Contacts of the helix formed by residues 196 - 205 (chain B) in PDB entry 5OC9
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 196 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.7 3.4 - - + -
185B THR* 3.4 41.5 - - - +
186B TRP* 4.0 23.1 - - + -
193B LYS* 4.6 1.6 - - - +
194B TYR 3.7 3.8 - - - +
195B GLN* 1.4 83.3 - - + +
197B ILE* 1.4 56.4 + - - +
198B ASP* 3.3 3.1 - - + -
199B SER* 3.1 22.8 + - - +
200B ILE* 3.0 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLN* 3.0 30.9 + - + +
196B PRO* 1.4 69.5 - - - +
198B ASP* 1.3 57.6 + - - +
200B ILE* 3.4 14.8 + - + +
201B ARG* 3.0 27.9 + - - +
209B ALA* 3.5 22.2 - - + +
212B PHE* 3.6 31.6 - - + +
213B GLY* 3.6 6.1 - - - +
216B GLU* 3.9 11.4 - - - +
268B MET* 3.8 17.3 - - - -
271B ARG* 5.6 2.2 - - - +
272B TRP* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PRO 3.3 0.8 - - - -
197B ILE* 1.3 77.2 - - - +
199B SER* 1.4 57.1 + - - +
201B ARG* 3.6 10.4 - - - +
202B GLY* 3.2 21.5 + - - -
271B ARG* 2.9 41.4 + - - -
272B TRP* 3.1 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 3.7 23.0 - - - +
185B THR* 4.9 4.2 + - - -
196B PRO* 3.1 23.4 + - - +
198B ASP* 1.4 77.9 - - - +
200B ILE* 1.4 62.9 + - - +
202B GLY* 3.4 3.6 + - - -
203B TYR* 3.4 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.1 12.6 - - + -
186B TRP* 3.5 59.5 - - + +
195B GLN* 3.7 10.8 - - - +
196B PRO* 3.0 29.5 + - + +
197B ILE* 3.4 17.7 + - + +
199B SER* 1.4 73.5 - - - +
201B ARG* 1.4 53.0 + - - +
203B TYR 3.4 0.2 + - - -
204B PHE* 2.8 41.8 + - + +
205B GLY 3.6 0.2 + - - -
208B ILE* 4.5 2.5 - - + -
209B ALA* 3.8 23.8 - - + +
212B PHE* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL 5.4 0.4 + - - -
90B LYS* 4.9 5.3 - - - +
122B ALA* 4.8 2.4 - - - +
123B GLU* 3.7 21.1 + - - -
197B ILE 3.0 16.8 + - - +
198B ASP* 3.6 9.2 - - - +
199B SER 3.3 0.2 - - - -
200B ILE* 1.4 73.3 - - - +
202B GLY* 1.3 63.4 + - - +
205B GLY* 3.0 42.7 + - - +
206B GLU* 2.8 28.8 + - - +
209B ALA* 3.5 6.0 - - + +
271B ARG 4.8 1.0 + - - -
272B TRP* 3.3 74.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 3.7 27.3 + - - +
121B MET 5.1 0.3 + - - -
122B ALA* 3.7 14.4 + - - +
198B ASP 3.2 11.8 + - - -
199B SER* 3.4 6.0 + - - -
201B ARG* 1.3 82.3 - - - +
203B TYR* 1.4 56.3 + - - +
543B ARG* 4.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 3.4 8.2 - - - +
174B HIS* 2.8 32.2 + + - -
175B ASP* 2.8 29.3 + - + -
178B ALA* 3.9 18.4 - - + -
179B LEU* 3.5 38.8 - - + +
182B LEU* 3.8 22.0 - - + -
199B SER 3.4 7.5 + - - +
201B ARG 3.2 0.4 - - - -
202B GLY* 1.4 78.2 - - - +
204B PHE* 1.3 84.5 + + + +
543B ARG* 2.8 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 4.8 0.4 - - - -
174B HIS* 4.5 3.6 - + - -
179B LEU* 3.9 12.1 - - + -
182B LEU* 3.8 9.0 - - + -
186B TRP* 3.6 23.6 - + - -
200B ILE* 2.8 32.6 + - + +
203B TYR* 1.3 102.3 - + + +
205B GLY* 1.3 57.8 + - - +
208B ILE* 3.3 39.5 - - + +
537B MET* 3.4 40.8 - - + -
538B CYS* 4.3 1.3 - - - -
543B ARG* 5.0 0.9 - - + -
544B PRO* 3.7 36.3 - - + +
546B SER* 3.4 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 4.8 2.0 - - - +
200B ILE 3.6 0.4 + - - -
201B ARG* 3.0 22.4 + - - -
203B TYR 3.7 0.4 - - - -
204B PHE* 1.3 80.0 - - - +
206B GLU* 1.3 62.6 + - - -
207B THR 3.4 2.9 - - - -
208B ILE 4.3 0.9 - - - -
209B ALA* 3.1 31.7 + - - +
546B SER* 3.7 17.5 - - - -
----------------------------------------------------------
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