SCit:
Tools for protein side chain conformation analysis and editing

This series of tools allows the analysis and editing of protein side chain conformations, as well as side chain positioning onto a protein backbone and the comparison of two series of side chains conformations. Protein coordinates must be specified using the Protein Data Bank format.

Note: SCit is based on the encoding of the protein using a Hidden Markov Model derived structural alphabet. Hence, it does not work for fragmented proteins.
More information in the help page below.
Additional help here.

To compare the conformations of the side chains of two PDB files, go here.

PDB File

PDB Id (ex: 1tim, or 1timA for chain A of the 1tim pdb entry)


Optionally, you can specify a sequence (1 letter code).
Specifying no sequence will let the file unaffected at this stage.

If specified, the sequence length MUST exactly match that of the PDB file. It will be used to :
1. subsitute amino acids not matching the PDB file sequence.
2. (re)position the side chains. For such purpose, only parts of the sequence specified in upercase will be considered. Lowercase letters of the sequence will remain unaffected.
If a sequence file upload is specified, the raw sequence will be ignored.

upload a Sequence (fasta format) :

or
paste your sequence (raw format)