Contacts of the helix formed by residues 294 - 306 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171P TYR* 3.6 1.9 + - - -
211P PHE 5.5 0.2 - - - -
237P THR* 5.3 0.7 - - - -
239P ARG* 3.4 32.3 - - - +
241P GLU* 4.2 6.5 - - - +
292P PHE 3.4 2.0 + - - +
293P LYS* 1.3 75.8 - - - +
295P VAL* 1.3 60.2 + - - +
296P ALA* 3.5 10.0 + - - +
297P GLU* 2.7 39.2 + - - +
298P GLY* 2.8 27.4 + - - -
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Residues in contact with VAL 295 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171P TYR* 3.8 7.6 - - - +
211P PHE* 3.6 45.2 + - + +
241P GLU* 3.1 33.1 + - + +
245P ALA* 4.0 10.3 - - + +
246P VAL* 3.8 34.1 - - + +
249P ALA* 4.5 1.3 - - + -
294P THR* 1.3 73.2 - - - +
296P ALA* 1.3 68.1 + - - +
299P VAL* 2.9 36.7 + - + +
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Residues in contact with ALA 296 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241P GLU* 4.8 1.8 + - - -
249P ALA* 4.3 13.3 - - + +
294P THR* 3.3 9.9 + - - +
295P VAL* 1.3 81.5 - - - +
297P GLU* 1.3 54.9 + - + +
300P THR* 2.5 35.6 + - - +
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Residues in contact with GLU 297 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292P PHE 4.2 1.4 - - - +
293P LYS* 3.3 20.6 - - + -
294P THR* 2.7 45.9 + - - +
296P ALA* 1.3 79.8 - - + +
298P GLY* 1.3 65.5 + - - +
300P THR* 3.3 6.0 + - - -
301P GLU* 3.0 24.5 + - - +
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Residues in contact with GLY 298 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171P TYR* 3.2 21.8 - - - -
213P TYR* 3.7 18.8 - - - -
293P LYS* 4.2 8.0 - - - +
294P THR 2.8 15.4 + - - -
297P GLU* 1.3 73.0 - - - +
299P VAL* 1.3 55.7 + - - +
301P GLU* 3.3 6.2 + - - +
302P TYR* 2.9 29.5 + - - +
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Residues in contact with VAL 299 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171P TYR* 3.6 24.0 + - + -
185P ALA* 4.7 3.8 - - + -
246P VAL* 4.2 16.6 - - + +
249P ALA* 3.7 17.9 - - + -
250P THR* 3.4 29.4 - - - +
295P VAL* 2.9 38.7 + - + +
298P GLY* 1.3 72.0 - - - -
300P THR* 1.3 58.6 + - - +
302P TYR* 3.3 5.6 + - - +
303P MET* 2.8 45.0 + - + +
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Residues in contact with THR 300 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249P ALA* 3.8 25.1 - - + +
252P ALA* 5.6 2.9 - - + -
253P TYR* 4.3 20.5 - - + +
296P ALA 2.5 26.0 + - - +
297P GLU* 3.3 8.1 + - - -
299P VAL* 1.3 78.0 - - - +
301P GLU* 1.3 61.9 + - - +
303P MET* 3.1 5.7 + - - +
304P ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 301 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213P TYR* 3.3 24.3 + - - +
293P LYS* 2.9 39.5 + - - +
297P GLU 3.0 17.2 + - - +
298P GLY* 3.6 4.9 - - - +
300P THR* 1.3 77.3 - - - +
302P TYR* 1.3 61.9 + - - +
304P ALA* 3.4 8.1 + - + +
305P TRP* 3.1 21.4 + - + +
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Residues in contact with TYR 302 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171P TYR* 4.0 11.2 - + + -
172P GLY* 3.0 34.9 + - - -
173P PRO* 3.3 21.1 - - + -
174P ARG 5.1 0.4 + - - -
175P GLU* 2.6 34.6 + - - +
183P SER* 3.9 9.6 - - - -
185P ALA* 4.0 14.4 - - + -
186P PHE* 3.3 19.2 - + - -
213P TYR* 4.1 11.8 - - + -
298P GLY 2.9 16.9 + - - +
299P VAL* 3.4 6.1 - - - +
301P GLU* 1.3 74.6 - - - +
303P MET* 1.3 61.8 + - + +
305P TRP* 3.1 6.1 + + - -
306P LEU* 2.9 55.5 + - + +
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Residues in contact with MET 303 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185P ALA* 3.6 31.4 - - + +
189P ASN* 3.6 29.2 - - + +
250P THR* 3.6 29.2 - - + +
253P TYR* 3.5 36.5 + - + -
254P HIS* 3.9 9.0 - - - -
299P VAL* 2.8 37.8 + - + +
300P THR* 3.1 4.5 + - - +
302P TYR* 1.3 75.7 - - + +
304P ALA* 1.3 61.5 + - - +
306P LEU* 3.3 11.3 + - + -
307P ASN* 2.6 29.3 + - - +
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Residues in contact with ALA 304 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253P TYR* 3.4 21.1 + - + +
300P THR 3.0 12.3 + - - +
301P GLU* 3.5 11.9 - - - +
303P MET* 1.3 77.7 - - - +
305P TRP* 1.3 62.8 + - - +
307P ASN 3.1 21.1 + - - -
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Residues in contact with TRP 305 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173P PRO* 3.6 48.8 - - + +
174P ARG* 4.0 29.5 - - + +
213P TYR* 5.7 0.9 - - - +
301P GLU* 3.1 10.2 + - + +
302P TYR* 3.1 9.0 + + - +
304P ALA* 1.3 79.0 - - - +
306P LEU* 1.3 88.8 + - + +
307P ASN* 3.1 3.5 + - - +
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Residues in contact with LEU 306 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186P PHE* 4.1 24.9 - - + -
189P ASN* 3.6 38.1 + - + +
193P ASN* 5.2 1.4 + - - -
302P TYR* 2.9 53.7 + - + +
303P MET* 3.7 13.2 - - + +
304P ALA 3.2 0.6 - - - -
305P TRP* 1.3 91.9 - - + +
307P ASN* 1.3 74.8 + - - +
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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