  Simplified Go models, where only native contacts interact favorably, have
proven useful to characterize some aspects of the folding of small proteins.
The success of these models is limited by the fact that all residues interact
in the same way, so that the folding features of a protein are determined only
by the geometry of its native conformation. We present an extended version of a
C-alpha based Go model where different residues interact with different
energies. The model is used to calculate the thermodynamics of three small
proteins (Protein G, SrcSH3 and CI2) and the effect of mutations on the
wildtype sequence. The model allows to investigate some of the most
controversial areas in protein folding such as its earliest stages, a subject
which has lately received particular attention. The picture which emerges for
the three proteins under study is that of a hierarchical process, where local
elementary structures (LES) (not necessarily coincident with elements of
secondary structure) are formed at the early stages of the folding and drive
the protein, through the transition state and the postcritical folding nucleus
(FN), resulting from the docking of the LES, to the native conformation.
