Contacts of the helix formed by residues 213 - 218 (chain B) in PDB entry 2XAR
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 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B SER* 3.4 15.4 + - - -
193B PHE* 5.0 0.2 - - - -
194B LYS* 5.5 12.0 - - + +
211B GLU 3.7 3.9 + - - +
212B TYR* 1.3 80.1 - - - +
214B PRO* 1.3 60.9 - - - +
215B LEU* 3.0 39.0 - - - +
216B ASP* 2.8 48.6 + - - +
217B LEU 3.7 1.7 + - - -
224B ARG* 5.1 1.7 + - - -
228B ALA* 5.7 1.2 - - - +
231B ALA* 5.2 0.2 - - - +
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Residues in contact with PRO 214 (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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169B PRO 3.5 9.9 - - - +
170B LYS* 4.7 0.7 - - + -
171B CYS 3.3 23.8 - - - +
172B GLY* 3.9 3.8 - - - -
191B SER* 4.3 4.3 - - - +
193B PHE* 3.6 34.5 - - + -
212B TYR* 3.3 40.5 - - + +
213B ASP* 1.3 89.1 - - - +
215B LEU* 1.3 55.5 + - + +
216B ASP 3.2 0.2 - - - -
217B LEU* 3.2 1.8 + - - +
218B PHE* 3.0 35.1 + - + -
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Residues in contact with LEU 215 (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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171B CYS 5.1 0.7 - - - +
172B GLY* 3.6 31.4 - - - +
173B PHE* 3.9 11.0 - - - +
174B LEU* 3.8 38.8 - - + +
189B SER 4.9 2.5 - - - +
191B SER* 4.1 13.9 - - - +
213B ASP* 2.9 25.7 + - - +
214B PRO* 1.3 76.6 - - - +
216B ASP* 1.3 57.2 - - - +
218B PHE 3.9 0.3 - - - -
219B SER* 3.0 29.8 + - - -
224B ARG* 3.4 14.8 + - - +
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Residues in contact with ASP 216 (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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213B ASP* 2.8 34.1 + - - +
215B LEU* 1.3 76.9 - - - +
217B LEU* 1.3 64.5 + - - +
219B SER* 3.0 18.2 + - - -
224B ARG* 2.7 68.1 + - - +
225B VAL* 3.7 1.6 + - - +
227B GLU* 5.0 14.8 - - - +
228B ALA* 4.1 7.9 - - + +
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Residues in contact with LEU 217 (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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167B ILE* 4.1 16.6 - - + -
169B PRO* 3.7 21.1 - - + -
212B TYR* 3.4 30.3 - - + +
213B ASP 3.7 0.6 + - - -
214B PRO 3.2 9.4 + - - +
216B ASP* 1.3 81.5 - - - +
218B PHE* 1.3 62.0 + - + +
219B SER 3.5 0.3 + - - -
220B GLY 4.6 0.5 + - - -
225B VAL* 3.6 20.3 - - + +
228B ALA* 3.8 23.2 - - + +
229B ILE* 3.9 24.2 - - + -
232B LEU* 4.6 1.1 - - + -
295B VAL* 4.1 15.7 - - + -
301B LEU* 3.4 28.6 - - + +
371B ILE* 5.6 0.2 - - + -
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Residues in contact with PHE 218 (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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169B PRO* 3.7 33.7 - - + -
170B LYS 3.4 24.0 - - - -
172B GLY* 3.4 31.0 - - - +
212B TYR* 4.7 0.4 - - - -
214B PRO 3.0 25.6 + - - +
215B LEU 3.9 1.6 - - - +
217B LEU* 1.3 77.7 - - + +
219B SER* 1.3 61.5 + - - +
220B GLY* 3.0 7.9 + - - -
301B LEU* 3.5 47.8 - - + -
302B ASP* 4.7 7.7 - - - +
304B LEU* 4.2 4.7 - - + -
305B LEU* 3.8 34.3 - - + +
308B GLN* 4.0 11.2 - - - -
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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