---
title: "Monomer Types, Polymer Types and Natural Analogs"
slug: "monomer-types-polymer-types-and-natural-analogs"
updated: 2026-09-28T09:01:40Z
published: 2026-09-28T09:01:40Z
canonical: "docs.discngine.com/monomer-types-polymer-types-and-natural-analogs"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://docs.discngine.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Monomer Types, Polymer Types and Natural Analogs

Three fields classify every monomer: its **polymer type**, its **monomer type** and its **natural analog**. They come from HELM, the notation the service is built on, and they decide where a monomer can be used in a sequence and how tools interpret it. This article explains what each one means and how they constrain one another.

## Polymer type: which kind of chain

HELM writes a macromolecule as a set of polymer chains, each of one kind, connected to each other. The polymer type of a monomer says which kind of chain it can appear in.

| Polymer type | Chain | Typical monomers |
| --- | --- | --- |
| `PEPTIDE` | A peptide, amide bonds along the backbone | Natural and modified amino acids, N-terminal caps such as acetyl |
| `RNA` | A nucleic acid, in HELM's three-part model: sugar, phosphate, base | Ribose and deoxyribose variants, phosphate and thiophosphate linkers, bases |
| `CHEM` | Not a chain at all: a single chemical entity attached to one or more chains | Linkers, PEG spacers, fluorescent labels, small molecules conjugated to a peptide |

`RNA` covers DNA as well. HELM does not have a separate DNA polymer type; a deoxyribose sugar makes the chain DNA.

A symbol is unique **within a polymer type**. `A` is alanine in a peptide and adenine in a nucleic acid, and the two are different monomers that never collide. This is also why the polymer type of a monomer cannot be changed after creation: it is part of the monomer's identity.

## Monomer type: which role in the chain

The monomer type says how the monomer connects to its neighbours.

| Monomer type | Role | Attachment points |
| --- | --- | --- |
| `Backbone` | Sits in the chain and continues it | Usually `R1` and `R2`, one towards each neighbour |
| `Branch` | Hangs off a backbone monomer, and ends there | Usually `R1` only, towards the backbone |
| `Undefined` | No chain role; used for every `CHEM` monomer | Whatever the chemistry needs |

In a peptide, every amino acid is a `Backbone` monomer, whether natural or not. A `Branch` monomer in a peptide is something attached to a side chain, for example a group on the epsilon amine of a lysine. In a nucleic acid the sugars and phosphates are `Backbone`, and the bases are `Branch`: a base hangs off its sugar and does not continue the chain.

Not every combination exists. The application only offers the monomer types that are valid for the chosen polymer type:

|  | `PEPTIDE` | `RNA` | `CHEM` |
| --- | --- | --- | --- |
| `Backbone` | yes | yes | no |
| `Branch` | yes | yes | no |
| `Undefined` | no | no | yes |

A terminal group such as an acetyl cap is not a separate type. It is registered as `Backbone` or `Branch` with a single attachment point, and the chain simply stops there.

## Natural analog: which natural residue it stands in for

Most registered monomers are variants of a natural building block: a D-amino acid, an N-methylated residue, a fluorinated phenylalanine, a 2'-O-methyl ribose. The natural analog names that building block by its usual one-letter code.

| Polymer type | Codes |
| --- | --- |
| `PEPTIDE` | The twenty amino acids `A C D E F G H I K L M N P Q R S T V W Y`, and `X` for unknown or any |
| `RNA` | The bases `A C G U T`, and `N` for unknown or any; `r` for a ribose-like sugar and `p` for a phosphate-like linker |
| `CHEM` | `-`, not applicable |

The natural analog does not change the chemistry of a monomer. It is used by the tools that read sequences:

- an **alignment** matches a modified residue to its natural counterpart, so that `Nle` aligns with leucine rather than being treated as a gap;
- a **comparison** with a natural sequence, or a display in one-letter form, shows the analog;
- a **substitution analysis** groups monomers by the residue they replace.

Choose the analog by the role the monomer plays, not only by its skeleton. Norvaline is registered as an analog of valine when it is used as an isostere of valine, and as an analog of leucine when it replaces leucine, even though its straight propyl side chain is neither. When no natural residue is a sensible match, use `X` for a peptide and `N` for a nucleic acid.

For a `CHEM` monomer the analog is always `-`. Whatever value is submitted, the service stores `-`, because a linker or a label is not a variant of any natural residue.

## How the three fields interact

- The **polymer type** is chosen first and filters the other two lists.
- The **monomer type** must be valid for that polymer type, following the table above.
- The **natural analog** must belong to that polymer type's list, and is required for `PEPTIDE` and `RNA`.

Changing the monomer type or the natural analog of an existing monomer is a material change: it creates a new version and archives the previous state. See [Versioning and Deletion](/public/docs/monomer-versioning-and-deletion).

## Related

- [Attachment Points and CAP Groups](/public/docs/attachment-points-and-cap-groups): how `R1`, `R2` and `R3` are written and capped.
- [Import File Format](/public/docs/monomer-import-file-format): the columns that carry these three fields.