Contacts of the helix formed by residues 281 - 294 (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 GLU 281 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282C GLN* 1.3 76.0 + - + +
283C THR* 3.2 5.8 + - - +
284C LEU* 3.3 10.1 + - - +
285C ASN* 2.9 38.7 + - - +
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Residues in contact with GLN 282 (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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235C VAL* 4.9 15.2 - - - +
236C GLY* 3.8 28.5 + - - +
239C ALA* 4.4 12.3 - - + +
281C GLU* 1.3 83.5 - - + +
283C THR* 1.3 64.9 + - - +
285C ASN* 3.5 7.4 + - - +
286C GLN* 2.9 27.1 + - - +
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Residues in contact with THR 283 (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* 3.8 28.5 + - + +
238C GLY* 3.6 17.9 - - - +
239C ALA* 4.1 9.0 + - - +
242C VAL* 3.9 12.5 - - + +
265C VAL* 3.7 28.3 - - + -
281C GLU 3.2 4.1 - - - +
282C GLN* 1.3 80.1 - - - +
284C LEU* 1.3 63.4 + - - +
286C GLN* 3.5 3.6 + - - +
287C LEU* 3.1 19.7 + - + +
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Residues in contact with LEU 284 (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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265C VAL* 3.7 25.7 + - - +
266C GLY* 4.3 6.1 - - - -
267C ARG 4.8 3.1 - - - +
281C GLU* 3.3 12.0 + - - +
283C THR* 1.3 76.3 - - - +
285C ASN* 1.3 64.1 + - - +
286C GLN 3.0 1.3 - - - -
287C LEU* 2.6 39.3 + - + -
288C LEU* 2.8 44.3 + - + -
313C ASP* 3.8 37.0 - - + +
316C LEU* 4.1 14.8 - - + -
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Residues in contact with ASN 285 (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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281C GLU* 2.9 33.7 + - - +
282C GLN* 3.7 6.6 - - - +
284C LEU* 1.3 75.6 - - - +
286C GLN* 1.3 62.0 + - - +
288C LEU* 3.4 17.3 + - - +
289C VAL* 3.0 30.7 + - + +
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Residues in contact with GLN 286 (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* 3.7 34.2 - - + +
242C VAL* 4.0 6.5 - - + -
243C ARG* 3.0 36.5 + - - +
282C GLN 2.9 18.6 + - - +
283C THR 3.5 5.2 - - - +
284C LEU 2.8 0.2 + - - -
285C ASN* 1.3 73.6 - - - +
287C LEU* 1.3 66.6 + - - +
289C VAL* 3.0 21.4 + - - +
290C GLU* 2.9 42.6 + - - +
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Residues in contact with LEU 287 (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* 3.8 19.4 - - + +
246C PHE* 4.8 5.6 - - + -
259C ILE* 4.8 17.9 - - + -
262C ILE* 4.8 12.8 - - + -
265C VAL* 5.1 13.5 - - + -
266C GLY* 6.3 0.2 - - - -
283C THR* 3.1 13.8 + - + +
284C LEU* 2.6 20.8 + - + +
286C GLN* 1.3 72.2 - - - +
288C LEU* 1.3 66.5 + - - +
290C GLU* 3.0 3.3 + - - +
291C MET* 2.9 46.3 + - + -
316C LEU* 3.9 28.3 - - + -
322C PHE* 4.6 2.9 - - + -
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Residues in contact with LEU 288 (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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284C LEU* 2.8 40.6 + - + -
285C ASN* 3.5 20.6 - - - +
287C LEU* 1.3 77.7 - - + +
289C VAL* 1.3 62.3 + - + +
291C MET* 3.4 5.0 - - - +
292C ASP* 3.2 25.3 + - - +
315C ALA* 3.6 44.9 - - + +
316C LEU* 4.2 10.1 - - + -
321C ARG* 3.8 26.8 + - - +
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Residues in contact with VAL 289 (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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285C ASN* 3.0 19.7 - - + +
286C GLN* 3.0 15.8 + - - +
288C LEU* 1.3 76.0 - - + +
290C GLU* 1.3 62.9 + - + +
292C ASP* 3.6 4.0 + - - +
293C GLY* 2.9 24.6 + - - -
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Residues in contact with GLU 290 (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* 4.0 7.2 - - + -
243C ARG* 3.7 19.5 - - - +
246C PHE* 3.5 51.2 - - + +
250C LYS* 6.0 1.7 - - - -
286C GLN* 2.9 36.3 + - - +
287C LEU 3.5 4.7 - - - +
289C VAL* 1.3 74.2 - - - +
291C MET* 1.3 67.1 + - - +
293C GLY* 2.7 13.0 + - - -
294C PHE* 3.0 18.9 + - - +
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Residues in contact with MET 291 (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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195C LYS* 2.7 30.9 + - - +
246C PHE* 3.2 30.3 - - + -
259C ILE* 6.0 0.9 - - + -
287C LEU* 2.9 31.6 + - + -
288C LEU* 3.4 11.2 - - - +
290C GLU* 1.3 78.9 - - - +
292C ASP* 1.3 59.0 + - - +
294C PHE* 3.0 44.1 - - + -
302C VAL* 3.3 36.3 - - + -
316C LEU* 5.7 0.2 - - + -
320C GLY 4.8 0.9 - - - +
321C ARG* 4.1 19.7 - - + -
322C PHE* 4.1 17.3 - - + -
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Residues in contact with ASP 292 (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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195C LYS* 3.5 12.6 + - - +
288C LEU 3.2 7.3 + - - +
289C VAL* 3.8 4.0 - - - +
290C GLU 3.2 0.6 - - - -
291C MET* 1.3 77.3 - - - +
293C GLY* 1.3 60.5 + - - +
294C PHE 3.4 1.0 - - - +
320C GLY* 3.2 23.0 - - - +
321C ARG* 2.8 43.5 + - - +
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Residues in contact with GLY 293 (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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250C LYS* 3.9 11.0 + - - -
289C VAL 2.9 13.1 + - - -
290C GLU* 2.7 12.1 + - - -
292C ASP* 1.3 80.4 - - - +
294C PHE* 1.3 58.3 + - - -
295C ASP 4.0 0.3 + - - -
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Residues in contact with PHE 294 (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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195C LYS* 2.8 81.5 + - + -
246C PHE* 4.2 12.8 - + + -
250C LYS* 3.7 25.4 - - + +
290C GLU 3.0 15.6 + - - +
291C MET* 3.0 49.8 - - + -
292C ASP 3.4 1.1 - - - +
293C GLY* 1.3 79.4 - - - +
295C ASP* 1.3 67.6 + - - +
296C SER* 3.5 4.0 + - - -
300C ILE* 3.7 42.4 - - + -
302C VAL* 4.5 3.1 - - + -
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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