Q: Secondary Structure Designations

[Christian Cumbaa]

Julianne M. Braun wrote:

> Is there a standard method for designating primary and secondary
> structure of proteins?  I'm familiar with mixed case three letter
> abbreviations delimited by dashes or hyphens (e.g. Pro-Ala-Gly) and with
> one letter abbreviations (e.g. PAG) for primary structure, but if one
> also wants to designate known secondary structure how would that be
> done?  Are secondary structure designators placed between residues in
> the same string of text?  Is it more common to list out the residue
> range that has a certain structure?  If a list is common, would it
> normally include designation of secondary structure for all residues or
> just for those of known structure types (i.e. random coil residues would
> be left off the list)?  

I can't say anything about a standard presentation format for secondary
structure information, but the Moose query facility
(http://db2.sdsc.edu/moose/) presents secondary structure in the
following form.

      Sequence and secondary structure:

   1 GQGGGTHNQW NKPSKPKTNM KHMAGAAAAG AVVGGLGGYM LGSAMSRPMM 
       SSSSSTTT TT S   THH HHHHTT SSS S  SS SS E E TGGGGT   

  51 HFGNDWEDRY YRENMNRYPN QVYYRPVDQY NNQNNFVHDC VNITIKQHTV 
      SSTHHHHHH HHHHGGGT     EE SS  S STTHHHHHHH HHHHHHHHHH 

 101 TTTTKGENFT ETDIKIMERV VEQMCTTQYQ KESQAYYDGR RS 
     HHHHHTT  T HHHHHHHHHH HHHHHHHHHH HHHHHHHTTT    

That's from a "snapshot" entity query on the protein with PDB code
2PRP.  
Take a look at the Moose homepage for a reference on the particular
secondary structure classification system used.