Contacts of the helix formed by residues 294 - 306 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171F TYR* 3.6 2.0 + - - -
211F PHE 5.5 0.4 - - - -
237F THR* 5.3 0.4 - - - -
239F ARG* 3.4 30.5 - - - +
241F GLU* 4.2 6.5 - - - -
292F PHE 3.4 2.0 + - - +
293F LYS* 1.3 75.2 - - - +
295F VAL* 1.3 59.7 + - - +
296F ALA* 3.5 9.6 + - - +
297F GLU* 2.7 39.8 + - - +
298F GLY* 2.8 27.4 + - - -
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Residues in contact with VAL 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171F TYR* 3.8 7.9 - - - +
211F PHE* 3.6 44.7 + - + +
237F THR* 5.9 0.2 - - - +
241F GLU* 3.1 34.0 + - + +
245F ALA* 4.0 10.1 - - + +
246F VAL* 3.8 34.5 - - + +
249F ALA* 4.5 2.2 - - + -
294F THR* 1.3 73.3 - - - +
296F ALA* 1.3 65.9 + - - +
299F VAL* 2.9 32.9 + - + +
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Residues in contact with ALA 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F GLU* 4.8 1.4 + - - -
249F ALA* 4.3 12.5 - - + +
294F THR* 3.3 9.0 + - - +
295F VAL* 1.3 82.0 - - - +
297F GLU* 1.3 54.7 + - + +
300F THR* 2.5 36.3 + - - +
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Residues in contact with GLU 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F PHE 4.2 1.6 - - - +
293F LYS* 3.3 21.1 - - + -
294F THR* 2.7 47.5 + - - +
296F ALA* 1.3 79.4 - - + +
298F GLY* 1.3 64.4 + - - +
300F THR* 3.3 6.1 + - - -
301F GLU* 3.0 25.0 + - - +
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Residues in contact with GLY 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171F TYR* 3.2 21.3 - - - -
213F TYR* 3.7 18.5 - - - -
293F LYS* 4.3 8.4 - - - +
294F THR 2.8 14.2 + - - -
297F GLU* 1.3 75.8 - - - +
299F VAL* 1.3 55.3 + - - +
301F GLU* 3.3 5.8 + - - +
302F TYR* 2.9 29.6 + - - +
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Residues in contact with VAL 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F TYR* 3.6 23.8 + - + -
185F ALA* 4.7 4.0 - - + -
246F VAL* 4.2 16.6 - - + +
249F ALA* 3.7 17.9 - - + -
250F THR* 3.4 28.5 - - - +
295F VAL* 2.9 39.0 + - + +
298F GLY* 1.3 71.4 - - - -
300F THR* 1.3 58.6 + - - +
302F TYR* 3.3 4.9 + - - +
303F MET* 2.8 46.6 + - + +
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Residues in contact with THR 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F ALA* 3.8 25.6 - - + +
252F ALA* 5.6 2.5 - - + -
253F TYR* 4.3 21.6 - - + +
296F ALA 2.5 25.6 + - - +
297F GLU* 3.3 8.0 + - - -
298F GLY 3.3 0.2 - - - -
299F VAL* 1.3 77.6 - - - +
301F GLU* 1.3 61.3 + - - +
303F MET* 3.1 6.1 + - - +
304F ALA* 3.0 23.7 + - - +
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Residues in contact with GLU 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F TYR* 3.3 24.3 + - - +
293F LYS* 2.9 39.5 + - - +
297F GLU 3.0 17.1 + - - +
298F GLY* 3.3 5.3 + - - +
300F THR* 1.3 77.8 - - - +
302F TYR* 1.3 61.9 + - - +
304F ALA* 3.4 8.3 + - + +
305F TRP* 3.1 21.2 + - + +
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Residues in contact with TYR 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F TYR* 4.0 11.2 - + + -
172F GLY* 3.0 35.4 + - - -
173F PRO* 3.3 21.5 - - + -
174F ARG 5.2 0.2 + - - -
175F GLU* 2.6 34.7 + - - +
183F SER* 3.9 9.6 - - - -
185F ALA* 4.0 13.7 - - + -
186F PHE* 3.3 19.4 - - - -
213F TYR* 4.1 11.8 - - + -
298F GLY 2.9 17.3 + - - +
299F VAL* 3.4 5.4 - - - +
301F GLU* 1.3 74.6 - - - +
303F MET* 1.3 62.5 + - + +
305F TRP* 3.1 6.2 + + - -
306F LEU* 2.9 57.2 + - + +
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Residues in contact with MET 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F ALA* 3.6 31.4 - - + +
189F ASN* 3.6 28.9 - - + +
250F THR* 3.6 29.2 - - + +
253F TYR* 3.5 37.7 + - + -
254F HIS* 3.9 9.6 - - - -
299F VAL* 2.8 37.3 + - + +
300F THR* 3.1 4.4 + - - +
302F TYR* 1.3 74.2 - - + +
304F ALA* 1.3 61.4 + - - +
306F LEU* 3.3 11.3 + - + -
307F ASN* 2.6 28.6 + - - +
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Residues in contact with ALA 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F TYR* 3.4 20.5 - - + +
300F THR 3.0 11.4 + - - +
301F GLU* 3.5 11.9 - - + +
303F MET* 1.3 76.9 - - - +
305F TRP* 1.3 61.5 + - - +
307F ASN 3.1 21.8 + - - +
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Residues in contact with TRP 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PRO* 3.6 47.7 - - + +
174F ARG* 4.0 29.8 - - + +
213F TYR* 5.7 0.9 - - - +
301F GLU* 3.1 10.3 + - + +
302F TYR* 3.1 8.8 + + - +
304F ALA* 1.3 80.4 - - - +
306F LEU* 1.3 87.3 + - + +
307F ASN 3.1 3.9 + - - +
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Residues in contact with LEU 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F PHE* 4.1 25.4 - - + -
189F ASN* 3.6 37.2 + - + +
193F ASN* 5.2 1.4 + - - -
302F TYR* 2.9 53.4 + - + +
303F MET* 3.7 13.0 - - + +
304F ALA 3.2 0.4 - - - -
305F TRP* 1.3 91.9 - - + +
307F ASN* 1.3 73.9 + - - +
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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