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Figure 3
Comparative analysis of peptide geometry and properties in helices (light green) and strands (dark red). Data are derived from a nonredundant set of 1024 high-resolution protein structures. (a) KDE plot of Dratio, defined as the ratio of electron density at the midpoint of the carbonyl (C=O) bond to that of the amide (C—N) bond, comparing helices (light green) and strands (dark red). The density distributions reveal subtle differences in electron-density patterns, indicative of structural and electronic variations between the two secondary structures. (b) KDE plot of the distribution of the dihedral angle ω for helices (light green) and strands (dark red). The distributions illustrate the planarity of peptide bonds, with helices exhibiting a narrower distribution tightly centred around 180°, indicative of their structural rigidity. Strands display a broader distribution, reflecting increased geometric variability and flexibility in their peptide bonds. (c) KDE plot of the normalized mean atomic displacement parameters (ADP) of peptide atoms (O, C, N) in helices (light green) and strands (dark red). The distributions highlight the differences in atomic mobility between the two secondary-structure types. Helices display a broader range of ADP values, suggesting increased flexibility and dynamic movement compared with strands, which show a sharper peak indicative of greater rigidity. Higher ADP values typically correspond to greater atomic mobility or structural flexibility. (d) KDE plot of hydrogen-bond distances between main-chain nitrogen and oxygen atoms, comparing bonding patterns in helices (light green) and strands (dark red). The distributions illustrate distinct preferences in hydrogen-bond lengths, with helices showing a broader range and longer average bond distances, while strands exhibit shorter and more consistent distances. Hydrogen bonding serves as a key stabilizing force in both secondary structures.

IUCrJ
Volume 12| Part 3| May 2025|
ISSN: 2052-2525
https://doi.org/10.1107/S2052252525002106