Contacts of the helix formed by residues 276 - 287 (chain A) in PDB entry 5DO7
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 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A PHE 4.9 0.4 - - - +
261A ASP* 3.5 12.1 + - - +
262A LYS* 4.8 1.1 - - - +
263A ILE* 4.6 0.7 - - - -
275A GLY* 1.3 71.2 - - - -
277A PRO* 1.3 80.1 - - + +
278A ALA* 4.0 14.4 - - + +
279A GLU* 2.8 32.7 + - - -
280A MET* 2.8 20.4 + - - +
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Residues in contact with PRO 277 (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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257A PHE* 3.4 54.8 - - + +
258A GLN* 4.7 13.2 - - - +
260A PHE* 2.9 34.5 - - + +
263A ILE* 4.4 10.3 - - + -
275A GLY 3.9 4.0 - - - +
276A THR* 1.3 85.6 - - + +
278A ALA* 1.3 64.2 + - - +
280A MET* 2.8 6.5 + - + +
281A LEU* 2.8 22.6 + - - +
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Residues in contact with ALA 278 (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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258A GLN* 5.5 1.8 + - - -
276A THR* 3.3 11.3 - - + +
277A PRO* 1.3 76.1 - - - +
279A GLU* 1.3 54.1 + - - +
281A LEU* 2.9 13.8 + - - +
282A ASP* 2.8 37.4 + - - +
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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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262A LYS* 5.5 2.1 - - - -
273A PHE* 3.7 4.3 - - + -
275A GLY* 3.5 3.8 - - - -
276A THR* 2.8 50.3 + - - +
278A ALA* 1.3 75.7 - - - +
280A MET* 1.3 54.2 + - - -
282A ASP* 3.5 5.4 + - - +
283A PHE* 2.8 46.2 + - + +
334A ILE* 2.9 37.0 - - + +
337A LYS* 3.4 18.3 + - - -
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Residues in contact with MET 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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257A PHE* 3.5 26.0 - - + -
263A ILE* 4.0 22.0 - - + +
265A ILE* 4.7 16.8 - - + -
273A PHE* 3.3 42.1 - - + -
276A THR 2.8 11.2 + - - +
277A PRO* 2.8 11.0 + - + +
279A GLU* 1.3 66.8 - - - +
281A LEU* 1.3 62.4 + - - +
282A ASP 3.0 1.5 + - - -
284A PHE* 2.8 46.8 + - + +
297A PRO 4.8 0.9 - - - +
298A PHE* 5.2 2.2 - - - +
301A TYR* 3.4 41.7 - - + -
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Residues in contact with LEU 281 (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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257A PHE* 4.1 20.6 - - + -
258A GLN* 6.1 3.1 - - - +
277A PRO 2.8 14.1 + - - +
278A ALA* 3.4 13.2 - - - +
280A MET* 1.3 72.5 - - - +
282A ASP* 1.3 57.9 + - - +
285A ASN* 3.1 31.1 + - - +
291A CYS* 3.8 17.7 - - - -
297A PRO* 4.2 4.0 - - + -
301A TYR* 3.4 26.2 - - + +
311B CYS* 5.9 8.1 - - - -
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Residues in contact with ASP 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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278A ALA 2.8 12.8 + - - +
279A GLU* 3.7 9.0 - - - +
280A MET 3.0 0.6 - - - -
281A LEU* 1.3 75.4 - - - +
283A PHE* 1.3 69.2 + - + +
284A PHE 3.2 2.0 - - - -
285A ASN* 2.8 24.6 + - - +
286A ASP* 2.8 11.3 + - - +
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Residues in contact with PHE 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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273A PHE* 4.0 16.4 - - + -
279A GLU* 2.8 43.6 + - + +
282A ASP* 1.3 82.4 - - + +
284A PHE* 1.3 56.8 + - - +
286A ASP* 2.8 38.1 + - + +
287A CYS* 2.8 32.1 + - - -
329A TYR* 4.5 7.9 - + + -
332A SER* 3.8 21.8 - - - -
333A ALA* 5.1 8.5 - - + -
334A ILE* 4.6 22.4 - - + -
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Residues in contact with PHE 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 ILE* 6.3 0.7 - - + -
280A MET* 2.8 28.7 + - + +
283A PHE* 1.3 76.6 - - - +
285A ASN* 1.3 51.3 - - - +
287A CYS* 3.2 9.0 + - + +
288A GLY 2.2 36.9 + - - +
289A TYR* 3.7 16.2 - + + -
300A PHE* 5.3 0.4 - + - -
301A TYR* 3.2 46.0 - + + -
304A LEU* 3.7 40.2 - - + -
305A THR* 4.4 14.6 - - + -
325A ILE* 4.0 22.0 - - + -
329A TYR* 3.2 31.7 - + - -
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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 LEU* 3.1 21.5 + - - +
282A ASP* 2.8 9.8 + - - +
284A PHE* 1.3 76.3 - - - +
286A ASP* 1.3 62.4 + - - +
287A CYS 3.2 0.7 - - - -
288A GLY* 3.3 15.7 + - - -
289A TYR 3.7 1.6 + - - -
290A PRO* 3.1 48.8 - - + +
291A CYS 4.9 0.3 + - - -
301A TYR* 3.7 11.6 + - - -
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Residues in contact with ASP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASP 2.8 6.7 + - - +
283A PHE* 2.8 50.5 + - + +
285A ASN* 1.3 79.2 - - - +
287A CYS* 1.3 57.9 + - - +
288A GLY 3.7 0.2 + - - -
332A SER* 4.6 4.2 + - - -
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Residues in contact with CYS 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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283A PHE* 2.8 13.2 + - - -
284A PHE* 3.2 10.5 + - + +
286A ASP* 1.3 78.9 - - - +
288A GLY* 1.3 57.5 + - - +
289A TYR* 4.5 4.7 - - - -
325A ILE* 4.0 29.8 - - + +
328A ALA* 3.9 23.8 - - + -
329A TYR* 3.1 42.6 - - + -
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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