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Table 8 The HCV NS3 rules applied to the NS3 protease sequence.

From: How to find simple and accurate rules for viral protease cleavage specificities

P1 Decamer Rule match Mass (kDa) Mass (kDa)
C16 RGLLGCIITS HCVA 1.7 65.6
C47 TFLATCINGV HCVA 5.0 62.3
C52 CINGVCWTVY HCVA, HCVC 5.5 61.8
Q73 KGPVIQMYTN HCVC 7.7 59.6
M74 GPVIQMYTNV HCVC 7.8 59.4
V78 QMYTNVDQDL HCVC 8.3 59.0
C97 RSLTPCTCGS HCVA 10.3 56.9
C99 LTPCTCGSSD HCVA 10.5 56.7
S102 CTCGSSDLYL HCVB 10.7 56.5
T108 DLYLVTRHAD HCVB 11.4 55.8
G120 PVRRRGDSRG HCVB 12.8 54.4
S122 RRRGDSRGSL HCVC 13.0 54.2
I132 LSPRPISYLK HCVC 14.1 53.1
G137 ISYLKGSSGG HCVB 14.7 52.6
C159 FRAAVCTRGV HCVA 16.7 50.5
V163 VCTRGVAKAV HCVC 17.1 50.1
K165 TRGVAKAVDF HCVC 17.3 49.9
Q195 PPAVPQSFQV HCVC 20.6 46.6
A240 TLGFGAYMSK HCVC 25.1 42.2
C279 LADGGCSGGA HCVA 29.2 38.1
C289 YDIIICDECH HCVA, HCVC 30.2 37.1
C292 IICDECHSTD HCVA 30.5 36.7
G314 QAETAGARLV HCVC 32.6 34.6
V339 PNIEEVALST HCVB 35.2 32.0
L341 IEEVALSTTG HCVB 35.4 31.9
C368 RHLIFCHSKK HCVA, HCVC 38.3 28.9
N387 VALGINAVAY HCVC 40.3 26.9
L395 AYYRGLDVSV HCVB, HCVC 41.2 26.0
T402 VSVIPTSGDV HCVC 41.9 25.3
C428 DSVIDCNTCV HCVA, HCVC 44.5 22.7
C431 IDCNTCVTQT HCVA 44.9 22.4
S488 SGMFDSSVLC HCVC 51.2 16.1
C492 DSSVLCECYD HCVA 51.6 15.7
C494 SVLCECYDAG HCVA 51.8 15.4
A497 CECYDAGCAW HCVD 52.1 15.1
C499 CYDAGCAWYE HCVA 52.3 14.9
V511 PAETTVRLRA HCVB 53.6 13.6
L513 ETTVRLRAYM HCVB, HCVC 53.9 13.3
C525 PGLPVCQDHL HCVA 55.2 12.0
V535 EFWEGVFTGL HCVC 56.5 10.8
I542 TGLTHIDAHF HCVC 57.2 10.0
Q552 LSQTKQSGEN HCVC 58.4 8.8
A562 FPYLVAYQAT HCVB 59.5 7.8
C568 YQATVCARAQ HCVA, HCVC 60.1 7.1
C584 DQMWKCLIRL HCVA 62.0 5.2
C622 KYIMTCMSAD HCVA 66.3 1.0
  1. The table shows the result of applying the HCV NS3 cleavage rules to the NS3 protease amino acid sequence. Only decamers that are predicted to be cleaved are listed. The first column mentions the amino acid and the position in the NS3 sequence that occupies the P1 position in the decamer. The second column lists the decamer. The third column shows which HCV NS3 rules that the decamer matches to. The fourth and fifth column show the molecular masses of the cleavage products if NS3 is cleaved in that position.