Amino Acid Distributions


  • Distribution of amino acids in N', Ncap, N1, N2, N3 and N4 positions.

    The sequences of 299 high resolution structures with low homology have been surveyed . On the basis of backbone hydrogen bonding, 2 101 helices have been found in this database. The distribution of amino acids in all the database and in N', Ncap and the first helical positions ( N1 N2 N3 N4 )of helices have been extracted.
    Aftewards the amino acid ratios in helix positions have been calculated and compared to the general amino acid ratios in all sequence position in terms of amino acid propensity:

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    • Amino acid all N' Ncap N1 N2 N3 N4
    Ala 6844 153 82 221 238 241 265
    Arg 3437 72 56 83 75 76 112
    Asn 3802 100 201 47 86 65 55
    Asp 4862 140 313 101 234 205 61
    Cys 1134 31 16 17 18 19 42
    Gln 2893 66 34 97 105 138 94
    Glu 4506 92 77 155 317 270 80
    Gly 6475 197 218 126 120 108 50
    His 1783 45 47 32 48 39 35
    Ile 4272 135 28 103 61 72 212
    Leu 6366 218 80 180 101 134 289
    Lys 4624 76 60 124 114 98 87
    Met 1606 62 22 37 22 41 73
    Phe 3224 90 38 80 64 82 122
    Pro 3748 123 148 230 102 50 0
    Ser 4920 125 320 126 146 97 68
    Thr 4689 121 257 97 93 130 98
    Trp 1254 32 19 40 30 38 34
    Tyr 3007 80 48 83 43 71 100
    Val 5532 144 38 123 85 128 225

  • Amino acid propensities in Ncap position.

    The ratio between the amino acid percentage found in a defined position and the amino acid percentage found in the database is called "global propensity".
    If the percentage of an amino acid found in a position is different that the percentage in the database, the amino acid is then "preferred" (propensity >1) or "not favourable" (propensity<1) in this position. For example here is 5% of Asp in all the protein sequences and 10% in the N-cap position (See Table)so the global propensity for Asp in Ncap is 10 over 5 equal 2, Asp is a prefered amino acid in N-cap.
    Propensities higher than 1.0 are coloured in yellow, propensities higher than 2.0 are coloured in orange.

  • Asp, Asn, Ser and Thr are preferred in N-cap, in agreement with previous work [1]. This has been explained by the fact that Asp, Asn, Ser Thr side chains can easily hydrogen bond to the nitrogen backbone group of the N3 residue in replacement of the missing (i ,i+4) backbone backbone interaction [2] and so stabilise the N-termini of the helix.
    • Amino acid Number in the whole database Percentage in the whole database Number in the Ncap position Percentage in the Ncap position Global propensity
    Ala 6844 9% 82 4% 0.5±0.1
    Arg 3437 4% 56 3% 0.6±0.1
    Asp 3802 5% 201 10% 2.0±0.2
    Asn 4862 6% 313 15% 2.4±0.2
    Cys 1134 1% 16 1% 0.5±0.1
    Gln 2893 4% 34 2% 0.4±0.1
    Glu 4506 6% 77 4% 0.6±0.1
    Gly 6475 8% 218 10% 1.3±0.1
    His 1783 2% 47 2% 1.0±0.2
    Ile 4272 5% 28 1% 0.2±0.0
    Leu 6366 8% 80 4% 0.5±0.1
    Lys 4624 6% 60 3% 0.5±0.1
    Met 1606 2% 22 1% 0.5±0.1
    Phe 3224 4% 38 2% 0.4±0.1
    Pro 3748 5% 148 7% 1.5±0.1
    Ser 4920 6% 320 15% 2.4±0.2
    Thr 4689 6% 257 12% 2.1±0.1
    Trp 1254 2% 19 1% 0.6±0.1
    Tyr 3007 4% 48 2% 0.6±0.1
    Val 5532 7% 38 2% 0.3±0.0

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    NEXT. Amino acid propensities in N1 position.
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  • Amino acid propensities in N1 position.

    Here again the ratio between the amino acid percentage found in a defined position and the amino acid percentage found in the database is called "global propensity".
    The "local propensity" is defined by the ratio of the percentage found in a position inside the helix and the percentage found in all the positions (N1 to C1) in the helix (percentage not shown). A local propensity higer than 1 in a given position means that the amino acid is more prefered to be there than in other position in the helix.

