Structural preferences


  • Rotamer definition.

    Side chain orientation is defined by its Chi angles. When the angles distribution is discrete, the preferred angles can be defined by rotamers. In this work we focused only on sp3-sp3 bonding angles, because sp3-sp2 bonding angles are usually not discrete. According to the IUPAC-IUB Commission recommendations we use the three following rotamers:
    Rotamer Chi
    g- (gauche -) 60±60
    t (trans) 180±60
    g+ (gauche +) -60±60
    We focused on the two first side chains angles, Chi1 and Chi2. The Chi1 angle when it exist is always sp3-sp3, so the Chi1 propensities of all amino acids have been studied (except Ala, Gly and Pro). The Chi2 angles of Arg, Glu, Gln, Ile, Leu, Lys and Met are sp3-sp3 so their Chi1-Chi2 combinations have been studied. The Chi2 angles of Ser, Thr and Cys are not studied because they involve the position of an hydrogen atom so they are usually not defined in X-ray structures. The other amino acids have no Chi2 angles, or present sp3-sp2 Chi2 bonds so their Chi2 angles are not studied.

    • Chi1 and Chi2 angles of Glu.



    Example of a discrete distribution of Chi1/Chi2.
  • Rotamer distribution of Chi1 in the whole database.
    The same database of 299 structures have been used. The distribution of Chi1 rotamers has been extracted.
    (* Val has a different convention for rotamers : g- is -60, t is 60 and g+ is 180)
    NEXT. Preferences in N1.
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    • Number in the database Percentages
    Aminoacid total g- t g+ g- t g+
    Arg 3407 293 1162 1952 9% 34% 57%
    Asn 3785 597 1149 2039 16% 30% 54%
    Asp 4847 870 1541 2436 18% 32% 50%
    Cys 1134 183 314 637 16% 28% 56%
    Gln 2867 232 901 1733 8% 31% 60%
    Glu 4454 472 1452 2529 11% 33% 57%
    His 1777 244 582 951 14% 33% 54%
    Ile 4264 569 430 3265 13% 10% 77%
    Leu 6361 101 2053 4207 2% 32% 66%
    Lys 4546 367 1543 2634 8% 34% 58%
    Met 1601 141 460 999 9% 29% 62%
    Phe 3223 389 1108 1725 12% 34% 54%
    Ser 4903 2224 1161 1518 45% 24% 31%
    Thr 4685 2243 377 2065 48% 8% 44%
    Trp 1253 202 421 630 16% 34% 50%
    Tyr 2999 384 1021 1594 13% 34% 53%
    Val* 5524 1096 449 3978 20% 8% 72%
    Total 61630 10607 16124 34892 17% 26% 57%
    Chi1 distribution in the database.


  • Rotamer preferences of Chi1 in N1 position.
    Propensities are the ratio of the rotamer percentage in the position and the rotamer percentage in the database. The general preference in N1 is to be in t conformation (41% of the total in t at N1 against 26% in the database, propensity equal 1.6) but not Asn, Asp, Cys, His and Thr.
    NEXT. Preferences in N2.
    PREVIOUS. Distribution in database .
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    • Number in N1 position Percentages Propensities
    Aminoacid total g- t g+ g- t g+ g- t g+
    Arg 81 8 49 24 10% 60% 30% 1.1±0.4 1.8±0.2 0.5±0.1
    Asn 47 4 10 33 9% 21% 70% 0.5±0.3 0.7±0.2 1.3±0.1
    Asp 100 8 13 79 8% 13% 79% 0.4±0.2 0.4±0.1 1.6±0.1
    Cys 17 2 3 12 12% 18% 71% 0.7±0.5 0.6±0.4 1.3±0.2
    Gln 97 3 60 34 3% 62% 35% 0.4±0.2 2.0±0.2 0.6±0.1
    Glu 153 13 71 69 8% 46% 45% 0.8±0.2 1.4±0.2 0.8±0.1
    His 32 8 14 10 25% 44% 31% 1.8±0.7 1.3±0.3 0.6±0.2
    Ile 103 8 38 57 8% 37% 55% 0.6±0.2 3.7±0.6 0.7±0.1
    Leu 180 0 115 65 0% 64% 36% 0 2.0±0.1 0.5±0.1
    Lys 121 12 74 35 10% 61% 29% 1.2±0.4 1.8±0.2 0.5±0.1
    Met 37 1 14 22 3% 38% 59% 0.3±0.3 1.3±0.3 1.0±0.1
    Phe 80 4 55 21 5% 69% 26% 0.4±0.2 2.0±0.2 0.5±0.1
    Ser 125 56 21 48 45% 17% 38% 1.0±0.1 0.7±0.2 1.2±0.2
    Thr 97 34 4 59 35% 4% 61% 0.7±0.1 0.5±0.3 1.4±0.1
    Trp 41 5 20 16 12% 49% 39% 0.8±0.4 1.5±0.3 0.8±0.2
    Tyr 83 11 40 32 13% 48% 39% 1.0±0.3 1.4±0.2 0.7±0.1
    Val* 123 10 25 88 8% 20% 72% 0.4±0.1 2.5±0.6 1.0±0.1
    Total 1517 187 626 704 12% 41% 46% 0.7±0.1 1.6±0.1 0.8±0.0
    Chi1 propensities in N1 position.


