Sample LIGPLOT outputs

contents page  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.

Key to symbols.

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:-

 DIMPLOT of a domain-domain interface

contents page  LIGPLOT Operating Manual