From primary to tertiary structure

In the tertiary structure of a protein, amino acid residues which are distant in the primary structure get close to each other. As an example, let's see a tour along the polypeptide chain of green fluorescent protein, GFP, from the Aequorea victoria jellyfish. As the ball travels along the polypeptide chain (primary structure), the colour of the latter will adopt the rainbow colour scheme:

Water molecules:

Tour along the chain, in the style of a

Aequorea victoria, crystal jellyfish -- photo by Vern Krutein at flickr