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Secondary structure is often formally defined by the hydrogen bonds of your biopolymer, as affecting an atomic resolution structure.
In proteins, the secondary structure is placed because of the patterns of hydrogen bonds between backbone amide and carboxyl groups.
In nucleic acids, the secondary structure is placed because of the hydrogen bonding involving the nitrogenous bases.
The hydrogen bonding patterns may be significantly distorted, that makes an automated resolution of secondary structure difficult.
The secondary structure may be also defined good regular pattern of backbone dihedral angles in a particular region of your Ramachandran plot.
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