The apparent gap between the peptide and the top alpha helix, in which you see a patch of the yellow floor, is actually largely filled by bound water molecules resolved in the X-ray diffraction. The oxygens of these water molecules can be displayed with RasMol's "select hetero" command.
The peptide uses RasMol's Corey/Pauling/Koltun color scheme: carbon is gray, oxygen is red, and nitrogen is blue. Hydrogens would be white but are not resoved by X-ray crystallography.
This image was constructed from images in a RasMol "movie" script. The atomic coordinate file employed is 1VAB.PDB.