Contacts of the helix formed by residues 294 - 306 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171J TYR* 3.6 1.2 + - - -
211J PHE 5.5 0.7 - - - -
237J THR* 5.3 3.8 - - - -
239J ARG* 5.4 12.8 - - - +
241J GLU* 4.2 9.6 - - - +
292J PHE 3.4 5.3 + - - +
293J LYS* 1.3 75.2 - - - +
295J VAL* 1.3 59.4 + - - +
296J ALA* 3.5 9.8 + - - +
297J GLU* 2.7 38.9 + - - +
298J GLY* 2.8 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171J TYR* 3.8 8.3 - - - +
211J PHE* 3.6 44.9 + - + +
241J GLU* 3.1 33.7 + - + +
245J ALA* 4.0 10.3 - - + +
246J VAL* 3.7 33.9 - - + +
249J ALA* 4.5 2.2 - - + -
294J THR* 1.3 72.2 - - - +
296J ALA* 1.3 67.6 + - - +
299J VAL* 2.9 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 296 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241J GLU* 5.1 1.8 + - - -
249J ALA* 4.3 12.9 - - + +
294J THR* 3.3 9.2 + - - +
295J VAL* 1.3 81.2 - - - +
297J GLU* 1.3 54.1 + - + +
300J THR* 2.5 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292J PHE 4.2 1.2 - - - +
293J LYS* 3.3 21.8 - - + -
294J THR* 2.7 46.1 + - - +
296J ALA* 1.3 79.8 - - + +
298J GLY* 1.3 64.4 + - - +
300J THR* 3.3 6.1 + - - -
301J GLU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171J TYR* 3.2 22.2 - - - -
213J TYR* 3.7 17.9 - - - -
293J LYS* 4.2 8.2 - - - +
294J THR 2.8 14.6 + - - -
297J GLU* 1.3 74.7 - - - +
299J VAL* 1.3 55.8 + - - +
301J GLU* 3.3 6.0 + - - +
302J TYR* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 299 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171J TYR* 3.6 23.5 + - + -
185J ALA* 4.7 4.3 - - + -
246J VAL* 4.2 16.2 - - + +
249J ALA* 3.7 18.6 - - + -
250J THR* 3.4 28.5 - - - +
295J VAL* 2.9 39.1 + - + +
298J GLY* 1.3 71.4 - - - +
300J THR* 1.3 58.9 + - - +
302J TYR* 3.3 4.7 + - - +
303J MET* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 300 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249J ALA* 3.7 24.5 - - + +
252J ALA* 5.6 2.5 - - + -
253J TYR* 4.3 21.6 - - + +
296J ALA 2.5 26.4 + - - +
297J GLU* 3.3 8.0 + - - -
299J VAL* 1.3 78.1 - - - +
301J GLU* 1.3 62.0 + - - +
303J MET* 3.1 6.5 + - - +
304J ALA* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 301 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213J TYR* 3.3 24.3 + - - +
293J LYS* 2.9 38.9 + - - +
297J GLU 3.0 18.0 + - - +
298J GLY 3.6 4.3 - - - +
300J THR* 1.3 77.1 + - - +
302J TYR* 1.3 64.2 + - - +
304J ALA* 3.4 8.1 + - - +
305J TRP* 3.1 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 302 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171J TYR* 4.0 11.2 - + + -
172J GLY* 3.0 35.7 + - - -
173J PRO* 3.3 21.9 - - + +
174J ARG 5.2 0.2 + - - -
175J GLU* 2.6 34.3 + - - +
183J SER* 3.9 9.0 - - - -
185J ALA* 4.0 14.4 - - + -
186J PHE* 3.3 19.2 - - - -
213J TYR* 4.1 11.6 - - + -
298J GLY 2.9 16.2 + - - +
299J VAL* 3.4 6.1 - - - +
301J GLU* 1.3 75.0 - - - +
303J MET* 1.3 61.3 + - + +
305J TRP* 3.1 6.5 + + - -
306J LEU* 2.9 56.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 303 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J ALA* 3.6 33.7 - - + +
189J ASN* 3.6 28.9 - - + +
250J THR* 3.6 27.6 - - + +
253J TYR* 3.5 37.6 + - + -
254J HIS* 3.9 8.5 - - - -
299J VAL* 2.8 36.9 + - + +
300J THR* 3.1 4.5 + - - +
302J TYR* 1.3 75.0 - - + +
304J ALA* 1.3 61.5 + - - +
306J LEU* 3.3 10.6 + - + -
307J ASN* 2.6 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253J TYR* 3.4 20.9 + - + +
300J THR 3.0 11.7 + - - +
301J GLU* 3.5 11.2 - - + +
303J MET* 1.3 77.4 - - - +
305J TRP* 1.3 62.0 + - - +
307J ASN 3.1 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 305 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173J PRO* 3.6 48.5 - - + +
174J ARG* 4.0 30.3 - - + +
213J TYR* 5.7 0.7 - - - +
301J GLU* 3.1 10.2 + - + +
302J TYR* 3.1 9.0 + + - +
304J ALA* 1.3 79.0 - - - +
306J LEU* 1.3 88.8 + - + +
307J ASN* 3.1 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186J PHE* 4.1 24.5 - - + -
189J ASN* 3.6 38.1 + - + +
193J ASN* 5.2 0.9 + - - -
302J TYR* 2.9 53.9 + - + +
303J MET* 3.7 13.5 - - + +
304J ALA 3.2 0.4 - - - -
305J TRP* 1.3 90.9 - - + +
307J ASN* 1.3 75.5 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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