Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Normalized Amino Acid Indices quantifying 54 various attributesDescriptionFrom approximately 500 indices listed in www.genome.jp/aaindex as of 2005, a sample of 54 Amino Acid Indices were selected to represent the range of structural and functional attributes. Each index was normalized to have mean 0 and variation 1. FormatAA54 is a matrix of 54 indices (columns) quantifying attributes for the 20 amino acids (rows). Amino acids are represented by their single character abbreviation and sorted alphabetically. Indices are normalized to have mean = 0 and variation = 1. Sourcewww.genome.jp/aaindex Examplesdata(AA54) AA54 ResultsR version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(HDMD) Loading required package: psych Loading required package: MASS > png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HDMD/AA54.Rd_%03d_medium.png", width=480, height=480) > ### Name: AA54 > ### Title: Normalized Amino Acid Indices quantifying 54 various attributes > ### Aliases: AA54 > ### Keywords: datasets > > ### ** Examples > > data(AA54) Warning message: In data(AA54) : data set 'AA54' not found > AA54 Conformational parameter of beta-turn A -1.6532449 C 0.5542128 D 1.1647862 E -0.9017700 F -0.9017700 G 1.1647862 H 0.1315081 I -1.6532449 K 0.1315081 L -0.9017700 M -0.3851309 N 1.1647862 P 1.1647862 Q -0.3851309 R 0.5542128 S 0.5542128 T 0.1315081 V -1.6532449 W 1.1647862 Y 0.5542128 Chou-Fasman parameter of the coil conformation A -0.9425533 C 0.6256463 D 0.6909879 E -0.5178326 F -0.9425533 G 1.7037835 H 0.2335964 I -1.1059074 K -0.0277702 L -1.0078949 M -1.3346032 N 1.2137211 P 1.9978209 Q -0.4198201 R 0.2009256 S 1.1157086 T 0.2662672 V -1.2039199 W -0.7791992 Y 0.2335964 Average volume of buried residue A -1.42102675 C -0.80380367 D -0.64360828 E 0.07727081 F 1.21512846 G -2.01233590 H 0.36467999 I 0.40001719 K 0.45891253 L 0.37881466 M 0.44713346 N -0.39153630 P -0.53052916 Q 0.21861962 R 1.18214722 S -1.24198496 T -0.70014785 V -0.23840842 W 2.02081698 Y 1.21984037 Residue accessible surface area in folded protein A -0.809183910 C -1.066749081 D 0.264004300 E 0.221076771 F -0.852111439 G -0.895038967 H -0.036488399 I -1.109676609 K 2.281598134 L -0.895038967 M -0.551618740 N 0.822062169 P 0.264004300 Q 1.165482396 R 1.981105435 S 0.006439129 T 0.135221714 V -1.109676609 W -0.508691211 Y 0.693279584 Normalized frequency of beta-sheet Normalized frequency of beta-turn A -0.53898350 -0.68526415 C 0.43851806 -0.08582831 D -1.32641531 1.44000836 E -1.78801326 -0.11307540 F 0.95442166 -0.90324081 G -0.75620606 1.54899669 H -0.43037221 -0.11307540 I 1.55178372 -1.42093540 K -0.78335889 0.54085461 L 0.73719909 -1.33919415 M 0.05837857 -1.06672331 N -0.37606657 1.27652586 P -1.29926249 1.54899669 Q 0.19414267 -0.08582831 R -0.26745529 0.05040710 S -0.75620606 1.19478460 T 0.43851806 -0.03133415 V 1.82331193 -1.09397040 W 0.92726884 -1.06672331 Y 1.19879705 0.40461919 Normalized frequency of turn Size Amino acid composition A -1.3204081 -1.37920049 1.69083748 C 0.8856006 -1.10876902 -0.98260874 D 0.7257449 -1.37920049 0.23685796 E -1.1925235 -0.02704315 0.47137078 F 0.1182932 0.78425126 -0.65429079 G 1.1733409 -2.46092637 1.59703235 H -0.2014182 0.51381979 -1.40473183 I -1.0966101 0.24338832 -0.23216770 K 0.2781489 1.05468273 0.75278618 L -1.0006967 0.24338832 1.12800670 M -1.0966101 0.51381979 -1.54543953 N 1.3012254 -0.02704315 -0.32597283 P 1.4610811 0.24338832 0.09615026 Q -0.2973316 0.51381979 -0.51358309 R -0.7129564 1.32511420 -0.04455744 S 0.7896872 -1.10876902 0.94039644 T 0.1182932 -0.02704315 0.51827335 V -1.7040618 -0.02704315 0.75278618 W 0.6937738 1.05468273 -1.73304979 Y 1.0774274 1.05468273 -0.74809592 Relative mutability Molecular weight Number of hydrogen bond donors A 0.80451070 -1.5490010 -0.8173156 C -1.61507036 -0.5103075 -0.8173156 D 0.98597928 -0.1231462 0.1442322 E 0.86500023 0.3314036 0.1442322 F -0.97993033 0.9165190 -0.8173156 G -0.73797222 -2.0032267 -0.8173156 H -0.22381125 0.5915629 0.1442322 I 0.68353165 -0.1856754 -0.8173156 K -0.52625888 0.3009490 1.1057800 L -1.01017509 -0.1856754 -0.8173156 M 0.62304212 0.3987924 -0.8173156 N 1.83283265 -0.1548970 1.1057800 P -0.52625888 -0.7053461 -0.8173156 Q 0.59279736 0.2996528 1.1057800 R -0.25405601 1.2084286 3.0288756 S 1.40940596 -1.0306263 0.1442322 T 0.71377641 -0.5760762 0.1442322 V 0.01814686 -0.6399012 -0.8173156 W -1.67555988 2.1816774 0.1442322 Y -0.97993033 1.4348937 0.1442322 Positive charge Negative charge Helix-coil equilibrium constant A -0.4094473 -0.3248931 0.5828561 C -0.4094473 -0.3248931 -0.1353552 D -0.4094473 2.9240383 -0.6878254 E -0.4094473 2.9240383 0.9695852 F -0.4094473 -0.3248931 0.6933501 G -0.4094473 -0.3248931 -2.3452361 H 2.3202011 -0.3248931 0.1408799 I -0.4094473 -0.3248931 0.4171150 K 2.3202011 -0.3248931 0.9695852 L -0.4094473 -0.3248931 1.5220554 M -0.4094473 -0.3248931 0.9695852 N -0.4094473 -0.3248931 -0.6878254 P -0.4094473 -0.3248931 -1.4612837 Q -0.4094473 -0.3248931 -0.1353552 R 2.3202011 -0.3248931 0.4171150 S -0.4094473 -0.3248931 -1.2402956 T -0.4094473 -0.3248931 -1.2402956 V -0.4094473 -0.3248931 -0.1353552 W -0.4094473 -0.3248931 0.6933501 Y -0.4094473 -0.3248931 0.6933501 Alpha-helix indices Hydrophobicity factor Residue volume Polarity A 0.88582143 -0.45624827 -1.34649303 -0.08362743 C -0.86828041 -0.23215776 -0.76069138 -1.04998886 D 0.21926273 -1.12851979 -0.79958275 1.73759218 E 1.58746216 -1.12851979 -0.07766125 1.47741795 F 0.32450884 1.24683958 1.10123424 -1.16149210 G -1.42959300 -1.12851979 -2.03438471 0.25088229 H 1.02614957 -1.12851979 0.21645509 0.77123075 I 0.04385255 1.51574818 0.60293821 -1.16149210 K 1.02614957 0.21602325 0.77551893 1.10574048 L 0.95598550 1.02274907 0.60293821 -1.27299534 M 1.76287234 0.03675084 0.44980326 -0.97565336 N -0.79811634 -0.51002999 -0.45199101 1.21724372 P -1.42959300 1.20202148 -0.52248169 -0.12079518 Q 0.11401662 -0.59966619 0.12165709 0.80839850 R -0.13155764 -0.45624827 0.91163861 0.80839850 S -0.90336244 -1.12851979 -1.33677033 0.32521779 T -0.93844448 -0.72515688 -0.61971018 0.10221131 V -0.79811634 0.39529565 -0.05578499 -0.90131787 W 0.49991902 1.56056628 2.02490494 -1.08715660 Y -1.14893670 1.42611198 1.19846274 -0.78981463 Hydrophobicity value Heat capacity Normalized relative frequency of bend A -0.14803237 -1.20993437 -0.40210075 C -0.40773828 0.59997484 -0.83943088 D 1.66990901 -0.54680653 1.34721974 E 1.66990901 -0.14657059 0.05952549 F -1.18685602 0.41628753 -0.66935805 G 0.11167354 -1.67420805 1.90603046 H -0.14803237 1.35326083 -0.28062016 I -0.82326774 0.11969163 -1.32535324 K 1.66990901 1.13923985 0.15670996 L -0.82326774 0.37499995 -0.91231923 M -0.56356183 2.16889963 -1.56831442 N 0.21555591 -0.44485178 1.49299645 P 0.11167354 -0.62769623 1.46870033 Q 0.21555591 0.03711664 -0.40210075 R 1.66990901 -1.45007576 0.27819055 S 0.26749709 -0.94198669 0.59404009 T -0.09609119 -0.70605822 0.35107890 V -0.66744419 -0.27211845 -1.22816876 W -1.65432666 1.12407301 -0.49928522 Y -1.08297365 0.68676276 0.47255949 Normalized relative frequency of coil Average accessible surface area A -0.671552090 -0.78872925 C -0.766248037 -1.30026992 D 0.401668642 