Contacts of the helix formed by residues 173 - 185 (chain B) in PDB entry 2OBC
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 173 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 3.4 8.2 + - - +
172B THR* 1.3 81.2 + - - +
174B PRO* 1.4 76.8 - - - +
175B GLN* 3.5 8.7 + - - +
176B ALA* 2.9 17.7 + - - +
177B ARG* 3.0 22.2 + - - +
356B VAL 4.4 0.3 + - - -
358B PRO* 3.9 20.1 - - - +
359B ASP* 2.9 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B SER* 1.4 83.6 - - - +
175B GLN* 1.3 74.7 + - - +
177B ARG* 3.3 26.7 + - + +
178B ARG* 3.0 36.6 + - - +
358B PRO* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B SER* 3.7 3.3 + - - +
174B PRO* 1.3 95.7 - - - +
176B ALA* 1.3 58.4 + - - +
178B ARG* 3.3 12.4 + - - +
179B ASP* 3.0 23.9 + - - +
356B VAL* 3.5 15.4 - - + +
357B GLY* 3.8 25.1 - - - +
358B PRO* 3.6 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 5.5 1.6 - - + -
172B THR* 3.2 28.9 - - - +
173B SER* 2.9 21.2 + - - +
175B GLN* 1.3 74.9 - - - +
177B ARG* 1.3 64.4 + - - +
179B ASP* 3.4 2.7 + - - +
180B VAL* 3.1 29.8 + - + +
320B TYR* 4.0 16.9 - - + -
356B VAL* 3.8 11.1 - - + +
359B ASP* 3.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 4.2 24.4 - - + +
173B SER 3.0 12.5 + - - +
174B PRO* 3.5 31.0 + - + +
175B GLN 3.3 0.2 - - - -
176B ALA* 1.3 77.2 - - - +
178B ARG* 1.3 70.4 + - - +
180B VAL* 3.2 8.5 + - - +
181B GLN* 3.0 22.8 + - + +
207B ARG* 4.3 15.0 - - - +
210B GLU* 3.3 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PRO* 3.0 25.4 + - - +
175B GLN* 3.3 10.1 + - - +
177B ARG* 1.3 85.4 - - - +
179B ASP* 1.3 64.1 + - - +
181B GLN* 3.4 19.4 + - - +
182B LEU* 3.5 7.1 + - - +
209B SER 4.3 10.5 + - - -
210B GLU* 3.7 52.0 + - - +
211B LEU 4.9 4.0 + - - -
212B ASP* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B GLN 3.0 17.0 + - - +
176B ALA 3.7 5.4 - - - +
178B ARG* 1.3 76.8 - - - +
180B VAL* 1.3 61.2 + - - +
182B LEU* 3.3 16.9 + - - +
183B LEU* 3.3 23.8 + - - +
320B TYR* 2.4 27.0 + - + +
354B ARG* 3.0 38.4 + - - -
356B VAL* 4.0 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LYS* 4.7 11.7 - - - +
176B ALA* 3.1 17.0 + - + +
177B ARG* 3.5 9.4 - - + +
179B ASP* 1.3 74.5 - - - +
181B GLN* 1.3 55.0 + - - +
183B LEU* 3.0 6.1 + - - +
184B ARG* 2.7 42.4 + - - +
297B TRP* 3.6 19.7 - - + +
299B GLU* 3.5 27.4 - - - +
320B TYR* 3.6 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 3.0 18.9 + - - +
178B ARG 3.4 9.4 - - - +
180B VAL* 1.3 76.1 - - - +
182B LEU* 1.3 57.3 + - - +
184B ARG* 3.1 29.5 + - - +
185B ALA* 2.9 30.1 + - - +
205B THR 3.2 7.8 + - - -
206B VAL* 3.5 6.8 - - + +
207B ARG* 2.7 70.5 + - - +
210B GLU* 3.8 26.0 - - + +
211B LEU* 4.2 6.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
18B ARG* 4.7 2.9 - - - +
19B PHE* 3.9 22.2 - - + -
178B ARG 3.5 6.5 + - - +
179B ASP* 3.3 18.2 + - - +
180B VAL 3.2 0.4 - - - -
181B GLN* 1.3 78.8 - - - +
183B LEU* 1.3 67.3 + - + +
185B ALA* 3.3 12.2 + - - +
186B GLN* 3.8 15.6 + - - +
210B GLU 5.9 0.4 - - - +
211B LEU* 3.8 17.2 - - + +
212B ASP* 4.4 8.5 - - - +
214B GLN* 3.7 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLN* 4.7 12.8 - - - +
179B ASP* 3.3 37.2 + - - +
180B VAL 3.0 7.7 + - - +
182B LEU* 1.3 82.7 - - + +
184B ARG* 1.3 64.9 + - - +
185B ALA 3.5 0.3 + - - -
186B GLN* 3.6 19.9 + - + +
187B SER* 3.6 17.5 + - - -
297B TRP* 3.6 36.6 - - + -
318B ILE* 5.6 0.7 - - + -
320B TYR* 3.9 8.7 - - - +
354B ARG* 4.3 10.1 - - - +
363B HIS* 5.2 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLN* 4.6 3.0 - - - +
171B ILE* 5.3 7.1 - - - +
180B VAL* 2.7 27.0 + - + +
181B GLN* 3.1 26.3 - - - +
183B LEU* 1.3 72.5 - - - +
185B ALA* 1.3 62.8 + - - +
187B SER* 3.1 21.7 + - - -
190B ILE* 3.7 20.2 - - + +
204B LEU* 3.4 36.1 - - - +
205B THR 2.9 24.9 + - - -
206B VAL* 4.0 8.5 - - + -
207B ARG* 3.6 11.3 - - - +
227B PRO* 3.4 14.4 - - - +
297B TRP* 3.7 23.1 - - + +
299B GLU* 2.7 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 3.4 25.6 - - + +
181B GLN 2.9 16.7 + - - +
182B LEU 3.3 8.0 + - - +
183B LEU 3.2 1.0 - - - -
184B ARG* 1.3 76.6 - - - +
186B GLN* 1.3 56.0 + - - +
187B SER 3.5 0.2 - - - -
206B VAL* 3.8 25.6 - - + -
211B LEU* 4.4 8.7 - - + -
219B TYR* 4.3 12.9 + - + +
225B ARG* 3.2 20.5 + - - +
227B PRO* 4.8 1.6 - - - -
----------------------------------------------------------
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