Table 6

Rs and Rp for two proteins having the same fold belonging to the β class

Name of the protein

Number of residues

Number of aligned residues

Rs

Rp


Azurin (1azu)

126

84

1.12

(1.06)

0.33

(0.29)

Plastocyanin (5pcy)

99

84

1.33

(1.14)

0.46

(0.32)


The structures are aligned using the software SSM at EBI http://www.ebi.ac.uk/msd-srv/ssm webcite. The values calculated considering only the aligned amino acid residues are given in parenthesis. To quantify the sequence structure compatibility between the structures, two more parameters are computed over the aligned residues. (Rs)azu/pcy = 0.97 and (Rs)pcy/azu = 0.89. Each term contributing to the former corresponds to (ASAazu - <ASA>pcy)/<ASA>pcy, i.e., in Eq. (3) the observed value at a given position in the structure of azurin is compared to the average value corresponding to the aligned residue type at the same position in the sequence of plastocyanin. The opposite is done in the calculation of (Rs)pcy/azu.

Bahadur and Chakrabarti BMC Structural Biology 2009 9:76   doi:10.1186/1472-6807-9-76

Open Data