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Table 4 Frequencies of amino acids associated with altered intra-subtype Nef function

From: Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

Function Codona AA Subtypeb +/-c % Frequency p-value q-value
A B C D
CD4 88 G C - 10 2 20 2 <0.0001 <0.0001
  88 S C + 90 97 80 98 0.0001 0.0001
HLA-I 3 G A - 76 95 66 81 <0.0001 <0.0001
  8-12 SSIVG C - 82 48d 81 88 <0.0001 <0.0001
  8 R B + 10 30 7 12 <0.0001 <0.0001
  8 S B - 80 41 81 81 <0.0001 <0.0001
  9 R A + 5 9 4 0 0.05 0.06
  9 S C - 87 70 89 88 0.0008 0.001
  11 V A - 79 34 74 88 <0.0001 <0.0001
  14 P B - 89 63 93 94 <0.0001 <0.0001
  28 A B + 14 8 1 4 0.007 0.008
  40 H C + 86 79 51 93 <0.0001 <0.0001
  40 Y C - 10 14 46 5 <0.0001 <0.0001
  65 D B - 11 9 1 8 0.13 0.13
  65 E B + 86 90 97 87 0.08 0.09
  83 G A - 67 57 45 31 <0.0001 <0.0001
  89 F A/B +/- 16 5 97 5 <0.0001 <0.0001
  89 H B + 82 93 0 95 <0.0001 <0.0001
  98 D B + 85 7 47 31 <0.0001 <0.0001
  98 E B - 15 92 53 69 <0.0001 <0.0001
  102 H C - 9 25 16 1 <0.0001 <0.0001
  105 K C + 73 54 72 78 0.004 0.005
  105 Q B - 2 20 8 13 0.001 0.002
  105 R A/C -/- 23 26 20 9 0.03 0.04
  108 D C - 15 86 50 45 <0.0001 <0.0001
  108 E C + 84 13 50 55 <0.0001 <0.0001
  120 Y A - 60 93 35 62 <0.0001 <0.0001
  153 I B - 1 17 1 9 <0.0001 <0.0001
  153 V B + 99 80 99 87 <0.0001 <0.0001
  168 M A + 24 61 76 39 <0.0001 <0.0001
  182 Q C - 5 28 11 1 <0.0001 <0.0001
  191 L A - 61 3 0 1 <0.0001 <0.0001
  196 Q A - 36 0 0 0 <0.0001 <0.0001
  198 K B + 10 21 35 33 0.0002 0.0002
  202 F B + 62 10 23 62 <0.0001 <0.0001
  202 Y B - 35 90 69 38 <0.0001 <0.0001
  1. aNumbered according to HXB2.
  2. bIndicates the subtype in which the amino acid is associated with altered Nef function.
  3. cIndicates whether the amino acid is associated with increased (+) or decreased (-) Nef function.
  4. dThe consensus for subtype B is SSVVG and is 52% conserved.