  Phi-values are experimental measures of the effects of mutations on the
folding kinetics of a protein. A central question is which structural
information Phi-values contain about the transition state of folding.
Traditionally, a Phi-value is interpreted as the 'nativeness' of a mutated
residue in the transition state. However, this interpretation is often
problematic because it assumes a linear relation between the nativeness of the
residue and its free-energy contribution. We present here a better structural
interpretation of Phi-values for mutations within a given helix. Our
interpretation is based on a simple physical model that distinguishes between
secondary and tertiary free-energy contributions of helical residues. From a
linear fit of our model to the experimental data, we obtain two structural
parameters: the extent of helix formation in the transition state, and the
nativeness of tertiary interactions in the transition state. We apply our model
to all proteins with well-characterized helices for which more than 10
Phi-values are available: protein A, CI2, and protein L. The model captures
nonclassical Phi-values <0 or >1 in these helices, and explains how different
mutations at a given site can lead to different Phi-values.
