PreDom Help

DiD (View interface)

How to use

1. Select the domain structure database to view in the "Database" cell.
2. Enter the PDB ID in the [PDB ID] field, and click [Find chains] to list all the chain IDs in the specified PDB data on the next menu. Then select the chain ID from the list.
   To clear the chain list, click [Reset]. (The [PDB ID] field is also initialized.)
3. Click [View] to submit the query.

Description of the result

List of the domains (bottom left table)

The list of the domains in the specified data.

Field name	Description
domain	domain number
show	switch to show/hide the domain (uncheck to hide)
scheme of interface residues	buttons to change the scheme of the domain-domain interface residues
residue number	range of the residue number of the domain
interface area	area of the domain-domain interface (Å2) total: the area of the whole domain-domain interface core: the area of the domain-domain interface originating in the core interface residues

Amino acid sequence (top left box)

The amino acid sequence of the specified data. For each domain, the core interface residues are indicated with deep background color, while the peripheral interface residues are indicated with intermediate color. By placing the mouse pointer over one of the interface residues, the residue name and the residue number are displayed in the "interaction residue" field below.

3D Structure (right box)

The Jmol visualization of the specified data. Initially, the domain-domain interface residues are shown in cpk format, while other residues are shown in cartoon format. As with the amino acid sequence, the core interface residues are indicated with deep color. By placing the mouse pointer over one of the interface residues in the amino acid sequence, the residue color turns white to show its position in the structure.

Data about a residue (below the 3D structure)

By clicking one of the residues in the amino acid sequence, the data describing the residue are shown here.