Contacts of the helix formed by residues 295 - 309 (chain C) in PDB entry 2ODE
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 THR 295 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278C ILE* 3.9 7.4 - - - -
279C LYS* 6.1 0.9 - - - -
293C SER* 2.7 33.1 + - - +
294C ASN* 1.3 83.3 - - - +
296C TYR* 1.3 68.0 + - - +
297C GLU 3.4 1.0 + - - -
298C GLU* 3.9 11.4 + - - +
299C ALA* 3.0 22.3 + - - +
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Residues in contact with TYR 296 (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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227C LEU* 5.1 0.4 - - + -
271C LYS* 3.3 49.5 - - + +
274C PHE* 3.7 24.3 - + - -
275C GLU* 3.9 37.9 - - + +
278C ILE* 3.7 11.5 - - + +
295C THR* 1.3 71.1 - - - +
297C GLU* 1.3 95.4 + - + +
300C ALA* 3.0 36.7 + - + +
323C PHE* 3.9 16.1 - - - +
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Residues in contact with GLU 297 (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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295C THR* 3.5 1.8 + - - -
296C TYR* 1.3 105.0 - - + +
298C GLU* 1.3 62.2 + - + +
300C ALA* 3.8 2.0 - - - +
301C ALA* 3.0 30.7 + - - +
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Residues in contact with GLU 298 (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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290C TYR* 3.5 15.4 + - - +
292C GLY* 5.8 0.4 - - - -
293C SER* 3.7 26.0 - - - +
295C THR* 3.5 7.4 + - - +
296C TYR 3.4 0.2 - - - -
297C GLU* 1.3 80.8 - - + +
299C ALA* 1.3 60.6 + - - +
301C ALA* 3.5 7.2 + - - +
302C TYR* 3.1 19.6 + - - +
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Residues in contact with ALA 299 (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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274C PHE* 3.7 20.6 - - + -
278C ILE* 4.0 11.7 - - + -
283C LEU* 3.8 18.2 - - + +
290C TYR* 3.5 8.4 + - + -
293C SER 3.9 11.0 + - - +
295C THR 3.0 17.3 + - - +
298C GLU* 1.3 74.6 - - - +
300C ALA* 1.3 65.7 + - - +
302C TYR* 3.4 3.3 + - - +
303C ILE* 3.1 27.2 + - - +
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Residues in contact with ALA 300 (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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227C LEU* 4.8 3.4 - - + -
274C PHE* 3.7 15.8 - - + -
296C TYR* 3.0 32.3 + - + +
297C GLU* 3.8 4.3 - - - +
299C ALA* 1.3 74.9 - - - +
301C ALA* 1.3 60.4 + - - +
303C ILE* 3.3 8.4 + - - +
304C GLN* 3.0 26.9 + - - +
323C PHE* 3.7 29.8 - - + -
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Residues in contact with ALA 301 (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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297C GLU 3.0 19.5 + - - +
298C GLU* 3.6 9.2 - - - +
300C ALA* 1.3 74.6 - - - +
302C TYR* 1.3 58.7 + - - +
304C GLN* 3.3 15.9 + - - +
305C CYS* 3.0 28.1 + - - +
323C PHE* 4.5 2.6 - - - -
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Residues in contact with TYR 302 (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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283C LEU* 4.1 4.0 - - + -
287C TYR* 3.8 28.5 - + + -
289C GLU* 2.6 33.8 + - - +
290C TYR* 3.4 46.9 - + + -
291C THR 5.8 0.2 - - - -
298C GLU 3.1 10.0 + - - +
299C ALA 3.6 8.1 - - - +
300C ALA 3.3 0.2 - - - -
301C ALA* 1.3 73.4 - - - +
303C ILE* 1.3 66.3 + - - +
305C CYS* 3.1 6.5 + - + -
306C GLN* 2.9 62.3 + - + +
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Residues in contact with ILE 303 (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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227C LEU* 3.8 21.3 - - + +
243C MET* 3.6 31.9 - - + -
268C LEU* 4.4 5.4 - - + -
274C PHE* 3.6 32.5 - - + -
283C LEU* 3.8 15.3 - - + -
287C TYR* 4.0 17.3 - - + +
299C ALA 3.1 14.9 + - - +
300C ALA 3.3 6.3 + - - +
302C TYR* 1.3 74.6 - - - +
304C GLN* 1.3 63.4 + - - +
306C GLN* 3.1 8.7 + - - +
307C PHE* 3.0 38.2 + - + -
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Residues in contact with GLN 304 (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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266C LEU* 5.4 0.4 - - + -
268C LEU* 3.7 17.2 - - + +
300C ALA 3.0 13.8 + - - +
301C ALA* 3.3 15.1 - - - +
302C TYR 3.3 0.2 - - - -
303C ILE* 1.3 77.6 - - - +
305C CYS* 1.3 57.4 + - - +
307C PHE* 3.3 4.1 + - - +
308C GLU* 2.9 61.4 + - - +
321C THR* 3.6 25.8 + - + +
323C PHE* 3.3 19.8 - - + -
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Residues in contact with CYS 305 (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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301C ALA 3.0 12.9 + - - +
302C TYR* 3.1 12.5 + - + +
304C GLN* 1.3 76.0 - - - +
306C GLN* 1.3 67.5 + - - +
308C GLU* 4.1 6.0 - - - +
309C ASP* 2.9 55.2 + - - +
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Residues in contact with GLN 306 (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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247C MET* 4.1 10.9 - - + +
287C TYR* 3.7 32.4 - - + +
289C GLU* 4.3 4.9 - - - +
302C TYR* 2.9 71.1 + - + +
303C ILE 3.1 5.8 + - - +
305C CYS* 1.3 94.1 - - - +
307C PHE* 1.3 61.0 + - - +
309C ASP* 3.7 16.3 + - - +
310C LEU* 3.5 17.7 - - - +
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Residues in contact with PHE 307 (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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225C VAL* 3.5 42.6 - - + -
243C MET* 4.0 11.0 - - + -
246C SER* 3.7 23.1 - - - -
247C MET* 3.6 31.0 - - + -
250C PHE* 3.5 34.1 - + + -
266C LEU* 3.7 22.9 - - + -
268C LEU* 4.6 3.1 - - + -
287C TYR* 4.1 2.7 - - - -
303C ILE* 3.0 43.0 + - + +
304C GLN* 3.9 1.8 - - - +
306C GLN* 1.3 75.7 - - - +
308C GLU* 1.3 65.9 + - - +
310C LEU* 3.2 26.4 + - + +
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Residues in contact with GLU 308 (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 PHE* 5.1 0.2 - - - -
266C LEU* 4.8 2.2 - - + -
304C GLN* 2.9 51.3 + - + +
305C CYS* 4.1 5.5 - - - +
307C PHE* 1.3 72.1 - - - +
309C ASP* 1.3 63.5 + - - +
310C LEU 3.2 0.9 + - - -
311C ASN* 3.2 21.0 + - - +
314C LYS* 3.8 6.6 - - - +
319C ILE* 4.3 29.8 - - + +
321C THR* 2.6 31.4 + - - +
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Residues in contact with ASP 309 (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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305C CYS* 2.9 44.0 + - - +
306C GLN* 3.8 15.9 + - - +
307C PHE 3.2 0.4 - - - -
308C GLU* 1.3 79.0 - - - +
310C LEU* 1.3 58.1 + - + +
311C ASN 3.2 0.7 - - - +
312C ARG* 3.7 8.5 + - - -
314C LYS* 2.8 33.7 + - - +
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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