This study mathematically demonstrates that the conventional interpretation of Ramachandran space (the left-handed region) in tertiary protein structure formation is an error rooted in analytical bias. By extracting and analyzing 166,541 high-resolution structural residues from the RCSB Protein Data Bank (PDB), the right-handed absolute coordinates (phi = +68.45 degrees, psi = +53.21 degrees) were defined as the true values. Topological distance analysis revealed an observed mean distance of 163.55 degrees, recording a statistical deviation of 327.3 sigma based on the central limit theorem. Furthermore, comparative validation against generated structures (AlphaFold) and active functional sites (UniProt) identified an offset hierarchy from the theoretical pure mirror distance (161.615 degrees). These observational facts expose the conventional left-handed consensus as an artifact caused by "model bias" in crystallographic analysis, conclusively proving that biological structures are placed under geometric constraints driven by thermodynamic approval (system adaptability). Research ProvenanceThis research was conducted under the "Advanced Materials Resourcing Infrastructure (ARIM) Japan" project. Facility: Kyoto University Hub Project ID: JPMXP1226KT0010 (FY2026) RDE Dataset ID: b1353048-7724-455f-9083-f165086e9d78
Akira Tsuyoshi (Sun,) studied this question.