An amino group in its standard form consists of a nitrogen and two hydrogens attached to something. Foldit shows amino groups in their charged or "protonated" form, with three hydrogens. This form is what normally occurs in the aqueous solution inside a cell.
As a protein is built, amino acids are chained together by peptide bonds. This has the effect of removing two hydrogen atoms from the amino group of every amino acid added to the chain. The first amino acid in the chain, known as the N terminal, keeps all three hydrogens. See protein backbone for more detail.