We use several representations for showing proteins, including all-atom, stick, and Richardson cartoon representations. The colors are used to highlight specific parts (but that may be specific atoms, atom types, or structural characteristics, depending on the context). To learn more, Wikipedia has some nice articles about this:
http://en.wikipedia.org/wiki/Protein_structure
http://en.wikipedia.org/wiki/Alpha_helix
http://en.wikipedia.org/wiki/Beta_sheet