Contacts of the helix formed by residues 231 - 243 (chain A) in PDB entry 1ZJA
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 ASN 231 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ASP* 4.2 6.9 + - - -
206A SER* 2.9 13.7 + - - +
207A LYS 5.2 2.0 + - - -
209A PRO* 5.3 4.4 - - - +
230A PRO* 1.3 95.3 - - - +
232A LEU* 1.3 65.8 + - - +
233A HIS 3.5 1.8 - - - -
234A ARG* 3.3 26.4 + - - +
235A TYR* 3.1 53.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL 3.5 22.4 - - - +
203A ALA 3.3 24.5 - - - +
205A TYR* 4.1 18.4 - - + +
206A SER* 3.3 12.4 - - - +
227A THR 3.7 15.3 - - - +
229A GLY 3.4 13.4 + - - +
230A PRO 3.5 1.4 + - - -
231A ASN* 1.3 76.5 - - - +
233A HIS* 1.3 71.6 + - + +
235A TYR* 3.2 7.0 + - - +
236A LEU* 3.0 37.7 + - + +
266A PHE* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN 3.5 0.4 - - - -
232A LEU* 1.3 83.1 - - + +
234A ARG* 1.3 59.7 + - - +
236A LEU* 3.9 2.9 - - + +
237A GLN* 2.9 40.5 + - - +
262A GLN* 5.8 0.6 + - - +
265A LEU* 3.4 41.5 + - + +
266A PHE* 3.7 40.2 - + - -
271A ARG* 3.6 14.6 - - - +
273A GLU* 2.5 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 6.0 1.6 - - - +
230A PRO 5.6 0.2 - - - +
231A ASN* 3.3 35.3 + - - +
233A HIS* 1.3 79.5 - - - +
235A TYR* 1.3 69.9 + - + +
237A GLN* 3.8 9.0 - - - +
238A GLU* 2.9 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TRP* 3.3 56.9 - + + -
174A ASP* 2.5 36.8 + - - +
179A ARG* 3.7 23.9 + - - -
183A TYR* 3.9 3.7 + - - -
205A TYR* 4.9 4.0 - - + -
206A SER* 4.2 16.6 - - - -
231A ASN* 3.1 41.2 + - + +
232A LEU* 3.6 6.3 - - - +
234A ARG* 1.3 88.9 - - + +
236A LEU* 1.3 64.4 + - + +
238A GLU* 3.3 7.3 + - - +
239A MET* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TRP* 5.6 0.4 - - + -
202A VAL* 3.8 15.7 - - + +
205A TYR* 3.8 33.9 - - + -
232A LEU* 3.0 20.6 + - + +
233A HIS* 3.9 2.7 - - - +
234A ARG 3.4 0.2 - - - -
235A TYR* 1.3 76.8 - - - +
237A GLN* 1.3 62.9 + - - +
239A MET* 3.2 21.5 + - + +
240A HIS* 3.0 22.3 + - - +
266A PHE* 3.7 32.3 - - + -
272A LYS 4.4 0.3 - - - +
273A GLU* 3.5 39.4 - - + +
274A LEU* 4.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A HIS* 2.9 26.9 + - - +
234A ARG* 3.8 7.0 - - - +
236A LEU* 1.3 77.1 - - - +
238A GLU* 1.3 58.5 + - - +
240A HIS* 3.3 2.9 + - - +
241A GLU* 3.0 27.0 + - - +
271A ARG* 3.4 34.0 + - - +
272A LYS* 3.9 8.4 - - + +
273A GLU* 3.1 30.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 2.7 37.9 + - - +
180A GLU* 5.3 1.5 - - - +
183A TYR* 2.5 32.6 + - + +
234A ARG* 2.9 18.5 + - + +
235A TYR* 3.6 7.0 - - - +
236A LEU 3.2 0.2 - - - -
237A GLN* 1.3 75.4 - - - +
239A MET* 1.3 65.6 + - - +
241A GLU* 3.1 12.6 + - - +
242A LYS* 2.9 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 4.3 2.7 - - - -
173A TRP* 4.1 18.2 - - + -
183A TYR* 3.6 25.2 + - + -
186A LEU* 3.7 16.4 - - + -
199A PHE* 3.7 43.1 - - + -
205A TYR* 4.7 2.7 - - + -
235A TYR 2.9 13.5 + - - +
236A LEU* 3.2 32.7 + - + +
238A GLU* 1.3 75.8 - - - +
240A HIS* 1.3 58.7 + - - +
243A VAL* 3.0 28.9 + - - +
244A PHE* 3.5 16.3 + - + -
274A LEU* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU 3.0 10.3 + - - +
237A GLN 3.6 4.3 - - - +
238A GLU 3.1 0.2 - - - -
239A MET* 1.3 76.4 - - - +
241A GLU* 1.3 64.4 + - - +
244A PHE* 3.3 25.2 + - + +
245A ASP* 2.8 55.1 + - + +
272A LYS* 3.1 54.6 - - + +
273A GLU 3.1 23.5 + - - +
275A ASP* 5.5 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLN 3.0 15.9 + - - +
238A GLU* 3.1 16.7 + - - +
240A HIS* 1.3 80.9 - - - +
242A LYS* 1.3 86.8 + - - +
245A ASP* 3.9 10.8 - - - +
246A HIS* 3.1 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLU* 3.4 30.1 - - - +
183A TYR* 3.8 22.0 - - + -
187A ARG* 3.0 31.5 + - - +
238A GLU* 2.9 32.8 + - + +
241A GLU* 1.3 103.0 + - - +
243A VAL* 1.3 60.3 + - + +
246A HIS* 3.2 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 3.5 47.3 - - + +
186A LEU* 3.9 14.8 - - + -
187A ARG* 4.2 8.1 - - + +
190A LEU* 3.5 29.6 - - + -
239A MET 3.0 13.4 + - - +
241A GLU 3.4 0.4 - - - -
242A LYS* 1.3 84.6 - - - +
244A PHE* 1.3 78.3 + - + +
245A ASP 3.2 1.3 - - - -
246A HIS* 2.9 16.3 + - - +
247A TYR* 3.2 19.6 - - + -
----------------------------------------------------------
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