The palmprint is the segment which is long enough to contain all three catalytic motifs A, B and C, and no other sequence. The sequence between A and B is called V1, and the sequence between B and C is called V2. In typical (unpermuted) palm domains, the motifs appear in ABC order and the palmprint thus extends from the start of motif A through the end of motif C, i.e. is A+V1+B+V2+C. In permuted palm domains, the motifs appear in CAB order and the palmprint then extends from the start of motif C to the end of motif B, i.e C+V3+A+V1+B.
The palmcore is the segment obtained by expanding the palmprint by exactly 150aa on each flank. This design balances the conflicting goals (a) include as much of the palm domain as possible, and (b) don't overflow into neighboring domains or genes.
We define positions of the catalytic motifs by the location of the one essential residue in each motif, i.e. ASP in motif A, GLY in motif B and ASP in motif C. The ASP in motif C is the first D in the canonical [G/S]D[D/N] motif. These definitions are somewhat arbitrary, but enable unambiguous identification of the palmprint and palmcore boundaries if the catalytic residues ASP-GLY-ASP can be located.
Motif A has two additional residues before the essential ASP and thus starts at ASP − 3.
Motif B has one additional residue before the essential GLY and thus starts at GLY − 1.
Motif C has two additional residues before the essential ASP and thus starts at ASP − 3.