Fig. 9. DSSP assignments for similar structures: 4mbp and 1pot. (A) The DSSP assignment for two segments taken from two structurally similar proteins (periplasmic binding protein 4mbp [84] and putrescine binding protein 1pot [85] ) illustrates that the observed differences between these segments may originate from sequence differences. The boxed letters shown in the column next to the amino acid sequence give the final DSSP assignment: G = 310-helix, H = a-helix, T = turn, B = b-bridge, and S = bend. The next column shows the hydrogen bonds (>: hydrogen bond acceptor, <: hydrogen bond donor and X: both), with indications of the hydrogen bond length, i.e. i ® i+(3,4) for 310 and a-helices, respectively. (B) All the predictions from PSIPRED [87] , SSpro [88] and PROFphd [89; 90] (see chapter 28) correctly spot the a-helix signal in 4mbp, while missing this signal for 1pot. This may indicate that the altered sequence changed the structure significantly in this region. Here, 'h' refers to the DSSP class helix (H or G) and 'c' to the DSSP non-regular class. Note: the predictions are cut out from those for the entire protein.