Protein regular structure element

The term random coil" is sometimes used incorrectly to designate non-regular structure elements within a protein structure. There is, of course, nothing random about this the angles are well defined... 

Table 1.23. Proportion of regular structural elements present in various globular proteins...

Table 1.24. Normalized frequencies of amino acid residues in the regular structural elements of globular proteins...

Shown is the fraction of an amino acid in a regular structural element, related to the fraction of all amino acids of the same structural element. P = 1 means random distribution P > 1 means enrichment, P < 1 means depletion. The data are based on an analysis of 66 protein structures. 

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

The a-helix is the classic element of protein structure. A single a-helix can order as many as 35 residues whereas the longest strands include only about 15 residues, and one helix can have more influence on the stability and organization of a protein than any other individual structure element. a-Helices have had an immense influence on our understanding of protein structure because their regularity makes them the only feature readily amenable to theoretical analysis. 

There are different classes of protein sequence databases. Primary and secondary databases are used to address different aspects of sequence analysis. Composite databases amalgamate a variety of different primary sources to facilitate sequence searching efficiently. The primary structure (amino acid sequence) of a protein is stored in primary databases as linear alphabets that represent the constituent residues. The secondary structure of a protein corresponding to region of local regularity (e.g., a-helices, /1-strands, and turns), which in sequence alignments are often apparent as conserved motifs, is stored in secondary databases as patterns. The tertiary structure of a protein derived from the packing of its secondary structural elements which may form folds and domains is stored in structure databases as sets of atomic coordinates. Some of the most important protein sequence databases are PIR (Protein Information Resource), SWISS-PROT (at EBI and ExPASy), MIPS (Munich Information Center for Protein Sequences), JIPID (Japanese International Protein Sequence Database), and TrEMBL (at EBI). ... 

The complete pattern of folding of the polypeptide chain of a protein, whether regular or irregular, is called the tertiary structure. The tertiary structure of any protein is the sum of many forces and structural elements, many of which are the result of interactions between the side chain groups of amino acids in the protein. Some of these interactions are described below. 

---