Secondary Structure Content

The Secondary structure content analysis follows how much of a protein selection is alpha, beta, or unstructured at each frame. It is an excellent high-level summary when you want to monitor backbone-state changes through time.

Adding the plot

1. Open Path Analyzer.
2. Choose Secondary structure content in Observable.
3. Choose a Path.
4. Define a Protein residue selection.
5. Click Add Content Series.

Inputs

• The selection must contain atoms belonging to protein residues.
• Path Analyzer recomputes secondary structure along the path and reports percentages of:
• Alpha
• Beta
• Unstructured

View

• Content series: a multi-series time plot with values between 0 and 100 %.

Key equations

If \(N_{\alpha}(t)\), \(N_{\beta}(t)\), and \(N_{\mathrm{unstructured}}(t)\) are the residue counts at frame \(t\), and \(N_{\mathrm{res}}\) is the total number of selected protein residues, then Path Analyzer reports

\[ \%_{\alpha}(t)=100\frac{N_{\alpha}(t)}{N_{\mathrm{res}}},\qquad \%_{\beta}(t)=100\frac{N_{\beta}(t)}{N_{\mathrm{res}}},\qquad \%_{\mathrm{unstructured}}(t)=100\frac{N_{\mathrm{unstructured}}(t)}{N_{\mathrm{res}}} \]

Tip

• Use broad selections when you want a protein-wide summary.
• Use focused selections when you want to isolate one domain, helix bundle, or loop-rich region.
• Pair it with Ramachandran when you want both a summary and residue-level backbone detail.