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 (T
tructure) 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.
/ \ \ /---------
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 propellor
s 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.)