Contacts of the helix formed by residues 294 - 304 (chain A) in PDB entry 2O0K
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 PHE 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A VAL* 3.7 24.2 - - + -
159A ASN* 4.2 20.6 - - + -
257A CYS* 4.7 9.0 - - + -
258A ALA* 4.0 30.1 - - + +
284A ILE* 5.3 1.6 - - + -
286A THR* 3.1 31.4 - - + -
288A PRO* 4.2 8.5 - - + -
289A ASN 4.9 0.9 - - - -
292A ASN* 2.7 15.9 + - - +
293A HIS* 1.3 82.7 - - + +
295A TYR* 1.3 57.6 + - - +
297A ILE* 4.1 13.5 - - + -
298A TRP* 2.9 45.9 + + + +
356A PHE* 4.0 28.3 - + - -
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Residues in contact with TYR 295 (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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290A GLY 3.9 3.6 - - - +
291A LEU* 3.4 49.9 - - + +
292A ASN* 2.6 21.3 + - - +
294A PHE* 1.3 74.9 - - - +
296A ASP* 1.3 66.9 + - - +
297A ILE 3.2 0.2 - - - -
298A TRP* 4.2 1.9 - + - +
299A THR* 2.5 55.2 + - + +
356A PHE* 3.7 37.7 - + + -
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Residues in contact with ASP 296 (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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291A LEU 5.5 2.1 - - - +
292A ASN 3.7 5.1 + - - +
293A HIS* 3.3 12.5 + - - +
294A PHE 3.2 0.2 - - - -
295A TYR* 1.3 95.5 - - - +
297A ILE* 1.3 62.0 + - - +
299A THR* 4.1 10.7 - - - +
300A ALA* 3.4 19.9 + - - +
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Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 4.6 18.4 - - + -
257A CYS* 4.5 11.4 - - - -
263A PHE* 4.3 19.3 - - + -
267A TRP* 4.1 29.6 - - + +
284A ILE* 5.4 5.8 - - + -
293A HIS* 3.1 18.4 - - + +
294A PHE* 3.1 18.1 + - + +
296A ASP* 1.3 80.6 - - - +
298A TRP* 1.3 67.1 + - - +
300A ALA* 3.3 5.6 + - - +
301A ALA* 3.0 22.2 + - - +
306A SER* 4.3 2.1 + - - +
308A PHE* 5.0 21.5 - - + -
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Residues in contact with TRP 298 (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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157A VAL* 3.9 20.9 - - + -
159A ASN* 3.4 43.5 - - + +
294A PHE* 2.9 26.6 + + + +
295A TYR* 4.2 3.4 - + - +
297A ILE* 1.3 79.3 - - - +
299A THR* 1.3 57.7 + - - +
301A ALA* 3.1 4.8 + - - +
302A VAL* 2.8 62.3 + - + +
310A PRO* 3.8 12.6 - - + -
311A TYR 3.6 31.6 - - - -
312A THR* 3.8 18.2 - - + -
356A PHE* 3.6 28.3 - + + -
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Residues in contact with THR 299 (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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295A TYR* 2.5 46.4 + - + +
296A ASP* 4.2 11.4 - - - +
298A TRP* 1.3 84.8 - - - +
300A ALA* 1.3 63.6 + - - +
302A VAL* 4.0 2.6 - - - -
303A GLU* 2.9 43.7 + - - +
305A LYS* 5.1 7.2 - - - -
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Residues in contact with ALA 300 (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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296A ASP 3.4 18.6 + - - +
297A ILE* 3.3 4.4 + - - +
298A TRP 3.3 0.4 - - - -
299A THR* 1.3 80.1 - - - +
301A ALA* 1.3 56.6 + - - +
304A GLY 3.0 5.5 + - - -
305A LYS* 2.7 53.0 + - + +
306A SER* 2.9 23.0 + - - +
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Residues in contact with ALA 301 (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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157A VAL* 4.0 23.8 - - + -
297A ILE 3.0 13.1 + - - +
298A TRP 3.1 6.9 + - - +
300A ALA* 1.3 74.5 - - - +
302A VAL* 1.3 66.2 + - - +
303A GLU 3.1 2.1 + - - -
304A GLY* 3.5 10.5 + - - +
306A SER* 3.7 7.7 + - - +
308A PHE* 3.7 27.4 - - + +
310A PRO* 3.8 19.2 - - + +
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Residues in contact with VAL 302 (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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298A TRP* 2.8 69.0 + - + +
299A THR* 4.0 4.3 - - - +
301A ALA* 1.3 74.2 - - - +
303A GLU* 1.3 71.9 + - - +
310A PRO* 4.3 11.9 - - + +
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Residues in contact with GLU 303 (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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299A THR* 2.9 40.5 + - - +
301A ALA 3.1 0.4 - - - -
302A VAL* 1.3 89.8 - - - +
304A GLY* 1.3 57.6 + - - +
305A LYS* 3.2 39.9 - - + +
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Residues in contact with GLY 304 (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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300A ALA 3.0 4.3 + - - -
301A ALA 3.5 8.8 + - - -
303A GLU* 1.3 80.3 - - - +
305A LYS* 1.3 62.2 + - - +
306A SER 3.3 12.3 + - - +
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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