Str1_1: Question: When considering beta sheets, are consecutive residues of a strand closer than neighbouring residues on different strand? Write program that calculates the distance between Cbeta atoms of consecutive residues in a beta strand and the Cbeta atoms of the neighboring residues. Structure id "1bjt" is used from PDB.
Str1_2: Question: Do the bond lengths between Cα – C, C – N and N– Cα have similar lengths or not? Structure id "6aa3" is used from PDB.
Str1_3: # Question: Compute the phi and psi dihedral angles for Cα[i] when given the coordinates of C[i-1], N[i], Cα[i],C[i] and N[i+1] and plot the Ramachandran plot.Plot Proline and Glycine residues seperately. Also, plot the most unstable residues with the largest 5 B-factors(temperature). Structure id "6aa3" is used from PDB.
Str2: Question: Find the contact matrix of a protein. For two residues to be contacting distance between Cα atoms should be less than 7 Å. Find the relation between coordination number and B-factor. Find the relation between coordination number and Relative Surface Area. Is there any difference between core and surface in terms of the physicochemical properties of the aminoacids (small, large, hydrophobic, polar, charged etc.)
Str3: Question: Translate proteins such that centroid is at the origin and check if the sum of the coordinates are almost zero or not. Find an NMR structure and compare RMSD of the models with the first model. Align the structures 1xg5 chain A, 3gy0 chain A and 1edo by using MULTIPROT and write a code to calculate the RMSD value