Contacts of the helix formed by residues 159 - 183 (chain B) in PDB entry 2R9R
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 159 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLN* 5.8 1.7 + - - -
152B LEU* 4.8 4.9 - - - +
156B PRO 3.4 5.2 - - - +
157B GLU* 3.0 4.7 - - - -
158B SER* 1.3 90.3 + - - +
160B GLY* 1.3 65.7 + - - +
161B PRO* 3.4 18.3 - - - +
162B ALA* 3.1 22.3 + - - +
163B ARG* 3.2 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B SER* 1.3 72.0 - - - +
161B PRO* 1.3 70.3 - - - +
163B ARG* 3.1 24.0 + - - +
164B ILE* 3.2 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 4.7 13.2 - - + -
159B SER* 3.4 15.5 - - - +
160B GLY* 1.3 91.1 - - - +
162B ALA* 1.3 60.9 + - - +
164B ILE* 3.1 14.5 + - + +
165B ILE* 3.1 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 3.8 24.4 - - - +
155B TYR 3.6 8.5 - - - +
156B PRO* 3.4 17.0 - - + +
158B SER* 3.3 26.2 - - - +
159B SER* 3.1 17.1 + - - +
161B PRO* 1.3 80.1 - - - +
163B ARG* 1.3 61.2 + - - +
165B ILE* 3.4 4.9 + - - +
166B ALA* 3.2 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PRO* 3.0 21.5 - - + +
157B GLU* 3.0 36.2 + - - +
159B SER 3.2 7.6 + - - +
160B GLY* 3.1 14.7 + - - +
162B ALA* 1.3 77.3 - - - +
164B ILE* 1.3 69.2 + - + +
166B ALA* 2.9 9.3 + - - +
167B ILE* 2.8 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLY 3.2 17.5 - - - +
161B PRO* 3.2 14.8 - - + +
163B ARG* 1.3 80.4 - - + +
165B ILE* 1.3 59.5 + - + +
167B ILE* 3.2 7.7 + - + +
168B VAL* 2.9 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 3.2 51.6 - - + +
153B PHE* 3.7 35.4 - - + -
161B PRO* 3.1 15.3 + - + +
162B ALA 3.6 5.8 - - - +
164B ILE* 1.3 79.1 - - + +
166B ALA* 1.3 58.6 - - - +
168B VAL* 3.6 6.3 + - - +
169B SER* 2.8 34.6 + - - +
232B TRP* 3.9 15.6 - - + -
236B GLU* 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PRO* 4.0 26.7 - - + -
162B ALA 3.2 10.1 + - - +
163B ARG* 2.9 9.5 + - - +
165B ILE* 1.3 77.1 - - - +
167B ILE* 1.3 68.7 + - + +
169B SER* 3.1 6.0 + - - -
170B VAL* 3.1 27.0 + - - +
306B HIS* 3.9 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ARG* 2.8 28.7 + - + +
164B ILE* 3.6 11.0 - - + +
166B ALA* 1.3 74.9 - - + +
168B VAL* 1.3 63.7 + - + +
170B VAL* 3.2 11.1 + - + +
171B MET* 3.0 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 2.9 34.3 + - + +
165B ILE* 3.8 5.8 - - - +
167B ILE* 1.3 77.2 - - + +
169B SER* 1.3 57.5 + - - +
171B MET* 3.2 9.7 + - + +
172B VAL* 2.9 46.2 + - + +
232B TRP* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ILE* 2.8 22.2 + - - +
166B ALA* 3.1 10.7 + - - -
168B VAL* 1.3 78.1 - - - +
170B VAL* 1.3 58.4 + - - +
172B VAL* 3.5 1.7 + - - +
173B ILE* 3.0 35.5 + - - +
232B TRP* 3.4 19.8 + - - +
233B PHE* 5.0 0.3 - - - -
236B GLU* 2.8 28.3 + - - -
306B HIS* 3.8 16.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ALA 3.1 16.1 + - - +
167B ILE* 3.6 11.9 - - + +
169B SER* 1.3 72.1 - - - +
171B MET* 1.3 77.0 + - + +
173B ILE* 3.2 8.4 + - - +
174B LEU* 2.9 34.8 + - + +
303B LEU* 4.2 10.1 - - + -
306B HIS* 3.8 31.4 - - + +
510B PGW 4.1 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 3.0 32.9 + - + +
168B VAL* 3.5 11.4 - - + +
170B VAL* 1.3 95.5 - - + +
172B VAL* 1.3 58.7 + - + +
174B LEU* 3.4 17.5 + - + +
175B ILE* 2.9 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 2.9 36.7 + - + +
169B SER 3.9 3.8 - - - +
171B MET* 1.3 74.5 - - + +
173B ILE* 1.3 61.1 + - - +
175B ILE* 3.4 9.9 + - + +
176B SER* 2.9 27.0 + - - -
229B CYS* 3.9 28.3 - - - -
232B TRP* 4.1 24.7 - - + -
233B PHE* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER* 3.0 28.1 + - - +
