Table 1.
Proteins used for the analysis of molecular surfaces.
Table 2.
Atom types and relative atomic hydrophobicity (small correlation matrix, see text).
Figure 1.
Schematics of different representations of molecular surfaces.
Top row: representation of the hydrophobicity on the molecular surface, at (a) low, amino acid-level; and (b) high, atomic-level resolutions. Bottom row, the same representation for molecular surfaces probed with larger probes. Scheme upgraded from [29], which reports the mapping at low, amino acid-based hydrophobicity (i.e., a and c).
Table 3.
Fit for 12 atom types for different hydrophobicity scales.
Figure 2.
Comparison between the representation of atom-based properties, i.e., charges (left column; red = negative, blue = positive), atomic hydrophobicity (middle column; red = hydrophobic and blue = hydrophilic region); with amino acid-based properties, i.e., amino acid-based hydrophobicity (right column) on the molecular surface of ribonuclease (PDB ID: 1AFU).
The molecular surface is probed with decreasing geometrical resolution (from top to bottom).
Figure 3.
Evolution of the ratio between atom-based overall hydrophobicity and total molecular surface area (relative density of the atomic hydrophobicity); and of the ratio of the atomic and the amino acid overall hydrophobicities; vs. probe radii for 5 model proteins: lysozyme (1LYZ); ribonuclease-A (1AFU); human hemoglobin (1Y4F); human serum albumin (1AO6); human IgG (1HZH).
Figure 4.
Evolution of the ratio between the atomic hydrophilic area and the total molecular surface area; and of the ratio between the atomic and the amino acid hydrophilic areas; vs. probe dimensions for 5 model proteins: lysozyme (1LYZ); ribonuclease-A (1AFU); human hemoglobin (1Y4F); human serum albumin (1AO6); human IgG (1HZH).
Figure 5.
Evolution of the ratio between the atomic hydrophilicity and the total molecular surface area (hydrophilic relative density); and of the ratio between the atomic and the amino acid hydrophilicity relative densities; vs. probe dimensions for 5 model proteins: lysozyme (1LYZ); ribonuclease-A (1AFU); human hemoglobin (1Y4F); human serum albumin (1AO6); human IgG (1HZH).
Figure 6.
Evolution of the ratio between the atomic hydrophilicity and the hydrophilic area (hydrophilic specific density); and of the ratio between the atomic and the amino acid hydrophilicity specific densities; vs. probe dimensions for 5 model proteins: lysozyme (1LYZ); ribonuclease-A (1AFU); human hemoglobin (1Y4F); human serum albumin (1AO6); human IgG (1HZH).
Figure 7.
Evolution of the ratio between the atomic hydrophobic area and the total molecular surface area; and of the ratio between the atomic and the amino acid hydrophobic relative areas; vs. probe dimensions for 5 model proteins: lysozyme (1LYZ); ribonuclease-A (1AFU); human hemoglobin (1Y4F); human serum albumin (1AO6); human IgG (1HZH).
Figure 8.
Evolution of the ratio between the atomic hydrophobicity and the total molecular surface area (hydrophobic relative density); and of the ratio between the atomic and the amino acid hydrophobicity relative densities; vs. probe dimensions for 5 model proteins: lysozyme (1LYZ); ribonuclease-A (1AFU); human hemoglobin (1Y4F); human serum albumin (1AO6); human IgG (1HZH).
Figure 9.
Evolution of the ratio between the atomic hydrophobicity and the hydrophobic area (hydrophobic specific density); and of the ratio between the atomic and the amino acid hydrophobicity specific densities; vs. probe dimensions for 5 model proteins: lysozyme (1LYZ); ribonuclease-A (1AFU); human hemoglobin (1Y4F); human serum albumin (1AO6); human IgG (1HZH).
Table 4.
General comparison of the evolution of molecular surface properties with the probe radius, calculated at atom- and amino acid level.
Figure 10.
Evolution of the ratio between atom-based overall hydrophobicity and total molecular surface area (relative density of the atomic overall hydrophobicity); and of the ratio of the atomic and the amino acid overall hydrophobicities; vs. probe dimensions for hemoglobin subset.
Figure 11.
Density of the overall hydrophobicity on the molecular surface of hemoglobin subset, at small (top) and large (bottom) probe radius vs. the hydrophobicity of the residue 37.
The hydrophobicities of the residue 37 are, from left to right, Gly, Ala, Glu, Tyr and Trp [38].
Table 5.
Computing time (sec) for the construction of protein molecular surfaces on a personal computer.