Contacts of the helix formed by residues 196 - 201 (chain B) in PDB entry 7V3X
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 VAL 196 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ARG* 4.6 2.0 - - - +
157B SER* 4.6 9.6 - - - +
160B VAL* 5.4 1.8 - - + -
161B ARG* 4.0 36.6 + - + +
194B TYR* 3.7 13.0 - - + +
195B GLY* 1.3 78.1 - - - +
197B GLU* 1.3 71.8 + - - +
198B GLU* 2.9 5.1 + - - -
199B PHE* 2.9 23.0 + - - +
200B VAL* 3.5 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.8 22.7 - - + +
147B VAL* 5.9 4.0 - - + -
148B THR* 4.4 1.7 - - + +
160B VAL* 4.9 10.0 - - + +
164B LEU* 5.5 10.3 - - + -
182B THR* 3.6 15.5 - - + +
192B ALA* 3.3 22.7 - - + +
193B ARG 3.3 8.1 + - - -
194B TYR* 3.1 45.9 + - - +
195B GLY 3.4 1.7 + - - -
196B VAL* 1.3 84.4 + - - +
198B GLU* 1.3 63.4 + - - +
200B VAL* 3.5 9.7 + - - +
201B SER* 3.4 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 4.2 16.5 - - - +
184A ARG 4.9 1.6 - - - +
185A ILE* 5.4 5.0 - - - +
43B LEU* 3.9 11.4 - - + +
190B PRO* 4.9 1.0 - - - +
191B ILE* 3.3 33.2 + - + +
192B ALA* 3.2 26.3 + - + +
195B GLY* 3.4 27.1 - - - -
196B VAL 2.9 1.1 + - - -
197B GLU* 1.3 78.2 - - - +
199B PHE* 1.3 85.9 + - + +
201B SER* 3.3 6.9 + - - +
204B VAL* 3.6 12.2 - - + +
223B LEU* 6.1 0.7 - - + -
224B LYS* 2.9 22.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR 4.2 0.2 - - - -
48A SER* 3.6 34.5 - - - -
52A LYS* 4.0 11.2 - - - -
77A GLU* 5.6 4.0 - - - +
183A GLU* 3.4 37.2 - - + +
184A ARG 3.3 24.5 - - - -
185A ILE* 5.8 0.7 - - - -
193A ARG* 3.4 23.3 - - - -
161B ARG* 3.3 23.8 + - - +
195B GLY 3.7 5.2 - - - -
196B VAL* 2.9 12.0 + - - +
198B GLU* 1.3 95.5 - - - +
200B VAL* 1.3 60.2 + - - +
224B LYS* 4.2 2.5 - - - +
226B ARG* 2.4 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 5.9 5.3 - - - +
161B ARG* 3.5 46.0 - - + +
164B LEU* 4.2 6.1 - - + +
165B PHE* 3.8 39.5 - - + +
168B VAL* 4.2 18.6 - - + +
180B MET* 6.4 0.2 - - + -
196B VAL 3.9 8.3 - - - +
197B GLU* 3.7 9.9 - - - +
198B GLU 3.3 0.2 - - - -
199B PHE* 1.3 77.7 - - - +
201B SER* 1.3 65.9 + - - +
202B ASP* 3.8 2.4 + - - +
226B ARG* 3.4 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER* 3.2 23.5 + - - -
43B LEU* 3.8 24.6 + - - +
168B VAL* 5.1 1.5 - - - +
180B MET* 4.8 6.9 - - - +
197B GLU 3.4 10.2 + - - -
198B GLU 3.5 3.3 + - - -
200B VAL* 1.3 85.6 - - - +
202B ASP* 1.3 57.1 + - - +
203B ASN 3.3 19.1 - - - -
224B LYS* 2.8 29.5 + - - -
226B ARG* 3.2 4.0 + - - -
----------------------------------------------------------
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