Contacts of the helix formed by residues 173 - 180 (chain B) in PDB entry 1OUQ
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 ARG 173 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU 4.5 0.2 - - - -
172B LEU* 1.3 74.8 - - - +
174B ILE* 1.3 66.8 + - - +
176B GLU* 2.8 49.9 + - - +
177B ILE* 3.1 10.0 + - - +
200B THR* 4.3 6.1 - - - -
201B LYS* 3.5 36.1 - - - +
202B THR* 4.4 8.3 + - - +
288B GLY 6.0 0.7 - - - -
289B HIS* 4.8 12.8 + - + -
292B ARG* 3.6 27.9 - - - +
313B GLY 5.6 1.0 + - - -
314B GLY 5.7 2.4 + - - -
115C A3P 3.0 14.6 + - - -
124D A 4.2 11.2 + - - -
125D T 3.6 11.2 - - - +
116X T 2.5 47.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PHE* 4.1 24.9 - - + -
172B LEU 3.9 1.4 + - - +
173B ARG* 1.3 70.1 - - - +
175B ALA* 1.3 67.4 + - - +
177B ILE* 2.9 13.2 + - + +
178B ALA* 2.9 24.2 + - - +
258B THR* 4.1 19.1 - - - +
261B LEU* 4.1 15.8 - - + +
262B GLU* 3.9 28.5 - - + -
265B PHE* 4.6 1.8 - - + -
288B GLY* 4.1 27.1 + - - +
125D T 3.1 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B HIS* 6.2 1.3 - - + -
174B ILE* 1.3 74.5 - - - +
176B GLU* 1.3 66.1 + - - +
178B ALA* 3.7 4.8 - - - +
179B ARG* 3.1 42.4 + - - +
255B GLN* 5.1 0.2 + - - -
258B THR* 4.2 16.4 - - + -
124D A 4.2 6.1 - - - +
125D T 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 3.5 27.9 - - + +
173B ARG* 2.8 60.1 + - - +
175B ALA* 1.3 78.1 - - - +
177B ILE* 1.3 68.8 + - - +
179B ARG* 2.8 30.0 + - - +
180B ILE* 3.5 7.0 + - - +
197B ILE* 4.0 11.5 - - + +
199B ARG 3.5 21.5 - - - +
200B THR* 3.6 24.8 - - - +
201B LYS 3.7 2.3 + - - -
292B ARG* 5.5 0.7 + - - -
124D A 5.4 0.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
163B PHE* 3.9 37.5 - - + -
166B ILE* 3.9 25.6 - - + -
167B ALA* 4.2 18.4 - - + -
172B LEU* 3.9 25.8 - - + +
173B ARG 3.1 10.7 + - - +
174B ILE* 2.9 12.1 + - + +
176B GLU* 1.3 75.2 - - - +
178B ALA* 1.3 66.4 + - - +
180B ILE* 2.8 32.2 + - + +
239B PHE* 4.4 22.8 - - + -
261B LEU* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE 2.9 14.0 + - - +
175B ALA* 3.7 13.2 - - - +
177B ILE* 1.3 76.3 - - - +
179B ARG* 1.3 60.3 + - - +
180B ILE 3.2 2.9 + - - +
237B TYR* 4.2 17.0 - - - +
239B PHE* 5.2 9.2 + - - +
255B GLN* 4.0 18.9 - - + +
256B LEU* 3.9 26.5 + - - +
258B THR* 5.0 4.3 - - + -
261B LEU* 4.4 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ALA* 3.1 37.5 + - - +
176B GLU* 2.8 22.8 + - - +
178B ALA* 1.3 70.4 - - - +
180B ILE* 1.3 62.3 + - - -
181B ARG* 3.0 16.8 + - - +
184B ASP* 4.1 2.4 - - - +
199B ARG* 3.3 62.2 + - - +
200B THR* 4.7 4.2 - - - +
237B TYR* 3.8 12.7 - - + +
255B GLN* 3.9 26.4 + - - +
124D A 5.2 3.4 + - - -
126E ASP* 4.2 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 4.8 7.4 - - + -
172B LEU* 4.7 5.2 - - + -
176B GLU 3.5 3.1 + - - +
177B ILE* 2.8 41.9 + - + +
178B ALA 3.2 1.6 + - - +
179B ARG* 1.3 70.4 - - - +
181B ARG* 1.3 69.0 + - - +
184B ASP* 4.2 7.0 - - + -
185B ILE* 4.7 4.7 - - + -
195B ILE* 3.4 49.4 - - + -
196B HIS 5.7 0.9 - - - +
197B ILE* 4.5 10.8 - - + -
237B TYR* 3.6 4.1 - - - +
238B LEU* 2.8 45.3 + - + +
239B PHE* 4.5 2.7 + - + -
----------------------------------------------------------
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