Contacts of the helix formed by residues 161 - 171 (chain C) in PDB entry 2BZN
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 THR 161 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.5 24.5 + - + +
134C TYR* 2.5 22.8 + - - +
159C VAL* 4.4 0.3 - - - +
160C VAL* 1.3 88.8 - - + +
162C GLY* 1.3 65.4 + - - +
163C GLU* 2.6 26.9 + - - -
164C MET* 3.3 7.3 + - - +
165C VAL* 3.2 19.9 + - - +
196C TYR* 3.8 24.5 - - + +
204C GLU* 3.4 12.8 - - - +
205C CYS* 3.4 7.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C THR* 1.3 69.5 - - - +
163C GLU* 1.3 65.4 + - - +
165C VAL* 3.2 5.9 + - - +
166C GLU* 3.0 30.2 + - - +
204C GLU* 2.9 25.1 + - - +
205C CYS* 4.2 0.4 - - - -
208C ALA* 3.6 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.0 32.1 + - - -
21A ARG* 4.8 11.7 + - + +
134C TYR* 3.8 7.8 - - - -
161C THR* 2.6 28.2 + - - -
162C GLY* 1.3 72.7 + - - +
164C MET* 1.3 73.9 + - + +
166C GLU* 3.5 12.9 + - - +
167C GLU* 3.0 27.9 + - - +
204C GLU* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 4.2 15.5 - - - +
133C GLY 3.4 14.8 - - - +
134C TYR* 3.6 46.9 - - + +
139C VAL* 3.4 33.2 - - + -
159C VAL* 3.5 25.6 - - + -
161C THR 3.3 5.8 + - - +
162C GLY 3.1 0.6 - - - -
163C GLU* 1.3 84.0 + - - +
165C VAL* 1.3 64.5 + - - +
167C GLU* 3.3 22.3 + - + +
168C LEU* 3.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C VAL* 3.9 11.4 - - + +
161C THR 3.2 16.0 + - - +
162C GLY* 3.4 7.2 - - - +
164C MET* 1.3 77.2 - - - +
166C GLU* 1.3 57.3 + - - +
168C LEU* 3.3 2.1 + - - +
169C ILE* 2.9 35.7 + - + +
176C ILE* 3.9 25.5 - - + +
205C CYS* 3.4 35.7 - - + +
208C ALA* 4.1 2.5 - - + -
209C ALA* 3.7 38.4 - - + +
216C ILE* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C GLY 3.0 20.6 + - - +
163C GLU* 3.7 11.6 - - - +
165C VAL* 1.3 74.7 - - - +
167C GLU* 1.3 64.5 + - - +
169C ILE* 3.2 1.9 + - - +
170C LEU* 2.9 35.6 + - + +
208C ALA* 4.0 26.5 - - + +
212C LEU* 3.7 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 2.5 53.3 + - - -
139C VAL* 3.8 19.4 - - + +
143C LYS* 5.5 1.2 + - - -
163C GLU* 3.0 17.3 + - - +
164C MET* 3.7 13.2 - - + +
165C VAL 3.3 0.2 - - - -
166C GLU* 1.3 78.8 - - - +
168C LEU* 1.3 53.0 + - - +
170C LEU* 3.4 7.4 + - - +
171C SER* 2.6 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLY 4.1 6.5 - - - +
138C PHE* 3.9 34.1 - - + -
139C VAL* 4.0 24.5 - - + -
142C VAL* 4.1 14.4 - - + +
156C ALA 4.6 5.6 - - - +
157C GLY* 4.9 0.2 - - - -
159C VAL* 3.9 25.1 - - + -
164C MET* 3.0 23.6 + - + +
167C GLU* 1.3 76.9 - - - +
169C ILE* 1.3 60.3 + - - +
171C SER* 3.3 10.6 + - - -
172C GLY 3.3 1.0 + - - -
173C ALA* 3.0 27.5 + - + +
176C ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 3.4 36.7 + - - +
40C ASN* 3.0 25.5 + - - -
165C VAL* 2.9 25.1 + - + +
166C GLU 3.7 4.0 - - - +
168C LEU* 1.3 78.0 - - - +
170C LEU* 1.3 62.2 + - - +
172C GLY* 3.1 4.0 + - - -
173C ALA 3.5 13.9 - - - +
174C ASP 4.8 2.9 - - - +
176C ILE* 3.7 18.2 - - + -
209C ALA* 3.7 37.7 - - + +
212C LEU* 3.9 16.4 - - + -
214C GLY* 4.1 14.4 - - - -
215C HIS 4.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 3.8 30.0 + - - +
166C GLU* 2.9 28.6 + - + +
167C GLU* 3.8 7.0 - - - +
169C ILE* 1.3 76.6 - - - +
171C SER* 1.3 60.0 + - - +
172C GLY 3.4 0.9 + - - -
212C LEU* 4.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C VAL* 3.5 28.5 - - - +
142C VAL* 4.0 6.5 - - - -
143C LYS* 3.3 53.5 + - - +
146C ARG* 4.3 2.3 - - - +
167C GLU* 2.6 24.3 + - - +
168C LEU* 3.6 9.2 - - - -
169C ILE 3.1 0.6 - - - -
170C LEU* 1.3 78.3 - - - +
172C GLY* 1.3 54.9 + - - +
173C ALA 3.9 0.2 - - - -
----------------------------------------------------------
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