User Manual

Table of contents

Types of 2D diagrams in the 2DProts database

The 2DProts database contains two kinds of diagrams: A diagram that visualizes secondary structures comprising a domain of a single protein, and a multiple 2D diagram that combines diagrams of domains of all proteins that comprise a family.

2D diagram of secondary structures of individual protein domains

A 2D diagram of secondary structure of a domain visualizes relative distance between single secondary structure elements, as well as position of amino acids that comprise each element in the sequence of the domain.

The 2D diagram contains two types of symbols that represent secondary structures:

  • an arrow, which represents a protein sheet, and
  • a bar, which represents a protein helix.

Both symbols can be coloured in two ways:

  • Using rainbow colours, which means that the secondary structure is part of more than 80 % of proteins in its protein family. The exact colour of a secondary structure depends on its position in the domain. The colour spectrum starts on green (start of sequence that represents the domain) and goes through orange, red, purple, and blue all the way to cyan (end of sequence that represents the domain).
  • Using grey, which means that the secondary structure is part of lea than 80 % of proteins in the protein family.

On the right, you can see an example of a 2D diagram of domain 1n1mA02.

Multiple 2D diagram from whole protein families

A multiple 2D diagram shows diagram of all domains of a whole protein family in one picture. Diagrams of individual protein domains are rotated and moved to similar positions. There are three types of multiple 2D diagrams offered in the 2DProts database. The type of multiple 2D diagram can be changed using tabs located above the picture currently displayed multiple 2D diagram.

Default type (i.e., with transparency and averages)

In the default type of multiple 2D diagram, each domain shown is transparent. Therefore, the unstable parts are less visible in big families.

The average protein is shown as well. It contains secondary structures which are in at least 80 % of protein domains in the family. The position and orientation of each secondary structure is computed as an average through all domains that contain this secondary structure. The average protein is visualized using filled dark grey secondary structure symbols (arrows and bars).

The example on the right shows the default type of the multiple 2D diagram for protein family 2.140.10.20.

Second type (i.e., no transparency, no averages)

In the second type, all domains are shown with 100 % visibility. Therefore, the multiple 2D diagram of this type shows structures that are present only in small number of domains very noticeably. The average protein structure is not shown.

The example on the right shows the second type of the multiple 2D diagram for protein family 2.140.10.20.

Third type (i.e., no transparency, with averages)

In the third type, all domains are shown with 100 % visibility. Therefore, the multiple 2D diagram of this type shows structures that are present only in small amount of domains very noticeably.

The average protein is shown as well. It contains secondary structures which are in at least 80 % of protein domains in the family. The position and orientation of each secondary structure is computed as an average through all domains that contain this secondary structure. The average protein is visualized using filled dark grey secondary structure symbols (arrows and bars).

The example on the right shows the third type of the multiple 2D diagram for protein family 2.140.10.20.

Each protein domain is represented in the 2DProts database via its identifier in the CATH format (e.g., 1r9nA01), and its 2D diagram is searchable using this identifier. It is also possible to search for all domains of a specific protein using its PDB ID (e.g., 1r9n). The search field of the 2DProts database also accepts substrings that are at least 3 characters long (e.g., 1r9n, 1r9, r9n).

Protein families are also represented in the 2DProts database via a CATH identifier (e.g., 2.140.10.20) that can be used in the search field to obtain a multiple 2D diagram of a family. Substrings that are at least 3 characters long are also supported (e.g., 2.140.10, 2.140, 140.10.20).

2DProts output pages

2D diagram of individual protein domains page

2DProts output page for each domain contains three parts

  • diagram for the given part
  • name of family to which the domain belonges
  • links to old versions of diagrams of this domain

Multiple 2D diagram of whole families page

2DProts output page for each family contais four parts

  • multiple diagrams for the given family
  • name of all domains which belonges to the given family
  • name of all clusters which belonges to the given family
  • links to old versions of diagrams of this domain

Multiple 2D diagram of whole clusters page

2DProts output page for each family contais four parts

  • multiple diagrams for the given family
  • name of family to which the domain belonges
  • links to old versions of diagrams of this domain

Custom entry 2DProts multiple picture

In section "Custom entry" you can create custom multi image from provided domains. All the domains in their latest version have to be from one family.

Filtering PDB entries

See RCSB filtering guide (PDF, 600 kB) for information on filtering PDB entries by experimental method and resolution using RCSB advanced search.