Predefined sets

Names of predefined sets can be used in selection strings. They are matched at the level of the elements they contain.

Residue sets

Set Residues
water
ions
DNA
RNA
ligand
acidic asp, glu
acyclic ala, arg, asn, asp, cys, glu, gln, gly, ile, leu, lys, met, ser, thr, val
aliphatic ala, gly, ile, leu, val
aromatic his, phe, trp, tyr
basic arg, his, lys
buried ala, cys, ile, leu, met, phe, trp, val
charged arg, asp, glu, his, lys
cyclic his, phe, pro, trp, tyr
hydrophobic ala, gly, ile, leu, met, phe, pro, trp, tyr, val
large arg, glu, gln, his, ile, leu, lys, met, phe, trp, tyr
medium asn, asp, cys, pro, thr, val
negative asp, glu
neutral ala, asn, cys, gln, gly, his, ile, leu, met, phe, pro, ser, thr, trp, tyr, val
polar arg, asn, asp, cys, glu, gln, his, lys, ser, thr
positive arg, his, lys
small ala, gly, ser
surface arg, asn, asp, glu, gln, gly, his, lys, pro, ser, thr, tyr

The Dashboard page defines water, ions, DNA, RNA and ligand for its selection menu.

Atom sets

Set Atoms
backbone C, CA, N, O
backbone+h C, CA, N, O, HN, HN1, HN2
sidechain SG, SD, CB, CG, CD, CD1, CD2, CE, CE1, CE2, CE3, CG1, CG2, CZ, CZ2, CZ3, CH2, ND1, ND2, NE, NE1, NE2, NH1, NH2, NZ, OD1, OD2, OG, OG1, OE1, OE2, OH, HD1, HE1, HE2, HE, HE21, HE22, HH23, HH11, HH12, HG, HG1, HH21, HD22, HD21, HZ1, HZ2, HZ3, HH

One-letter residue names

ALA=A, ARG=R, ASN=N, ASP=D, ASX=B, CYS=C,
GLU=E, GLN=Q, GLX=Z, GLY=G, HIS=H, ILE=I, LEU=L,
LYS=K, MET=M, PHE=F, PRO=P, SER=S, THR=T, TRP=W
TYR=Y, VAL=V, XAA=X, SEL=U

Source of the one-letter table, as given on the original page: www.ensembl.org/Docs/Pdoc/bioperllive/Bio/SeqUtils.htm

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