Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived from the mutational data. To interpret these data, we have developed models that are based (a) on the substructural cooperativity of helices and hairpins, and (b) on splitting up mutation-induced stability changes of a protein into components for its substructures. We obtain a consistent structural interpretation of mutational Phi-values by fitting few parameters that describe the degrees of structure formation of helices and hairpins in the transition state. Our models explain how mutations at a given site can lead to different Phi-values, and capture non-classical Phi-values smaller than 0 or larger than 1, which have been difficult to interpret. Non-classical Phi-values simply arise, e.g., if mutations stabilize a helix or hairpin, but destabilize its tertiary interactions. References: [1] C. Merlo, K. A. Dill, and T. R. Weikl, PNAS 102, 10171 (2005). [2] T. R. Weikl and K. A. Dill, J. Mol. Biol. 365, 1578 (2007). [3] T. R. Weikl, Biophys. J., in press (2008).