Contacts of the helix formed by residues 236 - 252 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B PHE 3.0 3.2 + - - -
235B VAL* 1.3 74.8 - - - +
237B VAL* 1.3 65.2 + - - +
238B GLY 2.7 6.0 + - - -
239B ALA* 2.8 21.8 + - - +
240B ALA* 3.2 12.3 + - - +
243B ARG* 5.6 0.2 + - - -
279B GLU* 4.6 7.1 - - - +
282B GLN* 4.7 8.9 + - - -
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 4.6 5.6 - - + -
234B PHE* 3.3 35.8 + - + +
235B VAL 3.2 5.5 + - - +
236B GLY* 1.3 75.7 - - - +
238B GLY* 1.3 59.7 + - - +
240B ALA* 3.9 7.2 - - - +
241B ARG* 2.9 60.3 + - + +
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Residues in contact with GLY 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 4.4 1.2 - - - -
233B LEU* 3.9 21.9 - - - +
234B PHE 4.4 3.4 + - - -
236B GLY 2.7 5.9 + - - +
237B VAL* 1.3 73.8 - - - +
239B ALA* 1.3 63.4 + - - +
241B ARG* 3.2 6.0 + - - +
242B VAL* 3.1 25.1 + - - +
283B THR* 3.7 23.2 - - - +
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B GLY* 2.8 15.9 + - - +
238B GLY* 1.3 70.4 - - - +
240B ALA* 1.3 59.2 + - - +
242B VAL* 3.1 2.7 + - - -
243B ARG* 2.9 33.4 + - - +
282B GLN* 4.5 14.4 - - + +
283B THR* 4.1 9.0 + - - +
286B GLN* 3.5 43.0 - - + +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLY 3.2 8.7 + - - +
237B VAL* 3.9 10.3 - - - +
239B ALA* 1.3 79.0 - - - +
241B ARG* 1.3 57.1 + - - +
243B ARG* 3.4 30.3 + - - +
244B ASP* 2.9 27.2 + - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLU* 5.1 9.9 + - - -
150B TYR* 3.5 29.6 + - + +
229B ASP* 4.0 19.8 + - - +
230B PHE* 3.8 16.1 - - + -
233B LEU* 3.9 33.5 - - - +
237B VAL* 2.9 36.5 + - + +
238B GLY 3.4 7.9 - - - +
239B ALA 3.1 0.4 - - - -
240B ALA* 1.3 75.1 - - - +
242B VAL* 1.3 60.7 + - - +
244B ASP* 3.2 4.0 + - - +
245B LEU* 2.8 30.4 + - - +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 4.4 16.6 - - + -
238B GLY 3.1 15.1 + - - +
239B ALA* 3.1 6.6 + - - +
241B ARG* 1.3 74.8 - - - +
243B ARG* 1.3 62.2 + - - +
245B LEU* 3.3 9.8 + - + +
246B PHE* 3.1 54.9 + - + -
265B VAL* 6.2 0.7 - - + -
283B THR* 4.1 24.5 - - + +
286B GLN* 4.1 3.8 - - + -
287B LEU* 3.9 27.6 - - + +
290B GLU* 3.9 7.6 - - + -
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Residues in contact with ARG 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ALA* 2.9 10.7 + - - +
240B ALA* 3.5 36.0 + - - +
242B VAL* 1.3 77.1 - - - +
244B ASP* 1.3 61.9 + - - +
246B PHE* 3.4 2.3 + - - +
247B ALA* 3.1 22.0 + - - +
286B GLN* 3.4 41.1 + - - +
290B GLU* 3.6 16.4 - - - +
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Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TYR* 3.3 36.4 + - + +
240B ALA 2.9 15.2 + - - +
241B ARG* 3.5 9.2 - - - +
243B ARG* 1.3 71.5 - - - +
245B LEU* 1.3 67.3 + - - +
247B ALA* 3.0 8.9 + - - +
