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Solvent Accessibility and Contact ResiduesNACCESS (by S. Hubbard and J. Thornton 1992-1996) is a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids, and is available for free from this site for researchers at academic and non profit-making institutions. It can be downloaded from the NACCESS website. The program uses the Lee & Richards (1971, J. Mol. Biol., 55, 379-400) method, whereby a probe of given radius is rolled around the surface of the molecule, and the path traced out by its centre is the accessible surface. Typically, the probe has the same radius as water (1.4 Angstroms) and hence the surface described is often referred to as the solvent accessible surface. The calculation makes successive thin slices through the 3D molecular volume to calculate the accessible surface of individual atoms. The accessibility macros import multiple residue accessibility files (.rsa-files) generated by NACCESS into EXCEL, extract the sequences from these files into a sequence alignment and color-code the alignment according to side-chain accessibility. Contact residues at interfaces can be identified by calculating the residue accessibilities of the isolated components of a complex as well as of the entire complex and calculate the relative and absolute differences in solven accessible surface area. Atom surface accessibility file format (*.asa-files) Examples: Click the "HowTo" button for step by step instructions on how to process multiple .rsa files to color code alignments for residue accessibility and to identify interface residues |
Convert surface accessibility values to a color code
Identify residues contributing to an interface Problem: Under Windows, the xxx_GetFile utilities do not keep the file extensions of the imported files in the worksheet name and therefore do not recognize the individual worksheets properly. For the moment, these macros will only work correctly if you remove the .rsa filename extensions from the filenames. I will correct the problem as soon as possible. Macros:RSA_GetFiles reads the .rsa residue surface accessibility files whose filenames are listed in the first column of the worksheet "Files" into separate worksheets of the active workbook. RSA_CollectData collects the sequences, residue labels and accessibility data from multiple .rsa worksheets into individual worksheets RSA_ExtractSeq extracts the sequences from the "SEQ" worksheet to a horizontal alignment (works only for sequences with less than 250 residues) RSA_GapFromAlig propagates alignment information from the horizontal alignment to the worksheets collected by "RSA_CollectData" RSA_GapFromLbl gaps the worksheets collected by "RSA_CollectData" according to the residue label RSA_GAPFromSeq gaps the worksheets collected by "RSA_CollectData" according to the gaps placed in the "SEQ" worksheet RSA_ValColorBlue converts relative accessibility values to a color code RSA_ValColorRed converts relative solvent accessibilitiy differences to a color code |
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Last Modified by A.Honegger |
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