Contacts of the helix formed by residues 278 - 294 (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 ASP 278 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F GLU* 1.3 73.2 + - + +
280F ARG 3.1 2.0 - - - +
281F GLU* 2.6 39.3 + - - +
282F GLN* 2.9 30.3 + - - +
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Residues in contact with GLU 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F PHE 3.8 6.7 - - - +
231F VAL* 5.4 2.2 - - - -
232F GLU 4.8 4.9 - - - +
233F LEU* 2.6 61.2 + - - +
234F PHE 3.6 10.6 - - - +
235F VAL* 4.3 7.6 + - - +
236F GLY 5.0 1.9 + - - -
238F GLY 5.1 1.0 + - - -
278F ASP* 1.3 80.2 - - + +
280F ARG* 1.3 61.2 - - + +
282F GLN* 3.5 11.6 + - - +
283F THR* 2.9 32.0 + - - +
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Residues in contact with ARG 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F VAL* 3.6 29.8 - - + +
264F ALA 3.0 24.0 + - - -
265F VAL* 3.3 27.4 - - + +
267F ARG* 3.3 49.7 + - - +
278F ASP 2.8 1.8 + - - +
279F GLU* 1.3 79.5 - - + +
281F GLU* 1.3 60.8 + - - +
283F THR* 4.4 5.8 - - - -
284F LEU* 3.0 30.0 + - - +
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Residues in contact with GLU 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F ASP* 2.6 33.0 + - - +
280F ARG* 1.3 73.8 - - - +
282F GLN* 1.3 59.1 + - + +
284F LEU* 3.5 18.1 - - + +
285F ASN* 2.8 47.6 + - - +
313F ASP* 5.6 0.2 - - - +
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Residues in contact with GLN 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E ARG* 5.2 1.1 + - - +
235F VAL* 4.9 9.9 - - - +
236F GLY* 4.5 18.1 + - - -
239F ALA* 4.2 11.0 - - + +
278F ASP* 2.9 30.2 + - - +
279F GLU* 3.8 8.5 - - - +
281F GLU* 1.3 76.0 - - + +
283F THR* 1.3 66.2 + - - +
285F ASN* 3.4 5.3 + - - +
286F GLN* 3.0 25.8 + - - +
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Residues in contact with THR 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F PHE* 4.4 14.9 + - + -
233F LEU* 4.9 1.0 - - - +
238F GLY* 3.5 39.1 - - - +
239F ALA* 3.9 8.9 + - - +
242F VAL* 3.7 11.3 - - + +
265F VAL* 3.9 23.0 - - + +
279F GLU* 2.9 23.1 + - - +
280F ARG* 4.4 4.0 - - - -
282F GLN* 1.3 77.2 - - - +
284F LEU* 1.3 62.2 - - - +
286F GLN* 3.5 3.3 + - - +
287F LEU* 3.3 18.0 + - - +
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Residues in contact with LEU 284 (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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265F VAL* 3.8 22.3 - - - +
266F GLY* 4.2 3.1 - - - -
267F ARG 5.4 5.6 - - - +
280F ARG 3.0 21.8 + - - +
281F GLU* 3.5 18.6 - - + +
283F THR* 1.3 72.4 - - - +
285F ASN* 1.3 76.3 + - - +
286F GLN 3.1 1.6 - - - -
287F LEU* 2.9 21.7 + - + +
288F LEU* 3.0 21.9 + - + +
313F ASP* 3.1 30.1 - - + +
316F LEU* 3.8 37.9 - - + -
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Residues in contact with ASN 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E ARG* 3.7 22.5 - - - +
310E ASP* 5.4 3.0 + - - -
281F GLU* 2.8 34.9 + - - +
282F GLN* 3.9 5.4 - - - +
284F LEU* 1.3 78.9 - - - +
286F GLN* 1.3 60.9 + - - +
288F LEU* 3.4 23.0 + - - +
289F VAL* 3.0 29.1 + - - +
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Residues in contact with GLN 286 (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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308E ARG* 3.7 19.8 - - - +
311E ILE* 4.0 18.3 - - - +
239F ALA* 3.4 37.0 - - + +
242F VAL* 3.7 9.6 - - + -
243F ARG* 2.8 22.2 - - + +
282F GLN 3.0 17.6 + - - +
283F THR 3.6 5.8 - - - +
284F LEU 3.0 0.4 + - - -
285F ASN* 1.3 74.1 - - - +
287F LEU* 1.3 65.4 + - - +
289F VAL* 3.3 6.6 + - - +
290F GLU* 2.7 52.4 + - + +
