Contacts of the helix formed by residues 296 - 303 (chain A) in PDB entry 2AZE
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 ASP 296 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 5.4 2.0 - - - -
259A LEU* 3.6 22.8 - - + +
260A PRO* 3.2 17.0 - - - +
261A PHE* 3.2 62.8 + - + +
295A ASP* 1.3 75.8 + - - +
297A ILE* 1.3 84.4 + - - +
299A VAL* 3.0 4.7 + - - +
300A LEU* 2.7 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 3.6 20.9 - - - +
229A GLN* 3.4 45.3 - - + +
232A ALA* 5.3 5.4 - - + -
233A PHE* 4.7 12.1 - - + -
295A ASP* 3.4 21.7 - - + +
296A ASP* 1.3 93.0 + - - +
298A GLU* 1.3 57.4 + - - +
300A LEU* 3.2 10.3 + - - +
301A LYS* 2.8 42.8 + - + +
837C GLU 5.8 0.9 - - - +
838C SER* 4.7 10.1 - - - +
842C SER* 4.7 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A HIS* 4.4 9.6 - - + -
295A ASP* 3.4 25.3 + - + +
296A ASP 3.2 0.8 - - - -
297A ILE* 1.3 78.6 - - - +
299A VAL* 1.3 56.9 + - - +
301A LYS* 3.3 25.0 + - - +
302A ARG* 2.9 80.8 + - - +
842C SER* 4.2 19.7 + - - +
846C GLN* 5.0 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 4.3 10.3 - - + -
263A ILE* 4.0 25.1 - - + -
294A HIS* 4.5 7.4 - - + -
295A ASP 3.1 16.6 + - - +
296A ASP* 3.0 10.5 + - - +
298A GLU* 1.3 77.4 - - - +
300A LEU* 1.3 60.0 + - + +
302A ARG* 3.2 7.6 + - - +
303A MET* 2.9 46.6 + - - +
246B VAL* 4.8 2.2 - - + -
251B LEU* 3.9 19.1 - - + -
254B ILE* 4.1 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA* 4.0 19.7 - - + +
233A PHE* 3.8 31.2 - - + -
236A LEU* 4.2 15.3 - - + -
259A LEU* 4.0 18.2 - - + -
261A PHE* 5.2 0.2 - - + -
296A ASP* 2.7 25.8 + - + +
297A ILE* 3.4 11.0 - - - +
299A VAL* 1.3 75.7 - - + +
301A LYS* 1.3 58.1 + - - +
303A MET* 3.3 5.9 + - - -
304A GLY 3.3 4.2 + - - -
305A MET* 2.9 50.7 + - + +
306A ALA 4.9 0.2 - - - -
246B VAL* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 2.9 39.6 + - - -
228A LEU* 4.2 23.4 - - - +
232A ALA* 5.4 2.0 - - + +
297A ILE* 2.8 33.8 + - + +
298A GLU* 3.5 29.9 + - - +
299A VAL 3.3 0.2 - - - -
300A LEU* 1.3 71.9 - - + +
302A ARG* 1.3 59.6 + - + +
304A GLY* 2.9 20.6 + - - -
305A MET 4.6 2.2 - - - +
306A ALA* 4.3 13.5 - - + +
310A GLU* 3.5 41.2 - - + +
842C SER* 5.5 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A HIS* 3.2 34.9 + - - -
298A GLU* 2.9 60.4 + - - +
299A VAL* 3.8 1.3 - - - +
301A LYS* 1.3 72.5 - - + +
303A MET* 1.3 59.9 + - - +
304A GLY* 3.1 5.4 + - - -
253B SER* 5.1 1.9 + - - +
254B ILE* 3.4 38.5 + - + +
846C GLN* 3.8 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.9 21.5 - - + -
239A ARG* 3.4 29.4 - - - +
299A VAL* 2.9 36.4 + - + +
300A LEU* 3.5 11.2 - - + +
301A LYS 3.2 0.2 - - - -
302A ARG* 1.3 75.1 - - - +
304A GLY* 1.3 58.7 + - - +
305A MET* 3.7 20.6 - - + +
246B VAL* 3.9 7.6 - - + -
250B ASP* 3.5 40.8 - - + +
253B SER* 4.4 10.1 - - - +
254B ILE* 4.7 1.6 - - + -
----------------------------------------------------------
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