Contacts of the helix formed by residues 232 - 246 (chain A) in PDB entry 3EIJ
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 SER 232 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LYS* 5.5 1.0 - - - +
227A CYS* 4.0 4.0 - - - -
228A GLY* 4.8 2.0 - - - +
231A MET* 1.3 74.3 - - - +
233A THR* 1.3 64.6 + - - +
234A THR* 3.5 12.3 + - - -
235A ASP* 3.0 30.5 + - - +
236A VAL* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A CYS* 3.7 21.9 - - - -
232A SER* 1.3 71.3 - - - +
234A THR* 1.3 64.5 + - - +
236A VAL* 3.3 2.6 + - - +
237A GLU* 2.8 30.2 + - - +
272A GLY 4.6 4.9 - - - +
273A ILE* 3.8 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 3.2 10.4 + - - -
233A THR* 1.3 78.8 + - - +
235A ASP* 1.3 66.4 + - - +
237A GLU* 3.3 9.4 + - + +
238A LYS* 2.9 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU* 5.4 3.8 - - - +
197A LYS* 3.8 31.9 + - - +
198A SER* 3.4 20.9 + - - -
231A MET* 2.9 33.8 - - + +
232A SER* 3.0 27.9 + - - +
234A THR* 1.3 78.3 - - - +
236A VAL* 1.3 59.4 + - - +
238A LYS* 3.3 8.1 + - - +
239A SER* 2.9 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO* 4.9 3.8 - - + -
223A LEU* 5.2 2.0 - - + +
227A CYS* 3.8 22.4 - - + -
231A MET* 3.8 22.7 - - + -
232A SER 3.2 15.1 + - - +
233A THR 3.6 6.5 - - - +
234A THR 3.2 0.2 - - - -
235A ASP* 1.3 75.9 - - - +
237A GLU* 1.3 62.7 + - - +
239A SER* 3.2 11.1 + - - -
240A PHE* 3.1 45.4 + - + -
273A ILE* 3.8 33.2 - - + +
274A LEU* 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR 2.8 17.3 + - - +
234A THR* 3.7 9.3 - - + +
236A VAL* 1.3 76.7 - - - +
238A LYS* 1.3 62.8 + - + +
240A PHE* 3.2 3.5 + - - +
241A ASP* 3.0 32.5 + - - +
274A LEU* 4.1 14.1 - - + +
278A TYR* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU* 6.0 4.6 - - - +
198A SER* 3.9 19.3 - - - +
234A THR* 2.9 41.3 + - + +
235A ASP* 3.6 11.4 + - - +
237A GLU* 1.3 76.5 - - + +
239A SER* 1.3 61.7 + - - +
241A ASP* 3.3 12.0 + - - +
242A LYS* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 2.7 21.9 + - - -
201A PRO* 3.2 33.5 - - - +
202A VAL* 3.6 19.7 - - - +
235A ASP 2.9 14.1 + - - -
236A VAL 3.2 9.9 - - - -
238A LYS* 1.3 76.9 - - - +
240A PHE* 1.3 62.1 + - - +
242A LYS 3.2 2.3 + - - -
243A LEU* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO* 5.6 0.9 - - + -
205A VAL* 5.4 0.2 - - + -
223A LEU* 4.2 23.1 - - + -
236A VAL* 3.1 40.7 + - + +
237A GLU 3.2 4.0 + - - +
239A SER* 1.3 80.4 - - - +
241A ASP* 1.3 65.7 + - - +
243A LEU* 3.5 23.8 - - + +
244A LEU* 3.0 29.5 + - + +
261A VAL* 4.8 1.8 - - + -
264A PHE* 3.8 25.4 - + + -
265A ILE* 3.6 39.0 - - + -
268A ALA* 3.8 14.6 - - + -
273A ILE* 5.1 0.2 - - + -
274A LEU* 3.7 13.7 - - + -
278A TYR* 3.3 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLU* 3.0 24.8 + - - +
238A LYS* 3.4 14.8 - - - +
239A SER 3.2 0.2 - - - -
240A PHE* 1.3 77.4 - - - +
242A LYS* 1.3 61.3 + - - +
244A LEU 3.4 1.9 + - - -
245A LYS* 3.2 26.7 + - - +
278A TYR* 2.6 34.8 + - - -
282A TYR* 3.5 26.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
161A GLU* 3.8 19.6 + - - -
202A VAL* 4.3 26.6 - - + +
238A LYS 3.1 10.1 + - - +
239A SER 3.8 5.6 - - - +
241A ASP* 1.3 77.5 - - - +
243A LEU* 1.3 58.3 + - - +
245A LYS* 3.0 11.9 + - + -
246A ASP* 2.7 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO* 4.6 3.4 - - + +
202A VAL* 3.8 40.8 - - + +
205A VAL* 3.8 39.0 - - + -
206A SER* 5.2 1.1 - - - +
239A SER* 2.9 16.5 + - - +
240A PHE* 3.5 33.0 - - + +
241A ASP 3.3 0.2 - - - -
242A LYS* 1.3 77.6 - - - +
244A LEU* 1.3 59.5 + - - +
246A ASP* 3.9 2.5 - - + -
247A LEU* 3.4 27.9 + - - +
250A LEU* 4.0 18.4 - - + +
261A VAL* 4.8 13.9 - - + -
264A PHE* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE 3.0 19.3 + - - +
241A ASP 3.8 0.4 - - - +
242A LYS 3.1 0.2 - - - -
243A LEU* 1.3 75.9 - - - +
245A LYS* 1.3 62.3 + - - +
247A LEU* 3.4 16.0 - - + +
248A PRO* 4.5 2.1 - - - +
261A VAL* 4.2 7.6 - - + -
265A ILE* 4.1 15.5 - - + -
278A TYR* 3.6 20.4 - - + +
282A TYR* 3.5 38.8 - - + +
288A CYS* 4.9 1.6 - - - -
291A ALA* 4.1 29.4 - - + +
294A ALA* 3.9 27.8 - - + -
295A LEU* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASP* 3.2 18.8 + - - +
242A LYS* 3.0 16.0 + - + +
244A LEU* 1.3 75.5 - - - +
246A ASP* 1.3 64.1 + - - +
247A LEU 3.1 8.1 + - - -
248A PRO* 3.5 12.1 - - - +
282A TYR* 4.7 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 4.9 4.7 - - + +
242A LYS* 2.7 58.1 + - - +
243A LEU* 3.9 5.4 - - + +
244A LEU 3.5 0.2 - - - -
245A LYS* 1.3 77.3 - - - +
247A LEU* 1.3 56.8 + - - +
248A PRO* 3.5 2.0 - - - -
249A GLU* 3.2 26.9 + - + +
250A LEU* 3.0 37.7 + - + +
----------------------------------------------------------
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