LIGPLOT symbols:-
- Ligand bonds are shown with thick lines (here in purple).
- Non-ligand bonds (ie belonging to those protein
residues to which
the ligand is hydrogen-bonded) are shown with thin (orange) bonds.
- Hydrogen bonds are shown by dashed (green) lines with
the length of the bond printed in the middle.
- Hydrophobic contacts between protein and ligand are indicated by
the (brick-red) spoked arcs. Protein residues involved only in
these contacts with the ligand are shown by a single spoked arc. Other
atoms involved in hydrophobic contacts have spokes coming out of the
individual atoms.
- Atomic accessibilities are (optionally) shown by shaded circles
around the atoms. The thicker and darker the circle, the more buried and
solvent inaccessible the atom. Exposed, highly accessible surface atoms are
surrounded by a thinner, lighter circle.
- Chain identifiers (where relevant) are shown in parentheses
after the residue names.
Note that the parameter file, ligplot.prm, allows you to
alter these symbols in terms of:-
- Line-thicknesses
- Line colours
- Atom sizes
- Atom colours
- Text sizes
- Text colour
- Whether certain atoms or interactions are shown at all
- Whether atom or residue names are printed on the plot
- etc
See section 5 of the Operating Manual.