LIGPLOT
Operating Manual
a. Sample LIGPLOT outputs
Example 1: Chymotrypsin (8gch)
The LIGPLOT diagrams below illustrate the catalytic triad (His
57, Asp 102 and Ser 195) in the active site of the serine
protease chymotrypsin. The ligand bound is a 3-residue inhibitor
Gly-Ala-Trp.
The plots show the ligand's Trp 252 residue nestling in the highly
hydrophobic specificity pocket of the enzyme's active site.
Standard
colour LIGPLOT. (Black-and-white
version).
With
atomic accessibilities calculated by NACCESS.
Schematic
peptide representation.
Example 2: SH2 domain (1sha)
LIGPLOT diagram of the interactions between phosphopeptide A (Tyr-Val-Pro-Met-Leu,
phosphorylated Tyr) and the SH2 domain of the
V-src tyrosine
kinase transforming protein. The ligand (residues
201-205 of
chain B) has its phosphorylated tyrosine shown towards the bottom
of the picture.
Standard
colour LIGPLOT
Example 3: Fab B1312-myohaemerythrin complex (2igf)
A "schematic peptide" LIGPLOT diagram. The molecule shown is an
antibody-peptide complex (ligand residues 69-75, chain
P).
Each peptide residue is shown by a circle at the C-alpha position,
and only those sidechains which are involved in hydrogen bonds are depicted.
Schematic
LIGPLOT diagram
Example 4: Pancreatic trypsin inhibitor (2ptc)
LIGPLOT diagram of part of the pancreatic trypsin inhibitor
(residues 15-22, chain I), in a complex with beta-trypsin.
Note that the plot includes non-standard options - such as the absence
of atoms in the plot, and the ligand bonds being coloured by atom type.
Colour
LIGPLOT with non-standard options
Example 5: MHC class 1 complex (1vab)
LIGPLOT diagram of MHC class 1 complex with sendai virus nucleoprotein
(residues 1-9, chain P).
Standard
colour LIGPLOT
Schematic
ligand; protein residues bond-only
Standard
ligand; schematic protein residues
b. Sample DIMPLOT outputs
Example 1: A dimer interface
DIMPLOT diagram of the residues interacting across the dimer interface
of iron superoxide dismutase (3sdp).
DIMPLOT
of a dimer interface
Example 2: A domain-domain interface
DIMPLOT diagram of the residues interacting across the interface
between domains 2 and 3 in deoxyribonuclease I (1atn). The domains are
defined as:-
Domain 1: Residues 1 - 136, chain A; and residues 338 - 371,
chain A.
Domain 2: Residues 137 - 178, chain A; and residues 272 - 337,
chain A.
Domain 3: Residues 179 - 267, chain A.
DIMPLOT
of a domain-domain interface
LIGPLOT
Operating Manual