248B GLN* 2.9 47.0 + - - +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TYR* 3.8 19.7 - - + -
223B PHE* 4.5 17.8 - - + -
225B ILE* 3.9 36.1 - - + -
230B PHE* 4.6 12.3 - - + -
241B ARG 2.8 20.1 + - - +
242B VAL* 3.4 9.0 - - + +
244B ASP* 1.3 75.2 - - - +
246B PHE* 1.3 70.9 + - + +
248B GLN* 3.5 3.6 + - - +
249B ALA* 3.1 20.4 + - - +
257B VAL* 3.6 30.3 - - + -
259B ILE* 5.1 7.4 - - + -
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B VAL* 3.1 42.8 + - + +
243B ARG 4.1 0.4 - - - +
244B ASP 3.1 0.2 - - - -
245B LEU* 1.3 87.8 - - + +
247B ALA* 1.3 67.7 + - - +
248B GLN 3.1 1.1 - - - -
249B ALA* 3.0 12.0 + - + +
250B LYS* 3.0 35.8 + - - +
257B VAL* 5.3 6.7 - - + -
259B ILE* 5.4 2.5 - - + -
287B LEU* 4.1 19.5 - - + -
290B GLU* 3.6 42.8 - - + +
291B MET* 4.5 3.1 - - + -
294B PHE* 4.1 24.5 - + + -
300B ILE* 5.4 2.5 - - + -
302B VAL* 3.9 30.7 - - + -
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ARG 3.1 13.7 + - - +
244B ASP* 3.0 13.8 + - - +
246B PHE* 1.3 77.1 - - - +
248B GLN* 1.3 72.5 + - - +
250B LYS* 3.3 10.3 + - - +
251B ALA* 3.2 19.2 + - - +
290B GLU* 5.3 0.2 + - - -
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Residues in contact with GLN 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TYR* 3.4 29.1 + - + +
223B PHE* 4.0 13.9 - - + -
244B ASP* 2.9 47.8 + - - +
245B LEU* 3.7 6.1 - - - +
247B ALA* 1.3 81.5 - - - +
249B ALA* 1.3 67.3 + - - +
251B ALA* 3.0 15.4 + - - +
252B HIS* 2.9 34.1 + - + +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 4.3 6.0 - - - -
245B LEU 3.1 14.5 + - - +
246B PHE* 3.0 18.7 + - + +
248B GLN* 1.3 77.9 - - - +
250B LYS* 1.3 62.1 + - - +
252B HIS 3.2 0.3 + - - -
253B ALA* 3.1 21.0 + - - +
255B CYS* 3.5 16.6 - - - -
257B VAL* 3.8 24.9 - - + -
300B ILE* 3.9 16.4 - - + -
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B PHE* 3.0 24.3 + - + +
247B ALA* 3.7 9.0 - - - +
248B GLN 3.2 0.2 - - - -
249B ALA* 1.3 76.5 - - - +
251B ALA* 1.3 60.4 + - - +
252B HIS 3.3 1.0 + - - -
253B ALA* 3.5 14.3 + - - +
290B GLU* 5.1 7.6 + - - -
293B GLY 3.6 20.4 + - - -
294B PHE* 3.9 22.6 - - - +
298B GLU* 5.5 5.7 - - + +
300B ILE* 3.9 18.4 - - + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ALA 3.2 11.5 + - - +
248B GLN* 3.0 16.8 + - - +
250B LYS* 1.3 75.7 - - - +
252B HIS* 1.3 68.7 + - + +
253B ALA 3.7 0.2 - - - -
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Residues in contact with HIS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TYR 5.3 1.1 - - - -
151B LYS* 6.5 0.2 - - + -
152B PRO* 3.7 33.8 - - + +
221B PRO* 4.0 18.9 - - + +
223B PHE* 3.8 21.1 - + + -
248B GLN* 2.9 37.8 + - + +
249B ALA 3.7 3.1 - - - +
251B ALA* 1.3 86.3 - - + +
253B ALA* 1.3 63.2 + - - +
254B PRO 3.0 16.0 - - - +
255B CYS* 3.9 2.6 - - + +
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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