Pmv predefined sets:

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, sln, 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

Atom Sets:

‘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 Character 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

#from www.ensembl.org/Docs/Pdoc/bioperllive/Bio/SeqUtils.htm