Homework 2: (Due Thursday, 09/13)
We define the distance between two structures as the norm of
the vector differences.
The distance between protein structures with coordinate vectors
coor1(:,1:3) and coor2(:,1:3) is norm(coor1-coor2). In this exercise we compute
the distances between different representations of the same protein. Your
report should include the programs, plots and explanations of the results as
requested below.
- Extract
the coordinates of the protein 1LAP from the protein data bank
- Read
the CA coordinates of this protein. Plot the chain of the CA-s and the
contact matrix. Assign secondary structures. You may also use the plot3
facility.
- Instead
of the CA-s it is possible to read the N atoms. Modify the code to read
the N-s instead of the CA-s. Be careful not to lose any N! Stored the
coordinates in a different array from the CA array. Compute the distance
between the N vector representation of the protein chain and the CA vector
of the protein. Repeat the process after placing the geometric centers of
the two protein presentations at the origin. Any changes after the shifts
of the geometric centers?