The assumption that the intrinsic α-helical
propensities of the amino acids are position independent
was critical in several helix/coil transition theories.
In the first paper of these series, we reported that this
is not the case for Gly and nonpolar aliphatic amino acids
(Val, Leu, Met, and Ile). Here we have analyzed the helical
intrinsic propensities of noncharged polar residues (Ser,
Thr, Asn, and Gln) at different positions of a model polyalanine-based
peptide. We found that Thr is more favorable (by ∼0.3
kcal/mol) at positions N1 and N2 than in the helix center,
although for Ser, Asn, and Gln the differences are smaller
(±0.2 kcal/mol), and in many cases within the experimental
error. There is a reasonable agreement (±0.2 kcal/mol)
between the calculated free energies, using the ECEPP/2
force field equipped with a hydration potential, and the
experimental data, except at position N1.