Table 5

Structural and sequential properties of loop-type specific words in Wset_≥30

Words characteristic

shared words^a

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)

AverageZ_max

9.4

15*

9.7

8.5

11.6*

(± standard deviation)

(± 4.7)

(± 9.5)

(± 5.3)

(± 3.9)

(± 7.0)

Average nb_pos*

3.0

4.6*

3.3

2.7

3.8

(± standard deviation)

(± 1.6)

(± 1.7)

(± 1.8)

(± 1.5)

(± 1.8)

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 Z_max criterion (cf. Method section) and the number of significant position of a word (nb_pos*). 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 Wset_≥30. ^a: words sharing by long and short loops

Regad et al. BMC Bioinformatics 2010 11:75   doi:10.1186/1471-2105-11-75