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.