Typical pharmacophore features include hydrophobic centroids, aromatic rings, hydrogen bond acceptors or donors, cations, and anions.  These pharmacophore points may be located on the ligand itself or may be projected points presumed to be located in the receptor.
The features need to match different chemical groups with similar properties, in order to identify novel ligands.  Ligand-receptor interactions are typically "polar positive", "polar negative" or "hydrophobic". A well-defined pharmacophore model includes both hydrophobic volumes and hydrogen bond vectors.