Related Experiment Video

Updated: Aug 17, 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

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

Bioinformatics (Oxford, England)
|May 23, 2003
PubMed
Abstract

More Related Videos

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling10:27

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations05:57

Synthesizing 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 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.
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
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 Cycloalkanes02:29

Conformations of Cycloalkanes

Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that was based on the...
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
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 Cyclohexane02:02

Chair Conformation of Cyclohexane

The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...