170B VAL 3.6 3.6 - - - +
172B VAL* 1.3 77.2 - - - +
174B LEU* 1.3 63.9 + - - +
176B SER* 2.6 25.9 + - - +
177B ILE* 3.1 19.8 + - + +
233B PHE* 3.9 19.1 - - + -
236B GLU* 5.8 1.1 - - - +
299B ARG 3.7 20.9 - - - +
302B LYS* 3.5 39.7 - - + +
303B LEU* 3.8 29.8 - - + -
306B HIS* 4.4 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 2.9 25.1 + - + +
171B MET* 3.8 24.0 - - + +
173B ILE* 1.3 76.3 - - - +
175B ILE* 1.3 63.0 + - + +
177B ILE* 3.3 13.4 + - + +
178B VAL* 3.1 30.1 + - + +
303B LEU* 4.2 26.2 - - + -
510B PGW 4.3 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B MET* 2.9 31.8 + - + +
172B VAL* 3.7 8.7 - - + +
174B LEU* 1.3 74.9 - - + +
176B SER* 1.3 61.0 + - - +
178B VAL* 3.4 5.8 + - - +
179B SER* 2.9 28.8 + - - -
225B VAL* 4.0 19.7 - - + -
229B CYS* 4.1 7.9 - - - -
509B PGW 3.9 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL 2.9 13.6 + - - -
173B ILE* 2.6 24.9 + - - -
175B ILE* 1.3 77.7 - - - +
177B ILE* 1.3 59.8 + - - +
179B SER* 4.1 3.7 - - - -
180B PHE* 3.2 14.7 + - - +
226B GLU* 5.4 0.2 - - - -
229B CYS* 3.8 24.9 - - - -
233B PHE* 3.6 8.7 - - - -
299B ARG* 2.8 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ILE* 3.1 30.4 + - + +
174B LEU* 3.6 18.8 - - + +
175B ILE 3.1 0.2 - - - -
176B SER* 1.3 79.2 - - - +
178B VAL* 1.3 68.1 + - - +
180B PHE* 3.2 7.2 + - - +
181B CYS* 3.0 32.8 + - - -
297B ILE* 4.8 9.9 - - + -
299B ARG* 4.3 15.0 - - + +
300B ILE* 3.3 38.4 - - + -
303B LEU* 4.7 2.5 - - + -
505B PGW 4.4 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 3.1 18.3 + - + +
175B ILE* 3.9 3.8 - - - +
177B ILE* 1.3 76.3 - - - +
179B SER* 1.3 58.1 + - - +
181B CYS* 3.3 1.9 + - - +
182B LEU* 3.0 54.0 + - + +
505B PGW 3.6 37.9 - - + +
508B PGW 4.6 27.1 - - + -
509B PGW 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE 2.9 18.4 + - - -
176B SER* 4.1 4.0 - - - -
178B VAL* 1.3 75.8 - - - +
180B PHE* 1.3 65.0 + - - +
182B LEU* 3.4 6.2 + - - +
183B GLU* 3.2 29.6 + - - +
222B PHE* 3.8 19.4 + - - -
225B VAL* 3.6 30.4 - - - +
226B GLU* 5.0 4.0 + - - +
296B ARG* 6.2 0.2 - - - -
299B ARG* 5.8 0.4 - - - -
509B PGW 4.0 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER 3.2 18.9 + - - +
177B ILE* 3.2 4.5 + - - +
179B SER* 1.3 77.5 - - - +
181B CYS* 1.3 71.6 + - - +
183B GLU* 3.4 26.5 + - - +
184B THR* 4.2 8.6 - - + +
293B ARG* 3.4 37.1 + - + -
294B ILE* 4.8 4.0 - - - -
296B ARG* 3.4 41.0 - - + +
297B ILE* 3.7 42.8 - - + -
299B ARG* 4.0 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE* 3.0 29.3 + - - +
178B VAL* 3.6 9.6 - - - +
180B PHE* 1.3 85.2 - - - +
182B LEU* 1.3 61.1 + - - +
183B GLU 3.0 4.5 - - - -
184B THR* 2.6 31.3 + - - -
185B LEU* 4.0 4.2 + - - +
297B ILE* 5.4 4.0 - - - -
505B PGW 4.5 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL* 3.0 37.6 + - + +
179B SER 3.9 4.3 - - - +
181B CYS* 1.3 75.4 - - - +
183B GLU* 1.3 61.2 + - - +
184B THR 3.0 2.5 + - - -
185B LEU* 3.1 35.4 + - + -
188B PHE* 3.2 29.5 - - + +
222B PHE* 4.0 11.0 - - + -
505B PGW 3.8 27.4 - - + -
508B PGW 4.3 22.9 - - + -
509B PGW 4.3 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B SER* 3.2 21.5 + - - +
180B PHE* 3.4 16.7 + - - +
181B CYS 3.0 1.0 + - - -
182B LEU* 1.3 76.3 - - - +
184B THR* 1.3 59.9 + - - +
185B LEU 3.5 0.8 + - - -
188B PHE* 5.3 1.5 - - - +
189B ARG* 4.0 18.2 + - - +
211B GLY* 3.3 36.7 - - - +
212B TYR* 3.8 9.1 - - - -
222B PHE* 3.6 29.3 - - + +
226B GLU* 5.0 0.7 - - - +
293B ARG* 3.7 15.0 + - - +
296B ARG* 2.9 44.2 + - - -
----------------------------------------------------------
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