Table 2.
Consolidation of CDPro and DSSP Structure Annotations into Generalized Helix, Strand, Turn, and Unordered Categories
| Defined Structure Categories | CDPro Structures | DSSP Structures | CPPTRAJ Implementation of DSSP |
|---|---|---|---|
| helix | helix (regular) | α-helix | α-helix |
| helix (distorted) | 3–10 helix | 3–10 helix | |
| β-strand | strand (regular) | β-strand | parallel β-sheet |
| strand (distorted) | antiparallel β-sheet | ||
| turn | turn | turn | turn |
| bend | |||
| other | unordered | π-helix | π-helix |
| β-bridge | none | ||
| irregular/loop | |||
| turn (1 residue) | |||
| bend (1 residue) |
We choose a consolidation scheme similar to Kardos et al. (86), in which the π-helix secondary structure is counted as unordered because of its lack of distinction as a stable secondary structure. The DSSP was implemented using the AMBERTOOLS trajectory analysis software CPPTRAJ, which contains an alternate set of structure codes despite using the DSSP algorithm.