Figure 1

SMS sequence and structure window. This SMS example screen displays the pdb file 1cho.pdb, highlighting the residue Leu46 in chain E. SMS sequence frame, from where all the SMS modules and features can be accessed, is shown at the top of this figure. The sequence is colored according to physical-chemical properties of the amino acids. The blue and red lines underneath the amino acid sequence represent the secondary structure elements (beta strands and helices respectively), according to the pdb file annotation. As the user scrolls the mouse over the sequence, information about the residues appears in the "residue info" box. Pull-down menu on the top of the sequence frame is also shown, demonstrating choice of SMS modules and rendering. SMS structure frame (Chime wiondow) is shown at the bottom of this figure. This figure was centered on the Leu_46 (painted in red) of the E chain. The other residues drawn in stick presentation are the residues that make contacts with the Leucine, colored according to the contacts they make, corresponding to the first two lines of the Protein Dossier in Figure 2.