If you want to find out which proteins interact with your favorite protein, then DIP (Database of Interacting Proteins) is your place. Go to http://dip.doe-mbi.ucla.edu/dip/Search.cgi?SM=3 and enter your favorite protein into the "node" field (you can try Sup35 which is the prion-like protein in yeast).
You will get a short table that looks like this:
Notice where the cursor is (bottom left). Click on the code under the DIP Node heading.
In a new browser window, you will get another page that looks like this:
You want to click on the link that says "graph" as shown in the top right corner.
Now you should see a linkage map that illustrates your favorite protein (red node, or dot) connected to many other nodes. Each node is a protein and you can click on each node to find out more about each protein in the network.
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