Contacts of the helix formed by residues 279 - 294 (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 GLU 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B LEU 4.8 8.3 - - - +
234B PHE 4.6 5.8 - - - +
235B VAL* 3.0 45.2 - - - +
236B GLY 4.6 2.0 - - - +
278B ASP* 1.3 80.8 - - - +
280B ARG* 1.3 53.1 + - - +
281B GLU* 3.1 2.6 - - - +
282B GLN* 3.0 37.6 + - - +
283B THR* 2.2 41.1 + - - +
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Residues in contact with ARG 280 (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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231B VAL* 4.2 27.8 - - + +
264B ALA 3.5 24.3 + - - +
265B VAL* 3.6 26.5 - - + +
267B ARG* 4.7 28.8 - - - +
278B ASP 2.7 11.7 + - - +
279B GLU* 1.3 72.6 - - - +
281B GLU* 1.3 68.0 + - - +
283B THR* 3.5 5.9 - - - -
284B LEU* 2.8 38.1 + - - +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASP* 3.2 35.3 + - - +
279B GLU 4.5 0.2 - - - +
280B ARG* 1.3 92.1 + - - +
282B GLN* 1.3 54.4 + - + +
284B LEU* 3.7 7.7 - - - +
285B ASN* 2.7 49.1 + - - +
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Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 5.7 1.6 - - - +
236B GLY* 4.7 11.1 + - - -
239B ALA* 4.5 10.7 - - + +
279B GLU* 3.0 44.8 + - - +
280B ARG 3.3 0.6 - - - -
281B GLU* 1.3 75.2 - - + +
283B THR* 1.3 66.1 + - - +
285B ASN* 3.2 13.0 + - - +
286B GLN* 2.8 25.1 + - - +
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Residues in contact with THR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 4.2 18.3 + - + +
238B GLY* 3.7 35.2 - - - +
239B ALA* 4.3 9.7 + - - +
242B VAL* 4.1 10.2 - - + +
265B VAL* 4.2 19.2 - - + +
279B GLU* 2.2 33.9 + - - +
280B ARG* 3.5 8.1 - - - -
282B GLN* 1.3 73.8 - - - +
284B LEU* 1.3 61.5 + - - +
286B GLN* 3.2 4.9 + - - +
287B LEU* 3.1 18.4 + - - +
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Residues in contact with LEU 284 (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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265B VAL* 3.7 17.4 - - + +
266B GLY* 3.6 26.2 - - - -
267B ARG 5.9 1.6 - - - +
280B ARG 2.8 21.1 + - - +
281B GLU* 3.7 7.4 - - - +
283B THR* 1.3 68.4 - - - +
285B ASN* 1.3 71.3 + - - +
286B GLN 2.9 1.6 - - - -
287B LEU* 2.6 32.2 + - + +
288B LEU* 2.9 26.7 + - + +
313B ASP* 4.1 28.9 - - + +
315B ALA* 5.7 0.2 - - + -
316B LEU* 4.0 21.3 - - + -
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLU* 2.7 37.4 + - - +
282B GLN* 3.3 12.3 - - - +
284B LEU* 1.3 73.6 - - - +
286B GLN* 1.3 63.2 + - - +
288B LEU* 3.1 18.3 + - - +
289B VAL* 3.0 27.7 + - + +
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Residues in contact with GLN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ALA* 3.5 37.3 - - + +
242B VAL* 4.1 8.5 - - + -
243B ARG* 3.4 32.6 + - + +
282B GLN 2.8 12.9 + - - +
283B THR 3.3 10.1 - - - +
285B ASN* 1.3 72.9 - - - +
287B LEU* 1.3 68.4 + - - +
289B VAL* 3.0 26.8 + - - +
290B GLU* 3.0 41.5 + - - +
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Residues in contact with LEU 287 (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* 3.9 17.8 - - + +
246B PHE* 4.1 19.1 - - + -
259B ILE* 4.9 13.7 - - + -
262B ILE* 4.4 19.1 - - + -
265B VAL* 5.3 9.9 - - + -
283B THR 3.1 9.6 + - - +
284B LEU* 2.6 29.5 + - + +
