EnzDes shows nitrogen as blue, oxygen as red, and sulfur as yellow. Otherwise, each "nub" or bend in a sidechain represents a carbon atom. (The black nub on proline is a special case.)
See also: Sidechain Bonding Gallery.
The default "hydro" coloring in Foldit tells you whether the amino acid at a particular segment is hydrophobic or hydrophilic. The shape of the sidechain may tell you which amino acid is where, but there are times when a little more information is useful.
EnzDes and CPK make it easier to tell one sidechain from another. They also give clues about how the sidechains can form hydrogen bonds. The Sidechain Bonding Gallery provides more detail about hydrogen bonding.
In both EnzDes and CPK, the sulfur atoms in cysteine and methionine show up in bright yellow.
Nitrogen atoms are dark blue, and oxygen atoms are red.
The last atom in proline's sidechain is a special case, colored in black. All sidechains start out bonded to the alpha carbon in the protein backbone. Proline curves around in a "cycle", and the last carbon atom in proline's sidechain ends up bonded to the nitrogen atom in the "amino group" of backbone. The black cap reflects this unusual bonding pattern.