Contacts of the helix formed by residues 232 - 247 (chain B) in PDB entry 3R9X
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 SER 232 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLN 3.7 1.5 + - - -
231B LEU* 1.3 74.5 - - - +
233B LEU* 1.3 66.6 + - - +
234B GLU* 3.8 14.2 + - - +
235B ASP* 3.0 39.0 + - - +
236B PHE* 3.3 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 4.2 26.7 - - + +
150B ARG* 3.9 58.3 - - + +
184B LYS* 4.0 15.5 - - + -
232B SER* 1.3 72.4 - - - +
234B GLU* 1.3 75.5 + - - +
235B ASP 2.8 1.7 + - - -
236B PHE* 2.9 20.6 + - + +
237B PHE* 3.5 39.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B SER* 3.9 13.7 - - - +
233B LEU* 1.3 84.8 - - - +
235B ASP* 1.3 57.4 + - - +
237B PHE* 3.4 20.1 + - - +
238B LYS* 3.0 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ALA 4.7 0.7 - - - +
222B ILE* 4.1 20.2 - - + +
230B GLN 5.1 0.2 - - - +
231B LEU* 3.7 25.7 - - + +
232B SER* 3.0 37.1 + - - +
233B LEU 2.8 1.8 + - - -
234B GLU* 1.3 77.3 - - - +
236B PHE* 1.3 60.1 + - - -
238B LYS* 3.1 30.9 + - - +
239B LEU* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 3.8 31.4 - - + -
193B TYR* 4.4 4.5 - - - +
196B PHE* 3.8 4.8 - + + -
197B LEU* 4.0 16.8 - - + -
200B ILE* 4.1 22.4 - - + -
201B PHE* 3.8 34.1 - + - -
228B VAL* 4.0 20.2 - - + -
231B LEU* 4.0 25.6 - - + -
232B SER 3.3 27.4 - - - -
233B LEU* 2.9 11.1 + - - +
235B ASP* 1.3 73.6 - - - +
237B PHE* 1.3 71.5 + - + +
239B LEU* 3.4 5.6 - - - +
240B TYR* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 5.3 0.2 - - + -
151B THR* 3.5 22.0 - - + -
184B LYS* 4.2 16.4 - - + -
185B PHE* 3.4 57.1 - + + -
193B TYR* 3.5 22.4 - - - -
233B LEU* 3.5 48.9 - - + -
234B GLU* 3.6 22.4 - - - +
235B ASP 3.3 0.4 - - - -
236B PHE* 1.3 75.9 - - + +
238B LYS* 1.3 65.2 + - - +
240B TYR 3.2 1.2 + - - -
241B ARG* 2.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ALA* 3.5 37.0 + - + +
234B GLU* 3.0 24.6 + - - +
235B ASP* 3.1 29.7 + - - +
237B PHE* 1.3 81.1 - - - +
239B LEU* 1.3 58.1 + - - +
241B ARG* 3.6 5.3 + - - +
242B LEU* 3.3 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 3.7 17.9 - - + -
200B ILE* 4.9 5.4 - - + -
208B LEU* 5.6 0.2 - - + -
212B ILE* 4.5 18.2 - - + -
216B LEU* 4.5 3.6 - - + +
217B LEU* 3.9 20.2 - - + -
220B ALA* 3.9 16.4 - - + -
222B ILE* 3.9 23.8 - - + -
231B LEU* 4.8 7.9 - - + -
235B ASP 2.9 28.6 + - - +
236B PHE* 3.4 17.5 - - + +
238B LYS* 1.3 76.8 - - - +
240B TYR* 1.3 64.5 + - - +
241B ARG 3.3 0.2 - - - -
242B LEU* 3.6 11.2 - - + +
243B ILE* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 3.9 15.5 - + + -
187B VAL* 4.2 11.0 - - + -
188B LYS 4.6 3.6 + - - -
189B ASP 4.1 4.3 + - - -
192B ASN* 3.6 21.4 + - - +
193B TYR* 3.5 46.9 + + + -
196B PHE* 3.6 44.2 - + + -
236B PHE 2.9 20.1 + - - +
237B PHE 3.7 2.9 - - - +
239B LEU* 1.3 78.1 - - - +
241B ARG* 1.3 59.4 + - - +
243B ILE* 3.2 8.9 + - + +
244B GLU* 2.8 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 4.4 16.4 - - + -
237B PHE 2.9 15.1 + - - +
238B LYS* 3.8 6.1 - - - +
240B TYR* 1.3 76.0 - - - +
242B LEU* 1.3 64.5 + - - +
244B GLU* 3.1 22.7 + - - +
245B ASP* 2.9 61.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 3.1 41.6 - - + +
219B GLU* 3.4 26.0 - - + +
220B ALA* 3.5 29.8 - - + +
238B LYS* 3.3 13.2 + - + +
239B LEU* 3.6 11.4 - - - +
241B ARG* 1.3 78.0 - - - +
243B ILE* 1.3 57.5 + - - +
245B ASP* 3.8 8.2 + - + +
246B SER* 2.8 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 4.0 27.8 - - + -
212B ILE* 4.0 24.2 - - + -
213B PRO* 5.1 4.3 - - + -
216B LEU* 4.5 16.6 - - + -
239B LEU* 2.9 23.6 - - + +
240B TYR* 3.2 11.1 + - + +
241B ARG 3.1 0.6 - - - -
242B LEU* 1.3 73.9 - - - +
244B GLU* 1.3 62.0 + - - +
245B ASP 2.9 5.7 + - - -
246B SER* 3.1 4.1 + - - -
247B GLY* 2.9 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 5.3 1.5 - - - -
186B PRO 4.8 7.4 - - - +
188B LYS* 4.5 18.9 + - - +
240B TYR* 2.8 53.1 + - + +
241B ARG* 3.4 28.7 - - - +
243B ILE* 1.3 72.7 - - - +
245B ASP* 1.3 63.3 + - - +
246B SER 4.8 1.4 - - - -
247B GLY* 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 2.9 50.7 + - - +
242B LEU* 3.9 9.4 - - + +
244B GLU* 1.3 84.6 - - - +
246B SER* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 4.4 14.8 - - - +
242B LEU 2.8 17.9 + - - -
243B ILE* 3.1 3.7 + - - -
244B GLU 4.8 0.6 - - - +
245B ASP* 1.3 81.5 - - - +
247B GLY* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ILE* 2.9 25.1 + - - +
244B GLU 5.3 2.0 - - - -
246B SER* 1.3 82.4 - - - +
----------------------------------------------------------
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