Contacts of the helix formed by residues 213 - 219 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A SER* 3.3 21.9 + - - -
194A LYS* 5.5 11.9 - - + +
211A GLU 3.7 4.3 + - - +
212A TYR* 1.3 80.1 - - - +
214A PRO* 1.3 56.6 - - - +
215A LEU* 3.0 32.1 - - - +
216A ASP* 2.8 53.8 + - - +
217A LEU 3.7 1.7 + - - -
224A ARG* 5.1 1.6 + - - -
228A ALA* 5.7 1.2 - - - +
231A ALA* 5.2 0.6 - - - +
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Residues in contact with PRO 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PRO 3.5 9.2 - - - +
170A LYS* 4.7 1.1 - - + -
171A CYS 3.3 25.6 - - - +
172A GLY* 3.9 3.6 - - - -
191A SER* 4.3 3.6 - - - +
193A PHE* 3.6 34.8 - - + -
212A TYR* 3.3 41.5 - - + +
213A ASP* 1.3 90.3 - - - +
215A LEU* 1.3 56.0 + - + +
216A ASP 3.2 0.2 - - - -
217A LEU* 3.2 1.7 + - - +
218A PHE* 3.0 36.4 + - + -
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A CYS 5.1 0.2 - - - +
172A GLY* 3.6 31.1 - - - +
173A PHE* 3.8 10.5 - - - +
174A LEU* 3.9 38.6 - - + +
189A SER 4.9 2.7 - - - +
191A SER* 4.1 14.4 - - - +
213A ASP* 2.9 24.3 + - - +
214A PRO* 1.3 77.3 - - - +
216A ASP* 1.3 57.9 + - - +
218A PHE 3.9 0.7 - - - -
219A SER* 3.1 30.3 + - - -
224A ARG* 3.5 15.7 + - - +
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Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ASP* 2.8 35.8 + - - +
215A LEU* 1.3 75.0 - - - +
217A LEU* 1.3 64.0 + - - +
219A SER* 3.0 18.4 + - - -
224A ARG* 2.7 69.4 + - - +
225A VAL* 3.7 1.9 + - - +
227A GLU* 5.0 13.9 - - - +
228A ALA* 4.0 9.5 + - + +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 4.1 17.3 - - + -
169A PRO* 3.7 21.1 - - + -
212A TYR* 3.4 29.6 - - + +
213A ASP 3.7 1.8 + - - -
214A PRO 3.2 8.1 + - - +
216A ASP* 1.3 80.3 - - - +
218A PHE* 1.3 61.1 + - + +
220A GLY 4.7 0.3 + - - -
225A VAL* 3.6 19.3 - - + +
228A ALA* 3.7 18.3 - - + +
229A ILE* 3.8 29.6 - - + -
232A LEU* 4.7 1.3 - - + -
295A VAL* 4.3 10.1 - - + -
301A LEU* 3.3 36.6 - - + +
371A ILE* 5.6 0.7 - - + -
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Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PRO* 3.7 33.7 - - + -
170A LYS 3.4 23.8 - - - -
172A GLY* 3.3 31.2 - - - +
212A TYR* 4.7 0.4 - - - -
214A PRO* 3.0 26.7 + - + +
215A LEU 3.9 1.1 - - - +
217A LEU* 1.3 77.7 - - + +
219A SER* 1.3 62.1 + - - +
220A GLY* 3.1 5.6 + - - -
301A LEU* 3.7 40.8 - - + -
302A ASP* 4.8 7.5 - - - +
304A LEU* 4.2 5.6 - - + -
305A LEU* 3.8 44.1 - - + +
308A GLN* 4.0 11.4 - - - -
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Residues in contact with SER 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU 3.1 18.9 + - - -
216A ASP 3.0 16.4 + - - -
217A LEU 3.3 0.2 - - - -
218A PHE* 1.3 77.1 - - - +
220A GLY* 1.3 58.5 + - - +
221A SER* 3.0 18.6 + - - -
224A ARG* 3.3 38.0 - - - +
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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