Secondary Structure Length

Search by the length of helix or sheet secondary structure elements.

This search queries the PDB by the length of helices and/or beta sheets as calculated by DSSP or Stride. Choose first the "Secondary Structure Method" (DSSP or Stride), then the "Helix Subtype" and/or the "Beta Strand Subtype" and enter integer numbers in the "Between ... and ..." text boxes for a range of residue length. The upper or lower limit of the range can be left empty.

Examples:

  1. Enter 50 in the first box after "Helix Length" and "Between". Leave all pull down menus to their defaults and all other text boxes empty.

    This search will retrieve all structures that have at least one very long (at least 50 residues) helix of any kind according to DSSP.

  2. Select Stride from the "Secondary Structure Method" pull down menu. Select Alpha Helix from the "Helix Subtype" pull down menu and enter "Between 20 and 30". Select Beta Strand from the "Beta Strand Subtype" pull down menu and enter "Between 20 and 30".

    This search will retrieve all structures that according to Stride have at least one moderately long alpha helix (20 to 30 residues) and at least one moderately long beta sheet (20 to 30 residues).