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Table 3 Structural and sequential properties of words in W set≥30 according to the statistical word type

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

Words characteristic W set≥30 UR w NS w OR w
Average RMSd w (Å) 0.85 0.94 0.89 0.74*
(± standard deviation) (± 0.4) (± 0.4) (± 0.4) (± 0.3)
Average RMSd dev (Å) 2.72 2.67 2.69 2.76
(± standard deviation) (± 0.6) (± 0.6) (± 0.6) (± 0.7)
AverageZmax 10.3 9.5 8.8 14.0*
(± standard deviation) (± 6.1) (± 3.8) (± 4.0) (± 8.4)
Average nbpos* 3.3 3.0 2.9 4.1*
(± standard deviation) (± 1.8) (± 1.7) (± 1.6) (± 1.8)
Average dZ-score 31.1 29.0 27.4 39.5*
(± standard deviation) (± 9.7) (± 5.7) (± 5.3) (± 13.8)
  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*). The coverage of sequential space is analysed using the Euclidian distance between Z-score vectors (cf. Method section) (dZ-score). 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 shared by long and short loops.