Contacts of the helix formed by residues 202 - 212 (chain B) in PDB entry 2AR0
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 ASP 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A LYS* 4.3 28.0 + - - +
200B ASP 4.3 0.2 + - - -
201B LEU* 1.3 75.2 - - - +
203B GLY* 1.3 67.4 + - - +
204B ASP* 3.1 12.9 - - - +
205B THR* 2.8 44.9 + - - -
206B GLN* 3.0 8.5 + - - -
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Residues in contact with GLY 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LEU 3.6 1.8 + - - -
202B ASP* 1.3 72.5 - - - +
204B ASP* 1.3 55.5 + - - +
206B GLN* 3.1 20.3 + - - +
207B ASP* 2.9 35.4 + - - +
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Residues in contact with ASP 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A PRO* 6.1 5.7 - - + +
261A LYS* 5.6 1.6 + - - +
303A HIS* 4.3 8.0 + - - -
170B ARG* 2.6 24.9 + - - -
202B ASP* 2.9 13.3 + - - +
203B GLY* 1.3 73.7 - - - +
205B THR* 1.3 62.6 + - - +
207B ASP* 3.3 10.3 + - - +
208B PHE* 3.1 19.2 + - - +
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LYS* 5.4 0.2 - - - +
303A HIS* 4.4 5.5 + - - -
169B PRO* 4.3 10.8 - - + -
170B ARG* 3.8 38.9 + - + +
201B LEU* 4.0 27.8 - - + -
202B ASP* 2.8 33.2 + - - -
204B ASP* 1.3 72.7 - - - +
206B GLN* 1.3 66.2 + - - +
208B PHE* 3.2 3.9 + - + +
209B GLN* 3.0 24.0 + - + +
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Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU* 2.6 51.8 + - + +
199B ASP* 3.9 11.9 + - - +
201B LEU* 3.6 14.0 + - + +
202B ASP 3.0 11.5 + - - +
203B GLY* 3.1 20.8 + - - +
205B THR* 1.3 77.6 - - - +
207B ASP* 1.3 62.2 + - - +
209B GLN* 3.3 8.5 + - - +
210B ILE* 3.0 35.1 + - + +
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Residues in contact with ASP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLY* 2.9 25.2 + - - +
204B ASP* 3.5 15.0 - - - +
205B THR 3.2 0.2 - - - -
206B GLN* 1.3 80.3 - - - +
208B PHE* 1.3 56.6 + - - +
210B ILE* 4.3 5.3 - - - +
211B HIS* 2.8 56.1 + - + +
212B ARG* 5.2 3.8 + - - +
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ARG* 3.4 68.9 - - - +
171B GLU 4.1 0.7 - - - -
172B VAL* 3.6 26.2 - - + -
204B ASP 3.1 12.1 + - - +
205B THR* 3.2 13.0 + - - +
207B ASP* 1.3 77.1 - - - +
209B GLN* 1.3 59.2 + - - +
212B ARG* 2.6 67.0 + - + +
213B ALA* 2.7 28.4 + - - -
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Residues in contact with GLN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B GLN 5.0 0.8 + - - -
169B PRO* 3.1 17.2 - - + +
170B ARG* 2.6 34.1 + - - -
171B GLU 4.4 0.8 + - - -
188B ASP* 4.7 4.3 + - - +
191B VAL* 3.8 16.9 - - - +
198B LEU* 4.2 27.1 - - + -
201B LEU* 4.5 2.0 - - + -
205B THR* 3.0 19.7 + - - +
206B GLN 3.3 6.7 + - - +
208B PHE* 1.3 81.3 - - - +
210B ILE* 1.3 60.9 + - - +
213B ALA* 3.4 19.0 + - - +
214B PHE* 3.5 42.0 + - + -
236B ILE* 5.4 2.9 - - - +
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LYS* 6.3 0.4 - - - +
198B LEU* 4.3 16.4 - - + -
206B GLN* 3.0 25.9 + - + +
207B ASP* 3.7 7.9 - - - +
209B GLN* 1.3 81.9 - - - +
211B HIS* 1.3 77.8 + - + +
235B ASP* 4.1 19.3 - - + +
236B ILE* 3.9 5.1 - - - +
237B GLU* 3.1 31.4 + - + +
238B GLY 2.9 18.7 + - - -
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Residues in contact with HIS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ASP* 2.8 44.7 + - + +
210B ILE* 1.3 92.2 - - + +
212B ARG* 1.3 76.6 + - + +
213B ALA 3.9 0.2 - - - -
214B PHE 5.1 2.5 - - - +
215B ILE* 5.8 1.2 - - - +
237B GLU* 3.4 33.1 - - + +
238B GLY* 3.0 43.5 + - - +
239B ASN* 3.9 4.7 + - - +
240B LEU* 5.5 9.1 - - + +
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Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ARG* 2.9 43.6 - - - +
204A ASP* 4.8 2.4 + - - -
172B VAL* 3.8 18.8 - - + +
207B ASP* 5.2 4.9 + - - +
208B PHE* 2.6 50.1 + - + +
211B HIS* 1.3 90.6 - - + +
213B ALA* 1.3 63.5 + - - +
214B PHE 3.3 4.6 + - - -
215B ILE* 4.2 11.6 - - + +
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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