Contacts of the helix formed by residues 236 - 252 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234C PHE 3.0 3.0 + - - -
235C VAL* 1.3 72.9 - - - +
237C VAL* 1.3 66.3 + - - +
238C GLY 2.9 4.7 + - - +
239C ALA* 3.0 17.3 + - - +
240C ALA* 3.2 13.6 + - - +
282C GLN* 3.8 21.6 + - - -
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Residues in contact with VAL 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C LEU* 4.0 15.0 - - + -
234C PHE* 3.3 36.3 + - + +
235C VAL 3.4 3.3 + - - +
236C GLY* 1.3 75.1 - - - +
238C GLY* 1.3 62.2 + - - +
240C ALA* 3.5 6.2 + - - +
241C ARG* 3.1 54.2 + - + +
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Residues in contact with GLY 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C PHE* 3.3 20.0 - - - -
233C LEU* 4.0 12.2 - - - +
234C PHE 4.3 3.4 + - - -
236C GLY 2.9 1.6 + - - -
237C VAL* 1.3 79.9 - - - +
239C ALA* 1.3 61.0 + - - +
242C VAL* 3.1 25.3 + - - +
283C THR* 3.6 20.9 - - - -
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Residues in contact with ALA 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C GLY* 3.0 11.6 + - - +
238C GLY* 1.3 74.2 - - - +
240C ALA* 1.3 52.1 + - - +
242C VAL* 2.8 8.8 + - - +
243C ARG* 2.8 38.3 + - - +
282C GLN* 4.4 17.6 - - + +
283C THR* 4.1 6.4 + - - +
286C GLN* 3.7 35.5 - - + +
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C GLY 3.2 12.2 + - - +
237C VAL* 4.0 6.5 - - - +
239C ALA* 1.3 78.5 - - - +
241C ARG* 1.3 57.2 + - - +
243C ARG* 3.3 17.3 - - - +
244C ASP* 2.9 28.2 + - - +
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Residues in contact with ARG 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C TYR* 3.8 34.7 + - + -
229C ASP* 3.4 18.2 + - - +
230C PHE* 3.4 25.6 - - + -
233C LEU* 3.4 38.6 - - - +
237C VAL* 3.1 31.7 + - + +
239C ALA 3.1 0.6 - - - -
240C ALA* 1.3 75.3 - - + +
242C VAL* 1.3 61.6 + - - +
244C ASP* 3.8 8.1 - - + +
245C LEU* 3.0 27.7 + - - +
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Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 3.6 16.8 - - + -
238C GLY 3.1 18.1 + - - +
239C ALA* 2.8 7.5 + - - +
241C ARG* 1.3 74.1 - - - +
243C ARG* 1.3 65.9 + - - +
245C LEU* 3.1 13.1 - - + +
246C PHE* 2.9 45.9 - - + -
283C THR* 3.9 23.3 - - + +
286C GLN* 4.0 4.3 - - + -
287C LEU* 3.8 28.0 - - + +
290C GLU* 4.0 5.8 - - + -
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Residues in contact with ARG 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C ALA* 2.8 19.3 + - - +
240C ALA* 3.3 17.4 - - - +
242C VAL* 1.3 78.0 - - - +
244C ASP* 1.3 65.4 + - - +
246C PHE* 3.1 3.3 + - - +
247C ALA* 3.0 22.1 + - - +
286C GLN* 3.0 43.0 + - - +
290C GLU* 3.7 13.9 + - - +
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Residues in contact with ASP 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C TYR* 3.2 49.3 + - - +
240C ALA 2.9 14.4 + - - +
241C ARG* 3.8 7.0 - - - +
243C ARG* 1.3 77.5 - - - +
245C LEU* 1.3 66.7 + - - +
247C ALA* 3.0 10.1 + - - +
248C GLN* 2.9 30.8 + - - +