  • Rotamer preferences of Chi1 in N2 position.
    Many amino acids (Asn, Asp, Glu, His, Ser and Trp) show a preference for the g- conformation.
    NEXT. Preferences in N3.
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    • Number in N2 position Percentages Propensities
    Aminoacid total g- t g+ g- t g+ g- t g+
    Arg 75 5 37 33 7% 49% 44% 0.8±0.4 1.4±0.2 0.8±0.1
    Asn 86 19 14 53 22% 16% 62% 1.4±0.3 0.5±0.1 1.1±0.1
    Asp 234 54 23 157 23% 10% 67% 1.3±0.2 0.3±0.1 1.3±0.1
    Cys 18 4 5 9 22% 28% 50% 1.4±0.7 1.0±0.4 0.9±0.2
    Gln 104 9 59 36 9% 57% 35% 1.1±0.4 1.8±0.2 0.6±0.1
    Glu 313 45 108 160 14% 35% 51% 1.4±0.2 1.1±0.1 0.9±0.1
    His 48 12 16 20 25% 33% 42% 1.8±0.6 1.0±0.2 0.8±0.2
    Ile 61 3 12 46 5% 20% 75% 0.4±0.2 2.0±0.6 1.0±0.1
    Leu 102 1 52 49 1% 51% 48% 0.6±0.7 1.6±0.2 0.7±0.1
    Lys 112 8 53 51 7% 47% 46% 0.9±0.3 1.4±0.2 0.8±0.1
    Met 22 1 11 10 5% 50% 45% 0.5±0.5 1.7±0.4 0.7±0.2
    Phe 64 2 43 19 3% 67% 30% 0.3±0.2 2.0±0.2 0.6±0.1
    Ser 146 81 19 46 55% 13% 32% 1.2±0.1 0.5±0.1 1.0±0.1
    Thr 93 18 3 72 19% 3% 77% 0.4±0.1 0.4±0.2 1.8±0.1
    Trp 30 12 11 7 40% 37% 23% 2.5±0.7 1.1±0.3 0.5±0.2
    Tyr 43 5 28 10 12% 65% 23% 0.9±0.4 1.9±0.3 0.4±0.1
    Val* 85 7 7 71 8% 8% 84% 0.4±0.2 1.0±0.4 1.2±0.1
    Total 1636 286 501 849 17% 31% 52% 1.0±0.1 1.2±0.1 0.9±0.0
    Chi1 propensities in N2 position.


