Abstract: AimTo establish a new amino acid structure descriptor that can be applied to polypeptide QSAR studies. MethodsThe new amino acid structure descriptor c-scales were derived from a principal components analysis of 167 amino acid structure descriptor indexes by theoretic calculation. The c₁,c₂,c₃-scales were related to 3D structural features of amino acid such as steric, electronic and conformation properties etc. G/PLS regression method was used to find out the relationship between the c-scales and the biological activity and developed QSAR models of the polypeptides. ResultsUsing the established method, we developed accordingly QSAR models of Bitter tasting dipeptide, ACE inhibitors and bradykinin-potentiating pentapeptides and their r² and XV-r² were more than 0.70. ConclusionThe c-scales can quantitatively describe the 3D structural features of any coded and non-coded amino acid and can be used to establish a QSAR model of good predictability.