Contacts of the helix formed by residues 288 - 297 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D GLY 3.1 1.2 - - - -
287D HIS* 1.3 77.2 - - - +
289D ALA* 1.3 67.4 + - - +
290D GLN 3.2 0.9 - - - -
291D PHE* 3.1 2.4 + - - +
292D LEU* 2.9 30.8 + - + +
387D PHE* 3.5 31.1 - - + -
390D THR* 4.5 22.0 - - + -
391D VAL* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D GLN 3.1 27.2 + - - +
282D THR* 3.6 16.4 - - - +
283D ALA 3.5 21.1 - - - +
284D GLY* 4.0 13.0 - - - +
286D GLY* 3.7 5.6 + - - +
288D ALA* 1.3 77.8 - - - +
290D GLN* 1.3 63.0 + - - +
292D LEU* 3.0 13.0 + - - +
293D GLN* 3.2 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D GLY 5.0 3.2 + - - +
285D GLY 4.1 7.3 - - - +
286D GLY 3.2 15.6 + - - +
287D HIS* 3.9 27.2 + - - +
289D ALA* 1.3 79.3 - - - +
291D PHE* 1.3 63.6 + - - +
293D GLN* 3.6 3.8 + - - +
294D ASP* 3.2 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D HIS 3.3 18.9 + - - +
288D ALA* 3.1 9.8 + - - +
290D GLN* 1.3 81.8 - - - +
292D LEU* 1.3 64.6 + - + +
294D ASP* 3.1 12.4 + - - +
295D MET* 3.1 61.6 + - + +
387D PHE* 3.6 35.0 - + + -
504D HEM 4.2 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D GLN* 3.3 42.0 + - + +
274D ASP* 5.6 0.9 - - - +
281D GLN* 3.5 39.7 - - + +
282D THR* 4.9 6.5 - - - -
288D ALA* 2.9 19.2 + - + +
289D ALA* 3.0 6.2 + - - +
291D PHE* 1.3 79.0 - - + +
293D GLN* 1.3 63.0 + - - +
295D MET* 3.1 14.5 + - + +
296D ARG* 3.6 2.9 + - - +
343D ARG* 5.8 1.8 - - - +
387D PHE* 3.9 20.9 - - + -
391D VAL* 4.3 16.6 - - + -
504D HEM 4.4 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D THR* 2.7 37.9 + - - +
289D ALA 3.2 8.9 + - - +
290D GLN* 4.5 3.4 - - - +
292D LEU* 1.3 80.0 - - - +
294D ASP* 1.3 62.4 + - - +
296D ARG* 3.2 52.7 + - - +
297D ARG* 3.9 3.6 + - - +
308D CYS* 5.6 4.6 - - - -
311D GLU* 4.6 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D LYS* 4.1 21.2 + - - +
260D ALA* 5.5 3.1 - - - +
290D GLN* 3.2 15.1 + - + +
291D PHE* 3.1 15.7 + - - +
293D GLN* 1.3 77.9 - - - +
295D MET* 1.3 64.4 + - - +
297D ARG* 3.0 44.5 + - - +
298D TYR* 3.5 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D ALA* 5.5 7.6 - - + -
261D GLY 5.0 5.4 - - - +
263D SER* 3.8 21.1 - - - +
265D GLY* 4.1 25.4 - - - +
266D GLN* 4.0 23.6 - - + +
271D GLN* 4.6 7.0 - - - +
291D PHE* 3.1 52.7 + - + +
292D LEU* 3.1 11.8 + - + +
294D ASP* 1.3 79.0 - - + +
296D ARG* 1.3 63.1 + - - +
298D TYR* 3.0 28.2 + - - +
299D MET* 3.7 11.9 - - + +
504D HEM 4.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D GLN* 2.9 26.4 + - - +
275D VAL* 3.9 19.4 - - - +
282D THR* 4.6 8.1 - - - +
292D LEU 3.9 8.5 - - - +
293D GLN* 3.4 46.1 + - - +
294D ASP 3.1 0.6 - - - -
295D MET* 1.3 73.1 - - - +
297D ARG* 1.3 63.9 + - - +
298D TYR 2.8 6.7 + - - -
299D MET* 2.9 26.7 + - + -
304D ARG* 3.0 32.0 + - + +
307D LEU* 3.8 33.1 + - - +
308D CYS* 4.5 9.3 - - - +
311D GLU* 2.9 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D GLU 4.8 0.7 - - - +
120D LEU* 4.5 0.7 - - - +
121D PRO* 3.5 20.7 - - + +
238D LYS* 4.9 11.9 - - - +
258D GLU 4.6 5.3 + - - -
259D PHE* 4.1 25.6 - - - -
293D GLN 3.9 2.3 + - - +
294D ASP* 3.0 33.6 + - - +
296D ARG* 1.3 77.3 - - - +
298D TYR* 1.3 83.6 + - + +
299D MET 3.5 1.1 - - - +
304D ARG* 3.5 24.3 + - - +
----------------------------------------------------------
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