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.

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. [https://proteopedia.org/wiki/images/b/b5/Surfacedistance-reports.spt A script that you can download] (right click, save link as) reports the average surfacedepth values for each amino acid, secondary structures, and common chemical elements. In the list below, average values were normalized to a maximum depth of 10.0 Å, and averaged. For this small sample of 3 enzymes:

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. [https://proteopedia.org/wiki/images/b/b5/Surfacedistance-reports.spt A script that you can download] (right click, save link as) reports the average surfacedepth values for each amino acid, secondary structures, and common chemical elements. In the list below, average surfacedistance values were normalized to a maximum depth of 10.0 Å, and averaged for these 3 models. 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.

Jmol/Depth from surface: Difference between revisions

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 The asterisk "<span style="font-size:200%;">&#8270;</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. [https://proteopedia.org/wiki/images/b/b5/Surfacedistance-reports.spt A script that you can download] (right click, save link as) reports the average surfacedepth values for each amino acid, secondary structures, and common chemical elements. In the list below, average values were normalized to a maximum depth of 10.0 Å, and averaged. For this small sample of 3 enzymes:
+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. [https://proteopedia.org/wiki/images/b/b5/Surfacedistance-reports.spt A script that you can download] (right click, save link as) reports the average surfacedepth values for each amino acid, secondary structures, and common chemical elements. In the list below, average surfacedistance values were normalized to a maximum depth of 10.0 Å, and averaged for these 3 models. 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.