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Residues in contact with LEU 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F VAL* 3.7 17.3 - - + +
246F PHE* 4.8 7.4 - - + -
259F ILE* 5.0 13.7 - - + -
262F ILE* 5.1 6.3 - - + -
265F VAL* 6.2 6.3 - - + -
283F THR 3.3 8.8 + - - +
284F LEU* 2.9 13.5 + - + +
286F GLN* 1.3 77.8 - - - +
288F LEU* 1.3 67.6 + - + +
290F GLU* 3.0 3.8 + - - +
291F MET* 2.8 45.7 + - + -
316F LEU* 3.7 31.0 - - + -
321F ARG* 5.7 0.2 - - + -
322F PHE* 4.3 14.6 - - + -
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Residues in contact with LEU 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F LEU* 3.0 24.8 + - + +
285F ASN* 3.5 30.3 - - - +
287F LEU* 1.3 78.4 - - + +
289F VAL* 1.3 62.8 + - + +
291F MET* 3.6 0.7 + - - +
292F ASP* 2.9 33.8 + - - +
315F ALA* 3.7 24.7 - - + +
316F LEU* 3.2 32.1 - - + -
321F ARG* 2.8 37.9 - - - +
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Residues in contact with VAL 289 (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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307E ASN* 5.5 5.4 - - - +
308E ARG* 3.1 42.0 - - + +
285F ASN* 3.0 17.2 + - + +
286F GLN* 3.8 11.9 - - - +
287F LEU 3.1 0.2 - - - -
288F LEU* 1.3 74.9 - - + +
290F GLU* 1.3 63.2 + - - +
292F ASP* 3.5 6.9 + - - +
293F GLY* 2.8 26.2 + - - -
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Residues in contact with GLU 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E ARG* 5.2 3.5 + - - -
242F VAL* 4.1 5.4 - - + -
243F ARG* 3.1 19.4 - - - +
246F PHE* 3.3 56.3 - - + +
286F GLN* 2.7 51.0 + - - +
287F LEU 3.0 0.9 + - - +
289F VAL* 1.3 77.4 - - - +
291F MET* 1.3 59.6 + - - +
293F GLY* 2.7 20.6 + - - -
294F PHE* 3.1 16.5 + - - +
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Residues in contact with MET 291 (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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195F LYS* 3.0 51.9 + - + +
196F GLY* 4.4 2.0 - - - -
246F PHE* 4.0 5.1 - - + -
287F LEU* 2.8 39.2 + - + +
288F LEU 3.8 4.5 - - - +
290F GLU* 1.3 74.2 - - - +
292F ASP* 1.3 60.2 + - - +
293F GLY 3.4 0.2 + - - -
294F PHE* 2.4 55.0 - - + -
302F VAL* 3.8 23.6 - - + -
320F GLY 5.1 1.3 - - - -
321F ARG* 3.8 39.0 - - + +
322F PHE* 4.6 7.6 - - + -
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Residues in contact with ASP 292 (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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195F LYS* 3.8 11.0 + - - +
288F LEU 2.9 14.2 + - - +
289F VAL* 3.8 7.0 - - - +
290F GLU 3.1 0.4 - - - -
291F MET* 1.3 75.4 - - - +
293F GLY* 1.3 59.3 + - - +
294F PHE 3.5 0.8 + - - +
320F GLY 4.9 3.3 - - - +
321F ARG* 2.2 59.6 + - - +
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Residues in contact with GLY 293 (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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250F LYS* 4.3 5.6 + - - -
289F VAL* 2.8 13.6 + - - -
290F GLU* 2.7 12.2 + - - -
292F ASP* 1.3 79.7 - - - +
294F PHE* 1.3 57.1 + - - -
295F ASP 4.2 0.5 + - - -
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Residues in contact with PHE 294 (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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195F LYS* 2.5 63.2 + - + -
246F PHE* 3.8 20.4 - + + -
250F LYS* 2.5 26.7 - - + +
290F GLU 3.1 13.9 + - - +
291F MET* 2.4 56.5 - - + -
292F ASP 3.5 0.5 - - - +
293F GLY* 1.3 79.0 - - - +
295F ASP* 1.3 66.6 + - - +
296F SER* 3.9 8.7 - - - -
300F ILE* 3.5 42.0 - - + -
302F VAL* 5.0 0.2 - - + -
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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