A simplified representation of
protein structure which emphasizes the
secondary structure elements (SSEs). An
alpha helix becomes a circle and a
beta strand becomes a triangle - both connected by straight lines. The result is somewhere between a
3D and a
2D picture; spatial proximity is preserved between SSEs along with the chirality of the connections. This latter property is of great importance to
topological studies of a protein - this is where the name (
Topologically
Oriented
Protein
Structure) comes from.
Chirality information is in the connection of the lines to the elements - attachment to the 'top' of an element (the C-terminus) is indicated by a connection right to the center. The 'base' attachment is shown as a connection to the edge of the circle or triangle. This information is duplicated in the orientation of the triangles (the strand elements) which are either up or down:
/\ ______
---------/ _\________\__ / A beta hairpin.
/ \ \ /---------
------ \/
UP DOWN
Most cartoons are generated automatically, by a program that uses some sort of
simulated annealing. However, not all
folds are amenable to this, notably
beta propellors which look horrid. These errant rogues have to be hand-finished by a team of goblins. (I guarantee, no-one will still be reading by this point.)