Hydrogen bonds and ion pairs involving side chains play vital roles in protein functions such as molecular recognition and catalysis. Despite the wealth of structural information about hydrogen bonds and ion pairs at functionally crucial sites on proteins, the dynamics of these fundamental chemical interactions are not well understood largely due to the lack of suitable experimental tools in the past. NMR spectroscopy is a powerful tool for investigations of protein dynamics, but the vast majority of NMR methods had been applicable only to the backbone or methyl groups. Recently, a substantial progress has been made in the research on the dynamics of hydrogen bonds and ion pairs involving lysine side-chain NH3 + groups. Together with computational/theoretical approaches, the new NMR methods provide unique insights into the dynamics of hydrogen bonds and ion pairs involving lysine side chains. Here, the methodology and its applications are reviewed.