    • Amino acid Number in the whole database Percentage in the whole database Number in N1 positions Percentage in N1 positions Global propensity Local propensity
    Ala 6844 9% 221 11% 1.2±0.1 0.8±0.1
    Arg 3437 4% 83 4% 0.9±0.1 0.8±0.1
    Asn 3802 5% 47 2% 0.5±0.1 0.6±0.1
    Asp 4862 6% 101 5% 0.8±0.1 0.9±0.1
    Cys 1134 1% 17 1% 0.6±0.2 0.8±0.2
    Gln 2893 4% 97 5% 1.3±0.1 0.9±0.1
    Glu 4506 6% 155 7% 1.3±0.1 0.9±0.1
    Gly 6475 8% 126 6% 0.7±0.1 1.6±0.2
    His 1783 2% 32 2% 0.7±0.1 0.8±0.2
    Ile 4272 5% 103 5% 0.9±0.1 0.9±0.1
    Leu 6366 8% 180 9% 1.1±0.1 0.8±0.1
    Lys 4624 6% 124 6% 1.0±0.1 0.9±0.1
    Met 1606 2% 37 2% 0.9±0.2 0.7±0.1
    Phe 3224 4% 80 4% 0.9±0.1 0.9±0.1
    Pro 3748 5% 230 11% 2.3±0.2 5.8±0.6
    Ser 4920 6% 126 6% 1.0±0.1 1.3±0.1
    Thr 4689 6% 97 5% 0.8±0.1 1.0±0.1
    Trp 1254 2% 40 2% 1.2±0.2 1.2±0.2
    Tyr 3007 4% 83 4% 1.0±0.1 1.1±0.2
    Val 5532 7% 123 6% 0.8±0.1 0.9±0.1

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    NEXT. Amino acid propensities in N2 position.
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  • Amino acid propensities in N2 position.

    A good example of global/local propensity is Pro in N2 : its global propensity is equal to 1.0 meaning that Pro is found in the same proportion in N2 than in the database. However its local propensity is equal to 2.6 meaning that the proportion of Pro in N2 is higher than the proportion of Pro inside helices. In fact Pro is not favourable at all in the helix because Pro can not make backbone backbone hydrogen bonds, except in the N-termini where those bonds are not required.

    The most globally preferred polar amino acid in N2 are Glu, Asp, Gln, and the most locally preferred amino acids are Asp, Glu, Ser.

    • Amino acid Number in the whole database Percentage in the whole database Number in N2 positions Percentage in N2 positions Global propensity Local propensity
    Ala 6844 9% 238 11% 1.3±0.1 0.9±0.1
    Arg 3437 4% 75 4% 0.8±0.1 0.7±0.1
    Asn 3802 5% 86 4% 0.8±0.1 1.1±0.2
    Asp 4862 6% 234 11% 1.8±0.1 2.0±0.2
    Cys 1134 1% 18 1% 0.6±0.2 0.8±0.2
    Gln 2893 4% 105 5% 1.4±0.2 1.0±0.1
    Glu 4506 6% 317 15% 2.6±0.2 1.8±0.1
    Gly 6475 8% 120 6% 0.7±0.1 1.6±0.2
    His 1783 2% 48 2% 1.0±0.2 1.2±0.2
    Ile 4272 5% 61 3% 0.5±0.1 0.5±0.1
    Leu 6366 8% 101 5% 0.6±0.1 0.5±0.1
    Lys 4624 6% 114 5% 0.9±0.1 0.8±0.1
    Met 1606 2% 22 1% 0.5±0.1 0.4±0.1
    Phe 3224 4% 64 3% 0.7±0.1 0.7±0.1
    Pro 3748 5% 102 5% 1.0±0.1 2.6±0.4
    Ser 4920 6% 146 7% 1.1±0.1 1.5±0.2
    Thr 4689 6% 93 4% 0.7±0.1 1.0±0.1
    Trp 1254 2% 30 1% 0.9±0.2 0.9±0.2
    Tyr 3007 4% 43 2% 0.5±0.1 0.6±0.1
    Val 5532 7% 85 4% 0.6±0.1 0.6±0.1

    PREVIOUS. Amino acid propensities in N1 position.
    NEXT. Amino acid propensities in N3 position.
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  • Amino acid propensities in N3 position.

