PDB HSExposure Computation

Question

[lubw06]

I would like to compute the half sphere exposure using the BioPython PDB HSExposure module from a set of PDB files.

I have a question regarding the interpretation of HSExposure output.

I was able to run HSExposureCA on ‘1t09.cif’. However I am still not sure what values are HSEa-up, HSEa-down, HSEb-up, or HSEb-down. The first element of the ca_cb_list is shown below:

hse.ca_cb_list[0]: (Vector 67.26, -5.69, -42.49, Vector 67.82, -6.19, -43.15)

Are these the HSE values? Or am I looking at the wrong results?

I will appreciate it if anyone could help me understand the output or point me to a proper documentation explaining the output?

Answer 1

[Mensur Dlakic]

A working example from here, with small modifications. Note that this prints only the first 10 residues, and uses 1ako.pdb as input:

from Bio import PDB

pdbfile=open('1ako.pdb')
p=PDB.PDBParser()
s=p.get_structure('X', pdbfile)
m=s[0]
RADIUS=12.0

hse=PDB.HSExposureCB(m, RADIUS)
residue_list=PDB.Selection.unfold_entities(m,'R')
hse=PDB.HSExposureCA(m, RADIUS)
residue_list=PDB.Selection.unfold_entities(m,'R')
for r in residue_list[:10]:
    print(r.get_resname(), r.xtra)

It prints out:

('MET', {'EXP_HSE_B_U': 14, 'EXP_HSE_B_D': 15})
('LYS', {'EXP_CB_PCB_ANGLE': 0.36779144132803365, 'EXP_HSE_A_D': 16, 'EXP_HSE_A_U': 14, 'EXP_HSE_B_U': 12, 'EXP_HSE_B_D': 18})
('PHE', {'EXP_CB_PCB_ANGLE': 0.5011565950966005, 'EXP_HSE_A_D': 19, 'EXP_HSE_A_U': 27, 'EXP_HSE_B_U': 24, 'EXP_HSE_B_D': 22})
('VAL', {'EXP_CB_PCB_ANGLE': 0.42791751525779714, 'EXP_HSE_A_D': 26, 'EXP_HSE_A_U': 19, 'EXP_HSE_B_U': 19, 'EXP_HSE_B_D': 26})
('SER', {'EXP_CB_PCB_ANGLE': 0.47380644203839845, 'EXP_HSE_A_D': 27, 'EXP_HSE_A_U': 23, 'EXP_HSE_B_U': 24, 'EXP_HSE_B_D': 26})
('PHE', {'EXP_CB_PCB_ANGLE': 0.3983307352464271, 'EXP_HSE_A_D': 27, 'EXP_HSE_A_U': 23, 'EXP_HSE_B_U': 25, 'EXP_HSE_B_D': 25})
('ASN', {'EXP_CB_PCB_ANGLE': 0.46401180501955763, 'EXP_HSE_A_D': 21, 'EXP_HSE_A_U': 25, 'EXP_HSE_B_U': 22, 'EXP_HSE_B_D': 24})
('ILE', {'EXP_CB_PCB_ANGLE': 0.7672368218765522, 'EXP_HSE_A_D': 24, 'EXP_HSE_A_U': 20, 'EXP_HSE_B_U': 23, 'EXP_HSE_B_D': 21})
('ASN', {'EXP_CB_PCB_ANGLE': 0.8444275895178895, 'EXP_HSE_A_D': 22, 'EXP_HSE_A_U': 11, 'EXP_HSE_B_U': 10, 'EXP_HSE_B_D': 23})
('GLY', {'EXP_CB_PCB_ANGLE': 0.8558605272890972, 'EXP_HSE_A_D': 26, 'EXP_HSE_A_U': 9, 'EXP_HSE_B_U': 9, 'EXP_HSE_B_D': 26})

Answer 2

[Mensur Dlakic]

The original paper has an explanation for each of these parameters. Don't remember for HSEa, but HSEb-up and -down are whole numbers in the range 0 to 40 or so. What you listed above seem like Calpha and Cbeta coordinates.