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Residues in contact with LEU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C TYR* 5.0 6.5 - - + -
223C PHE* 4.7 13.9 - - + -
225C ILE* 3.0 44.4 - - + -
230C PHE* 5.8 4.3 - - + -
241C ARG 3.0 14.5 + - - +
242C VAL* 3.1 13.9 - - + +
244C ASP* 1.3 83.5 + - - +
246C PHE* 1.3 81.7 + - + +
248C GLN* 3.2 6.3 + - - +
249C ALA* 2.9 24.7 + - - +
257C VAL* 3.7 27.8 - - + -
259C ILE* 4.7 10.1 - - + -
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Residues in contact with PHE 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C VAL* 2.9 43.5 - - + -
243C ARG 3.1 3.9 + - - +
245C LEU* 1.3 97.6 - - + +
247C ALA* 1.3 65.0 + - - +
249C ALA* 3.4 10.6 - - + +
250C LYS* 3.1 36.8 + - + +
257C VAL* 5.8 1.8 - - + -
259C ILE* 5.3 4.3 - - + -
287C LEU* 4.6 10.3 - - + -
290C GLU* 3.5 41.7 - - + +
291C MET* 3.2 36.8 - - + -
294C PHE* 4.2 16.4 - + + -
300C ILE* 6.0 2.7 - - + -
302C VAL* 4.4 8.3 - - + -
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Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C ARG 3.0 13.2 + - - +
244C ASP* 3.0 13.0 + - - +
246C PHE* 1.3 76.3 - - - +
248C GLN* 1.3 63.7 + - + +
250C LYS* 3.7 6.4 + - - +
251C ALA* 3.5 20.1 + - - +
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Residues in contact with GLN 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C TYR* 3.4 34.6 + - + +
223C PHE* 3.6 19.1 - - + -
244C ASP* 2.9 31.4 + - - +
245C LEU* 3.3 8.3 - - - +
247C ALA* 1.3 77.3 - - + +
249C ALA* 1.3 68.3 + - - +
251C ALA* 3.1 15.9 + - - +
252C HIS* 3.2 40.5 + - - -
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PHE* 4.2 6.7 - - - -
245C LEU 2.9 13.4 + - - +
246C PHE* 3.2 17.2 + - + +
248C GLN* 1.3 77.2 - - - +
250C LYS* 1.3 58.2 + - - +
252C HIS 3.2 0.3 + - - -
253C ALA* 2.9 23.7 + - - +
255C CYS* 3.0 23.4 - - - -
257C VAL* 3.8 26.0 - - + -
300C ILE* 4.2 14.1 - - + -
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C PHE* 3.1 22.7 + - - +
247C ALA* 4.1 6.5 - - - +
248C GLN 3.2 0.2 - - - -
249C ALA* 1.3 71.6 - - + +
251C ALA* 1.3 61.9 + - - +
252C HIS 3.1 5.9 + - - -
253C ALA* 3.3 15.0 + - - +
290C GLU* 6.0 1.6 - - - -
293C GLY 3.9 19.2 + - - -
294C PHE* 3.7 24.0 - - - +
295C ASP 5.0 2.5 - - - +
298C GLU* 4.7 10.3 - - + +
300C ILE* 3.7 20.2 - - + -
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Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C ALA 3.5 11.0 + - - +
248C GLN* 3.1 13.7 + - - +
250C LYS* 1.3 79.5 - - - +
252C HIS* 1.3 75.0 + - + +
253C ALA 5.1 0.9 - - - +
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Residues in contact with HIS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C PRO* 4.7 14.6 - - + +
221C PRO* 3.6 22.4 - - + +
223C PHE* 3.9 20.3 - + + -
248C GLN* 3.2 41.5 + - - +
249C ALA 3.2 5.4 + - - +
250C LYS 3.1 0.2 - - - -
251C ALA* 1.3 92.9 + - + +
253C ALA* 1.3 62.3 + - - +
254C PRO* 2.9 16.5 - - - +
255C CYS* 4.1 4.5 - - - -
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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