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Table 5 Structural and sequential properties of loop-type specific words in W set≥30

From: Mining protein loops using a structural alphabet and statistical exceptionality

Words characteristic shared wordsa short-long specific words long-long specific words flanking-region unspecific words flanking-region specific words
Average RMSd w (Å) 0.90 0.80* 0.74 0.83 0.88
(± standard deviation) (± 0.4) (± 0.4) (± 0.4) (± 0.4) (± 0.4)
AverageZmax 9.4 15* 9.7 8.5 11.6*
(± standard deviation) (± 4.7) (± 9.5) (± 5.3) (± 3.9) (± 7.0)
Average nbpos* 3.0 4.6* 3.3 2.7 3.8
(± standard deviation) (± 1.6) (± 1.7) (± 1.8) (± 1.5) (± 1.8)
  1. The upper part of the table corresponds to the analysis of word structural properties. The intra-word structural variability is analysed using the Root Mean Square deviation (RMSd) between fragments corresponding to the same word (RMSd w ). The inter-word structural variability is analysed using the RMSd between fragments of two different words (RMSd dev ). The lower part of the table corresponds to the analysis of sequential properties of words. The intra-word amino-acid preferences of a word are analysed using Zmax criterion (cf. Method section) and the number of significant position of a word (nbpos*). Numbers within brackets indicate standard deviations. *: significant differences according to the Kruskal-Wallis test. The RMSd dev are computed on a subset of 890 words of W set≥30. a: words sharing by long and short loops