Structural preferences


  • Chi1 Chi2 preferences in N2.

    The table presents propensities of Chi1/Chi2 combination for the amino acids having two sp3-sp3 bonds in N2 position. Distribution in database is not displayed for clarity. It appears that the combinations g- g+, and g+ g- are higly preferred (propensity is 6 and 3.2 respectively). Those conformations only obsereved with Glu and Gln, the other amino acid being mainly t g-,t t, t g+
    • Distribution
    Chi1/Chi2 Arg Gln Glu Ile Leu Lys Met Total
    total 75 104 313 61 102 112 22 789
    g- g- 0 1 0 0 1 0 0 2
    g- t 5 2 14 3 0 6 1 31
    g- g+ 0 6 31 0 0 2 0 39
    t g- 7 27 15 5 39 8 4 105
    t t 28 30 86 7 11 42 6 210
    t g+ 2 2 7 0 2 3 1 17
    g+ g- 0 17 91 1 4 6 0 119
    g+t 26 8 40 36 42 33 4 189
    g+g+ 7 11 29 9 3 12 6 77
    Percentage
    Chi1/Chi2 Arg Gln Glu Ile Leu Lys Met Total
    g- g- 0% 1% 0% 0% 1% 0% 0% 0%
    g -t 7% 2% 4% 5% 0% 5% 5% 4%
    g- g+ 0% 6% 10% 0% 0% 2% 0% 5%
    t g- 9% 26% 5% 8% 38% 7% 18% 13%
    t t 37% 29% 27% 11% 11% 38% 27% 27%
    t g+ 3% 2% 2% 0% 2% 3% 5% 2%
    g+ g- 0% 16% 29% 2% 4% 5% 0% 15%
    g+ t 35% 8% 13% 59% 41% 29% 18% 24%
    g+ g+ 9% 11% 9% 15% 3% 11% 27% 10%
    Propensity
    Chi1/Chi2 Arg Gln Glu Ile Leu Lys Met Total
    g- g- 0 1±1 0 0 1±1 0 0 0.4±0.3
    g- t 0.9±0.4 0.3±0.2 0.7±0.2 0.4±0.2 0 0.7±0.3 0.6±0.7 0.6±0.1
    g- g+ 0 4±2 3.0±0.8 0 0 4±4 0 6±1
    t g- 1.6±0.7 2.3±0.5 0.6±0.2 3±1 1.4±0.2 1.1±0.4 2±1 1.2±0.4
    t t 1.4±0.2 1.6±0.3 1.2±0.1 1.6±0.7 2.9±1.0 1.5±0.2 1.5±0.6 1.6±0.1
    t g+ 2±2 0.9±0.8 1.2±0.6 0 2±2 1.4±0.9 2±2 1.6±0.4
    g+ g- 0 4±1 4.0±0.6 0.7±0.8 0.5±0.3 1.7±0.8 0 3.2±0.4
    g+ t 0.8±0.1 0.2±0.1 0.4±0.1 1.0±0.1 0.7±0.1 0.7±0.1 0.5±0.2 0.5±0.1
    g+ g+ 0.9±0.3 0.6±0.2 0.6±0.1 0.9±0.3 1.5±1.0 0.8±0.2 1.1±0.4 0.8±0.1



  • Chi1 Chi2 preferences in the middle of helix.

    The table presents propensities of Chi1/Chi2 combination for the amino acids having two sp3-sp3 bonds between N4 and C4 positions. Here the combinations g- g+, and g+ g- are no more preferred (propensity is 0 and 0.5 respectively).
    • Distribution
    Chi1/Chi2 Arg Gln Glu Ile Leu Lys Met Total
    total 624 559 705 827 1364 739 375 5193
    g- g- 1 3 1 6 1 6 1 19
    g- t 10 4 12 13 0 6 5 50
    g- g+ 0 0 0 1 0 0 0 1
    t g- 61 97 83 21 454 82 37 835
    t t 222 96 192 10 69 240 62 891
    t g+ 13 14 13 2 9 18 11 80
    g+ g- 4 4 5 8 70 22 0 113
    g+ t 274 251 237 654 738 301 147 2602
    g+ g+ 36 89 157 112 23 59 112 588
    Percentage
    Chi1/Chi2 Arg Gln Glu Ile Leu Lys Met Total
    g- g- 0% 1% 0% 1% 0% 1% 0% 0%
    g- t 2% 1% 2% 2% 0% 1% 1% 1%
    g- g+ 0% 0% 0% 0% 0% 0% 0% 0%
    t g- 10% 17% 12% 3% 33% 11% 10% 16%
    t t 36% 17% 27% 1% 5% 32% 17% 17%
    t g+ 2% 3% 2% 0% 1% 2% 3% 2%
    g+ g- 1% 1% 1% 1% 5% 3% 0% 2%
    g+ t 44% 45% 34% 79% 54% 41% 39% 50%
    g+ g+ 6% 16% 22% 14% 2% 8% 30% 11%
    Propensity
    Chi1/Chi2 Arg Gln Glu Ile Leu Lys Met Total
    g- g- 0.4±0.5 0.6±0.5 0.3±0.3 0.8±0.4 0.1±0.1 1.6±1.0 0.4±0.5 0.5±0.2
    g- t 0.2±0.1 0.1±0.1 0.3±0.1 0.1±0.1 0 0.1±0.5 0.2±0.1 0.2±0.1
    g- g+ 0 0 0 0.6±0.9 0 0 0 0
    t g- 1.7±0.3 1.6±0.2 1.6±0.2 0.9±0.3 1.2±0.1 1.7±0.3 1.1±0.3 1.4±0.1
    t t 1.3±0.1 0.9±0.1 1.2±0.1 0.2±0.1 1.4±0.2 1.3±0.1 0.9±0.2 1.1±0.1
    t g+ 1.7±0.7 1.2±0.5 1.0±0.4 1±1 0.7±0.3 1.3±0.4 1.4±0.7 1.1±0.2
    g+ g- 0.3±0.2 0.2±0.1 0.1±0.1 0.4±0.2 0.7±0.1 0.9±0.3 0 0.5±0.1
    g+ t 1.0±0.1 1.2±0.1 1.0±0.1 1.3±0.1 1.0±0.1 1.0±0.1 1.0±0.1 1.1±0.1
    g+ g+ 0.5±0.1 0.9±0.1 1.5±0.2 0.9±0.1 0.9±0.3 0.6±0.1 1.2±0.1 0.9±0.1

  • Summary of chi1/chi2 preferences.

    Glu and Gln present specific preferences for g-g+ and g+g- in N-termini positions, especially in N2. In the next step, hydrogen bonding is studied. The structural preferences of Glu, Asp, Asn are well explained by the hydrogen bonds found in N-termini positions.
    BACK. Back to the "Helix N-termini" page.