The term nub in Foldit refers to the bends in a sidechain.
Each of the nubs represents an atom.
All nubs are technically assigned Greek letter positions, but these are almost always rendered in Latin characters, so things get a little confusing.
In the PDB and similar sources, the beta carbon is identified as "CB", meaning "carbon, beta position". The next Greek letter is gamma, which becomes "G", so "CG" would be the second nub in the lysine sidechain seen here. Delta is next, so "CD" for the third nub.
Epsilon is next, which becomes "E", so CE for the fourth nub of lysine.
Zeta follows epsilon, so "Z" is the next position. In lysine, nitrogen is the last heavy atom of the sidechain, so you may see as "NZ".
In CPK/EnzDes coloring, the non-carbon nubs can be:
- red - oxygen
- blue - nitrogen
- yellow - sulfur
When a nub is the default color (gray in CPK, green in EnzDes) it's carbon.
See the Amino Acid Gallery to compare and contrast all those nubs.