CASTp: Computed Atlas of Surface Topography of proteins

Abstract

Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These include pockets located on protein surfaces and voids buried in the interior of proteins. The measurement includes the area and volume of pocket or void by solvent accessible surface model (Richards' surface) and by molecular surface model (Connolly's surface), all calculated analytically. CASTp can be used to study surface features and functional regions of proteins. CASTp includes a graphical user interface, flexible interactive visualization, as well as on-the-fly calculation for user uploaded structures. CASTp is updated daily and can be accessed at http://cast.engr.uic.edu.

Figure 1

An intuitive graphic user interface allows users to request a CASTp calculation by typing the four letter PDB name of a protein structure, by keyword searching or by submitting their own molecular structure in the PDB format. For visualization, the user has the choice of using MDL's Chime plug-in (Windows, MacOS and IRIX only) or Mage (11) java applet. In addition, users may also elect to have results emailed back as files.

Figure 2

Visualization of ATP binding pocket automatically identified on the structure of the catalytic subunit of protein kinase A (pdb 2cpk). It is the largest pocket and contains the following residues: L49, G50, T51, G52, S53, F54, G55, R56, V57, A70, K72, L74, V79, N84, H87, T88, E91, L95, V104, M120, E121, Y122, V123, E127, D166, K168, E170, N171, L173, T183, D184, G186, F187, G200, T201 and F327. A large number of these residues are known to be functionally important (see http://www.sdsc.edu/kinases/) (12).