Jmol/Depth from surface: Difference between revisions
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The asterisk "<span style="font-size:200%;">⁎</span>" means "all atoms". The atom expression must be enclosed in curly brackets "{...}". Anything after "#" is a comment, which is not part of the command to Jmol. | The asterisk "<span style="font-size:200%;">⁎</span>" means "all atoms". The atom expression must be enclosed in curly brackets "{...}". Anything after "#" is a comment, which is not part of the command to Jmol. | ||
Three enzymes that are roughly spherical with 527-575 amino acids each are [[2ace]], [[1crl|1CRL]], and [[1o86]]. Their maximum surfacedepth values are 10.25, 9.58, and 7.94 Å respectively. A script that you can download reports the average surfacedepth values for each amino acid, secondary structures, and common chemical elements. Average values were normalized to a maximum depth of 10.0 Å, and averaged. For this small sample of 3 enzymes: | |||
*The sidechain of Trp was deepest (2.5). | |||
*In order of increasing depth: the sidechains nitrogens and oxygens of charged amino acids (Asp, Glu, Lys, Arg) 0.8 < the sidechain O,N of Asn, Gln 1.1 < the entire sidechains of Val, Leu, Ile 1.4 < the entire sidechains of Phe, Tyr, Trp 2.3 Å. | |||
*Lys and Glu (0.3, 0.5) are shallower than Asp and Arg (~1). | |||
*In order of increasing depth: atoms in coil 1.3 < helices 1.6 < β strands 2.4 Å, | |||
</StructureSection> | </StructureSection> | ||