286B GLN* 1.3 70.6 - - - +
288B LEU* 1.3 63.7 + - - +
290B GLU* 3.1 3.5 + - - +
291B MET* 2.9 43.0 + - + +
316B LEU* 4.0 24.5 - - + -
322B PHE* 4.8 1.1 - - + -
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Residues in contact with LEU 288 (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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284B LEU* 2.9 28.7 + - + +
285B ASN* 3.3 22.0 - - - +
287B LEU* 1.3 75.6 - - - +
289B VAL* 1.3 64.5 + - + +
291B MET* 3.6 5.0 - - + +
292B ASP* 2.9 31.4 + - - +
315B ALA* 4.3 22.4 - - + +
316B LEU* 3.9 31.2 - - + -
321B ARG* 4.1 34.1 - - - +
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Residues in contact with VAL 289 (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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285B ASN* 3.0 19.4 + - + +
286B GLN* 3.0 25.5 + - - +
288B LEU* 1.3 76.4 - - + +
290B GLU* 1.3 62.9 - - - +
292B ASP* 3.4 8.5 + - - +
293B GLY* 2.8 25.2 + - - -
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Residues in contact with GLU 290 (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* 3.9 10.5 - - + -
243B ARG* 3.6 18.7 - - - +
246B PHE* 3.6 47.8 - - + +
250B LYS* 5.1 8.8 + - - -
286B GLN* 3.0 37.1 + - - +
287B LEU 3.6 4.7 - - - +
289B VAL* 1.3 77.6 - - - +
291B MET* 1.3 63.3 + - - +
293B GLY* 2.8 16.4 + - - +
294B PHE* 3.0 20.9 + - - +
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Residues in contact with MET 291 (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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195B LYS* 2.8 36.0 + - + +
246B PHE* 4.5 3.5 - - + -
287B LEU* 2.9 32.3 + - + +
288B LEU* 3.6 11.2 - - + +
290B GLU* 1.3 74.4 - - - +
292B ASP* 1.3 67.6 + - - +
293B GLY 2.8 4.5 + - - -
294B PHE* 3.4 25.8 + - + -
302B VAL* 3.2 41.3 - - + -
316B LEU* 5.8 0.7 - - + -
320B GLY 4.9 2.7 - - - +
321B ARG* 4.7 23.6 - - + -
322B PHE* 3.5 34.1 - - + -
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Residues in contact with ASP 292 (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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195B LYS* 3.2 15.2 + - - +
288B LEU 2.9 18.8 + - - +
289B VAL* 3.5 7.5 - - - +
291B MET* 1.3 76.8 - - - +
293B GLY* 1.3 58.6 + - - +
294B PHE 4.4 0.2 - - - +
320B GLY 4.8 3.1 - - - +
321B ARG* 2.9 47.1 + - - +
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Residues in contact with GLY 293 (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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250B LYS* 3.6 15.2 + - - -
289B VAL* 2.8 12.1 + - - -
290B GLU* 2.8 15.4 + - - -
292B ASP* 1.3 79.5 - - - +
294B PHE* 1.3 57.3 + - - -
295B ASP 4.2 0.5 + - - -
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Residues in contact with PHE 294 (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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195B LYS* 2.8 74.9 + - + -
246B PHE* 4.1 13.2 - + + -
250B LYS* 3.9 23.1 - - - +
290B GLU 3.0 21.6 + - - +
291B MET* 3.4 31.1 + - + -
292B ASP 4.4 0.2 - - - +
293B GLY* 1.3 80.1 - - - +
295B ASP* 1.3 67.7 + - - +
296B SER* 4.0 7.0 - - - -
300B ILE* 3.4 46.7 - - + -
302B VAL* 4.0 7.0 - - + -
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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