Lists

Three-letter code-names for Lists For easy reference, programmatic simplicity, and long-term maintainability we have given each list a three-letter mnemonic, like ′acc′ for accessibility tables, ′chi′ for torsion angle tables, etcetera. These are summarized in this table and worked out in depth in the remainder of this webpage.

Code	Type of data
	Administration
sou	WHAT IF interpretation of PDB files
	Geom
chi	Torsion angles
tau	Backbone bond angles
acc	Molecular surface area
asa	Accessible surface area
dsp	Secondary structure overview
	Residue contacts
cc1	Cα-Cα distance <  12.5 Ångström
cc2	Residue spheres closer than 0.25 Ångström
cc3	Residue spheres closer than 2.5 Ångström
cc4	Residues with an atom pair closer than 0.25 Ångström
cc5	Residues with an atom pair closer than 2.5 Ångström
cc6	Residues with a side chain atom pair closer than 0.25 Ångström
cc7	Residues with a side chain atom pair closer than 2.5 Ångström
cc8	Residues in different chains with a side chain atom pair closer than 2.5 Ångström
cc9	Cβ-Cβ distance <  12.5 Ångström
	Other contacts
cli	Residues with a atomic contact to ligand <  1.0 Ångström
cnu	Residue-nucleic acid spheres closer than 1.0 Ångström
iod	Residue distance to nearest (positive) ion
ion	Short residue-ion distances, grouped per ion
cys	Cysteine bridges
sbr	Salt bridges
sbh	Salt bridges assuming histidine is positive
	Quality / Validation
qua	First generation packing quality per residue
nqa	Second generation packing quality per residue
flp	Residues ′flipped′ for better hydrogen bonds
rot	Residue rotamer scores

Use of DSSP

In many Lists DSSP secondary structure assignments are added for your convenience. Be aware though, that these are the WHAT IF translation of DSSP output. So, 3₁₀-helices and π-helices are called H, just like normal helices. Further, loops are called blank in DSSP, while in Lists this became a - (minus sign) to ease your parcing problems...