Contacts of the helix formed by residues 224 - 234 (chain A) in PDB entry 2BZN
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 224 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A SER* 1.3 81.1 - - - +
225A PRO* 1.4 74.4 - - + +
226A GLY* 3.1 2.0 - - - -
227A ASP* 3.0 44.1 + - - +
228A VAL* 3.5 7.3 + - - +
230A LYS* 6.2 0.2 - - - -
244A MET* 3.6 10.0 - - - +
189C ARG 5.3 0.4 - - - -
190C LYS* 3.2 51.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A CYS* 1.4 88.1 - - + +
226A GLY* 1.3 61.3 + - - +
228A VAL* 3.1 14.3 + - + +
229A ALA* 3.0 22.2 + - - +
244A MET* 3.8 6.3 - - + -
307A ASP* 3.5 29.2 - - - +
308A ILE* 4.0 33.9 - - + +
311A GLY* 4.4 0.9 - - - -
312A ILE* 4.2 3.6 - - - +
190C LYS 3.8 4.5 - - - +
191C LYS* 3.3 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A CYS* 3.1 2.0 - - - -
225A PRO* 1.3 78.2 - - - +
227A ASP* 1.3 56.9 + - - +
229A ALA* 3.4 2.4 + - - +
230A LYS* 3.0 38.0 + - - +
189C ARG 4.4 0.9 - - - -
190C LYS 2.8 21.8 + - - -
191C LYS 3.6 1.2 + - - -
192C THR 3.8 4.5 - - - -
193C GLY* 3.6 22.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.3 34.8 - - + +
13A LYS* 5.7 0.2 - - - -
221A GLY 3.8 3.1 - - - +
222A CYS* 3.7 19.6 - - - -
223A SER* 2.9 33.6 + - - -
224A CYS* 3.0 23.6 + - - +
226A GLY* 1.3 73.3 - - - +
228A VAL* 1.3 65.9 + - - +
230A LYS* 3.3 15.7 + - - +
231A ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 4.3 8.1 - - + -
222A CYS* 3.9 9.9 - - + -
224A CYS 3.8 12.8 - - - +
225A PRO* 3.1 12.9 + - + +
227A ASP* 1.3 77.6 - - - +
229A ALA* 1.3 60.5 + - - +
231A ALA* 3.2 4.2 + - - +
232A PHE* 3.1 46.8 + - + -
239A VAL* 4.0 16.2 - - + -
241A LEU* 4.1 25.4 - - + -
244A MET* 4.3 8.1 - - + -
308A ILE* 4.5 6.5 - - + -
312A ILE* 3.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.7 4.4 - - + +
225A PRO 3.0 12.2 + - - +
226A GLY 3.7 7.9 - - - +
228A VAL* 1.3 77.4 - - - +
230A LYS* 1.3 51.3 + - - +
232A PHE* 3.3 10.5 + - - +
233A GLY* 2.7 32.6 + - - -
312A ILE* 4.3 10.7 - - + +
315A THR* 3.4 35.9 - - + +
327A LEU* 3.9 7.4 - - + +
192C THR 3.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 2.8 48.9 + - + +
13A LYS* 4.5 4.0 - - - +
15A VAL* 2.9 30.0 + - + -
16A LEU* 4.8 4.6 - - - +
17A LEU* 3.7 21.1 - - + -
199A LEU* 3.8 4.8 - - + +
226A GLY 3.0 19.8 + - - +
227A ASP* 3.6 12.7 + - - +
228A VAL 3.3 0.2 - - - -
229A ALA* 1.3 78.1 - - - +
231A ALA* 1.3 57.9 + - - +
233A GLY 4.3 0.2 - - - +
234A ALA* 2.8 30.3 + - - +
333A PHE* 3.5 12.7 - - + -
189C ARG 5.0 3.6 + - - -
193C GLY* 3.9 24.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.8 19.4 - - + -
199A LEU* 4.8 0.2 - - - -
202A VAL* 3.7 4.1 - - + +
218A SER* 3.8 18.4 - - - +
222A CYS* 4.8 0.2 - - - -
227A ASP 3.0 14.4 + - - +
228A VAL* 3.2 8.7 + - - +
230A LYS* 1.3 75.6 - - - +
232A PHE* 1.3 61.5 + - - +
234A ALA* 3.3 12.5 + - - +
235A GLY 3.4 0.7 + - - -
236A ALA* 3.1 24.0 + - - +
239A VAL* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 6.1 1.3 - - - -
48A VAL* 6.2 0.2 - - + -
49A PRO* 3.5 31.0 - - + -
50A ILE* 3.9 13.9 - - + -
228A VAL* 3.1 40.5 + - + -
229A ALA* 3.6 9.4 - - - +
231A ALA* 1.3 75.2 - - - +
233A GLY* 1.3 58.1 + - - +
235A GLY* 2.9 21.7 + - - -
236A ALA 3.3 19.1 + - - +
237A ASP 3.5 20.6 - - - -
239A VAL* 3.7 19.7 - - + -
312A ILE* 4.2 11.2 - - + -
324A LEU* 4.1 26.5 - - + -
327A LEU* 3.7 15.7 - - + +
328A SER* 3.6 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.9 0.9 - - - -
229A ALA 2.7 21.4 + - - -
230A LYS* 3.2 3.6 + - - -
232A PHE* 1.3 72.4 - - - +
234A ALA* 1.3 58.4 + - - +
327A LEU* 4.2 4.9 - - - +
328A SER* 3.3 21.8 - - - +
331A THR* 3.4 33.6 - - - +
333A PHE* 4.0 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 3.7 21.8 - - + -
202A VAL* 3.8 13.4 - - + +
203A MET* 3.8 34.9 - - + +
206A ALA* 4.1 3.5 - - - +
207A ASP* 5.7 0.5 - - - +
230A LYS 2.8 16.2 + - - +
231A ALA 3.6 6.5 - - - +
232A PHE 3.1 0.4 - - - -
233A GLY* 1.3 75.6 - - - +
235A GLY* 1.3 56.8 + - - +
236A ALA 3.7 0.7 - - - -
328A SER* 4.7 0.7 - - - -
333A PHE* 3.9 9.4 - - + -
----------------------------------------------------------
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