Contacts of the helix formed by residues 243 - 255 (chain B) 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 PHE 243 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASN* 5.2 2.9 - - - -
184B VAL* 3.6 36.3 - - + +
188B LEU* 5.7 0.2 - - - +
200B LEU* 3.9 20.3 - - + +
204B SER* 4.2 10.1 + - - -
207B PHE* 3.4 36.2 + - + -
208B LYS* 4.8 0.2 - - - -
209B ARG* 3.7 37.0 - - + -
211B PHE* 3.8 22.2 - + - -
241B GLU 3.8 0.2 + - - -
242B SER* 1.3 72.6 - - - +
244B GLN* 1.3 63.5 + - - +
246B VAL* 3.1 7.7 + - + +
247B ALA* 3.0 21.8 + - - +
272B TYR* 3.7 9.4 - - - -
401B ADP 3.7 31.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 4.2 8.1 - - + +
204B SER 4.5 7.5 + - - +
205B GLU* 5.6 5.6 - - - -
242B SER* 3.2 12.9 + - - +
243B PHE* 1.3 79.3 - - - +
245B ALA* 1.3 55.7 + - - +
247B ALA* 3.3 7.9 + - - +
248B ASP* 2.8 66.6 + - - +
259B ILE* 4.2 19.1 - - - +
261B TYR* 3.9 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLU* 4.1 27.1 - - + +
242B SER* 2.9 22.9 + - - +
244B GLN* 1.3 73.2 - - - +
246B VAL* 1.3 65.5 + - - +
248B ASP* 3.2 13.2 + - - +
249B ALA* 3.0 23.7 + - - +
295B VAL* 4.0 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR* 6.4 0.2 - - + -
184B VAL* 4.9 6.7 - - + -
185B ALA* 4.2 34.8 - - + +
188B LEU* 4.6 5.6 - - + -
211B PHE* 3.7 46.7 - - + -
242B SER 4.2 2.7 - - - +
243B PHE* 3.1 8.7 + - - +
245B ALA* 1.3 76.4 - - - +
247B ALA* 1.3 63.3 + - - +
249B ALA* 3.2 4.9 + - - +
250B THR* 3.0 26.9 + - - +
295B VAL* 3.7 20.0 - - + -
299B VAL* 4.2 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 3.8 18.3 - - + +
200B LEU* 4.3 5.8 - - + -
243B PHE 3.0 12.3 + - - +
244B GLN* 3.4 12.3 - - - +
246B VAL* 1.3 77.1 - - - +
248B ASP* 1.3 52.6 + - - +
250B THR* 3.2 1.8 + - - -
251B LEU* 2.8 41.2 + - + +
259B ILE* 3.4 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLN* 2.8 51.6 + - - +
245B ALA* 3.3 12.9 - - - +
247B ALA* 1.3 73.0 - - - +
249B ALA* 1.3 64.0 + - - +
251B LEU* 3.9 5.2 - - - +
252B ALA* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ALA 3.0 10.1 + - - +
246B VAL 3.6 7.9 - - - +
248B ASP* 1.3 78.5 - - - +
250B THR* 1.3 61.7 + - - +
252B ALA* 3.5 7.2 - - - +
253B TYR* 3.2 17.7 + - - +
295B VAL* 4.3 10.5 - - + +
296B ALA* 4.3 15.0 - - + +
299B VAL* 3.7 25.0 - - + +
300B THR* 3.8 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ALA* 4.6 0.9 - - - -
188B LEU* 4.1 20.0 - - + +
189B ASN 4.5 1.3 - - - +
192B LEU* 3.9 21.8 - - + -
246B VAL* 3.0 17.8 + - - +
247B ALA* 3.5 10.3 - - - -
249B ALA* 1.3 73.7 - - - +
251B LEU* 1.3 68.0 + - + +
252B ALA 3.1 1.3 - - - -
253B TYR* 3.1 3.8 + - - +
254B HIS* 3.1 25.0 + - + +
299B VAL* 3.4 16.7 - - - +
303B MET* 3.6 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 5.5 1.3 - - + -
192B LEU* 3.8 22.7 - - + -
198B PRO* 3.9 19.1 - - + -
247B ALA* 2.8 28.5 + - + +
248B ASP* 4.2 4.7 - - - +
250B THR* 1.3 76.4 - - + +
252B ALA* 1.3 57.0 + - - +
254B HIS* 3.3 2.6 + - - +
255B LYS* 2.8 27.5 + - - -
256B LYS 3.5 18.1 + - - +
257B GLY 3.1 30.3 - - - +
258B GLN* 4.0 8.7 - - - +
259B ILE* 4.4 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ASP 3.0 18.7 + - - +
249B ALA* 3.5 8.7 - - - +
251B LEU* 1.3 78.8 - - - +
253B TYR* 1.3 61.7 + - - +
255B LYS* 3.2 26.1 - - - +
300B THR* 5.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA 3.2 10.4 + - - +
250B THR 3.1 9.0 + - - +
252B ALA* 1.3 79.8 - - - +
254B HIS* 1.3 76.0 + + - +
255B LYS* 3.2 11.4 + - - +
300B THR* 4.3 19.4 - - + +
303B MET* 3.5 40.6 + - + -
304B ALA* 3.4 31.7 + - + +
307B ASN* 4.0 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ASN* 2.8 32.9 + - - -
192B LEU* 3.8 37.1 - - + +
193B ASN* 3.4 23.6 + - - -
250B THR* 3.1 30.4 + - + +
251B LEU 4.0 3.1 - - - +
253B TYR* 1.3 88.9 - + - +
255B LYS* 1.3 69.2 + - - +
256B LYS* 3.0 27.3 + - + +
303B MET* 3.9 6.3 - - - -
307B ASN* 4.5 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU 2.8 9.8 + - - -
252B ALA* 3.2 25.1 + - - +
253B TYR 3.2 8.8 - - - +
254B HIS* 1.3 79.5 - - - +
256B LYS* 1.3 58.9 + - - +
----------------------------------------------------------
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