Contacts of the helix formed by residues 178 - 188 (chain C) in PDB entry 2OB1
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 ASP 178 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ASP* 2.9 25.1 + - + +
176C LEU 4.7 0.2 - - - -
177C ASN* 1.3 76.2 - - - +
179C ILE* 1.3 55.1 + - - +
180C THR* 3.2 13.5 + - - -
181C GLU* 3.0 33.8 + - + +
182C THR* 2.8 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU 5.4 1.3 - - - +
177C ASN 3.7 4.6 + - - -
178C ASP* 1.3 73.1 + - - +
180C THR* 1.3 67.7 + - - +
182C THR* 3.4 6.5 + - + -
183C THR* 2.9 36.9 + - + +
211C GLU 5.6 0.2 - - - +
214C LEU* 3.6 33.4 - - + -
215C LEU* 4.0 30.5 - - + +
218C THR* 3.5 42.2 - - + +
219C ILE* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ASP* 3.2 8.5 + - - -
179C ILE* 1.3 83.6 - - - +
181C GLU* 1.3 64.9 + - - +
183C THR* 3.3 7.8 + - - +
184C ARG* 3.0 55.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ALA 3.8 7.1 - - - +
174C CYS* 3.7 17.6 - - - -
175C ASP* 2.9 36.7 + - - +
178C ASP* 3.0 28.8 + - - +
180C THR* 1.3 76.7 - - - +
182C THR* 1.3 57.6 + - - +
184C ARG* 3.7 8.6 - - - +
185C LEU* 2.9 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 5.3 1.1 - - + -
127C ILE* 5.7 2.9 - - + -
174C CYS* 3.4 13.2 - - - -
175C ASP 3.2 12.8 + - - -
176C LEU* 3.7 28.5 - - + -
178C ASP 2.8 22.0 + - - -
179C ILE* 3.7 10.1 - - + -
181C GLU* 1.3 73.6 - - - +
183C THR* 1.3 62.7 + - + +
185C LEU* 3.5 1.6 + - - +
186C LEU* 2.9 42.8 + - + +
215C LEU* 4.1 17.5 - - + -
219C ILE* 4.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ILE* 2.9 25.6 + - + +
180C THR* 3.3 12.0 + - - +
182C THR* 1.3 73.3 - - + +
184C ARG* 1.3 56.4 + - - +
186C LEU* 3.1 7.9 + - + +
187C ASP* 2.8 43.9 + - - +
218C THR* 3.2 34.5 - - + -
219C ILE* 6.3 0.4 - - + -
222C LYS* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C THR* 3.0 45.1 + - - +
181C GLU* 3.7 8.1 - - + +
183C THR* 1.3 80.0 + - - +
185C LEU* 1.3 62.0 + - - +
187C ASP* 3.3 25.0 + - - +
188C VAL* 3.5 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ILE* 4.5 14.1 - - + -
161C PRO* 3.7 31.0 - - + -
162C PHE* 3.9 11.0 - - + -
172C ALA* 3.7 24.9 - - + -
173C ALA 3.6 24.2 - - - +
174C CYS* 3.6 21.1 - - + -
181C GLU* 2.9 20.0 + - + +
182C THR* 3.7 5.4 - - + +
184C ARG* 1.3 76.5 - - - +
186C LEU* 1.3 64.0 + - + +
188C VAL* 3.1 21.3 + - - +
189C CYS* 3.3 15.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C VAL* 4.1 33.9 - - + -
125C VAL* 5.3 0.2 - - + -
127C ILE* 4.2 14.4 - - + -
182C THR* 2.9 28.9 + - + +
183C THR* 3.6 4.3 - - + +
185C LEU* 1.3 77.1 - - + +
187C ASP* 1.3 57.3 + - - +
189C CYS* 4.1 5.4 - - - -
190C THR* 2.6 49.9 + - + +
219C ILE* 4.0 30.5 - - + -
222C LYS* 3.7 28.9 - - + -
223C PHE* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C THR* 2.8 25.4 + - - +
184C ARG* 3.3 17.8 - - - +
185C LEU 3.2 0.2 - - - -
186C LEU* 1.3 74.8 - - - +
188C VAL* 1.3 61.8 + - + +
189C CYS 3.8 0.5 + - - -
190C THR 3.8 10.9 - - - +
191C LYS* 5.3 5.4 + - - -
222C LYS* 2.7 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C PRO* 4.2 14.1 - - + -
162C PHE* 3.9 27.6 - - + -
170C LYS* 4.0 6.6 - - - -
184C ARG 3.8 11.7 - - - +
185C LEU* 3.1 18.4 + - - +
187C ASP* 1.3 80.3 - - + +
189C CYS* 1.3 58.9 + - - +
190C THR 3.9 0.4 - - - -
----------------------------------------------------------
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