  • Rotamer preferences of Chi1 in N3 position.
    Here is no more amino acid preferences for the g- conformation. Amino acid with a big side chain are prefered in t conformation, the shorter side chain amino preferring the g+ conformation.
    NEXT. Preferences inside the hellix.
    PREVIOUS. Preferences in N2 .
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    • Number in N3 position Percentages Propensities
    Aminoacid total g- t g+ g- t g+ g- t g+
    Arg 76 2 47 27 3% 62 36 0.3±0.2 1.8±0.2 0.6±0.1
    Asn 65 1 11 53 2% 17 82 0.1±0.1 0.6±0.2 1.5±0.1
    Asp 204 3 15 186 1% 7 91 0.1±0.0 0.2±0.1 1.8±0.1
    Cys 19 0 5 14 0% 26 74 0 1.0±0.4 1.3±0.2
    Gln 137 6 23 108 4% 17 79 0.5±0.3 0.5±0.1 1.3±0.1
    Glu 270 6 64 200 2% 24 74 0.2±0.1 0.7±0.1 1.3±0.1
    His 39 0 10 29 0% 26 74 0 0.8±0.2 1.4±0.2
    Ile 72 2 9 61 3% 13 85 0.2±0.2 1.2±0.4 1.1±0.1
    Leu 134 0 76 58 0% 57 43 0 1.8±0.2 0.7±0.1
    Lys 98 2 52 44 2% 53 45 0.3±0.2 1.6±0.2 0.8±0.1
    Met 41 1 16 24 2% 39 59 0.3±0.3 1.4±0.3 0.9±0.1
    Phe 82 1 49 32 1% 60 39 0.1±0.1 1.7±0.2 0.7±0.1
    Ser 97 39 13 45 40% 13 46 0.9±0.1 0.6±0.2 1.5±0.2
    Thr 131 27 2 102 21% 2 78 0.4±0.1 0.2±0.1 1.8±0.1
    Trp 38 0 26 12 0% 68 32 0 2.0±0.3 0.6±0.2
    Tyr 71 1 40 30 1% 56 42 0.1±0.1 1.7±0.2 0.8±0.1
    Val* 128 7 9 112 5% 7 88 0.3±0.1 0.9±0.3 1.2±0.1
    Total 1702 98 467 1137 6% 27% 67% 0.3±0.1 1.0±0.1 1.2±0.1
    Chi1 propensities in N3 position.

  • Rotamer preferences of Chi1 inside the helix (N4 to C4).
    The g- conformation is still higly unfavoured. Only 3% of the side chain are in g-.
    NEXT. Summary of rotamer preferences.
    PREVIOUS. Preferences in N3 .
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    • Number between N4 and C4 Percentages Propensities
    Aminoacid total g- t g+ g- t g+ g- t g+
    Arg 621 11 296 314 2% 48% 51% 0.2±0.1 1.4±0.1 0.9±0.1
    Asn 415 0 97 318 0% 23% 77% 0 0.8±0.1 1.4±0.1
    Asp 493 3 118 372 1% 24% 75% 0 0.8±0.1 1.5±0.1
    Cys 126 4 39 83 3% 31% 66% 0.2±0.1 1.1±0.2 1.2±0.1
    Gln 558 7 207 344 1% 37% 62% 0.2±0.1 1.2±0.1 1.0±0.0
    Glu 701 13 288 400 2% 41% 57% 0.2±0.1 1.3±0.1 1.0±0.1
    His 204 2 113 89 1% 55% 44% 0.1±0.1 1.7±0.2 0.8±0.1
    Ile 827 20 33 774 2% 4% 94% 0.2±0.1 0.4±0.1 1.2±0.1
    Leu 1364 1 532 831 0% 39% 61% 0.0±0.1 1.2±0.1 0.9±0.0
    Lys 737 12 341 383 2% 46% 52% 0.2±0.1 1.4±0.1 0.9±0.0
    Met 375 6 110 259 2% 29% 69% 0.2±0.1 1.0±0.1 1.1±0.1
    Phe 505 2 339 163 0% 67% 32% 0.0±0.0 2.0±0.1 0.6±0.0
    Ser 461 86 136 239 19% 30% 52% 0.4±0.0 1.2±0.1 1.7±0.1
    Thr 497 72 2 423 14% 0% 85% 0.3±0.1 0.1±0.1 1.9±0.1
    Trp 192 4 125 63 2% 65% 33% 0.1±0.1 1.9±0.2 0.7±0.1
    Tyr 446 4 295 147 1% 66% 33% 0.1±0.0 1.9±0.1 0.6±0.1
    Val* 865 36 23 806 4% 3% 93% 0.2±0.1 0.3±0.1 1.3±0.1
    Total 9387 283 3094 6008 3% 33% 64% 0.2±0.1 1.3±0.1 1.1±0.1
    Chi1 propensities in N4 to C4 position.


  • Summary of rotamer Chi1 preferences.
    The structural preferences are different in N1, N2, N3 and inside the helix. Hydrogen bonding and steric clashes are the major causes of these differences: Firstly the hydrogen bonding possibility in N1, N2, N3 are different than those inside the helix (N4 to C4) where the NH backbone group are involved in (i, i+4) hydrogen bonds. Secondly the side chain are more confined inside the helix than in N1, N2, N3.
    The N2 position presents the higher proportion (17%) of g- conformation. In this position Asn, Asp, (Gln,) Glu, His, Ser and Trp have a propensity higher than 1 for this conformation. In the next step, Chi1/Chi2 propensity are studied.

    NEXT. Chi1/Chi2 Preferences in N2 .
    PREVIOUS. Preferences in N4 to C4 .
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