We detect and characterize the structure and time evolution of a collapse-inducing nucleus in a small folding protein. The analysis requires a combination of kinetic and time-dependent thermodynamic data obtained from a coarse grained simulation of dominant folding pathways resolved at a topological level. A new sequence-dependent dynamic invariant, the set of F values, is introduced to infer which portions of the protein are involved in the formation of the nucleus and thus identify the site mutations that significantly affect the folding process. The theoretical results are corroborated by experimental findings which also support the topological nucleation scenario. Furthermore, the structural evolution of the nucleus is investigated well beyond the submillisecond range.