Abstract
Transmembrane (TM) proteins are of great importance in various biological functions. However, there are a small number of TM proteins whose three-dimensional structures are determined. According to the previous bioinformatics studies, residue at helix contact in transmembrane helix (TMH) bundle frequently changes into another residue with similar volume. The volume of the residue near the center of the protein scarcely changes. The properties of the conserved amino acid in the TMH bundle and of the contacting residues between TMH must be valuable for knowing the principles of the structure formation of the TM protein. In this study, the conservation tendency of the amino acid residue is analyzed in several TM protein datasets. It is shown that the residues are more conservative at the inner positions of the TMH bundle. Furthermore, the residues in contact region tend to be conserved. The analysis presented here will be valid also for the prediction of the TM protein structures.
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