Welcome to the ProtSA web application. ProtSA will calculate, for your protein of interest, the average solvent accessible surface area (SASA) of each atom and residue in the unfolded-state ensemble. All you need to provide is the sequence of your protein. The accessibilities calculated by ProtSA for any residue are strongly sequence dependent and may be useful to understand mutational studies in proteins and to improve parameterizations of protein folding energetics.

In addition, if you provide a structural model (a PDB code, or your own file in PDB format), folded SASA and differences between the folded and unfolded SASA, per atom and per residue, will be calculated. Color-coded sequences summarize the results, and the structural model provided is returned with the B-factor column containing the ratio between the residue folded SASA and its unfolded SASA, allowing a straightforward three-dimensional visualization of exposure changes associated to protein folding.

The results will be e-mailed to the address you provide. You can find a more detailed explanation of this service in a separate page. The description of the method used for the calculation appears in the main reference (Bernadó et al. (2006)), though this server has some modifications, which are explained in the information page (see also the paper describing this server: Estrada et al. (2009)). Next to each field of the form, there is an information icon which leads you to the description of this field, below in this same page.

Thank you for using our service, and we hope that you find the results useful for your research or task. Please, cite Estrada et al. (2009) and Bernadó et al. (2006) if you use ProtSA.

Input form

If you want to apply ProtSA to a set of sequences, please contact us (J. Sancho, contact details) to do those calculations off-line. Future versions of ProtSA will manage such computationally demanding calculations.

Please, fill in all fields. Only ASCII printable characters are allowed.

Title for this job
Send file:
PDB id
Protein sequence (1 chain only)
Solvent radius (Å) (greater than 0.0, 1.4 is a usual value)
Unfolded conformations to generate (between 1-2000; 2000 suggested, see below)
E-Mail address to return results

Description of the fields

Title for this job

To help you in identifying your different jobs, you can add a title (max. 200 ASCII characters), which will appear inside the e-mail message containing your job results.

Send file

You can submit a text file with your protein in PDB format. ProtSA will calculate the unfolded SASA for each protein chain separately and, if the coordinates for all atoms are in the file, they will be used for folded SASA calculations.

PDB id

If your protein is in the PDB, you can submit its PDB id, and ProtSA will fetch the file in PDB format and do the same calculations as if you had provided the file through Send file.

Protein sequence

You can submit the sequence of your protein, each aminoacid represented by its one-letter uppercase code, without blanks. This way, only one protein chain can be provided, and ProtSA only calculates the unfolded SASA. For instance, you would enter the sequence for the LDL receptor ligand-binding module 5 (PDB id 1ajj) as:  PCSAFEFHCLSGECIHSSWRCDGGPDCKDKSDEENCA 

Solvent radius

SASA depends on the radius of the solvent sphere defining the protein surface. Values are in Å. A typical value is 1.4, though any value greater than or equal to 0.0 can be entered.

Unfolded conformations to generate

This is the number of conformations generated for each protein chain in the unfolded state. The greater, the better the approximation. Previous tests showed differences lower than 0.5% between calculations using 2000 and 4000 conformations. For two independent calculations on 2000 conformations, residue-type averaged solvent exposures are equivalent within 0.2%. Therefore, 2000 is a good upper limit. Permitted range is [1-2000].

E-Mail address

ProtSA will send the results to this e-mail address. Please, double-check you entered it right.

Contact

These are the author’s affiliations and e-mail addresses (replace dashes and adjacent spaces by the at symbol):

• Jorge Estrada: jorge.estrada — unizar.es
  Dep. Bioquímica y Biología Molecular y Celular. Facultad de Ciencias. Universidad de Zaragoza (Spain).
  Biocomputation and Physics of Complex Systems Institute. Universidad de Zaragoza (Spain).
• Pau Bernadó: pau.bernado — irbbarcelona.org
  Biomolecular NMR. Insitute for Research in Biomedicine. Parc Cientific de Barcelona (Spain).
• Martin Blackledge: martin.blackledge — ibs.fr
  Institut de Biologie Structurale Jean-Pierre Ebel. Grenoble (France).
• Javier Sancho: jsancho — unizar.es
  Dep. Bioquímica y Biología Molecular y Celular. Facultad de Ciencias. Universidad de Zaragoza (Spain).
  Biocomputation and Physics of Complex Systems Institute. Universidad de Zaragoza (Spain).

Please, send any technical question regarding this service to Jorge Estrada.

References