Understanding protein structure is important not just for an accurate mechanistic understanding of its function, but also for the extraction of protein structural features for further downstream applications. Geometrically, Cartesian coordinate system (CCS) and spherical coordinate system (SCS, ρ, θ and φ) are two interconvertible coordinate systems, and are like two sides of one coin. As an alternative to the default CCS approach, this perspective puts forward an inter-atomic SCS (IASCS) approach towards protein structure description with just two parameters, i.e., θ and φ. In addition, this perspective argues that since CCS has been the default approach for the past 50 years, the time is now ripe to take a look at the other side of the coin, and that this IASCS approach can find its potential applications in protein structure prediction, structural comparison and side chain placement in future.