Matrix representation of residue co-locations in a protein structure (1AP6) (modified from ). A protein sequence (1AP6) was compared to itself with DOTLET using different matrices, SCM (A), CCM (B), HCM (C), the combined SCHM (D) and NFM (G) and Blosum62 (F). Comparison of randomized 1AP6 using SCHM is seen in (I). The 2D (SeqX Residue Contact Map) and 3D (DeepView/Swiss-PDB Viewer) views of the structure are illustrated in (E) and (H). The black/gray parts of the dot-plot matrices indicate the respective compatible residues, except the Blosum62 comparison (F), where the diagonal line indicates the usual sequence similarity. The dot-plot parameters are otherwise the same for all matrices.