SUITE = PACT + INCA + SPIRE + RACE + LACE + SUIT

PACT: Peptidic Atomic Coordinates Tool

Provide input for PACT to represent disordered regions in PDB-style format (e.g., for use with INCA):

Radius of spacer probe (Å):
Disordered-residue offset distance (Å):
Peptidic-structure data (in PDB or FASTA format):

Optional residue list (in LACE format):

Interpretation of optional residue list:
Positive listing (disordered residues listed, ordered residues unlisted)
Negative listing (disordered residues unlisted, ordered residues listed)

Sample PACT Input and Output:

No. Input Output Remarks
1 ifnpacti.pdb ifnpacto.pdb input manually derived from PDB ID 1FG9 chains A and B
2 toxpacti.pdb toxpacto.pdb input manually derived from PDB ID 1PRT chains A through F
3 ps1pacti.faa ps1pacto.pdb sequence-based representation of disordered oligopeptides
4 ps2pacti.faa ps2pacto.pdb sequence-based representation of disordered oligopeptides
5 ps3pacti.faa ps3pacto.pdb sequence-based representation of disordered oligopeptides

Notes:

  1. PACT facilitates representation of peptidic structures containing disordered residues, with or without ordered residues, in PDB-style format suitable as input for naccess.
  2. PACT regards a residue as disordered in PDB-format input data if its atomic coordinates are already assigned the spdbv-style missing-atom placeholder value of 9999.999.
  3. PACT represents disordered residues by assigning them positions on the Z-axis, such that the constituent atoms of each disordered residue share the same coordinates.
  4. To avoid problems with naccess ASA calculation, adequate spacing should be ensured between all residues (e.g., using the default spacer-probe radius and offset distance).
  5. To be regarded as disordered by SAPPHIRE, each disordered residue should be explicitly represented with PDB ATOM records for at least two of its constituent atoms.