Contacts of the helix formed by residues 298 - 308 (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 LEU 298 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194F PHE 5.2 1.2 + - - -
196F GLN* 4.0 28.0 + - - +
198F ARG* 5.0 1.3 - - - +
206F ARG* 4.6 9.6 - - + +
207F SER* 3.4 35.2 - - - +
210F GLU* 3.5 22.4 - - - +
297F LEU* 1.3 72.8 - - - +
299F LEU* 1.3 58.7 + - - +
300F ASP* 4.0 8.7 - - + +
301F ASP* 2.8 54.3 + - - +
302F PHE 3.0 9.0 + - - -
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Residues in contact with LEU 299 (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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209F MET* 3.9 18.6 - - + +
210F GLU* 3.3 18.4 + - + +
213F PHE* 3.6 39.9 - - + -
221F PHE* 3.9 11.7 - - + -
232F PHE* 4.3 23.3 - - + -
236F VAL* 5.0 6.1 - - + -
250F LEU* 5.5 3.1 - - + -
252F ILE* 3.7 29.8 - - + -
297F LEU 3.4 3.7 + - - -
298F LEU* 1.3 71.1 - - - +
300F ASP* 1.3 65.3 + - - +
302F PHE* 3.0 17.3 + - + +
303F VAL* 3.0 27.2 + - + +
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Residues in contact with ASP 300 (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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207F SER* 2.9 35.8 + - - -
209F MET* 3.3 39.1 + - + +
298F LEU* 3.2 7.6 - - + +
299F LEU* 1.3 75.9 - - - +
301F ASP* 1.3 67.6 + - - +
303F VAL* 3.7 3.3 + - - +
304F GLU* 3.2 21.3 + - - +
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Residues in contact with ASP 301 (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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193F TYR* 3.6 33.3 - - + +
194F PHE 5.0 7.6 + - - +
196F GLN* 5.2 0.9 - - - +
297F LEU* 4.8 7.1 - - + +
298F LEU* 2.8 47.6 + - - +
300F ASP* 1.3 75.8 - - - +
302F PHE* 1.3 60.1 + - - +
304F GLU* 3.4 6.9 + - - +
305F ILE* 2.9 29.8 + - - +
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Residues in contact with PHE 302 (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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232F PHE* 3.8 27.8 - + - -
235F ILE* 3.8 21.5 - - + -
236F VAL* 3.8 24.5 - - + -
250F LEU* 3.8 28.7 - - + -
297F LEU* 4.1 20.1 - - + +
298F LEU 3.0 8.8 + - - +
299F LEU* 3.0 17.5 + - + +
301F ASP* 1.3 73.8 - - - +
303F VAL* 1.3 64.2 + - - +
305F ILE* 3.2 13.7 + - + +
306F ILE* 3.0 30.5 + - + +
329F PHE* 5.6 5.2 - + - -
341F PHE* 4.1 29.8 - + - -
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Residues in contact with VAL 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F MET* 3.9 26.9 - - + -
225F TYR* 5.6 2.0 - - + +
227F LEU* 4.2 20.6 - - + -
232F PHE* 4.2 15.3 - - + -
299F LEU* 3.0 20.6 + - + +
300F ASP 3.8 6.1 - - - +
302F PHE* 1.3 72.8 - - - +
304F GLU* 1.3 65.2 + - - +
306F ILE* 3.3 8.5 + - - +
307F LYS* 2.9 56.9 + - + +
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Residues in contact with GLU 304 (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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193F TYR* 2.8 26.7 + - - +
300F ASP 3.2 12.4 + - - +
301F ASP* 3.5 11.8 - - - +
302F PHE 3.3 0.2 - - - -
303F VAL* 1.3 78.4 - - - +
305F ILE* 1.3 54.2 + - - +
307F LYS* 3.5 3.8 + - - +
308F SER* 2.7 37.9 + - - +
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Residues in contact with ILE 305 (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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193F TYR* 3.4 45.3 - - + +
297F LEU* 4.9 8.7 - - + -
301F ASP 2.9 20.5 + - - +
302F PHE* 3.3 20.2 - - + +
304F GLU* 1.3 74.8 - - - +
306F ILE* 1.3 61.0 + - - +
308F SER* 2.8 16.0 + - - -
309F GLN* 2.8 28.1 - - - +
320F VAL* 3.7 38.6 - - + -
329F PHE* 6.1 0.4 - - + -
341F PHE* 4.6 16.4 - - + -
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Residues in contact with ILE 306 (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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227F LEU* 5.4 1.1 - - + -
230F TYR* 4.1 36.0 - - + +
232F PHE* 4.4 15.3 - - + -
235F ILE* 4.0 26.5 - - + -
302F PHE* 3.0 32.9 + - + +
303F VAL* 3.3 16.4 - - + +
305F ILE* 1.3 82.1 - - + +
307F LYS* 1.3 69.9 + - + +
309F GLN* 3.4 22.1 - - + +
311F LEU* 5.9 0.5 - - - +
331F LEU* 5.8 3.1 - - + -
338F VAL* 4.7 11.5 - - + +
341F PHE* 4.5 17.0 - - + -
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Residues in contact with LYS 307 (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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225F TYR 3.6 11.3 + - - -
226F LYS* 3.4 29.8 + - - +
227F LEU* 4.0 3.8 - - - -
230F TYR* 3.6 38.7 + - + +
303F VAL* 2.9 40.4 + - + +
304F GLU* 4.2 3.6 - - - +
306F ILE* 1.3 76.0 - - + +
308F SER* 1.3 59.4 + - - +
309F GLN 3.0 16.4 + - - +
311F LEU* 5.6 1.2 - - - +
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Residues in contact with SER 308 (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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304F GLU* 2.7 28.0 + - - +
305F ILE* 2.8 13.2 + - - -
307F LYS* 1.3 73.6 - - - +
309F GLN* 1.3 66.4 + - - +
310F ASP 4.0 1.0 + - - -
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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