Contacts of the helix formed by residues 236 - 252 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F PHE 3.1 2.6 + - - -
235F VAL* 1.3 76.0 - - - +
237F VAL* 1.3 63.4 + - - +
238F GLY 3.0 4.8 + - - +
239F ALA* 3.2 11.5 + - - +
240F ALA* 3.1 22.6 + - - +
243F ARG* 4.8 1.2 + - - -
279F GLU* 5.0 1.6 + - - -
282F GLN* 4.5 12.4 + - - -
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Residues in contact with VAL 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D PHE* 5.9 6.5 - - + -
233F LEU* 3.8 7.0 - - + -
234F PHE* 3.4 38.5 + - + +
235F VAL 3.3 4.0 + - - +
236F GLY* 1.3 75.9 - - - +
238F GLY* 1.3 52.6 + - - +
240F ALA* 3.6 6.8 + - + +
241F ARG* 2.8 70.9 + - + +
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Residues in contact with GLY 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F PHE* 4.4 1.1 - - - -
233F LEU* 2.9 32.0 - - - +
234F PHE 4.4 0.4 + - - -
236F GLY 3.0 1.4 + - - -
237F VAL* 1.3 74.3 - - - +
239F ALA* 1.3 57.9 + - - +
241F ARG* 3.3 5.0 + - - +
242F VAL* 2.7 32.9 + - - +
279F GLU* 5.1 0.8 + - - -
283F THR* 3.5 21.3 - - - +
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Residues in contact with ALA 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F GLY* 3.2 12.1 + - - +
238F GLY* 1.3 74.8 - - - +
240F ALA* 1.3 58.0 + - - +
242F VAL* 3.0 13.2 + - - +
243F ARG* 3.0 32.6 + - - +
282F GLN* 4.2 17.0 - - + +
283F THR* 3.9 5.9 + - - +
286F GLN* 3.4 28.6 - - + +
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Residues in contact with ALA 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E ARG* 5.7 2.7 - - - +
236F GLY 3.1 14.5 + - - +
237F VAL* 3.9 7.4 - - - +
239F ALA* 1.3 77.0 - - - +
241F ARG* 1.3 57.9 + - + +
243F ARG* 2.9 30.6 + - - +
244F ASP* 3.0 27.4 + - - +
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Residues in contact with ARG 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F TYR* 3.1 36.5 + - + +
229F ASP* 2.9 32.5 + - - +
230F PHE* 3.7 27.8 - - + -
233F LEU* 2.8 25.4 - - - +
237F VAL* 2.8 41.4 + - + +
238F GLY 3.6 4.5 - - - +
239F ALA 3.2 0.2 - - - -
240F ALA* 1.3 73.9 - - - +
242F VAL* 1.3 61.4 + - - +
244F ASP* 3.5 6.6 - - - +
245F LEU* 2.8 30.7 + - - +
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Residues in contact with VAL 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F PHE* 5.2 6.1 - - + -
238F GLY 2.7 26.6 + - - +
239F ALA* 3.2 9.6 - - - +
241F ARG* 1.3 77.4 - - + +
243F ARG* 1.3 61.1 + - - +
245F LEU* 3.4 6.0 + - + +
246F PHE* 3.0 44.3 + - + -
283F THR* 3.7 26.0 - - + +
286F GLN* 3.7 7.6 - - + -
287F LEU* 3.7 33.4 - - + +
290F GLU* 4.1 1.6 - - + -
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Residues in contact with ARG 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E ARG* 3.0 58.3 + - - +
268E HIS* 5.2 6.5 - - - +
280E ARG* 3.5 24.7 - - - +
311E ILE* 4.6 9.3 - - - +
236F GLY 4.8 1.0 + - - -
239F ALA* 3.0 17.4 + - - +
240F ALA* 2.9 44.3 + - - +
242F VAL* 1.3 73.9 - - - +
244F ASP* 1.3 63.8 + - - +
246F PHE* 3.4 2.9 + - - +
247F ALA* 3.0 24.1 + - - +
286F GLN* 2.8 32.5 + - - +
290F GLU* 3.1 17.1 - - - +
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Residues in contact with ASP 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F TYR* 4.9 18.2 - - - +
240F ALA 3.0 19.4 + - - +
241F ARG* 3.5 9.2 - - - +
243F ARG* 1.3 76.3 - - - +
