Journal article
Distance distributions in proteins: a six parameter representation
We present a statistical analysis of protein structures based on interatomic C-alpha distances. The overall distance distributions reflect in detail the contents of sequence-specific substructures maintained by local interactions (such as alpha-helixes) and longer range interactions (such as disulfide bridges and beta-sheets).
We also show that a volume scaling of the distances makes distance distributions for protein chains of different length superimposable. Distance distributions were also calculated specifically for amino acids separated by a given number of residues. Specific features in these distributions are visible for sequence separations of up to 20 amino acid residues.
A simple representation, which preserves most of the information in the distance distributions, was obtained using six parameters only. The parameters give rise to canonical distance intervals and when predicting coarse-grained distance constraints by methods such as data-driven artificial neural networks, these should preferable be selected from these intervals.
We discuss the use of the six parameters for determining or reconstructing 3-D protein structures.
Language: | English |
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Year: | 1996 |
Pages: | 733-740 |
ISSN: | 1460213x , 02692139 , 17410134 and 17410126 |
Types: | Journal article |
DOI: | 10.1093/protein/9.9.733 |
ORCIDs: | Lund, Ole |