Note

This website is presently under development. The primary website for MOPAC is still http://openmopac.net until the majority of its contents have been migrated here.

XENO

This keyword is only used when the default atomic labels in a PDB file are not to be used, i.e., when `RESIDUES <residues.html>`__ or `RESIDUES0 <residues.html>`__ is present.

For non-standard residues and hetero groups

By default, the method that recognizes amino acid residues only recognizes the standard twenty amino-acid residues, but some proteins contain residues which have extra molecular fragments attached. Other residues, particularly where there is a break in a chain, have atoms missing and therefore they do not correspond to any of the 20 standard residues.  In some cases, even though some atoms are missing, the remaining residue is one of the standard 20 residues.  This results in the residue being misidentified. Many hetero groups (small molecules, e.g., water, sulfate, glucose) that are associated with a protein are automatically recognized.  Unidentified residues are given the label “UNK”, and any heterogroups not recognized are given the label “HET”. In order to allow these unusual species to be correctly recognized, the keyword XENO is provided. ````

XENO, from the Greek ξενοσ, xenos, for ‘stranger’, defines unusual residues in a protein and unusual heterogroups in terms of the residue’s number and chain letter. The format of XENO is:

---

XENO=([C]Res=L[{,;}[C]Res=L][{,;}[C]Res=L]…) where [C] is the chain letter, if used, Res is the residue number, and L is the one-letter symbol for the residue, e.g. XENO=(A55=K;78=L,C3=P)or a three-letter identifier, for example: XENO=(B1123=ATP,B1157=SO4).  These two styles can be used in any order in the keyword, e.g.,: XENO=(A12=G,B1157=8OG,B45=D,A787=ATP,B1157=8OG,123=BIT)

If the one letter abbreviation is used, e.g., K for lysine or L for leucine, this will be replaced in the run by the standard three-letter identifier.  If the chain letter is omitted, chain A will be assumed.

When a prosthetic group is present, e.g. the the extra fragment in bacteriorhodopsin, on Lys216: -COCHRNH-;   R = CH₂CH₂CH₂CH₂N=CHCH=CMeCH=CHCH=CMeCH=CHC₉H₁₅, an alternative to using XENO is to delete the connection between the normal residue (here lysine) and the prosthetic (here retinal), using CVB

If XENO is not used, the checks on possible problems in the PDB file will still work, but the label for partial or the modified residues will be incorrect or reported as “UNK" or, for heterogroups, "HET", instead of the more descriptive label which would result from using XENO.

See also: `RESIDUES <residues.html>`__, `RESEQ <reseq.html>`__, `CHAINS <chains.html>`__, and `START_RES <start_res.html>`__.