10.Identify the glycosylation motif and the subtype-specific conserve motif (it should contain 14-15 amino acids).

>B conserve:

TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAGAGCATTT

TATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACAT

>Bprotein:

C T R P N N N T R K S I H I G P G R A F Y A T G E I I G D I R Q A H

subtypeB specific sequence R A F Y A

>E conserve:

TGTACCAGACCCTCCAACAATACAAGAACAAGTATAACTATAGGACCAGGGACAGTATTC

TATAGAACAGGAGACATAATAGGAGATATAAGAAAAGCATATTGTGAGAT

>E protein:

C T R P S N N T R T S I T I G P G T V F Y R T G D I I G D I R K A Y C E

subtypeE specific sequence T V F Y R

11. Translate the text sequences from 9. to the three dimensional structure by sending your protein sequences to the appropriate site.

12. The three dimensional structure of each V3 loop should be displayed by the PDB viewer.

 
 

subtype B

subtype E

13. Superimpose the V3 loop of each subtype together, the region that different in structure should be marked and displayed in different colors.

 
 

H1

H2

H3

H4

H5

H6

H7

H8