How to Select Charged, Polar, or Hydrophobic Residues in Seconds

If you’ve ever had to color-code or isolate specific residues in a large molecular system, you know how frustrating it can be to identify residues based on their charge, polarity, or hydrophobicity manually. For molecular modelers analyzing electrostatic interactions, solvation, or binding pockets, being able to quickly filter residues with specific chemical properties can significantly accelerate your workflow and improve the quality of your simulations and visualization.

The Node Specification Language (NSL) in SAMSON includes a range of attributes that let you specify exactly which residues you’re interested in—without tedious visual inspection or scripting.

Identifying charged residues

Use the residue.charge attribute (short name: r.c) to target residues based on the side chain charge:

• r.c neg: negatively charged (e.g. ASP, GLU)
• r.c pos: positively charged (e.g. LYS, ARG, HIS)
• r.c neu: neutral residues

For example, to highlight positively charged residues in your model, simply enter:

You can also combine multiple values:

This selects all neutral or positive residues.

Filtering by polarity

Residues can also be filtered by polarity using residue.polarity (r.p):

• r.p acidic: acidic polar residues
• r.p basic: basic polar residues
• r.p polar: all polar residues (includes basic and acidic)
• r.p nonpolar: hydrophobic residues like LEU, VAL

To find residues with strong dipole interactions, you could use:

Or limit the view to hydrophobic cores with:

Hydrophobicity scale filtering

Want to go a step further and filter based on gradations of hydrophobicity? Use the residue.hydrophobicity attribute, which is based on the Kyte-Doolittle scale:

This selects more hydrophilic residues. You can focus on more hydrophobic ones by inverting the range:

Or tune the precision even further:

Why it matters

This ability to rapidly identify specific chemical residue types is especially useful for:

• Analyzing charge distribution in macromolecules
• Studying binding site electrostatic complementarity
• Visualizing pKa-related state changes
• Optimizing protein-ligand docking interfaces

Rather than spending time looking up exact residue types and cross-referencing publications, use attributes like r.c, r.p, and r.hydrophobicity in SAMSON to narrow your selection and see only what you need.

Learn more in the full documentation: Residue attributes in SAMSON.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the SAMSON platform at www.samson-connect.net.