The alpha carbon is the central point of all amino acids. The segment shown here is joined to two others by peptide bonds. (Stick + polar H view, EnzDes coloring.)
The alpha carbon is the central point in the backbone of every amino acid.
The alpha carbon (α-carbon or Cα) is what connects the amino group to the acid carboxyl group, giving amino acids their name.
The alpha carbon also serves as the point of attachment for the sidechains of 19 out of 20 amino acids used in protein building.
Glycine is the only amino acid with no sidechain. In glycine, a hydrogen atom takes the spot where a sidechain is attached to the alpha carbon in the other amino acids.
The alpha carbon also has a hydrogen attached opposite the sidechain. (Or, in the case of glycine, it has a hydrogen opposite the hydrogen that replaces the sidechain.)
The alpha carbon is always atom 2.
Segment-to-segment differences are often reported as the distance between the alpha carbons.
In Foldit, a band drawn to or from the backbone in effect connects to the alpha carbon. The banding functions, such as band.AddBetweenSegments use the alpha carbon (atom 2) as the default atom unless another atom is specified.
A Foldit cutpoint temporarily breaks the peptide bond between two segments. A "cut band" connects the alpha carbons of the two segments until the cutpoint is closed.
See protein backbone for more on the backbone components shown here.