Contacts of the helix formed by residues 278 - 294 (chain A) 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 ASP 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A HIS* 1.3 87.8 + - - +
279A GLU* 1.3 77.3 + - + +
280A ARG* 3.3 24.9 + - - +
281A GLU* 3.5 24.7 - - - +
282A GLN* 4.1 5.4 + - - +
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PHE 6.1 0.7 - - - +
233A LEU* 4.5 13.7 - - + +
234A PHE 4.1 12.8 - - - +
235A VAL* 4.0 15.5 - - + +
236A GLY* 3.1 31.8 + - - +
238A GLY 4.7 1.9 + - - +
239A ALA 4.7 1.0 + - - -
278A ASP* 1.3 82.3 + - + +
280A ARG* 1.3 56.0 + - - +
281A GLU 3.2 1.3 - - - -
282A GLN* 3.2 40.3 + - - +
283A THR* 2.6 44.9 + - - +
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Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A VAL* 3.5 32.1 - - - +
264A ALA 3.7 17.0 + - - -
265A VAL* 3.7 23.3 - - + +
267A ARG* 4.4 27.1 - - + +
277A HIS* 3.5 25.6 - - - +
278A ASP* 3.4 21.5 + - - +
279A GLU* 1.3 77.1 - - - +
281A GLU* 1.3 55.9 + - - +
283A THR* 3.7 5.7 - - - -
284A LEU* 2.7 40.4 + - + +
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A HIS* 4.5 7.4 - - + -
278A ASP* 3.5 25.5 - - - +
280A ARG* 1.3 79.8 - - + +
282A GLN* 1.3 58.8 + - + +
284A LEU* 3.8 7.9 - - - +
285A ASN* 2.8 49.8 + - - +
313A ASP* 5.5 2.8 - - - +
241B ARG* 5.1 9.0 + - - -
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A VAL* 5.1 7.3 - - - +
236A GLY* 3.9 13.8 - - - +
239A ALA* 4.5 12.6 - - + +
278A ASP 4.1 5.1 + - - +
279A GLU* 3.2 40.4 + - - +
280A ARG 3.2 0.2 - - - -
281A GLU* 1.3 78.0 - - + +
283A THR* 1.3 66.7 + - - +
285A ASN* 3.4 6.8 + - - +
286A GLN* 3.0 23.7 + - - +
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Residues in contact with THR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PHE* 3.7 36.7 + - + -
233A LEU* 6.1 0.2 - - - +
238A GLY* 3.9 23.1 - - - +
239A ALA* 4.3 8.5 - - - +
242A VAL* 4.4 7.2 - - + +
265A VAL* 3.8 19.1 - - + -
279A GLU* 2.6 28.0 + - - +
280A ARG* 3.7 5.1 - - - -
282A GLN* 1.3 77.9 - - - +
284A LEU* 1.3 61.5 + - - +
286A GLN* 3.3 5.4 + - - +
287A LEU* 3.1 19.6 + - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL* 3.7 25.7 - - + +
266A GLY* 4.1 4.3 - - - -
267A ARG 4.3 7.6 - - - +
280A ARG* 2.7 22.6 + - + +
281A GLU* 3.9 8.1 - - - +
283A THR* 1.3 70.2 - - - +
285A ASN* 1.3 69.6 + - - +
286A GLN 3.0 1.6 - - - -
287A LEU* 3.0 24.0 + - + +
288A LEU* 2.9 32.8 + - + +
313A ASP* 3.9 33.7 - - + +
316A LEU* 3.8 26.0 - - + -
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Residues in contact with ASN 285 (chain A).
