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Multi sequence aligment file

  1. Upload FASTA file
  2. Access CLUSTALW, and upload or enter FASTA file. I uploaded five T1 type RNase T1/Po1/He1/Ms/F1, and color-code T1 (PDB ID:2B4U).
    Example of FASTA file

  3. Click "Execute Multiple Aligment"

  4. Save "clustalw.aln"
  5. Example of aligment file

The ConSurf Server

AccessThe ConSurf Server
  1. Analyze Nucleotides or Amino Acids?
  2. →Amino-Acids

  3. Is there a known protein structure?
  4. →YRS
    →Enter PDB ID or upload PDB file

    Click "next"

  5. Do you have a Multiple Sequence Aligment(MSA) to upload?
  6. →Upload aligment file(***.aln)
    →Enter sequence name corresponding PDB file at "Indicate the Query Sequence Name" (PDB ID:2BU4 is corresonds to sequence name T1. So I type T1.)

  7. Do you have a tree file to upload?
  8. →No

  9. Enter Job title and your E-Mail adress, and click "submit"

  10. When the calculation is finished, click "Follow the instructions to produce a PyMol figure (For users of PyMol)"

  11. Save "PDB FILE" and "consurf new.py"

Color-code on PyMOL

  1. Open PDB file
  2. Run → consurf_new.py
  3. Show → surface

  4. Flexible ←--------------------------------------→ Conserved