Classification of Hexapeptide Folds

The folding patterns of hexapeptide fragments have been determined from the atomic coordinates of the protein structures using the standard procedure of Kabsch and Sander [66]. Every residue is given a secondary structure descriptor. To reduce complexity, residues were classified as helical h (G, H or I in Kabsch-Sander nomenclature), extended strand s (E), P turn t (T) or remained unassigned n. With these four structural classes there are still 4096 possible folding patterns for hexapep- 

The type of information that can be retrieved from this database is best illustrated by two characteristic examples shown in Ikble 17.2. The first example compiles hexapeptides related to the C-terminal part of the first and main a helix in the bacterial protein barnase (Ikble 17.2a), the structure of which is known from X-ray analysis [67], but is not contained in our database. Of over 30,000 related peptides generated, nine could be found in the database. They are moderately similar to the query peptide as reflected by rms distances greater than 0.1 and similarity indices below 0.8. Seven of the nine related peptides adopt full or partial helical folds in their respective protein structures, whereas only two less related peptides are found in partially extended conformations. This highly consistent picture is also borne out by the cumu- 

Fold type Fold weight Number of peptides Percentage of all peptides 

However, such conclusions may not hold in general. This is evident in the second example (Table 17.2 b), where a segment of the first a helix in hen egg white lysozyme is examined. This helical segment has been shown also to be formed early in the folding process by similar NMR experiments [40]. A search for related peptides uncovers fifteen peptides of moderate similarity, of which only one adopts a fully helical fold and three are partially helical in their respective protein struetures. In 

Peptide Similar peptides From protein Peptide distance Similarity index Secondary structure Folding pattern Pattern weight Fold score 

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