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* 2.8 44.6 + - - +
282A GLN* 3.8 6.3 - - - +
284A LEU* 1.3 76.0 - - - +
286A GLN* 1.3 56.9 + - - +
288A LEU* 3.3 17.9 + - - +
289A VAL* 2.9 33.6 + - + +
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ALA* 3.7 36.3 - - + +
242A VAL* 3.9 10.5 - - + -
243A ARG* 3.3 25.6 + - + +
282A GLN 3.0 13.4 + - - +
283A THR 3.4 8.5 - - - +
284A LEU 3.0 0.8 - - - -
285A ASN* 1.3 72.5 - - - +
287A LEU* 1.3 68.0 + - - +
289A VAL* 3.0 18.3 + - - +
290A GLU* 2.5 56.3 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A VAL* 3.9 17.1 - - + +
246A PHE* 4.1 19.3 - - + -
259A ILE* 4.6 14.6 - - + -
262A ILE* 4.5 14.4 - - + -
265A VAL* 5.1 10.5 - - + -
283A THR 3.1 9.1 + - - +
284A LEU* 3.0 21.3 + - + +
286A GLN* 1.3 79.7 - - - +
288A LEU* 1.3 63.3 + - + +
290A GLU* 3.0 1.0 + - - -
291A MET* 2.9 43.8 + - + +
316A LEU* 3.6 30.7 - - + -
322A PHE* 4.6 1.6 - - + -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LEU* 2.9 30.8 + - + +
285A ASN* 3.4 19.5 - - - +
287A LEU* 1.3 71.9 - - + +
289A VAL* 1.3 63.0 + - + +
291A MET* 3.4 5.9 + - + +
292A ASP* 3.0 30.7 + - - +
313A ASP* 5.4 0.4 - - - +
315A ALA* 3.7 28.0 - - + +
316A LEU* 4.0 33.2 - - + -
321A ARG* 4.3 31.4 - - + +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASN* 2.9 18.7 + - + +
286A GLN* 3.0 26.0 + - - +
288A LEU* 1.3 77.4 - - + +
290A GLU* 1.3 63.7 + - - +
292A ASP* 3.5 8.7 + - - +
293A GLY* 2.8 24.9 + - - -
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A VAL* 3.8 19.3 - - + +
243A ARG* 3.4 19.8 - - - +
246A PHE* 3.7 39.0 - - + +
250A LYS* 4.8 10.4 + - - -
286A GLN* 2.5 43.2 + - - +
287A LEU 3.6 5.6 - - - +
289A VAL* 1.3 77.3 - - - +
291A MET* 1.3 69.3 + - - +
293A GLY* 2.9 10.3 + - - +
294A PHE* 3.1 18.4 + - - +
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 2.6 51.6 + - + +
196A GLY* 4.0 22.9 - - - +
246A PHE* 4.4 3.1 - - - -
287A LEU* 2.9 35.6 + - + +
288A LEU* 3.6 9.6 - - + +
290A GLU* 1.3 77.8 - - - +
292A ASP* 1.3 52.4 + - - +
293A GLY 3.0 1.0 + - - -
294A PHE* 3.4 6.6 + - + -
302A VAL* 4.1 18.2 - - - -
320A GLY 4.8 1.1 - - - +
321A ARG* 4.0 30.1 - - + +
322A PHE* 3.8 37.0 - - + -
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Residues in contact with ASP 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 3.3 13.1 + - - +
288A LEU 3.0 14.9 + - - +
289A VAL* 3.6 7.9 - - - +
291A MET* 1.3 75.8 - - - +
293A GLY* 1.3 59.4 + - - +
320A GLY* 4.6 4.0 - - - +
321A ARG* 2.9 45.1 + - - +
155B ASN* 5.0 9.4 - - - +
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Residues in contact with GLY 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LYS* 4.6 9.6 + - - -
289A VAL 2.8 15.4 + - - -
290A GLU* 2.9 8.7 + - - -
292A ASP* 1.3 79.3 - - - +
294A PHE* 1.3 61.7 + - - +
295A ASP 4.0 0.7 + - - -
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Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 2.7 73.5 + - + -
246A PHE* 4.3 13.5 - + + -
250A LYS* 3.9 24.9 - - - +
290A GLU 3.1 12.6 + - - +
291A MET* 3.4 22.9 + - - -
293A GLY* 1.3 77.4 - - - +
295A ASP* 1.3 67.7 + - - +
296A SER* 3.3 15.7 + - - -
300A ILE* 3.2 54.5 - - + -
302A VAL* 4.1 18.2 - - + -
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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