Figure 3
From: (PS)2-v2: template-based protein structure prediction server
The S2A2 substitution matrix. The scores are high if the residue-structure (RS) letters with similar residue types and the same secondary structure are aligned (red blocks). When two identical RS letters (e.g. diagonal entries) are aligned, the substitution scores are very high. In contrast, the scores are low when helix letters are aligned with strand letters (blue blocks).