Contacts of the helix formed by residues 161 - 171 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F TYR* 2.7 20.1 + - - +
159F VAL* 4.3 0.3 - - - +
160F VAL* 1.3 88.5 - - + +
162F GLY* 1.3 66.2 + - - +
163F GLU* 2.6 28.2 + - - -
164F MET* 3.3 5.9 + - - +
165F VAL* 3.2 20.6 + - - +
196F TYR* 3.7 24.7 - - + +
204F GLU* 3.3 11.2 - - - +
205F CYS* 3.4 6.5 - - - -
18H ARG* 3.2 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F THR* 1.3 70.6 - - - +
163F GLU* 1.3 65.3 + - - +
165F VAL* 3.2 5.3 + - - +
166F GLU* 2.9 31.7 + - - +
204F GLU* 2.9 25.0 + - - +
208F ALA* 3.7 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F TYR* 3.7 10.6 - - - -
161F THR* 2.6 28.6 + - - -
162F GLY* 1.3 71.1 + - - +
164F MET* 1.3 67.8 + - - +
166F GLU* 3.5 10.8 + - - +
167F GLU* 3.0 27.7 + - - +
18H ARG* 3.0 31.2 + - - -
21H ARG* 4.7 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F GLY 3.5 13.7 - - - +
134F TYR* 3.6 50.7 - - + +
139F VAL* 3.4 33.4 - - + -
159F VAL* 3.4 28.5 - - + -
161F THR 3.3 4.7 + - - +
162F GLY 3.2 0.4 - - - -
163F GLU* 1.3 82.1 + - - +
165F VAL* 1.3 65.9 + - - +
167F GLU* 3.7 21.8 - - + +
168F LEU* 3.0 38.5 + - + +
21H ARG* 4.3 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F VAL* 3.7 12.3 - - + +
161F THR 3.2 16.8 + - - +
162F GLY* 3.4 9.0 - - - +
164F MET* 1.3 77.8 - - - +
166F GLU* 1.3 58.1 + - - +
168F LEU* 3.3 1.9 + - - +
169F ILE* 3.0 37.0 + - + +
176F ILE* 3.9 21.0 - - + +
205F CYS* 3.4 36.1 - - + +
208F ALA* 4.2 0.9 - - + -
209F ALA* 3.8 35.7 - - + +
216F ILE* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F GLY 2.9 21.8 + - - +
163F GLU* 3.7 9.0 - - - +
165F VAL* 1.3 75.7 - - - +
167F GLU* 1.3 58.3 + - - +
169F ILE* 3.3 1.6 + - - +
170F LEU* 2.9 41.1 + - + +
208F ALA* 4.0 26.7 - - + +
212F LEU* 3.7 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F VAL* 3.8 11.9 - - + +
143F LYS* 5.4 1.7 + - - -
163F GLU* 3.0 16.8 + - - +
164F MET* 3.7 19.7 - - + +
166F GLU* 1.3 76.0 - - - +
168F LEU* 1.3 54.2 + - - +
170F LEU* 3.4 8.0 + - - +
171F SER* 2.7 44.0 + - - +
21H ARG* 2.7 53.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F GLY 4.2 2.9 - - - +
138F PHE* 4.0 33.2 - - + -
139F VAL* 4.0 27.4 - - + -
142F VAL* 4.2 8.6 - - + +
156F ALA 4.4 5.4 - - - +
157F GLY* 4.9 0.4 - - - -
159F VAL* 3.9 25.6 - - + -
164F MET* 3.0 26.9 + - + +
167F GLU* 1.3 72.9 - - - +
169F ILE* 1.3 66.5 + - - +
171F SER* 3.2 12.0 + - - -
172F GLY 3.2 1.2 + - - -
173F ALA* 3.0 26.0 + - + +
176F ILE* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ARG* 3.6 32.4 + - + +
40F ASN* 3.0 18.2 + - - -
165F VAL* 3.0 25.0 + - + +
166F GLU 3.7 3.1 - - - +
168F LEU* 1.3 75.0 - - - +
170F LEU* 1.3 58.2 + - - +
172F GLY 3.0 17.0 + - - -
173F ALA 3.4 14.6 - - - +
174F ASP 4.7 4.0 - - - +
176F ILE* 3.7 17.0 - - + -
209F ALA* 3.7 38.1 - - + +
212F LEU* 3.7 18.8 - - + -
214F GLY* 4.1 11.7 - - - -
215F HIS 4.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ARG* 3.6 33.7 + - - +
166F GLU* 2.9 27.3 + - + +
167F GLU* 3.6 7.0 - - - +
169F ILE* 1.3 74.1 - - - +
171F SER* 1.3 58.7 + - - +
172F GLY* 3.6 0.5 + - - -
212F LEU* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F VAL* 3.4 25.3 - - - +
142F VAL* 3.8 9.3 - - - +
143F LYS* 3.5 51.5 + - - +
146F ARG* 4.4 2.6 - - - +
167F GLU* 2.7 23.3 + - - +
168F LEU* 3.5 10.1 - - - -
169F ILE 3.1 0.6 - - - -
170F LEU* 1.3 76.1 - - - +
172F GLY* 1.3 57.4 + - - +
173F ALA 3.8 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