Lysine with the nubs identified. For lysine, the nubs are all carbon atoms, with nitrogen as the last heavy atom. The Greek letter position names are shown, along with their Roman equivalents. EnzDes coloring shown.

The term nub in Foldit refers to the bends in a sidechain.

Each of the nubs represents an atom.

The first nub as a sidechain leaves the backbone is always carbon, and is known as the beta carbon.

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".

As the lysine example shows, nubs are often carbon, but they can be other elements. Use EnzDes or CPK coloring in View Options to identify which atom is which.

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.

For proline, there is also a black nub. This is a special case, where the final carbon atom in proline's sidechain ends up bound to the nitrogen atom in amino group of the backbone.

See the Amino Acid Gallery to compare and contrast all those nubs.

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