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Example:


The selectivity filter of
the KcsA K+ channel
(1K4C)

Zhou, YF et al. (2001)
Nature, 414, 43-48.

PoreLogo

STEP 2: Family PoreLogo
(Click here for examples of input/output files)



a) Please specify a list-file of pore-lining residues:


The list-file of pore-lining residues should be in a PoreWalker-like format (see example file). Please click here to get instructions on how to prepare your list-file.




b) Please specify chain:

Please specify PDB identificative of the the protein chain to be used to generate your PoreLogo. The chain identificative **MUST** correspond to one of the chains included in the uploaded pore-lining residues list file.




c) Please specify the 3D-coordinates of the channel protein:


Please provide a text-file of the 3D-coordinates of the protein structure in the current wwPDB format




d) Please upload your multiple alignment file:

The multiple sequence alignment (MSA) file should be in FASTA, GDE or A2M format. Please click here to get instructions on how to prepare your MSA.
**PLEASE NOTE** that the first sequence in the alignment **MUST** be your reference protein, i.e. the protein for which you are also providing a pore-lining residues text file and a PDB file







Please enter your E-Mail address:


 

 

 

 

 

 

 

The development of PoreLogo has been partly funded by the BBSRC and by the FEBS Short-Term Fellowships Program spacer

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Related resources


Analysis of transmembrane protein
channels from 3D structure

Enzyme 3D structures organized by
the E.C. numbering hierarchy

Structural analyses of all PDB
entries