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Related Concept Videos

Residual Plots01:07

Residual Plots

A residual plot is a statistical representation of data used to analyze correlation and regression results. It helps verify the requirements for drawing specific conclusions about correlation and regression. To obtain the residual plot, first, the residual for each data value is calculated, which is simply the vertical distance between the observed and the predicted value obtained from the regression equation.
When the residual values are plotted against the variable x, it is called a residual...
Raman Spectroscopy: Overview01:20

Raman Spectroscopy: Overview

The underlying principle of Raman spectroscopy is based on the interaction between light and matter, specifically molecules' inelastic scattering of photons. When a monochromatic beam of light, typically from a laser source, interacts with a sample, most scattered light has the same frequency as the incident light. This is known as Rayleigh scattering.
However, a small fraction of the scattered light exhibits a frequency shift due to the exchange of energy between the incident photons and the...
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.
Parallel-axis Theorem01:06

Parallel-axis Theorem

The parallel-axis theorem provides a convenient and quick method of finding the moment of inertia of an object about an axis parallel to the axis passing through its center of mass. Consider a thin rod as an example. There is a striking similarity between the process of finding the moment of inertia of a thin rod about an axis through its middle, where the center of mass lies, and about an axis through its end using the conventional method. In the conventional method, the concept of linear mass...
Arrhenius Plots02:34

Arrhenius Plots

The Arrhenius equation relates the activation energy and the rate constant, k, for chemical reactions. In the Arrhenius equation, k = Ae−Ea/RT, R is the ideal gas constant, which has a value of 8.314 J/mol·K, T is the temperature on the kelvin scale, Ea is the activation energy in J/mole, e is the constant 2.7183, and A is a constant called the frequency factor, which is related to the frequency of collisions and the orientation of the reacting molecules.
The Arrhenius equation can be used to...
Plotting and Calibrating the Root Locus01:19

Plotting and Calibrating the Root Locus

Root loci often diverge as system poles shift from the real axis to the complex plane. Key points in this transition are the breakaway and break-in points, indicating where the root locus leaves and reenters the real axis. The branches of the root locus form an angle of 180/n degrees with the real axis, where n is the number of branches at a breakaway or break-in point.
The maximum gain occurs at the breakaway points between open-loop poles on the real axis, while the minimum gain is observed...

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Related Experiment Video

Updated: Jun 2, 2026

Measuring Sensitivity to Viewpoint Change with and without Stereoscopic Cues
08:04

Measuring Sensitivity to Viewpoint Change with and without Stereoscopic Cues

Published on: December 4, 2013

Revisiting the Ramachandran plot from a new angle.

Alice Qinhua Zhou1, Corey S O'Hern, Lynne Regan

  • 1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

Protein Science : a Publication of the Protein Society
|May 4, 2011
PubMed
Summary
This summary is machine-generated.

Steric constraints alone dictate polypeptide backbone dihedral angles (phi and psi), as confirmed by analyzing 850 protein structures. This finding supports Ramachandran

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Raman and IR Spectroelectrochemical Methods as Tools to Analyze Conjugated Organic Compounds
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Raman and IR Spectroelectrochemical Methods as Tools to Analyze Conjugated Organic Compounds

Published on: October 12, 2018

Related Experiment Videos

Last Updated: Jun 2, 2026

Measuring Sensitivity to Viewpoint Change with and without Stereoscopic Cues
08:04

Measuring Sensitivity to Viewpoint Change with and without Stereoscopic Cues

Published on: December 4, 2013

Raman and IR Spectroelectrochemical Methods as Tools to Analyze Conjugated Organic Compounds
09:11

Raman and IR Spectroelectrochemical Methods as Tools to Analyze Conjugated Organic Compounds

Published on: October 12, 2018

Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • The Ramachandran plot, based on steric constraints, defines allowed backbone dihedral angles (phi and psi) in polypeptides.
  • Previous work suggested the backbone angle tau influences allowed phi/psi combinations, particularly in the 'bridge region'.

Purpose of the Study:

  • To analyze the distribution of backbone dihedral angles in a large dataset of high-resolution protein structures.
  • To validate Ramachandran and colleagues' predictions regarding the influence of tau on phi/psi angle distributions.
  • To determine if steric constraints alone sufficiently explain observed backbone angle distributions.

Main Methods:

  • Analysis of phi/psi angle distributions in 850 non-homologous proteins.
  • Structures were resolved to 1.7 Å or less with sidechain B-factors < 30 Ų.
  • Examination of the dependence of phi/psi distributions on the backbone angle tau.

Main Results:

  • The distribution of phi/psi angles across 87,000 residues demonstrated the predicted dependence on tau.
  • The findings align with Ramachandran and colleagues' original predictions.
  • No additional energetic factors beyond sterics are required to explain the data.

Conclusions:

  • Steric constraints are sufficient to explain the observed backbone dihedral angle distributions in proteins.
  • The influence of the backbone angle tau on phi/psi distributions is confirmed.
  • Recent hypotheses invoking additional energetic contributions like hydrogen bonding are unnecessary.