Figure 1

An example of an aa-sphere This example demonstrates an aa-sphere for the 26-th amino acid of Ubiquitin [PDB:1UBQ]. Each amino acid is represented by a ball centered in its α-carbon position. The tube corresponds to the protein backbone denoting the protein sequence. The Euclidean sphere with center in the 26-th amino acid (black) with radius 9 Å (gray). The different colors emphasize amino acids included in the aa-sphere. Some of the heavy atoms of the colored amino acids with their α-atoms outside the Euclidean sphere intersect with the sphere and thus the respective amino acids are also included in the aa-sphere. The figure has been generated by VMD [30].