This post is my answer for this question on Biostar:Drawing a protein:
Dear all I often find protein's image like this (...) Do you know if there's a program to draw them (I mean circles with letters).
I wrote a Java-Swing application named WirePeptide displaying a draggable peptide. This application is available on github at https://github.com/lindenb/jsandbox/blob/master/src/sandbox/WirePeptide.java. The user can save the image as PNG, SVG and HTML+Canvas.
Compile & Run
java -jar dist/wirepeptide.jar