Exercise on Primary Protein Structure |
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1. Go to the Protein Data Bank web site http://www.rcsb.org .
2. Locate the blue column on the left of the page and find the button for the tutorial. Take the tutorial if you haven't already done so.
The purpose of doing this exercise is to see a little of the variety in primary protein structure and to become more familiar with the different amino acids. In other words, this is a practice, and the most important thing is to do it, not to have the right answers. You can answer with 1-letter abbreviations for amino acids.
3. Go back to the Protein Data Bank home page and search for two of the following:
For each, click on Sequence Details and use the information to fill in the table. Use the sequence provided, which isn't necessarily the complete protein sequence.
protein |
1HKC |
5PTP |
1PFY |
number of residues |
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residue 1 |
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last residue |
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number of disulfide bonds |
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Write the sequence for residues 1-15. |
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Which amino acids occur more than once in 1-15? |
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Which amino acid is most common, if any? |
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Is this sequence mostly nonpolar, aromatic, polar, charged, or mixed? |
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Write the sequence for the last 15 residues. |
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Which amino acids occur more than once? |
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Which amino acid is most common, if any? |
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Is this sequence mostly nonpolar, aromatic, polar, charged, or mixed? |