Contacts of the helix formed by residues 168 - 179 (chain B) in PDB entry 3V4R
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 GLU 168 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 1.4 77.8 - - - +
169B ARG* 1.4 66.6 + - - +
170B ASN* 4.3 5.6 - - + +
171B GLU* 2.9 34.5 + - + +
172B LEU 3.0 10.4 + - - -
219B ASP* 3.3 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 3.4 5.5 + - - -
168B GLU* 1.4 71.6 - - - +
170B ASN* 1.4 57.4 + - - +
172B LEU* 3.1 26.3 + - - +
173B LEU* 3.3 14.8 + - + +
200B VAL* 5.3 11.0 - - + -
216B PHE* 5.1 16.2 - - + -
218B GLY 5.4 6.9 + - - +
219B ASP* 5.0 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLU* 3.1 6.4 - - + +
169B ARG* 1.4 77.6 - - - +
171B GLU* 1.4 55.5 + - - +
173B LEU* 3.4 16.6 + - + +
174B ARG* 3.1 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 4.3 11.9 - - + -
168B GLU* 2.9 29.4 + - + +
170B ASN* 1.4 70.8 - - - +
172B LEU* 1.4 56.9 + - - +
174B ARG* 3.2 18.7 + - - +
175B LYS* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 3.8 28.5 - - + -
161B LEU* 3.9 24.7 - - + -
167B ILE* 3.8 17.8 - - + +
168B GLU 3.0 9.7 + - - +
169B ARG* 3.1 12.3 + - - +
171B GLU* 1.4 73.8 - - - +
173B LEU* 1.3 57.9 + - - +
175B LYS* 3.1 4.9 + - + +
176B LEU* 2.9 48.4 + - + +
200B VAL* 3.8 39.3 - - + -
202B ILE* 4.8 6.5 - - + -
214B VAL* 5.1 9.2 - - + -
221B ILE* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ARG* 3.5 15.7 - - + +
170B ASN* 3.4 14.6 - - + +
171B GLU 3.3 0.2 - - - -
172B LEU* 1.3 77.2 - - + +
174B ARG* 1.4 50.6 + - - +
176B LEU* 3.0 7.4 + - + +
177B VAL* 2.8 40.4 + - + +
183B ARG* 3.9 17.9 - - - +
193B PHE* 3.7 26.7 - - + -
195B VAL* 3.6 34.1 - - + -
200B VAL* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ASN 3.1 13.8 + - - +
171B GLU* 3.2 24.4 + - - +
173B LEU* 1.4 72.0 - - - +
175B LYS* 1.4 52.4 + - - +
177B VAL* 3.2 7.9 + - - +
178B ASP* 2.8 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 3.5 25.2 - - + +
167B ILE* 5.5 4.3 - - + -
171B GLU* 2.8 21.0 + - - +
172B LEU* 3.5 8.7 - - - +
174B ARG* 1.4 72.3 - - - +
176B LEU* 1.4 56.9 + - - +
178B ASP* 3.6 8.3 - - - +
179B ILE* 3.3 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 4.6 3.8 - - + -
172B LEU* 2.9 50.8 + - + +
173B LEU* 3.0 8.5 + - - +
175B LYS* 1.4 75.0 - - - +
177B VAL* 1.4 64.1 + - - +
179B ILE* 3.1 26.5 + - + +
181B TYR* 3.3 21.3 + - + +
193B PHE* 4.0 31.9 - - + -
200B VAL* 4.4 0.9 - - + -
202B ILE* 4.2 23.3 - - + -
243B ILE* 4.1 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 2.8 28.1 + - + +
174B ARG* 3.9 6.7 - - - +
176B LEU* 1.4 71.0 - - - +
178B ASP* 1.4 53.4 + - - +
179B ILE 2.8 21.5 - - - +
180B GLN* 4.3 1.0 - - - -
181B TYR 3.5 16.2 - - - +
182B ALA* 5.8 0.7 - - - -
183B ARG* 5.8 1.6 - - + +
193B PHE* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG 2.8 18.8 + - - +
175B LYS* 3.6 11.9 - - - +
176B LEU 3.2 0.2 - - - -
177B VAL* 1.4 69.8 - - - +
179B ILE* 1.4 67.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU 5.6 0.2 - - - +
157B MET* 3.3 37.2 - - + +
159B VAL* 3.9 22.0 - - + +
175B LYS 3.3 12.1 - - - +
176B LEU* 3.1 17.9 - - + +
177B VAL 2.8 13.7 - - - +
178B ASP* 1.4 80.5 - - + +
180B GLN* 1.3 62.8 + - - +
181B TYR* 3.8 23.6 - - + -
243B ILE* 4.2 21.5 - - + +
244B PHE 4.4 4.5 - - - +
245B PRO* 3.6 18.4 - - + -
----------------------------------------------------------
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