - - + -
299B LEU* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TRP* 3.5 42.8 - - + +
238B GLY* 3.8 9.2 - - - +
239B CYS* 3.7 19.3 - - - +
242B TYR* 4.8 0.9 - - + -
250B PRO* 4.3 21.8 - - + -
251B PHE* 4.3 4.3 - - + -
266B ASN* 3.1 21.8 + - - +
268B TYR* 3.5 36.2 + - + +
282B ILE* 2.9 37.9 + - + +
283B GLN 3.6 4.4 - - - +
285B MET* 1.3 73.9 - - - +
287B GLN* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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