LIGPLOT Operating Manual

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

DIMPLOT diagram of the residues interacting across the dimer interface of iron superoxide dismutase (3sdp).

DIMPLOT of a dimer 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