Density Maps of VEGF


Probability density maps and encoded features of human vascular endothelial growth factor A (VEGF). Structure of VEGF is extracted from PDB ID 2FJG chain V and W. Number 1 to 31 in each cell of the table corresponds to each of the interacting atom types defined in Table 1 of the main text. The PDMs are shown in contours colored according to the interacting atom type: cyan for nitrogen, black for carbon, and magenta for oxygen. The contour level is set to 0.0005. Color spectrum of protein atoms in each cell are based on the corresponding ai,j values (reference). Solvent inaccessible atoms are colored in gray. The interactive presentation is prepared with Jmol.

Color code of ai,j for surface atom
0 = = = = = = = = = = = = = = = = = = = = = 1
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1, NH1
cutoff = 0.0005


2, C
cutoff = 0.0005


3, CH1E
cutoff = 0.0005


4, O
cutoff = 0.0005


5, CH0
cutoff = 0.0005


6, CH1S
cutoff = 0.0005


7, CH2E
cutoff = 0.0005


8, CH3E
cutoff = 0.0005


9, CR1E
cutoff = 0.0005


10, OH1
cutoff = 0.0005


11, OC
cutoff = 0.0005


12, OS
cutoff = 0.0005


13, CH2G
cutoff = 0.0005


14, CH2P
cutoff = 0.0005


15, NH1S
cutoff = 0.0005


16, NC2
cutoff = 0.0005


17, NH2
cutoff = 0.0005


18, CR1W
cutoff = 0.0005


19, CY2
cutoff = 0.0005


20, SC
cutoff = 0.0005


21, CF
cutoff = 0.0005


22, SM
cutoff = 0.0005


23, CY
cutoff = 0.0005


24, CW
cutoff = 0.0005


25, CRHH
cutoff = 0.0005


26, NH3
cutoff = 0.0005


27, CR1H
cutoff = 0.0005


28, C5
cutoff = 0.0005


29, N
cutoff = 0.0005


30, C5W
cutoff = 0.0005


31, HOH
cutoff = 0.0005

The page is made by H.P. Peng