Contacts of the helix formed by residues 186 - 195 (chain B) in PDB entry 2VT4
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 ASP 186 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 3.8 18.4 + - - +
185B GLU* 1.3 79.2 - - - +
187B PRO* 1.3 83.2 - - - +
188B GLN* 3.3 29.2 - - - +
189B ALA* 3.0 11.3 + - + +
190B LEU* 2.9 20.1 + - - +
317B ARG* 5.7 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLU 3.6 4.0 - - - +
186B ASP* 1.3 93.8 - - - +
188B GLN* 1.3 60.8 + - + +
190B LEU* 3.2 10.4 + - + +
191B LYS* 2.9 29.7 + - - +
112C PHE* 4.0 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ASP* 3.2 17.2 + - - +
187B PRO* 1.3 82.1 - - + +
189B ALA* 1.3 62.4 + - - +
191B LYS* 3.3 14.3 - - + +
192B CYS* 3.2 20.3 + - - +
202B VAL* 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 3.6 32.3 - - + -
186B ASP* 3.0 16.3 + - + +
188B GLN* 1.3 78.1 - - - +
190B LEU* 1.3 62.7 + - - +
192B CYS* 2.9 15.9 + - - +
193B TYR* 3.0 34.0 + - + +
202B VAL* 3.7 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP 4.2 11.0 - - - +
185B GLU* 3.6 29.6 - - - +
186B ASP 2.9 15.1 + - - +
187B PRO* 3.7 9.6 - - + +
189B ALA* 1.3 75.5 - - - +
191B LYS* 1.3 63.0 + - - +
193B TYR* 3.3 30.2 + - + +
194B GLN* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PRO 2.9 13.4 + - - +
188B GLN* 3.3 18.4 - - + +
190B LEU* 1.3 76.1 - - - +
192B CYS* 1.3 61.3 + - - +
194B GLN* 3.4 5.7 + - - +
195B ASP* 3.4 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLN 3.2 8.1 + - - +
189B ALA* 2.9 12.3 + - - +
191B LYS* 1.3 75.0 - - - +
193B TYR* 1.3 63.6 - - + +
194B GLN 3.0 6.1 + - - -
195B ASP* 3.1 9.6 + - - +
198B CYS* 2.1 52.9 - - - +
200B ASP* 3.8 26.5 - - - -
202B VAL* 4.7 7.2 - - + -
401B NA 2.7 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 4.7 9.2 + - - -
182B TRP* 3.6 28.3 - + - -
183B ARG* 3.3 50.5 + - + +
184B ASP 2.9 29.9 + - - -
189B ALA* 3.0 30.9 + - + +
190B LEU* 3.3 20.6 + - + +
192B CYS* 1.3 82.5 - - + +
194B GLN* 1.3 62.0 + - + +
195B ASP 3.6 0.2 - - - -
200B ASP 5.1 2.0 - - - -
202B VAL* 2.6 30.7 + - + -
401B NA 3.9 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 5.6 0.4 - - - -
190B LEU 3.4 14.1 + - - +
191B LYS* 3.4 4.9 + - - +
192B CYS 3.0 1.0 - - - -
193B TYR* 1.3 83.8 - - + +
195B ASP* 1.3 58.6 + - - +
196B PRO* 3.1 13.6 - - - +
179D MET* 4.5 9.6 - - - +
181D TRP* 5.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 4.9 0.4 - - - -
191B LYS* 3.4 14.3 + - + +
192B CYS* 3.1 5.2 + - - +
194B GLN* 1.3 77.6 - - - +
196B PRO* 1.4 58.0 - - - +
197B GLY* 3.0 21.4 + - - -
198B CYS* 2.9 36.0 + - + +
401B NA 2.5 26.8 - - - -
178D MET 4.6 2.5 - - - +
179D MET* 4.0 24.4 - - + +
403D SOG 5.6 2.6 + - - -
----------------------------------------------------------
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