S100B binds tightly to a 12-amino acid peptide derived from heterodimeric capping protein. In native intact capping protein, this sequence is in the C terminus of the α-subunit, which is important for capping the actin filament. This C-terminal region is proposed to act as a flexible "tentacle," extending away from the body of capping protein in order to bind actin. To this hypothesis, we analyzed the interaction between S100B and capping protein in solution. The C-terminal 28 amino acids of the α-subunit, the proposed tentacle, bound to S100B as a free synthetic peptide or a glutathione S-transferase fusion (Kd ∼0.4-1 μM). In contrast, S100B did not bind to whole native capping protein or functionally affect its capping activity. S100B does not bind, with any significant affinity, to the proposed α-tentacle sequence of whole native capping protein in solution. In the NMR structure of S100B complexed with the α -subunit-derived 12-amino acid peptide, the hydrophobic side of a short α-helix in the peptide, containing an important tryptophan residue, contacts S100B. In the x-ray structure of native capping protein, the corresponding sequence of the α-subunit C terminus, including Trp 271, interacts closely with the body of the protein. Therefore, our results suggest the α-subunit C terminus is not mobile as predicted by the tentacle model. Addition of non-ionic detergent allowed whole capping protein to bind weakly to S100B, indicating that the α-subunit C terminus can be mobilized from the surface of the capping protein molecule, presumably by weakening the hydrophobic binding at the contact site.