The graphical representation of pairwise distances between all C-alpha atoms can give you hints about:
- the architecture of the protein structure
- the contacts between secondary structure elements
- detection of domains in the structure
- the beauty of protein structures in 2D
Rows are active links providing the residue pop-up menu and can take you to other tools.
References
Richardson, J.S. (1981) The anatomy and taxonomy of protein structure. Adv. Protein Chem., 34, 167-339.
Example URL for direct computation of the distance matrix:
http://i.moltalk.org/dist_map/3/PDB/1QMZ/65/18.0/1.5/-1/-1/-1/-1
parameters:
- toolchain
- "dist_map"
- position
- "3"
- strxsrc
- "PDB" or "model"
- strxid
- 4-letter pdb code or model identifier
- chaincode
- ASCII value of chain identifier (A=65, B=66, ' '=32, ...)
- dthreshold
- distance threshold
- imgscale
- scale of image (1.0, 1.5, 2.0, 2.5, 3.0)
- hlresfrom
- highlight from residue number (+ insertion code)
- hlresto
- highlight to residue number (+ insertion code)
- clipfrom
- clip graphics from residue number (+ insertion code)
- clipto
- clip graphics to residue number (+ insertion code)
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