Contacts of the helix formed by residues 285 - 297 (chain B) in PDB entry 2V62
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 CYS 285 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 5.5 1.6 + - - -
241B LEU* 3.8 26.5 - - - -
244B LEU* 3.8 20.4 - - - -
245B CYS* 3.8 5.8 - - - -
275B VAL* 3.6 26.5 - - + +
276B LEU* 4.0 8.4 + - - +
279B ALA* 3.5 24.3 - - + +
283B SER 3.6 0.4 + - - -
284B SER* 1.3 71.1 + - - +
286B CYS* 1.3 59.0 + - - +
287B GLU* 3.3 3.1 - - - -
288B ILE* 3.3 12.0 + - + +
289B ALA* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 4.3 6.1 - - - -
204A GLU* 3.6 28.3 - - - -
276B LEU* 3.7 21.9 - - - +
284B SER* 3.1 21.2 + - - +
285B CYS* 1.3 77.7 - - - +
287B GLU* 1.3 67.6 + - - +
289B ALA* 3.7 1.9 - - - +
290B GLN* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS* 2.9 39.2 + - - -
144B LEU* 4.0 26.7 - - + +
284B SER* 4.0 1.2 + - - +
286B CYS* 1.3 80.6 + - - +
288B ILE* 1.3 59.3 + - - +
290B GLN* 3.4 1.6 + - - -
291B PHE* 2.9 29.4 + - - +
312B ILE* 3.3 32.1 - - - +
313B LEU* 4.2 3.1 - - + +
315B PRO* 3.9 27.5 - - + +
316B HIS* 5.2 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 4.4 5.4 - - + -
144B LEU* 4.4 14.6 - - + -
237B GLY 3.9 21.5 - - - +
240B MET* 3.7 45.1 - - + +
241B LEU* 4.1 9.0 - - + +
244B LEU* 3.9 26.5 - - + -
275B VAL* 4.2 14.1 - - + -
284B SER 5.4 0.2 - - - +
285B CYS* 3.3 16.1 + - + +
287B GLU* 1.3 76.0 - - - +
289B ALA* 1.3 57.7 + - - +
291B PHE* 3.3 7.1 + - + +
292B LEU* 3.0 34.2 + - + +
313B LEU* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 4.2 3.3 - - - +
272B PRO* 3.9 22.0 - - + +
275B VAL* 3.7 21.6 - - + +
276B LEU* 3.8 19.5 - - + -
285B CYS 2.8 21.9 + - - +
286B CYS 3.7 3.6 - - - +
288B ILE* 1.3 72.1 - - - +
290B GLN* 1.3 56.7 + - - +
292B LEU* 3.3 3.6 + - - +
293B VAL* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PRO* 5.4 0.9 - - - +
286B CYS 3.1 17.6 + - - +
287B GLU* 3.9 4.0 - - - +
289B ALA* 1.3 72.5 - - - +
291B PHE* 1.3 64.5 + - - +
293B VAL* 3.3 24.7 + - - +
294B CYS* 3.0 26.5 + - - +
312B ILE* 3.8 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.9 24.9 - - + -
233B VAL* 3.2 42.6 - - + -
236B LEU* 4.1 13.7 - - + -
237B GLY* 3.6 20.0 - - - -
240B MET* 3.8 20.4 - - + -
287B GLU 2.9 19.0 + - - +
288B ILE* 3.5 8.1 - - - +
290B GLN* 1.3 74.5 - - - +
292B LEU* 1.3 62.2 + - + +
294B CYS* 3.3 5.6 + - - +
295B ALA* 2.9 24.9 + - + +
309B LEU* 3.6 28.3 - - + +
312B ILE* 3.6 10.0 - - + +
313B LEU* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLU* 4.0 21.5 - - + +
237B GLY* 3.9 32.5 - - - +
238B TYR* 4.6 6.5 - - + +
241B LEU* 5.0 2.7 - - + -
267B LEU* 4.3 15.3 - - + -
268B LEU* 4.1 17.0 - - + +
271B LEU* 3.6 13.7 - - + +
275B VAL* 4.0 24.9 - - + -
288B ILE* 3.0 26.6 + - + +
289B ALA 3.9 3.4 - - - +
290B GLN 3.3 0.2 - - - -
291B PHE* 1.3 75.4 - - + +
293B VAL* 1.3 60.1 + - - +
295B ALA* 3.7 8.1 - - + +
296B HIS* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.9 27.8 - - + -
272B PRO* 4.3 15.7 - - + -
289B ALA 2.9 21.4 + - - +
290B GLN* 3.3 28.0 + - - +
292B LEU* 1.3 74.8 - - - +
294B CYS* 1.3 64.4 + - - +
296B HIS* 3.3 5.1 + - - +
297B SER* 3.2 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLN* 3.0 17.3 + - - +
291B PHE 3.4 8.5 - - - +
292B LEU 3.3 0.2 - - - -
293B VAL* 1.3 74.9 - - - +
295B ALA* 1.3 64.6 + - - +
297B SER* 2.8 26.8 + - - -
298B LEU* 3.8 10.7 + - - +
305B ASN* 5.2 7.4 - - - -
308B ALA* 5.0 10.1 - - - -
309B LEU* 3.6 28.0 - - + -
312B ILE* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ARG* 4.7 6.5 - - - +
233B VAL* 3.7 27.8 - - + +
234B GLU* 4.3 13.9 - - + +
291B PHE* 2.9 17.1 + - + +
292B LEU* 3.8 17.9 - - + +
293B VAL 3.3 0.2 - - - -
294B CYS* 1.3 75.2 - - - +
296B HIS* 1.3 62.6 + - - +
298B LEU* 3.3 31.2 + - + +
309B LEU* 4.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 5.3 4.3 - - + -
268B LEU* 3.4 53.9 + - + +
269B ASP* 4.0 15.0 + - - -
271B LEU* 4.3 7.6 - - + -
292B LEU 2.9 19.0 + - - +
293B VAL* 3.8 4.5 - - - +
294B CYS 3.2 0.2 - - - -
295B ALA* 1.3 79.0 - - - +
297B SER* 1.3 59.7 + - - +
298B LEU 3.1 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B VAL* 3.2 11.2 + - - -
294B CYS* 2.8 24.9 + - - -
296B HIS* 1.3 76.0 - - - +
298B LEU* 1.3 65.5 + - - +
299B ALA 3.6 2.3 + - - -
302B GLU* 3.7 6.4 + - - +
----------------------------------------------------------
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