Contacts of the helix formed by residues 294 - 306 (chain N) in PDB entry 2X86
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 THR 294 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171N TYR* 3.6 1.7 + - - -
211N PHE 5.5 0.2 - - - -
237N THR* 5.3 0.7 - - - -
239N ARG* 3.4 30.7 - - - +
241N GLU* 4.2 6.3 - - - -
292N PHE 4.6 1.6 - - - +
293N LYS* 1.3 75.5 - - - +
295N VAL* 1.3 60.5 + - - +
296N ALA* 3.5 9.7 + - - +
297N GLU* 2.7 39.5 + - - +
298N GLY* 2.8 27.2 + - - -
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Residues in contact with VAL 295 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171N TYR* 3.8 8.1 - - - +
211N PHE* 3.6 44.7 + - + +
241N GLU* 3.1 34.3 + - + +
245N ALA* 4.0 9.9 - - + +
246N VAL* 3.7 35.2 - - + +
249N ALA* 4.4 2.2 - - + -
294N THR* 1.3 72.6 - - - +
296N ALA* 1.3 66.8 + - - +
299N VAL* 2.9 37.3 + - + +
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Residues in contact with ALA 296 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241N GLU* 4.8 1.4 + - - -
249N ALA* 4.3 13.3 - - + +
294N THR* 3.3 9.2 + - - +
295N VAL* 1.3 81.6 - - - +
297N GLU* 1.3 55.5 + - + +
300N THR* 2.5 36.0 + - - +
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Residues in contact with GLU 297 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292N PHE 4.2 1.2 - - - +
293N LYS* 3.3 21.8 - - + -
294N THR* 2.7 46.7 + - - +
296N ALA* 1.3 80.0 - - + +
298N GLY* 1.3 64.9 + - - +
300N THR* 3.3 6.2 + - - -
301N GLU* 3.0 24.1 + - - +
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Residues in contact with GLY 298 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171N TYR* 3.2 22.2 - - - -
213N TYR* 3.7 18.2 - - - -
293N LYS* 4.2 7.8 - - - +
294N THR 2.8 15.0 + - - -
297N GLU* 1.3 74.0 - - - +
299N VAL* 1.3 56.5 + - - +
301N GLU* 3.3 6.0 + - - +
302N TYR* 2.9 30.0 + - - +
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Residues in contact with VAL 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171N TYR* 3.6 24.0 + - + -
185N ALA* 4.7 3.8 - - + -
246N VAL* 4.2 16.6 - - + +
249N ALA* 3.7 17.5 - - + -
250N THR* 3.4 28.7 - - - +
295N VAL* 2.9 38.1 + - + +
298N GLY* 1.3 70.8 - - - -
300N THR* 1.3 58.4 + - - +
302N TYR* 3.3 4.9 + - - +
303N MET* 2.8 46.2 + - + +
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Residues in contact with THR 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249N ALA* 3.8 24.0 - - + +
252N ALA* 5.6 2.5 - - + -
253N TYR* 4.3 21.6 - - + +
296N ALA 2.5 26.5 + - - +
297N GLU* 3.3 8.0 + - - -
299N VAL* 1.3 77.7 - - - +
301N GLU* 1.3 62.2 + - - +
303N MET* 3.1 7.1 + - - +
304N ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213N TYR* 3.3 23.0 + - - +
293N LYS* 2.9 38.8 + - - +
297N GLU 3.0 17.6 + - - +
298N GLY 3.3 4.7 + - - +
300N THR* 1.3 76.7 - - - +
302N TYR* 1.3 63.1 + - - +
304N ALA* 3.4 7.3 + - + +
305N TRP* 3.1 20.5 + - + +
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Residues in contact with TYR 302 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171N TYR* 4.0 11.0 - + - -
172N GLY* 3.0 36.9 + - - -
173N PRO* 3.3 21.0 - - + +
174N ARG 5.1 0.2 - - - -
175N GLU* 2.6 35.0 + - - +
183N SER* 3.9 10.1 - - - -
185N ALA* 4.0 14.4 - - + -
186N PHE* 3.3 19.3 - + - -
213N TYR* 4.1 12.2 - - + -
298N GLY 2.9 17.5 + - - +
299N VAL* 3.4 5.6 - - - +
301N GLU* 1.3 75.3 - - - +
303N MET* 1.3 61.3 + - + +
305N TRP* 3.1 6.5 + + - -
306N LEU* 2.9 56.6 + - + +
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Residues in contact with MET 303 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185N ALA* 3.6 32.1 - - + +
189N ASN* 3.6 29.2 - - + +
250N THR* 3.6 28.0 - - + +
253N TYR* 3.5 36.9 + - + -
254N HIS* 3.9 9.6 - - - -
299N VAL* 2.8 37.1 + - + +
300N THR* 3.1 4.2 + - - +
302N TYR* 1.3 75.8 - - + +
304N ALA* 1.3 61.9 + - - +
306N LEU* 3.3 11.7 + - + -
307N ASN* 2.6 29.4 + - - +
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Residues in contact with ALA 304 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253N TYR* 3.4 21.2 + - + +
300N THR 3.0 11.5 + - - +
301N GLU* 3.5 12.1 - - + +
303N MET* 1.3 77.5 - - - +
305N TRP* 1.3 61.7 + - - +
307N ASN 3.1 21.7 + - - +
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Residues in contact with TRP 305 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173N PRO* 3.6 48.4 - - + +
174N ARG* 4.0 29.8 - - + +
213N TYR* 5.7 0.9 - - - +
301N GLU* 3.1 9.6 + - + +
302N TYR* 3.1 9.7 + + - +
304N ALA* 1.3 80.6 - - - +
306N LEU* 1.3 88.2 + - + +
307N ASN* 3.2 3.1 + - - +
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Residues in contact with LEU 306 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186N PHE* 4.1 25.4 - - + -
189N ASN* 3.6 37.9 + - + +
193N ASN* 5.2 1.0 + - - -
302N TYR* 2.9 53.7 + - + +
303N MET* 4.1 12.6 - - + -
304N ALA 3.2 0.6 - - - -
305N TRP* 1.3 90.4 - - + +
307N ASN* 1.3 73.8 + - - +
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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