Index

2.Copyright notice

4. Description of the Output

3. Input description

The input form, which allows a user to specify the data needed by the program, is divided in seven panels:

• The Sequence of the polypeptide to be created is specified in the Sequence text Area.
• The Secondary Structure is specified in the SecStr text Area
• In the Angle Panel the user can either choose to use a set of predefined phi,psi angles.
• In the View Panel the user can choose the Output Mode by selecting either the graphical output or the text output.
• If the 'User Angles' radio-button is checked, the user is forced to enter in the State-Angles Panel the Letter of the Secondary Structure's state and to define the phi, psi angles of the state.
• The 'Submit Sequence...' button in the Action Panel activates the Create Module, whreas the 'Clear Form' button resets the input form.
• Finally in the PDB Panel the user can enter a PDB ID Code and by pressing the 'View...' button activates the program that retrieves the structure with the specified code, if exists, directly from the PDB Databank
• Errors appear in a new HTML Page.

3.1 Sequence Specification

A sequence can be either typed directly in the text area or pasted from a text editor. The sequence can be given in FASTA or Swiss-Prot Format. The Swiss-Prot Format contains information that is not useful to the program so it is recommended to use the FASTA format in order to increase the reliability of the transmitted data and reduce the time of data transmission. For convenience, it is also possible to enter a sequence as plain text by using the one-letter code of aminoacid residues. Spaces are allowed since they do not affect the results of the program. The maximum length of a sequence is 2.000 residues(15.000 atoms).

3.2 Secondary Structure Specification

The Secondary Structure can be either typed directly in the text area or pasted from a text editor. If the user leaves the Secondary Structure Text Area blanc, the program produces a polypeptide chain in an extended form (phi, psi angles = 180). The SecStr program of our Server can predict the secondary structure of a polypeptide, SCAR can recognize only 4 letters of Secondary Structure States(fig 1). It is recommended to enter the Secondary Structure as plain text. Spaces are allowed since they do not affect the results of the program.

3.3 Predefined Angles

SCAR's predefined angles are shown in the table below(Fig.1).

• The 'H' letter is used to define a-helical structures constist of a stretch of residues with phi = -57 psi = -47.
• The 'E' letter is used to define structures of parallel b-sheets which consist of residues with phi = -120 and psi = +115.
• The 'B' letter is used to define structures of antiparallel b-sheets which consist of residues with phi = -140 and psi = +135.
• The 'L' letter is used to define loops which consist of residues with phi = -60 and psi = -30.

If the 'Default Angles' radio-button in the Angle Panel is checked, the program uses the above predefined angles and state letters. If the 'User Angles' is checked, then the user is obliged to input up to 10 states of secondary structure with the ö and ø angles of each state specified at will.

3.4 Errors

Error messages are displayed in a new HTML Error Page.

Explanation of the error messages:

Error 1 : No Sequence Entered.

Error 2 : Check the Length of your Input.

The length of the Sequence is different than the length of the Secondary Structure.

Error 3 : Invalid Aminoacid Character.

The Sequence entered contains letters that cannot be used. Allowed characters are the 20 aminoacid letters and the Space character.

Error 4 : Unrecognized Secondary Structure Character.

The Secondary Structure either contains letters other than the 4 predefined('H', 'E', 'B', 'L') or it contains characters other than those entered by the user.

Error 5 : No Secondary Structure States entered.

3.5 Appendix

3.5.1 Input Form Layout