Related Experiment Video
Updated: Aug 17, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
CAP: conformation angles package-displaying the conformation angles of side chains in proteins
S S Sheik1, P Sundararajan, V Shanthi
1Bioinformatics Centre and Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India. sekar@physics.iisc.ernet.in
A new graphics package visualizes protein side chain angles, showing multiple conformations and rotameric states for amino acid residues. This tool aids in understanding protein structure and dynamics from the Protein Data Bank.
Area of Science:
- Structural Biology
- Computational Biology
- Biochemistry
Background:
- The Protein Data Bank (PDB) contains numerous protein structures solved by X-ray diffraction and NMR spectroscopy.
- Understanding amino acid residue conformations is crucial for protein function and dynamics.
Purpose of the Study:
- To develop a graphics package for visualizing protein side chain conformation angles.
- To analyze and display multiple conformations and rotameric states of amino acid residues.
Main Methods:
- Developed a graphics package for displaying side chain conformation angles.
- Integrated the package with all protein structures from the Protein Data Bank.
- Visualized multiple conformations of amino acid residues at high resolution.
Main Results:
- The package successfully displays side chain conformation angles for user-selected residues.
- It visualizes multiple conformations adopted by single amino acid residues.
- It shows the percentage distribution of side chain angles in different rotameric states.
Conclusions:
- The developed graphics package is a valuable tool for analyzing protein side chain conformations.
- It enhances the understanding of protein structure and amino acid flexibility.
- The package supports structural analysis of proteins from X-ray diffraction and NMR data.
More Related Videos
10:27Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling
Published on: October 21, 2018
05:57Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
Published on: April 26, 2024
Related Concept Videos
Newman Projections
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Conformations of Ethane and Propane
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered ethane, the...
Conformations of Cycloalkanes
Conformations of Cyclohexane
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...
Chair Conformation of Cyclohexane
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
Fischer Projections