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Related Concept Videos

Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Protein Folding01:22

Protein Folding

Overview

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Updated: May 8, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Geometry motivated alternative view on local protein backbone structures.

Jan Zacharias1, Ernst Walter Knapp

  • 1Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195, Berlin, Germany.

Protein Science : a Publication of the Protein Society
|September 5, 2013
PubMed
Summary

We introduce a novel (d, ϑ)-plot as an alternative to the Ramachandran plot for visualizing protein backbone structure. This new method offers enhanced discrimination of local structures and their handedness.

Keywords:
(d, ϑ)-plotalternative Ramachandran plotbackbone conformation plotgeneric helix parametersprotein geometryprotein secondary structure

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • The Ramachandran plot (R-plot) is a standard tool for visualizing protein backbone structure using (φ, ψ)-angles.
  • Limitations of the R-plot include disconnected periodic structural regimes and less clear discrimination of local structure features.

Purpose of the Study:

  • To present and evaluate an alternative method for displaying local protein backbone structure.
  • To introduce generic helical parameters (twist angle ϑ and helical rise d) as a basis for a new visualization tool.

Main Methods:

  • Utilized generic helical parameters (d, ϑ) instead of traditional (φ, ψ)-angles.
  • Developed a polar coordinate (d, ϑ)-plot for local structure analysis.
  • Created a web application to display the (d, ϑ)-plot alongside the R-plot.

Main Results:

  • The (d, ϑ)-plot offers a polar coordinate view, connecting periodic structural regimes.
  • It provides clearer discrimination of local structure handedness and better separation of secondary structure motifs.
  • The new plot exhibits advantages in visualizing local protein backbone structures compared to the R-plot.

Conclusions:

  • The (d, ϑ)-plot is a valuable alternative for classifying local polypeptide structures.
  • It offers distinct advantages over the R-plot, including improved visualization of structural features.
  • A web application is provided to facilitate the adoption of this new plotting method.