Guide to PISA

Getting started

PISA stands for Protein Interfaces Surfaces and Assemblies. It is available as a webservice at the EBI, via:

PISA is a tool for exploring macromolecular interfaces and surfaces, and for examining probable quaternery structure (also referred to as "assemblies"). It can do this using either precalculated data from the PDB archive, or coordinate data uploaded by the user.

The analyses are:

Other functions include: searching the PDB archive for interfaces formed by structural homologues; assessing the biological role of interfaces; and the ability to download and visualise the structures, interfaces and assemblies using a variety of software.

Use 3GCB as an example

The initial PISA start page has the 3GCB structure preselected so I will used this as an example to explore the use of PISA.

3GCB is GAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A/DELTAK454. Once the accession code has been entered PISA will give you some basic starting information on the page, namely:

The chains and ligands form the basic components of the "structures" that are used in the analyses later on. So for example in the 3GCB example, the structures are the main chain and the seven ligands: GOL residues 1001 and 1002, and SO4 residues 1101 to 1105.

You are then presented with a choice of three different aspects of the protein to explore:


This is probably a good place to start. The first section Interfacing Structures lists in a table the different "structures" found within the entry, between which interfaces can form.

Each structure is given a row number (in the column marked "NN") which links to the details of that structure (the rows in the table are grouped according to some scheme which isn't clear to me).

A structure is described by:

Other details of the structure include the numbers of atoms (Nat) and residues (Nres), and information about the surface of the structure:

If applicable the value of ΔG (the solvation free energy of folding for the structure) is also shown.

At the bottom there is a table of structure similarity. This gives an indication of which structures within the entry are similar to any other structures - a cyan block in the matrix indicates that the two structures are similar (black indicates that they are the same!), and clicking on the dot allows you to see the two structures superposed.


Interfaces between pairs of "structures" (i.e. chains and ligands) within the entry.

A results table shows details of each interface found, with one interface per row of the table:

For each structure the number of interfacing atoms (iNat) and residues (iNres) are indicated.

For each interface a number of quantities are listed:

A link (in the column labelled "x") launches the selected viewer to visualise the interface. Clicking on the interface number (in the column marked "NN") links to more detail about the interface in question.


This page gives information about the possible quaternery structures ("assemblies") that PISA predicts. The table summarises the predicted assemblies, and clicking on the id number goes to the details for that assembly.

The summary for each assembly consists of the following information:

Notation for structures

Structures are indicated using the following notation.

Full chains without a chain ID are denoted {-}. Ligands are denoted:


where R is the residue or ligand name, C is the chain, and N is the residue number. For example, [HEM]-:605 means protoporhyrin IX containing Fe (HEM) in chain without a chain ID, residue number 605.