In serine proteases (SPs), the H-bond between His57 and Asp102 and that between Gly193 and the transition state intermediate play a crucial role in enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low-barrier H-bond between His57 and Asp102, in complete agreement with NMR experiments on enzyme-transition state analogue complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate-enzyme adduct indicates that the Gly193-induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.