Contacts of the helix formed by residues 197 - 212 (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 PRO 197 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER* 3.7 31.2 - - - +
10F LEU 3.1 25.1 - - - +
11F ASP* 3.5 14.8 - - - +
189F ARG* 4.2 3.5 - - - +
196F TYR* 1.3 91.7 - - + +
198F GLN* 1.3 60.7 + - - +
199F LEU 3.4 0.7 - - - -
200F SER* 3.4 3.6 + - - -
201F ALA* 2.9 25.5 + - - +
334H ILE* 4.0 15.5 - - + -
336H VAL* 4.2 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASP* 3.2 15.1 + - - +
12F PHE* 3.7 23.8 - - + -
160F VAL* 5.1 0.2 - - - +
178F VAL* 3.1 24.6 + - - +
179F GLY* 3.3 19.4 - - - -
180F ILE 4.5 0.5 + - - -
182F PRO* 3.4 22.4 - - + +
189F ARG* 5.1 0.6 - - - +
196F TYR 3.3 5.1 + - - +
197F PRO* 1.3 72.1 - - - +
199F LEU* 1.3 57.4 + - - +
201F ALA* 3.3 7.7 + - - +
202F VAL* 2.8 36.6 + - - +
218F SER* 3.1 20.0 + - - +
219F ASP 3.7 5.1 + - - +
220F GLY 3.7 20.3 + - - +
221F GLY* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LEU* 3.1 30.4 + - + +
11F ASP* 4.0 11.7 - - - +
12F PHE* 3.9 23.5 - - + +
15F VAL* 3.6 39.5 - - + -
198F GLN* 1.3 73.7 - - - +
200F SER* 1.3 66.7 + - - +
202F VAL* 3.3 3.9 + - + +
203F MET* 2.9 33.7 + - + +
230F LYS* 3.8 12.6 - - + +
231F ALA* 4.7 0.4 - - - -
234F ALA* 3.5 28.5 - - + -
333F PHE* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER* 3.4 12.6 + - - -
10F LEU* 2.7 38.5 + - - +
196F TYR* 4.2 13.7 - - - -
197F PRO* 3.4 11.4 + - - -
199F LEU* 1.3 77.4 - - - +
201F ALA* 1.3 61.6 + - - -
203F MET* 3.4 16.6 + - - +
204F GLU* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F VAL* 3.7 26.0 - - + +
178F VAL* 3.9 17.0 - - + -
196F TYR* 3.7 17.2 - - + -
197F PRO 2.9 17.6 + - - +
198F GLN* 3.5 11.2 - - - +
200F SER* 1.3 77.3 - - - +
202F VAL* 1.3 56.7 + - - +
204F GLU* 3.4 0.7 + - - -
205F CYS* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PHE* 5.3 0.9 - - + -
178F VAL* 4.4 5.8 - - + -
198F GLN* 2.8 32.2 + - + +
199F LEU* 3.7 6.5 - - + +
201F ALA* 1.3 72.9 - - - +
203F MET* 1.3 58.0 + - - +
206F ALA* 2.9 34.7 + - - +
216F ILE* 3.7 9.5 - - + +
218F SER* 3.2 35.0 - - - +
231F ALA* 3.8 15.7 - - + +
234F ALA* 3.7 22.9 - - + +
236F ALA* 3.8 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 203 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LEU* 3.8 26.9 - - + -
199F LEU* 2.9 20.0 + - + +
200F SER* 3.5 31.4 - - - +
202F VAL* 1.3 75.1 - - - +
204F GLU* 1.3 63.0 + - - +
206F ALA* 3.8 1.9 - - - +
207F ASP* 3.2 30.8 + - - +
234F ALA* 3.8 28.5 - - + +
333F PHE* 4.6 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F VAL 4.5 0.7 - - - -
161F THR* 3.3 17.3 - - - +
162F GLY* 2.9 30.2 + - - +
196F TYR* 2.9 25.9 + - - -
200F SER 3.0 15.5 + - - +
201F ALA* 3.9 3.1 - - - +
203F MET* 1.3 77.1 - - - +
205F CYS* 1.3 63.5 + - - +
207F ASP* 3.5 7.0 + - - +
208F ALA* 3.2 20.4 + - - +
18H ARG* 4.6 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F VAL* 3.3 38.6 - - - -
161F THR* 3.4 5.6 - - - -
165F VAL* 3.4 28.8 - - + +
178F VAL* 3.5 30.5 - - + -
201F ALA 2.8 18.8 + - - +
202F VAL 4.2 1.6 - - - +
204F GLU* 1.3 71.7 - - - +
206F ALA* 1.3 59.7 + - - +
208F ALA* 3.4 3.3 + - - +
209F ALA* 2.9 31.0 + - - +
216F ILE* 3.7 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F VAL 2.9 19.6 + - - +
203F MET 3.8 3.8 - - - +
205F CYS* 1.3 77.7 - - - +
207F ASP* 1.3 65.6 + - - +
210F HIS* 2.9 39.3 + - + +
216F ILE* 3.7 14.3 - - + +
234F ALA 4.0 6.3 - - - +
235F GLY* 3.6 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 207 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F MET 3.2 17.1 + - - +
204F GLU* 3.8 6.1 - - - +
206F ALA* 1.3 80.5 - - - +
208F ALA* 1.3 63.5 + - - +
210F HIS* 3.9 5.3 + - - +
211F GLY* 3.0 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F GLY* 3.7 37.9 - - - +
165F VAL* 4.2 6.3 - - + -
166F GLU* 4.0 21.4 - - + +
169F ILE* 5.2 0.2 - - - -
204F GLU 3.2 7.8 + - - +
205F CYS 3.7 7.0 - - - +
206F ALA 3.3 0.2 - - - -
207F ASP* 1.3 78.9 - - - +
209F ALA* 1.3 62.7 + - - +
211F GLY* 3.5 7.2 + - - -
212F LEU* 3.6 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F VAL* 3.8 3.5 - - + +
169F ILE* 3.7 24.5 - - + -
205F CYS 2.9 20.0 + - - +
206F ALA 3.9 2.2 - - - +
208F ALA* 1.3 73.3 - - - +
210F HIS* 1.3 59.9 + - + +
212F LEU* 3.0 14.9 + - - +
214F GLY* 2.8 25.0 + - - +
215F HIS 3.9 13.7 - - - +
216F ILE* 3.5 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ARG* 6.2 0.4 - - - -
206F ALA* 2.9 32.3 + - + +
207F ASP* 4.2 5.6 + - - +
209F ALA* 1.3 78.8 - - + +
211F GLY* 1.3 58.4 + - - +
213F LYS* 3.0 20.5 + - - +
214F GLY 3.3 21.1 - - - -
215F HIS* 5.4 0.2 - + - -
216F ILE 4.7 0.2 + - - -
235F GLY* 3.1 26.9 - - - -
237F ASP* 2.7 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F ASP 3.0 16.5 + - - -
208F ALA 3.9 3.6 - - - -
209F ALA 3.2 0.4 - - - -
210F HIS* 1.3 76.3 - - - +
212F LEU* 1.3 60.8 + - - +
213F LYS* 3.4 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ARG* 3.0 32.0 + - - +
166F GLU* 3.7 43.7 - - + +
169F ILE* 3.7 28.5 - - + -
170F LEU* 4.1 24.2 - - + -
208F ALA 3.6 6.7 + - - +
209F ALA 3.0 8.6 + - - +
211F GLY* 1.3 77.6 - - - +
213F LYS* 1.3 72.7 + - - +
214F GLY 3.1 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