Table 4. Comparison of Protein Folding Variation Matrix (PFVM) for
mutation on residue 183 of P53_HUMAN. Top section: the sequence
fragment (170-200) of P53_HUMAN with numeric ruler. Bottom section: the
local folding variation in PFSC letters. The PFSC letters in each
vertical column represent the local folding variation for 5 successive
amino acids in sequence. The order of PFSC letters in each vertical
column is ranked from higher to lower according the frequency numbers of
folding shapes in PDB. The PFSC letters are marked by colors: red is for
typical helix fold; blue for typical beta fold; pink and light blue for
folds with partial helix or beta; black for irregular folds.
PFVM Embracing Known Structures
The PFVM can generate all possible folding confirmations for a protein
with an astronomical number, of course, it should embrace the protein
conformations of known 3D structures. For a protein, it usually may have
multiple structural data in PDB, but these 3D structures in some degrees
have difference in folding conformations because of different
measurement methods and environments. With PFVM, different conformations
in PFSC strings can be constructed by the PFSC letters from each column
in matrix, and the conformations for protein with known 3D structures
should be one of these PFSC strings.