Contacts of the helix formed by residues 288 - 296 (chain B) in PDB entry 7A62
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 ALA 288 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLN* 6.2 0.4 - - - +
286B GLY* 3.1 1.2 - - - -
287B HIS* 1.3 78.2 - - - +
289B ALA* 1.3 66.9 + - - +
290B GLN 3.2 0.9 - - - -
291B PHE 3.4 0.9 + - - -
292B LEU* 3.1 30.9 + - + +
387B PHE* 3.8 26.8 - - + -
390B THR* 4.3 24.2 - - + -
391B VAL* 4.7 5.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
281B GLN 3.1 28.6 + - - +
282B THR* 3.5 18.5 - - - +
283B ALA 3.7 13.2 - - - +
284B GLY* 4.1 12.1 - - - +
286B GLY* 3.7 8.7 + - - +
288B ALA* 1.3 77.2 - - - +
290B GLN* 1.3 62.6 + - - +
292B LEU* 3.3 3.1 + - - +
293B GLN* 3.0 27.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
284B GLY 5.3 1.9 + - - +
285B GLY 4.4 8.4 - - - +
286B GLY 3.2 18.7 + - - +
287B HIS* 4.7 8.9 - - - -
288B ALA 3.2 0.8 - - - -
289B ALA* 1.3 79.6 - - - +
291B PHE* 1.3 57.2 + - - +
293B GLN* 3.4 8.1 + - - +
294B ASP* 2.9 29.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
260B ALA* 6.2 1.6 - - + -
263B SER* 5.6 0.2 - - - -
265B GLY* 5.4 2.5 - - - -
287B HIS 3.7 18.4 + - - +
288B ALA 3.4 5.1 + - - +
289B ALA 3.3 0.6 - - - -
290B GLN* 1.3 78.3 - - - +
292B LEU* 1.3 65.1 + - + +
294B ASP* 3.1 9.8 + - - +
295B MET* 3.0 57.3 + - + +
387B PHE* 3.6 28.9 - + + -
503B HEM 3.7 41.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
265B GLY 6.0 0.4 - - - +
271B GLN* 3.0 39.2 + - + +
274B ASP* 5.5 1.1 - - - +
281B GLN* 3.7 34.8 - - + +
282B THR* 4.2 9.9 - - + -
288B ALA* 3.1 19.5 + - + +
289B ALA 3.8 4.0 - - - +
291B PHE* 1.3 78.7 - - + +
293B GLN* 1.3 62.4 + - - +
295B MET* 3.3 12.3 + - + +
296B ARG* 3.7 4.7 + - - +
343B ARG* 5.6 0.9 - - - +
387B PHE* 3.9 12.3 - - + -
391B VAL* 4.1 20.4 - - + -
503B HEM 3.6 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 2.3 54.3 + - + +
284B GLY 5.0 3.6 + - - -
289B ALA* 3.0 15.9 + - - +
290B GLN* 3.8 7.0 - - + +
292B LEU* 1.3 72.4 - - - +
294B ASP* 1.3 66.1 + - - +
296B ARG* 3.3 25.3 + - - +
297B ARG* 4.1 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LYS* 3.8 24.7 + - - -
260B ALA* 5.3 0.2 - - - +
290B GLN* 2.9 19.5 + - + +
291B PHE* 3.1 12.0 + - - +
293B GLN* 1.3 78.5 - - - +
295B MET* 1.3 78.3 + - + +
297B ARG* 2.8 55.9 + - - +
298B TYR* 3.6 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ALA* 4.4 13.5 - - + -
263B SER* 4.3 7.9 - - - -
265B GLY 3.7 19.3 - - - +
266B GLN* 3.6 28.7 - - - +
271B GLN* 4.7 2.7 - - - +
291B PHE* 3.0 53.1 + - + +
292B LEU* 3.3 12.5 + - + +
293B GLN 3.3 1.0 - - - -
294B ASP* 1.3 97.6 - - - +
296B ARG* 1.3 60.7 + - - +
297B ARG 3.1 0.2 - - - -
298B TYR* 3.1 31.9 + - + +
299B MET* 3.4 20.9 + - + +
503B HEM 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B GLN* 2.7 27.8 + - - +
275B VAL* 3.7 26.3 - - - +
282B THR* 4.0 20.9 + - - +
292B LEU 3.9 7.0 - - - +
293B GLN* 3.5 18.3 - - - +
294B ASP 3.1 1.4 - - - -
295B MET* 1.3 75.2 - - - +
297B ARG* 1.3 64.8 + - - +
299B MET* 3.1 27.9 + - + +
304B ARG* 3.2 35.6 - - + +
307B LEU* 3.7 29.3 - - - +
308B CYS* 4.1 15.4 - - - -
311B GLU* 3.5 19.0 + - - -
----------------------------------------------------------
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