Addaa adds an amino acid of type res_type with sequence number res_number to adjacent_res, which must be the first or last residue of a chain. The res_type is a three-letter residue name for one of the 20 standard amino acids (case is unimportant), and res_number can include an insertion code. The adjacent_res specification may contain just a part of that residue (such as one atom or bond) but not more than one residue. If adjacent_res is a single amino acid not part of a longer chain, the res_number is used to determine whether the new residue will be added N- or C-terminally.
The conformation can be specified with a keyword:
| keyword | description | φ (°) | ψ (°) |
|---|---|---|---|
| ext | extended (default) | 180 | 180 |
| alpha | alpha helix | –57 | –47 |
| abeta | antiparallel beta sheet | –139 | 135 |
| pbeta | parallel beta sheet | –119 | 113 |
or with a comma-separated pair of values:
phi,psi(the desired φ and ψ angles in degrees, respectively). If the new residue is added at the C-terminus, φ and ψ apply to the new residue, ψ measured as if the residue's OXT were the N of a further C-terminal residue. If the new residue is added at the N-terminus, φ applies to adjacent_res and ψ to the new residue (for which φ is undefined, as there is no heavy atom substituent to delineate the torsion angle around the residue's N-CA bond).
An added residue may not have an optimal geometry and may clash with other parts of the structure. Residues added with the alpha keyword are assigned the residue attribute value isHelix=true; those added with the abeta or pbeta keyword are assigned the residue attribute value isStrand=true (isSheet=true). However, the backbone dihedral angles are merely those appropriate for the designated conformational state and do not ensure that the added residue will fall within that type of secondary structure (which depends on the conformations of multiple residues). After building is complete, ksdssp can be used to evaluate and reassign secondary structure.
The temperature factor for the new residue is set to the highest currently found in the model.
Example:
addaa tyr,30 :29.a- add tyrosine in an extended conformation as residue 30, after residue 29 in chain A (the new residue will also be in chain A)
See also: swapaa, delete, ksdssp, Build Structure