Contacts of the helix formed by residues 286 - 293 (chain C) in PDB entry 2OB2
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 MET 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C LEU* 3.4 45.7 - - + +
81C ARG* 3.6 5.2 - - - +
231C TYR* 3.6 21.5 - - + +
285C ASP* 1.3 71.3 - - - +
287C TRP* 1.3 60.4 + - - +
288C GLU 3.2 0.4 - - - -
289C ILE* 3.6 31.5 - - + +
290C PHE* 2.9 29.5 + - - +
318C GLN* 3.0 29.7 + - - +
321C TYR* 3.0 28.7 + - + +
323C LEU* 3.8 23.6 - - + -
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Residues in contact with TRP 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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285C ASP* 3.0 8.4 + - - +
286C MET* 1.3 78.6 - - - +
288C GLU* 1.3 67.2 + - + +
290C PHE* 3.5 24.4 - + + +
291C ASN* 3.1 51.4 + - - +
311C LEU* 3.7 40.6 - - + -
314C LEU* 4.4 7.6 - - + -
315C LYS* 3.4 69.0 - - + +
318C GLN* 3.5 9.7 + - + +
319C THR* 3.6 24.0 - - + +
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Residues in contact with GLU 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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268C LYS* 2.8 39.5 + - - -
284C ASN* 3.4 21.0 - - - +
285C ASP* 2.7 33.5 + - - +
287C TRP* 1.3 78.2 - - + +
289C ILE* 1.3 51.8 + - - +
291C ASN* 3.3 5.1 + - - +
292C ALA* 2.8 41.8 + - + +
293C GLN* 5.2 0.9 - - - -
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Residues in contact with ILE 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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80C LEU* 4.2 18.2 - - + +
84C GLY* 5.0 8.3 - - - +
284C ASN* 3.8 23.6 - - + +
285C ASP 3.1 6.5 + - - +
286C MET* 3.6 38.1 - - + +
287C TRP 3.3 0.2 - - - -
288C GLU* 1.3 73.5 - - - +
290C PHE* 1.3 66.8 + - - +
293C GLN* 2.9 50.5 + - + +
294C ILE* 3.2 13.7 + - + -
323C LEU* 3.7 28.5 - - + -
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Residues in contact with PHE 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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76C TYR* 3.5 35.9 - + - -
79C TYR* 5.5 0.9 - + - -
80C LEU* 3.7 32.4 - - + +
286C MET 2.9 20.2 + - - +
287C TRP* 3.5 27.4 - + + +
289C ILE* 1.3 73.9 - - - +
291C ASN* 1.3 69.7 + - - +
294C ILE* 3.2 15.4 - - + +
299C ARG* 2.5 64.1 + - + -
302C LEU* 5.2 3.1 - - + -
303C ARG* 6.0 1.6 - - - -
308C LEU* 5.6 0.7 - - + -
311C LEU* 4.3 10.1 - - + -
314C LEU* 3.9 13.9 - - + -
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Residues in contact with ASN 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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287C TRP* 3.1 58.6 + - - +
288C GLU* 3.9 4.7 - - - +
289C ILE 3.2 0.2 - - - -
290C PHE* 1.3 96.0 - - - +
292C ALA* 1.3 60.0 + - + +
294C ILE 4.8 0.3 - - - +
299C ARG* 3.5 23.4 + - - +
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Residues in contact with ALA 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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288C GLU* 2.8 21.4 + - + +
291C ASN* 1.3 74.4 - - + +
293C GLN* 1.3 69.1 + - + +
294C ILE 3.7 3.1 - - - -
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Residues in contact with GLN 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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30C LEU* 4.6 5.0 - - - +
284C ASN* 3.4 31.3 + - - +
288C GLU 5.7 0.4 - - - -
289C ILE* 2.9 37.6 + - + +
292C ALA* 1.3 88.9 - - + +
294C ILE* 1.3 68.7 + - + +
295C PRO* 3.4 10.6 - - - +
325C LYS* 5.5 6.1 + - - +
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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