Contacts of the helix formed by residues 236 - 252 (chain E) in PDB entry 2CEA
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 GLY 236 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E PHE 2.9 3.4 + - - -
235E VAL* 1.3 71.9 - - - +
237E VAL* 1.3 64.6 + - - +
238E GLY 3.2 3.3 + - - -
239E ALA* 3.3 8.5 + - - +
240E ALA* 3.2 21.2 + - - +
243E ARG* 5.1 0.9 + - - -
279E GLU* 3.0 8.7 + - - -
282E GLN* 3.4 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E LEU* 3.8 13.9 - - + -
234E PHE* 3.1 41.4 + - + +
235E VAL 3.3 3.5 + - - +
236E GLY* 1.3 76.1 - - - +
238E GLY* 1.3 57.8 + - - +
240E ALA* 3.2 8.9 + - + +
241E ARG* 2.9 62.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E PHE* 4.3 7.5 - - - -
233E LEU* 3.8 17.6 - - - +
236E GLY 3.2 1.0 - - - -
237E VAL* 1.3 74.9 - - - +
239E ALA* 1.3 68.1 + - - +
241E ARG* 2.8 16.4 + - - +
242E VAL* 2.9 15.2 + - - +
279E GLU* 3.7 8.6 + - - -
283E THR* 3.7 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E GLY* 3.3 10.7 + - - +
238E GLY* 1.3 72.4 - - - +
240E ALA* 1.3 66.3 + - - +
242E VAL* 2.8 15.9 + - - +
243E ARG* 2.8 30.3 + - - +
282E GLN* 3.7 21.8 + - + +
283E THR* 3.9 8.8 + - - +
286E GLN* 3.5 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E GLY 3.2 9.5 + - - +
237E VAL* 3.3 11.7 - - - +
239E ALA* 1.3 78.6 - - - +
241E ARG* 1.3 58.4 + - + +
243E ARG* 3.2 27.8 + - - +
244E ASP* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E ILE* 5.9 1.0 - - - +
229E ASP* 4.9 10.9 + - - +
230E PHE* 4.2 23.9 - - + -
233E LEU* 4.3 20.4 - - - +
237E VAL* 2.9 39.5 + - + +
238E GLY* 2.8 9.6 + - - +
240E ALA* 1.3 76.0 - - + +
242E VAL* 1.3 63.8 + - - +
244E ASP* 4.0 4.6 - - - +
245E LEU* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E PHE* 3.8 21.8 - - + -
238E GLY 2.9 11.6 + - - +
239E ALA 2.8 7.7 + - - +
241E ARG* 1.3 76.9 - - - +
243E ARG* 1.3 65.8 + - - +
245E LEU* 3.2 10.7 + - + +
246E PHE* 3.2 31.9 + - + +
283E THR* 4.2 18.4 - - + +
286E GLN* 3.7 12.1 - - + -
287E LEU* 3.8 18.2 - - + -
290E GLU* 3.4 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E GLY 5.1 1.0 + - - -
239E ALA* 2.8 26.6 + - - +
240E ALA* 3.3 33.5 - - - +
242E VAL* 1.3 78.1 - - - +
244E ASP* 1.3 56.4 + - - +
246E PHE 3.5 0.3 + - - -
247E ALA* 3.0 23.8 + - - +
286E GLN* 2.5 45.6 - - - +
290E GLU* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E ALA 3.0 15.1 + - - +
241E ARG* 4.4 4.3 - - - +
243E ARG* 1.3 71.7 - - - +
245E LEU* 1.3 71.4 + - - +
246E PHE 3.0 1.6 - - - -
247E ALA* 2.9 9.6 + - - +
248E GLN* 2.9 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E PHE* 4.3 22.0 - - + -
225E ILE* 3.7 37.9 - - + -
230E PHE* 5.8 2.5 - - + -
241E ARG 3.2 17.7 + - - +
242E VAL* 3.2 10.4 + - + +
244E ASP* 1.3 81.0 + - - +
246E PHE* 1.3 71.8 + - + +
248E GLN* 3.4 5.5 + - + +
249E ALA* 3.0 23.2 + - - +
257E VAL* 3.5 32.1 - - + -
259E ILE* 4.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E VAL* 3.2 22.1 + - + +
244E ASP 3.0 0.4 - - - -
245E LEU* 1.3 97.9 - - + +
247E ALA* 1.3 67.1 + - - +
248E GLN 3.2 0.2 - - - -
249E ALA* 3.3 11.4 - - + +
250E LYS* 3.0 36.7 + - + +
257E VAL* 5.0 6.5 - - + -
259E ILE* 5.3 5.8 - - + -
287E LEU* 5.0 6.3 - - + -
290E GLU* 3.4 45.8 - - + +
291E MET* 3.1 39.3 - - + -
294E PHE* 3.7 27.6 - + + -
300E ILE* 5.7 1.3 - - + -
302E VAL* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E ARG 3.0 15.8 + - - +
244E ASP* 2.9 19.0 + - - +
246E PHE* 1.3 78.3 - - - +
248E GLN* 1.3 66.5 + - + +
250E LYS* 3.2 11.2 + - - +
251E ALA* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 248 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E PRO* 5.9 0.9 - - - +
223E PHE* 4.0 20.4 - - + -
244E ASP* 2.9 38.6 + - - +
245E LEU* 3.6 8.3 - - + +
247E ALA* 1.3 77.4 - - - +
249E ALA* 1.3 68.3 + - - +
251E ALA* 2.9 17.6 + - - +
252E HIS* 3.0 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E PHE* 4.3 6.9 - - - -
245E LEU 3.0 15.2 + - - +
246E PHE* 3.1 18.8 + - + +
248E GLN* 1.3 77.8 - - - +
250E LYS* 1.3 62.8 + - + +
252E HIS 3.2 0.3 + - - -
253E ALA* 3.1 24.4 + - - +
255E CYS* 3.6 16.2 - - - -
257E VAL* 3.8 25.6 - - + -
300E ILE* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E PHE* 3.0 29.0 + - - +
247E ALA* 3.5 9.2 - - - +
249E ALA* 1.3 77.6 - - + +
251E ALA* 1.3 63.5 + - - +
252E HIS 3.1 1.0 + - - -
253E ALA* 3.4 11.6 + - - +
290E GLU* 4.9 9.5 + - - +
293E GLY* 4.0 18.2 + - - -
294E PHE* 3.8 23.5 - - + +
298E GLU* 5.1 8.0 - - + +
300E ILE* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E ALA 3.1 12.0 + - - +
248E GLN* 2.9 18.3 + - - +
250E LYS* 1.3 78.4 - - - +
252E HIS* 1.3 71.5 + - + +
253E ALA 3.6 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 252 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E PRO* 3.9 27.5 - - + +
221E PRO* 3.6 19.6 - - + +
223E PHE* 3.7 22.5 - + + -
248E GLN* 3.0 38.4 + - - +
249E ALA 3.6 2.0 - - - +
251E ALA* 1.3 89.4 - - + +
253E ALA* 1.3 64.9 + - - +
254E PRO 3.1 12.0 - - - +
255E CYS* 3.8 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