    The most globally preferred polar amino acid in N3 are Glu, Gln, Asp, and the most locally preferred amino acids are Asp, Glu,Gln, Thr.
    • Amino acid Number in the whole database Percentage in the whole database Number in N3 positions Percentage in N3 positions Global propensity Local propensity
    Ala 6844 9% 241 11% 1.3±0.1 0.9±0.1
    Arg 3437 4% 76 4% 0.8±0.1 0.7±0.1
    Asn 3802 5% 65 3% 0.6±0.1 0.9±0.1
    Asp 4862 6% 205 10% 1.6±0.1 1.8±0.2
    Cys 1134 1% 19 1% 0.6±0.2 0.8±0.2
    Gln 2893 4% 138 7% 1.8±0.2 1.3±0.1
    Glu 4506 6% 270 13% 2.3±0.2 1.6±0.1
    Gly 6475 8% 108 5% 0.6±0.1 1.4±0.2
    His 1783 2% 39 2% 0.8±0.1 0.9±0.2
    Ile 4272 5% 72 3% 0.6±0.1 0.6±0.1
    Leu 6366 8% 134 6% 0.8±0.1 0.6±0.1
    Lys 4624 6% 98 5% 0.8±0.1 0.7±0.1
    Met 1606 2% 41 2% 1.0±0.2 0.7±0.1
    Phe 3224 4% 82 4% 1.0±0.1 0.9±0.1
    Pro 3748 5% 50 2% 0.5±0.1 1.3±0.2
    Ser 4920 6% 97 5% 0.7±0.1 1.0±0.1
    Thr 4689 6% 130 6% 1.0±0.1 1.4±0.2
    Trp 1254 2% 38 2% 1.1±0.2 1.1±0.2
    Tyr 3007 4% 71 3% 0.9±0.1 0.9±0.1
    Val 5532 7% 128 6% 0.9±0.1 1.0±0.1

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    NEXT. Amino acid propensities in interior (N4 to C4) positions.
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  • Amino acid propensities inside the helix (N4 to C4 positions).

    In the middle of the helix (N4 to C4), local preferences differ higly from N-termini preferences. For example Pro is very unfavourable in theses positions. Asp, Glu, Gln, which were locally preferred at N2,N3 positions are, naturally, not locally preferred in the interior positions.
    • Amino acid Number in the whole database Percentage in the whole database Number in interior positions Percentage in interior positions Global propensity Local propensity
    Ala 6844 9% 1554 14% 1.6±0.1 1.1±0.0
    Arg 3437 4% 624 5% 1.3±0.1 1.1±0.1
    Asn 3802 5% 416 4% 0.8±0.0 1.0±0.1
    Asp 4862 6% 493 4% 0.7±0.0 0.8±0.1
    Cys 1134 1% 126 1% 0.8±0.1 1.0±0.2
    Gln 2893 4% 559 5% 1.3±0.1 1.0±0.1
    Glu 4506 6% 705 6% 1.1±0.1 0.8±0.0
    Gly 6475 8% 368 3% 0.4±0.0 0.9±0.1
    His 1783 2% 204 2% 0.8±0.1 0.9±0.1
    Ile 4272 5% 827 7% 1.3±0.1 1.3±0.1
    Leu 6366 8% 1364 12% 1.5±0.1 1.1±0.1
    Lys 4624 6% 739 7% 1.1±0.1 0.9±0.1
    Met 1606 2% 375 3% 1.6±0.1 1.2±0.1
    Phe 3224 4% 505 4% 1.1±0.1 1.1±0.1
    Pro 3748 5% 44 0% 0.1±0.0 0.2±0.1
    Ser 4920 6% 462 4% 0.7±0.0 0.8±0.1
    Thr 4689 6% 497 4% 0.7±0.0 1.0±0.1
    Trp 1254 2% 192 2% 1.1±0.1 1.0±0.1
    Tyr 3007 4% 446 4% 1.0±0.1 1.1±0.1
    Val 5532 7% 865 8% 1.1±0.0 1.2±0.1

    PREVIOUS. Amino acid propensities in N3 position.
    NEXT. Summary of amino acids preferences.
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  • Summary of amino acid preferences.

    The amino acid preferences are different in N1, N2, N3 and inside the helix. Several effects can explain those differences : hydrogen bonding, steric clashes, hydrophobic effect, lost of entropy, macrodipole effect.
    We found than Asp, Asn, Glu, Gln, Ser and Thr have specific preferences for N-termini positions. In the next step, structural propensities are studied. The specificity of Asp, Asn, Glu, Gln, Ser and Thr is enlightened.

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