245F LEU* 1.3 64.4 + - - +
247F ALA* 3.2 9.0 + - - +
248F GLN* 3.1 36.6 + - - +
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Residues in contact with LEU 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F TYR* 2.4 52.0 - - + +
223F PHE* 5.6 3.8 - - + -
225F ILE* 2.9 42.8 - - + -
230F PHE* 5.5 1.6 - - + -
241F ARG 2.8 16.0 + - - +
242F VAL* 3.6 8.7 - - + +
244F ASP* 1.3 81.5 + - - +
246F PHE* 1.3 65.0 + - + +
248F GLN* 3.3 6.2 + - - +
249F ALA* 3.0 24.8 + - - +
257F VAL* 3.4 22.8 - - + +
259F ILE* 5.3 5.2 - - + -
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Residues in contact with PHE 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F VAL* 3.0 38.3 + - + +
243F ARG 3.9 1.1 - - - +
245F LEU* 1.3 86.0 - - + +
247F ALA* 1.3 66.3 + - - +
249F ALA* 3.0 12.7 + - + +
250F LYS* 2.9 31.1 + - + +
257F VAL* 5.7 3.6 - - + -
259F ILE* 5.9 4.0 - - + -
287F LEU* 4.6 8.5 - - + -
290F GLU* 3.3 50.3 - - + +
291F MET* 4.0 13.2 - - + -
294F PHE* 3.8 35.9 - + + -
300F ILE* 5.9 2.5 - - + -
302F VAL* 4.3 20.6 - - + -
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Residues in contact with ALA 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E VAL* 5.5 1.6 - - + -
232E GLU* 3.9 29.8 - - - +
243F ARG 3.0 14.7 + - - +
244F ASP* 3.2 13.2 + - - +
246F PHE* 1.3 76.5 - - - +
248F GLN* 1.3 65.6 + - + +
250F LYS* 3.6 6.6 + - - +
251F ALA* 3.2 20.3 + - - +
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Residues in contact with GLN 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F TYR* 4.4 16.2 - - - +
223F PHE* 4.8 10.1 - - + -
244F ASP* 3.1 25.6 + - - +
245F LEU* 3.6 7.6 - - - +
247F ALA* 1.3 79.1 - - - +
249F ALA* 1.3 60.9 + - - +
251F ALA* 2.8 22.8 + - - +
252F HIS* 2.9 48.6 + - + -
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Residues in contact with ALA 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F PHE* 5.1 4.7 - - + -
245F LEU 3.0 14.7 + - - +
246F PHE* 3.2 17.9 - - + +
248F GLN* 1.3 77.6 - - - +
250F LYS* 1.3 60.3 + - - +
253F ALA 3.2 17.5 + - - -
255F CYS* 3.3 20.1 - - - -
257F VAL* 3.6 28.9 - - + -
300F ILE* 3.5 17.2 - - + +
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Residues in contact with LYS 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F PHE* 2.9 18.6 + - + +
247F ALA* 3.9 6.3 - - - +
249F ALA* 1.3 78.0 - - - +
251F ALA* 1.3 61.6 + - - +
252F HIS 3.5 0.2 + - - -
253F ALA* 3.7 11.6 + - - +
293F GLY 4.7 3.4 - - - -
294F PHE* 2.5 49.4 - - + +
295F ASP* 3.5 9.0 + - - +
298F GLU* 5.1 11.0 - - + +
300F ILE* 3.6 16.9 - - + +
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Residues in contact with ALA 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E GLU* 6.0 0.7 - - - +
247F ALA 3.2 14.3 + - - +
248F GLN* 2.8 23.5 + - - +
250F LYS* 1.3 78.9 - - - +
252F HIS* 1.3 68.3 + - + +
253F ALA 5.2 0.7 - - - +
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Residues in contact with HIS 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F PRO* 4.9 11.9 - - + +
221F PRO* 3.8 18.3 - - + +
223F PHE* 3.5 38.3 - + + -
248F GLN* 2.9 44.5 + - + +
249F ALA 3.8 1.8 - - - +
251F ALA* 1.3 86.3 + - + +
253F ALA* 1.3 66.7 + - - +
254F PRO 3.1 11.5 - - - +
255F CYS* 3.8 1.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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