Contacts of the helix formed by residues 298 - 308 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194E PHE 5.1 0.2 + - - -
196E GLN* 3.6 38.1 + - - +
198E ARG* 4.3 2.4 - - - +
206E ARG* 4.7 11.7 - - + +
207E SER* 3.4 16.2 - - - +
210E GLU* 3.3 18.6 - - - +
297E LEU* 1.3 74.0 - - - +
299E LEU* 1.3 67.1 + - - +
300E ASP* 3.2 35.2 - - + +
301E ASP* 2.9 42.7 + - - +
302E PHE* 3.0 10.2 + - - +
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Residues in contact with LEU 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E MET* 3.7 14.1 - - + +
210E GLU* 2.9 20.1 + - + +
213E PHE* 3.7 42.8 - - + -
221E PHE* 4.2 15.3 - - + -
236E VAL* 4.9 8.5 - - + -
250E LEU* 4.0 20.0 - - + -
252E ILE* 4.0 22.7 - - + -
297E LEU 3.6 0.8 + - - -
298E LEU* 1.3 69.6 - - - +
300E ASP* 1.3 57.5 + - - +
302E PHE* 3.0 14.0 + - + +
303E VAL* 2.7 46.2 + - + +
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Residues in contact with ASP 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E SER* 2.5 34.9 + - - -
209E MET* 3.3 36.0 - - + +
210E GLU* 4.5 0.2 - - - +
298E LEU* 3.2 11.5 - - + +
299E LEU* 1.3 74.1 - - - +
301E ASP* 1.3 64.1 + - - +
303E VAL* 4.2 1.7 - - - +
304E GLU* 3.3 23.4 + - - +
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Residues in contact with ASP 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E TYR* 3.2 40.4 - - + +
194E PHE 4.8 6.1 + - - +
196E GLN* 5.4 0.3 - - - +
297E LEU* 4.4 9.2 - - + -
298E LEU* 2.9 44.6 + - + +
300E ASP* 1.3 79.6 - - - +
302E PHE* 1.3 55.9 + - - +
304E GLU* 3.2 8.0 + - - +
305E ILE* 2.9 31.9 + - - +
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Residues in contact with PHE 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ILE* 4.9 9.2 - - + -
236E VAL* 3.3 30.1 - - + -
250E LEU* 3.6 35.7 - - + -
297E LEU* 4.6 17.0 - - + +
298E LEU 3.0 10.2 + - - +
299E LEU* 3.0 13.4 + - + +
301E ASP* 1.3 72.9 - - - +
303E VAL* 1.3 68.8 + - + +
305E ILE* 3.2 15.7 + - + +
306E ILE* 3.0 39.3 + - + +
329E PHE* 6.0 1.1 - + - -
341E PHE* 3.9 35.7 - + - -
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Residues in contact with VAL 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E MET* 3.7 29.2 - - + -
221E PHE* 6.1 3.1 - - + -
225E TYR* 5.5 5.2 - - + +
227E LEU* 6.0 6.5 - - + -
299E LEU* 2.7 33.8 + - + +
300E ASP 4.2 3.8 - - - +
302E PHE* 1.3 73.3 - - + +
304E GLU* 1.3 58.5 + - - +
306E ILE* 3.4 9.7 - - + +
307E LYS* 2.9 66.7 + - + +
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Residues in contact with GLU 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E GLU* 5.7 0.2 - - - +
193E TYR* 2.7 33.1 + - - +
300E ASP 3.3 13.8 + - - +
301E ASP* 3.2 11.4 + - - +
303E VAL* 1.3 80.4 - - - +
305E ILE* 1.3 53.1 + - - +
307E LYS* 4.4 2.2 - - - +
308E SER* 2.6 41.6 + - - +
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Residues in contact with ILE 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E TYR* 3.4 46.9 - - + -
297E LEU* 4.9 12.1 - - + -
301E ASP 2.9 15.7 + - - +
302E PHE* 3.2 22.8 + - + +
304E GLU* 1.3 73.5 - - - +
306E ILE* 1.3 60.6 + - - +
308E SER* 3.2 17.3 + - - -
309E GLN* 3.3 25.1 - - - +
320E VAL* 3.7 36.1 - - + -
329E PHE* 6.0 0.4 - - + -
341E PHE* 4.9 12.1 - - + -
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Residues in contact with ILE 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E TYR* 3.4 45.5 + - + +
302E PHE* 3.0 29.4 + - + +
303E VAL* 3.4 17.3 - - + +
305E ILE* 1.3 76.9 - - - +
307E LYS* 1.3 70.6 + - + +
309E GLN* 3.2 27.5 + - + +
311E LEU* 5.5 4.7 - - + -
331E LEU* 6.2 0.2 - - + -
341E PHE* 3.8 46.9 - - + -
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Residues in contact with LYS 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E TYR 2.9 26.3 + - - -
226E LYS* 3.4 24.5 + - - +
227E LEU* 4.5 6.7 - - - +
230E TYR* 3.4 28.7 + - + +
303E VAL* 2.9 41.9 + - + +
304E GLU* 4.4 2.5 - - - +
306E ILE* 1.3 75.3 - - + +
308E SER* 1.3 56.4 + - - +
309E GLN 3.1 11.2 + - - +
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Residues in contact with SER 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E TYR* 5.5 0.9 + - - -
304E GLU* 2.6 27.8 + - - +
305E ILE* 3.2 10.6 + - - -
306E ILE 3.3 0.2 - - - -
307E LYS* 1.3 74.8 - - - +
309E GLN* 1.3 62.6 + - - +
310E ASP 4.4 0.3 + - - -
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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