Based on the computed transformation matrix (ComputeStructuralAlignment) the two structural chains are superimposed and a structural alignment is derived.

The first part of the output displays the summary result of the superimposition: root mean square deviation (RMSD) and the number of aligned residues.

The middle line in the structural alignment indicates the pairwise distance in Angstroms between the aligned residues: 1 for 0.0 to 1.0, 2 for 1.0 to 2.0, 3 for 2.0 to 3.0, and so on. An exclamation mark '!' indicates that the pairwise distance is larger than 10 A.

The structural alignment is a local alignment, not showing the complete sequences but only the part that can be structurally aligned. The underlying scoring system of the alignment algorithm depends only on the pairwise distances and thus is not equivalent to a sequence alignment. The interpretation of a structural alignment is not comparable to the interpretation of a sequence alignment. The second is a model for evolutionary processes whereas the structural alignment shows the structural equivalence between residues in both structures.

Verification

The structural alignment is back verified on both structures. Every pair in the structural alignment is compared to every other aligned pair in terms of their difference in the respective Calpha distances. Thus for two aligned pairs i and j we compute the Calpha distances in structure A as Ai-Aj and in structure B as Bi-Bj. For this we do not need the two structures to be superimposed. The structural alignment indicates the pairing of the residues. The difference between the Calpha distances in structure A and B is then displayed in the resulting graph: green if the distance is below half the threshold, yellow if the distance is at least half the threshold, red if the distance exceeds the threshold. No verification and colouring can be done in regions where gaps occur.

The interpretation of this graph allows the identification of local conformation changes such as domain movements. A region is well aligned if the colouring is mostly green. Red and yellow spots between regions which are themselves well aligned and thus mostly green, indicate a different conformation of the said regions between the two structures.

Example

My favority example: 1FIN/A and 1E1V/A both are CDK2 (cyclin-dependent kinase 2) and share 100% sequence identity. Yet, one (1FIN) is complexed with a cyclin, the other (1E1V) is free. The structural alignment indicates some difficulties in aligning two movable parts. The verification shows the different conformations of the N-terminal part vs. the C-terminal part.