ABSTRACT The transient receptor potential (TRP) superfamily is subdivided into several subfamilies on the basis of sequence similarity, which is highly heterogeneous but shows a molecular architecture that resembles the one present in members of the Kv channel superfamily. Because of this diversity, they produce a large variety of channels with different gating and permeability properties. Elucidation of these particular features necessarily requires comparative studies based on structural and functional data. The present study aims to compilate, analyze, and determine, in a coherent way, the relationship between intrinsic side‐chain flexibility and the allosteric coupling in members of the TRPV, TRPM, and TRPC families. Based on the recently determined structures of TRPV1 and TRPV2, we have generated protein models for single subunits of TRPV5, TRPM8, and TRPC5 channels. With these models, we focused our attention on the apparently crucial role of the GP dipeptide at the center of the S4‐S5 linker and discussed its role in the interaction with the TRP domain, specifically with the highly‐conserved Trp during this coupling. Our analysis suggests an important role of the S4‐S5L flexibility in the thermosensitivity, where heat‐activated channels possess rigid S4‐S5 linkers, whereas cold‐activated channels have flexible ones. Finally, we also present evidence of the key interaction between the conserved Trp residue of the TRP box and of several residues in the S4‐S5L, importantly the central Pro. Proteins 2017; 85:630–646. © 2016 Wiley Periodicals, Inc.