Trp contacts
Download Trp contacts for X-Ray
This algorithm is for the detection of contacts between tryptophan (Trp) residues and other amino acid residues in 3D structures of proteins.
The algorithm works with PDB file.
Instructions
Open up PDB file by any text editor and copy all its lines that start from "ATOM" to the "input (2)" 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 (2)" list.
On the "Distances" list one should type the number of Trp residue in a designated cell (if there are 2 Trp residues in a protein, first type "1" and see interactions of the first residue, then type "2" and see interactions of the second residue).
Results
On the "Distances" list one will see the table containing amino acid content of a protein and the number of amino acid residues that make contacts with Trp.
The algorithm considers that a given amino acid residue makes a contact with Trp in case if any atom of Trp is situated at the distance of less than 5 Angstrom from any atom of a given amino acid residue.
On the "results near" list one can find distances between centroids of 6-atomic and 5-atomic rings of Trp side chain and atoms from functional groups of amino acid residues (N, O, S), in case if a given residue is situated near Trp in a primary sequence (from -5 to +5 position), as well as angles between planes for aromatic residues and distances between centroids of their rings and centroids of Trp rings.
On the "results near" list one can find distances between centroids of 6-atomic and 5-atomic rings of Trp side chain and atoms from functional groups of amino acid residues (N, O, S), in case if a given residue is situated far from Trp in a primary sequence, as well as angles between planes for aromatic residues and distances between centroids of their rings and centroids of Trp rings.
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