Contacts of the helix formed by residues 231 - 236 (chain F) in PDB entry 2RHB
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 ALA 231 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ILE* 6.3 0.4 - - - +
227F LEU 4.2 1.2 + - - -
229F GLY* 3.5 3.8 - - - +
230F TYR* 1.3 80.8 - - - +
232F PHE* 1.3 60.9 + - - +
233F GLU* 3.2 7.0 - - + +
234F ALA* 3.6 6.4 + - + +
235F ILE* 3.2 27.4 + - - +
338F VAL* 3.2 28.3 - - + +
339F GLU 3.8 15.0 - - - +
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Residues in contact with PHE 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F PHE* 4.6 5.6 - + - -
221F PHE* 4.4 10.5 - + - -
222F ILE* 4.3 15.3 - - + +
227F LEU* 3.7 33.6 + - + -
230F TYR* 3.8 22.7 - - + -
231F ALA* 1.3 73.7 - - - +
233F GLU* 1.3 63.7 + - - +
234F ALA 3.1 3.0 + - - -
235F ILE* 3.9 3.8 - - + +
236F VAL* 3.4 25.0 + - + +
237F TYR* 3.2 41.8 + + + -
299F LEU* 4.3 17.3 - - + -
302F PHE* 3.8 32.3 - + - -
303F VAL* 4.2 13.2 - - + -
306F ILE* 4.4 16.4 - - + -
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Residues in contact with GLU 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F MET* 4.1 27.0 - - - +
222F ILE* 4.4 8.2 - - + +
231F ALA* 4.9 4.0 - - + -
232F PHE* 1.3 79.0 - - - +
234F ALA* 1.3 58.0 + - + +
237F TYR* 4.1 10.4 - - - +
238F GLY 4.3 3.8 + - - -
239F ASP* 4.4 10.4 + - - +
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Residues in contact with ALA 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F ALA* 3.6 9.3 + - + +
232F PHE 3.9 0.2 - - - -
233F GLU* 1.3 81.6 - - + +
235F ILE* 1.3 61.6 + - + +
238F GLY* 4.0 5.4 + - - -
239F ASP* 4.6 4.9 + - - +
246F GLY 4.1 1.4 - - - -
247F GLY* 2.9 27.9 + - - +
339F GLU 4.1 20.0 - - - +
340F THR* 5.4 4.5 - - - -
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Residues in contact with ILE 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F TYR 3.7 6.3 - - - +
231F ALA 3.2 20.5 + - - +
232F PHE* 4.6 1.3 - - + -
234F ALA* 1.3 76.3 - - + +
236F VAL* 1.3 66.4 + - + +
247F GLY* 3.3 4.3 - - - -
248F LEU 3.0 21.0 + - - -
249F HIS* 3.1 17.9 + - + +
250F LEU* 5.8 1.3 - - + -
302F PHE* 3.8 24.9 - - + -
306F ILE* 4.0 8.1 - - + -
338F VAL* 3.7 20.6 - - + -
340F THR* 4.0 9.6 - - - +
341F PHE* 3.5 54.5 - - + +
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Residues in contact with VAL 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F PHE* 3.7 26.2 - - + -
232F PHE* 3.4 31.5 + - + +
235F ILE* 1.3 79.9 - - + +
237F TYR* 1.3 65.5 + - - +
238F GLY 3.4 0.4 - - - -
248F LEU* 3.5 12.0 - - - -
249F HIS 4.5 2.7 - - - +
250F LEU* 3.8 26.2 - - + +
252F ILE* 4.3 10.1 - - + -
253F GLY* 3.4 16.4 - - - -
299F LEU* 5.0 3.4 - - + -
302F PHE* 3.8 31.0 - - + -
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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