5AI
This algorithm is for the detection of contacts between cations and amino acid residues in 3D structures of proteins.
The algorithm works with PDB file containing results of X-Ray crystallographic analysis.
Instructions
Open up PDB file by any text editor and copy all its lines that start from "ATOM" to the "Input PDB" list.
Copy just those lines that describe amino acid residues from the same chain.
Better delete lines that start from "ANISOU" from your input by the way of sorting.
Delete remaining lines of the previous file from the "Input PDB" list.
Copy the lines with information on atoms of cations after the lines with information on atoms of proteins.
Lines with information on atoms of cations start from "HETATM".
On the "Results" list one should type the abbreviation for a cation and the number of cation in designated cells (if there are 2 cations in a protein, first type "1" and see interactions of the first cation, then type "2" and see interactions of the second cation).
Results
On the "Results" list one will see the table containing amino acid content of a protein and the number of amino acid residues that make contacts with a cation.
The algorithm considers that a given amino acid residue makes a contact with a cation in case if that cation is situated at the distance of less than 5 Angstrom from any atom of a given amino acid residue.
On the "Results" list one can find a table with numbers (from PDB file) of all amino acid residues interacting with a cation.
On the "Results" list one can also find the information on the type of contacts. If main chain atom of O or N is situated closer to a cation than any other atom of an amino acid residue, the interaction is classified as "MC". If side chain atom of O, N, or S is situated closer to a cation than any other atom of an amino acid residue, the interaction is classified as "SC". If an atom C is situated closer to a cation than any other atom of an amino acid residue, the interaction is classified as "HC".
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