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Crystallographic shell-waters that originate from diffraction data are an essential component, but not bulk water, of protein structure and stability. It interacts with various polar and non-polar components of protein. Polar backbone is constituted by O-type and N-type atoms of all residues. Polar side-chains are O, N, S containing groups of amino acid residues. Notably, ordered shell-waters form bridge interactions. Disordered shell-water may occupy central hydrophobic-cavity of protein. While X-ray diffraction can detect the former, the latter is suitably detected by NMR method.
In this context, the question as to how to gain insight into these shell-water and protein interactions has been highly relevant.
In this end, POWAINDv1.0 has been a program that extracts detailed analytical information on interactions a] between shell-water and protein-atom/ residue groups and b] among multiple atoms (bridge interactions) of water with an atom/residue of a protein or vice-versa.
Features
- The program works in CYGWIN-32bit-UNIX like terminal in window environment (e.g. WINDOW 7)
- The program works for one PDB at a time for distances in "inp_dist" file (limit is 34), which is basically a vertically single column of decimal numbers e.g. 2.050 2.100 etc
- The program could interpret decimal numbers up to 3rd decimals.
- It can analyze any number of chains of a PDB file.
- It presents both absolute and normalized values of frequencies of HOH-protein interactions in range specific manner.
- Different types of interactions such as polar, O-type, N-type, C-type, non-polar etc are interpreted separately using normalized file. It is also possible to compute the contribution of components for a given type. For example, how much is the contribution of ASP-OD1 in polar-type interaction for a given chain can be worked out from the normalized file. For this, following reference distance table seems to be useful.
- The program point out about the favorable and unfavorable type of interactions It is noteworthy here that van der Waals interaction can result in either favorable or unfavorable interaction. Unfavorable as well as favorable interactions are identified by the program POWAINDv1.0.
- Program redirects bridge interactions from 1:2 to other any higher combinations Apart from the standard 1:1 type of Protein-Water interactions, different other types of bridge interactions are also been extracted by the program such as nW and nP moles of residue-type/atom-type associates with 1P and 1W moles respectively.
- Program redirects a total of 5 EXCEL and one combined text outputs. While EXCEL files are readily used in post-run analyses, the text file is useful for verification of any range specific value. All these named files are shown below.
- The program gives five EXCEL outputs which are named as: XXXX_Y_resi_gr.xls; XXXX_Y _resi_gr_normalized.xls; XXXX_Y _atom_gr.xls; XXXX_Y_atom_gr_normalized.xls; XXXX_Y_atm_multiplicity.xls & XXXX_Y.txt
Project Samples
