Contacts of the helix formed by residues 217 - 225 (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 ALA 217 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215E GLU 3.9 0.6 + - - -
216E LEU* 1.3 78.3 - - - +
218E MET* 1.3 70.4 + - - +
219E ASP* 3.8 4.3 - - - +
220E GLU* 3.7 12.1 + - + +
221E PHE* 3.2 16.6 + - - +
237E TYR* 4.4 0.9 - - - -
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Residues in contact with MET 218 (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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217E ALA* 1.3 78.5 - - - +
219E ASP* 1.3 61.7 + - + +
221E PHE* 3.1 3.5 + - - +
222E ILE* 3.0 43.1 + - + +
233E GLU* 3.4 36.1 - - + +
237E TYR* 3.6 48.5 + - + -
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Residues in contact with ASP 219 (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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217E ALA* 5.3 2.8 - - - +
218E MET* 1.3 76.3 + - + +
220E GLU* 1.3 64.6 + - - +
222E ILE* 3.7 16.8 - - + +
223E GLN* 3.0 34.7 + - - +
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Residues in contact with GLU 220 (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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216E LEU* 4.6 6.5 - - + -
217E ALA* 3.7 22.0 + - + +
219E ASP* 1.3 83.4 + - - +
221E PHE* 1.3 57.9 + - - +
223E GLN* 4.1 11.9 + - - +
224E ARG* 3.2 30.3 + - - +
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Residues in contact with PHE 221 (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* 3.2 43.1 - - + -
212E ASP* 3.6 12.1 - - + +
213E PHE* 3.4 33.9 - + + -
216E LEU* 4.2 10.3 - - + +
217E ALA 3.2 14.6 + - - +
218E MET 3.1 3.9 + - - +
220E GLU* 1.3 78.5 - - - +
222E ILE* 1.3 69.1 + - + +
224E ARG* 3.3 6.5 + - + +
225E TYR* 3.1 50.7 + + + +
237E TYR* 3.6 22.9 - + - +
299E LEU* 4.2 8.1 - - + -
303E VAL* 6.1 2.9 - - + -
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Residues in contact with ILE 222 (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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218E MET* 3.0 44.3 + - + +
219E ASP* 3.4 14.1 + - + +
221E PHE* 1.3 79.8 - - + +
223E GLN* 1.3 59.6 + - - +
226E LYS 3.3 2.3 + - - -
227E LEU* 2.7 47.8 + - + +
228E GLU* 3.3 29.6 + - - +
231E ALA* 6.4 0.4 - - - +
232E PHE* 5.0 14.8 - - + +
233E GLU* 5.5 2.0 - - + +
237E TYR* 4.6 12.1 - - + -
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Residues in contact with GLN 223 (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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219E ASP 3.0 17.5 + - - +
220E GLU* 4.6 10.5 + - - +
222E ILE* 1.3 75.9 - - - +
224E ARG* 1.3 70.7 - - - +
226E LYS* 3.0 16.5 + - - +
228E GLU* 5.3 2.7 - - - +
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Residues in contact with ARG 224 (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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212E ASP* 4.1 20.4 + - + +
216E LEU* 5.4 10.6 - - - +
220E GLU 3.2 21.8 + - - +
221E PHE* 3.5 9.0 - - - +
223E GLN* 1.3 84.7 - - - +
225E TYR* 1.3 77.3 + - + +
226E LYS 3.4 0.9 + - - -
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Residues in contact with TYR 225 (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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208E GLN* 3.9 6.8 - - - +
209E MET* 3.3 53.4 + - + -
212E ASP* 2.6 29.8 + - + -
221E PHE* 3.1 50.4 + + + +
222E ILE 4.4 0.9 - - - +
223E GLN 3.1 1.0 - - - -
224E ARG* 1.3 90.1 - - + +
226E LYS* 1.3 67.9 + - - +
227E LEU* 3.1 9.8 + - + +
303E VAL* 5.5 5.2 - - + +
307E LYS* 2.9 20.1 + - - -
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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