key6 - 3 Display Æ Render in solid 3D 4 Color Æ act on...

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MIT OpenCourseWare http://ocw.mit.edu 7.88J Protein Folding Problem Fall 2007 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms .
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1) Interhelical ion pairs: Glu20(chainA) with Lys15(chainB), Glu22(chainA) with Lys27(chainB), and Glu22(chain B) with Lys27(chainA). Another possible interaction = Lys15(chainA) with Glu20(chainB). Ok if you also gave intrahelical ion pairs for this question. 2) For the image, you should have shown Glu20, Lys15, Glu22, and Lys 27, from each chain. One of the Lys15—Glu20 pairs appears not to be interacting, so you didn’t have to show it. The exact steps I took to answer the question and create the image in Swiss-PdbViewer: 1. opened 2ZTA 2. right-clicked in “ribn” column in the control panel
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Unformatted text preview: 3. Display Æ Render in solid 3D 4. Color Æ act on ribbon 5. Color Æ by chain 6. Right clicked “v” column to show atoms as Van der Waal spheres. 7. Display Æ Render in solid 3D. 8. Right clicked “show” column to hide all atoms for now (now displaying only ribbon) 9. Select Æ group property Æ select basic amino acids a. Display these atoms by clicking under “show” column for each one. 10. Repeat for acidic amino acids 11. Now looking for acidic/basic pairs connecting the two helices; unclick all that do not appear to interact. 12. Rotated image for optimal orientation. 13. Pushed “Print Screen” button on my keyboard. Pasted directly into this word document. Cropped as desired....
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This note was uploaded on 11/11/2011 for the course BIO 7.344 taught by Professor Bobsauer during the Spring '08 term at MIT.

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key6 - 3 Display Æ Render in solid 3D 4 Color Æ act on...

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