Selecting Amino Acids by Polarity and Charge in SAMSON

When working with protein structures, molecular modelers often need to quickly select specific types of residues. For example, you might want to highlight all acidic residues in a protein to study interactions with a positively charged ligand, or perhaps isolate neutral amino acids to prepare a simplified model of a hydrophobic core. Knowing how to efficiently filter residues based on chemical properties like polarity and charge not only saves time but also helps focus analysis on biologically relevant features.

SAMSON’s Node Specification Language (NSL) offers a powerful and expressive way to define such selections. Two particularly useful attributes for this purpose are:

residue.charge (r.c): to specify amino acid side chain charges (negative, neutral, positive, or undefined)
residue.polarity (r.p): to define the polarity category of side chains (acidic, basic, polar, nonpolar, or undefined)

How It Works

Filtering by Charge

The residue.charge attribute categorizes amino acid side chains by their typical charge state:

negative or neg: acidic side chains (e.g., ASP, GLU)
neutral or neu: uncharged side chains (e.g., ALA, SER)
positive or pos: basic side chains (e.g., LYS, ARG)
undefined or un: unspecified charge

Example queries:

r.c neg

r.c neg

Selects amino acids with negatively charged side chains.

r.c neu, pos

1	r.c neu, pos

Selects amino acids that are either neutral or positively charged.

Filtering by Polarity

The residue.polarity attribute describes the general polarity behavior of side chains:

acidicPolar or acidic
basicPolar or basic
polar
nonpolar
undefined or un

Example queries:

r.p polar

r.p polar

Selects amino acids with polar side chains.

r.p acidic, basic

1	r.p acidic, basic

Selects amino acids with acidic or basic side chains.

Combining Criteria

Because NSL allows logical combinations, you can make very specific selections. For example:

r.aa and r.c pos and r.p basic

1	r.aa and r.c pos and r.p basic

This selects amino acid residues that are basic and positively charged—essentially residues like lysine or arginine.

A Closer Look at Use Cases

Some practical applications include:

Studying electrostatic surfaces by isolating negatively or positively charged areas
Building coarse-grained models based only on neutral or nonpolar residues
Visualizing amino acid environments in docking studies

This level of fine control over residue selection is particularly useful in combination with SAMSON’s visualization capabilities or simulation engines.

To learn more about residue properties in NSL and see all possible attributes, visit the official documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.