Contacts of the helix formed by residues 207 - 216 (chain D) 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 SER 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D PRO 3.6 0.8 - - - -
206D ARG* 1.3 80.8 - - - +
208D GLN* 1.3 55.7 + - - +
209D MET 3.5 4.4 + - - -
210D GLU* 2.8 30.3 + - - +
211D THR* 3.0 15.5 + - - -
298D LEU* 3.5 16.0 - - - +
300D ASP* 2.6 37.9 + - - -
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Residues in contact with GLN 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D SER* 1.3 71.8 - - - +
209D MET* 1.3 61.2 + - - +
211D THR* 3.5 16.8 + - - +
212D ASP* 3.0 51.8 + - - +
225D TYR* 3.8 5.2 - - - +
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Residues in contact with MET 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D SER* 3.0 1.4 + - - -
208D GLN* 1.3 77.4 - - - +
210D GLU* 1.3 56.5 + - - +
212D ASP* 3.4 1.2 + - - +
213D PHE* 2.9 23.3 + - - +
221D PHE* 3.3 25.6 - - + -
225D TYR* 3.4 43.0 + - + +
299D LEU* 4.1 9.2 - - + -
300D ASP* 3.3 48.0 - - - +
303D VAL* 3.6 36.1 - - + -
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Residues in contact with GLU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ARG* 2.8 32.5 + - - -
203D PHE* 4.9 0.2 - - - -
205D PRO* 3.4 10.6 - - + +
206D ARG* 2.8 15.8 + - - -
207D SER* 2.8 13.9 + - - +
209D MET* 1.3 73.1 - - - +
211D THR* 1.3 66.5 + - - +
213D PHE* 3.2 13.1 + - - +
214D LEU* 3.3 20.1 + - - +
252D ILE* 3.6 22.3 - - + +
297D LEU 3.9 0.9 - - - +
298D LEU* 3.2 20.9 - - - +
299D LEU* 2.9 40.0 + - + +
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Residues in contact with THR 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D PRO* 3.6 22.0 + - + +
207D SER 3.0 15.0 + - - -
208D GLN* 3.6 23.9 + - - +
210D GLU* 1.3 76.6 - - - +
212D ASP* 1.3 62.5 + - - +
214D LEU* 3.6 2.8 + - - +
215D GLU* 3.3 49.1 + - - +
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Residues in contact with ASP 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D GLN* 3.0 32.4 + - - +
209D MET 3.6 4.7 - - - +
210D GLU 3.2 0.2 - - - -
211D THR* 1.3 77.2 - - - +
213D PHE* 1.3 64.8 + - - +
215D GLU* 4.6 8.2 - - - +
216D LEU* 2.9 47.7 + - + +
221D PHE* 3.9 2.0 - - - -
224D ARG* 4.0 21.3 + - - -
225D TYR* 2.7 33.8 + - + -
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Residues in contact with PHE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D MET 2.9 14.7 + - - +
210D GLU* 3.2 9.6 + - - +
212D ASP* 1.3 74.1 - - - +
214D LEU* 1.3 61.9 + - + +
216D LEU 3.4 4.5 - - - +
221D PHE* 3.5 32.5 - + + -
232D PHE* 4.8 1.8 - + - -
236D VAL* 3.7 29.2 - - + -
237D TYR* 3.4 46.9 + + - -
252D ILE* 3.6 33.0 - - + -
253D GLY* 4.4 5.2 - - - -
256D LYS* 2.9 45.4 + - + +
299D LEU* 3.8 15.9 - - + -
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Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D PHE* 4.8 11.7 - - + +
205D PRO* 3.6 34.5 - - + -
210D GLU 3.3 9.5 + - - +
211D THR 4.0 3.6 - - - +
212D ASP 3.2 0.4 - - - -
213D PHE* 1.3 77.4 - - + +
215D GLU* 1.3 61.6 + - + +
252D ILE* 4.0 20.6 - - + -
255D ALA* 4.2 6.1 - - + -
256D LYS* 2.8 53.2 + - + +
259D GLN* 3.2 41.6 - - - +
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Residues in contact with GLU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D THR* 3.3 38.7 + - - +
212D ASP* 4.1 8.0 - - - +
214D LEU* 1.3 78.9 - - + +
216D LEU* 1.3 75.1 + - + +
217D ALA 3.9 0.3 + - - -
256D LYS* 4.3 0.7 + - - -
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D ASP* 2.9 39.5 + - + +
213D PHE 3.4 4.9 - - - +
215D GLU* 1.3 83.0 - - + +
217D ALA* 1.3 64.8 + - - +
220D GLU* 3.8 21.5 - - + -
221D PHE* 4.5 13.5 - - + +
224D ARG* 3.5 49.6 - - - +
256D LYS* 2.6 29.6 + - - -
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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