0.57537927 E -0.403246907 0.89145316 F -0.450594881 -0.88438317 G 3.368808313 -0.92597184 H -0.008680462 0.16365150 I -0.434812223 -0.99667263 K 0.133363459 2.33873920 L -0.576856144 -0.79704695 M -0.340116276 -0.55167376 N 1.995717082 0.55458493 P -0.419029565 0.19692240 Q 0.086015485 0.91224750 R -0.592638801 1.99355307 S 0.212276748 -0.19817002 T -0.797813353 -0.07340399 V -0.213855014 -0.95924274 W -0.419029565 -0.50176731 Y -0.103376409 0.35080054 Percentage of buried residues Percentage of exposed residues A 0.6201393 -0.82857188 C 1.6966074 -1.28134340 D -0.8775556 0.75612844 E -1.0179645 0.98251420 F 0.9477600 -1.05495764 G 0.6669422 -1.05495764 H -0.1755111 0.03169401 I 1.3221837 -0.91912619 K -1.6264030 2.34082876 L 1.0413659 -0.78329473 M 0.6669422 -0.60218612 N -0.7371467 0.71085129 P -0.5967378 0.52974268 Q -1.0179645 1.02779135 R -1.5327970 1.52584002 S -0.1287081 -0.05886030 T -0.3627230 -0.05886030 V 1.2285778 -0.87384903 W 0.5265333 -0.73801758 Y -0.6435407 0.34863407 Transfer free energy Relative frequency of occurrence A 0.58921351 1.30694740 C 1.44108847 -1.45728273 D -0.68859892 0.09456577 E -0.83057808 0.57951842 F 0.87317183 -0.48737742 G 0.58921351 1.16146161 H 0.02129687 -1.31179693 I 1.15713015 0.14306103 K -2.39234884 0.43403263 L 0.87317183 1.98588112 M 0.73119267 -1.26330166 N -0.54661976 -0.34189162 P -0.26266145 0.04607050 Q -0.83057808 -0.43888215 R -1.82443220 0.04607050 S 0.02129687 0.91898528 T -0.12068229 0.43403263 V 1.01515099 0.77349948 W 0.58921351 -1.74825432 Y -0.40464060 -0.87533954 Average relative probability of helix Net charge Side chain volume A 1.35039582 0.000000 -1.2387074 C -0.74806099 0.000000 -0.7684688 D 0.10686586 -2.179449 -0.8949657 E 1.81671955 -2.179449 -0.2899804 F 0.14572617 0.000000 1.1812338 G -1.48640690 0.000000 -1.9949390 H 0.37888804 0.000000 0.1775082 I 0.26230710 0.000000 0.5762485 K 0.80635146 2.179449 0.7549941 L 0.76749115 0.000000 0.5762485 M 1.70013862 0.000000 0.5927480 N -0.47603881 0.000000 -0.3807282 P -1.91387033 0.000000 -0.8427169 Q 0.49546897 0.000000 0.2242570 R -0.04857539 2.179449 0.8924908 S -1.05894348 0.000000 -1.1892086 T -0.78692130 0.000000 -0.5842233 V -0.28173726 0.000000 -0.0287368 W -0.16515632 0.000000 2.0062137 Y -0.86464193 0.000000 1.2307326 Hydropathy index Normalized frequency of beta-sheet unweighted A 0.76666277 -0.57547202 C 1.00101383 0.14386800 D -1.00770958 -1.25484871 E -1.00770958 -1.37473871 F 1.10145000 0.82324469 G 0.03013085 -0.45558202 H -0.90727341 -0.61543535 I 1.67058830 1.86229140 K -1.14162447 -0.93514203 L 1.43623724 0.14386800 M 0.80014149 -0.29572868 N -1.00770958 -1.09499537 P -0.37161383 -1.29481204 Q -1.00770958 -0.01598533 R -1.34249681 -0.13587534 S -0.10378404 0.06394134 T -0.07030532 1.06302470 V 1.57015213 1.70243806 W -0.13726277 1.02306137 Y -0.27117766 1.22287804 Normalized frequency of left-handed alpha-helix Refractivity A -0.56198068 -1.353551279 C 0.11187778 1.597483474 D 0.22418753 -0.634336319 E -0.46694936 -0.140462860 F -0.46694936 0.999389571 G 3.62803669 -1.761043829 H -0.21641224 0.286746977 I -0.48422778 0.028543172 K 0.30194043 0.237923173 L -0.52742384 0.002253518 M -0.70884727 0.270785287 N 1.55462603 -0.514154184 P -0.60517674 -0.734801072 Q 0.07732094 -0.112295266 R -0.05226723 0.742124689 S -0.21641224 -1.164827771 T -0.51014541 -0.727289688 V -0.50150620 -0.454063117 W -0.70884727 2.232195277 Y 0.12915621 1.199380248 Average side chain orientation angle Normalized frequency coil A 0.04432906 -0.8760163 C 1.30031907 0.1261325 D -1.13777919 0.2298031 E -1.06389742 -0.7723457 F 1.59584614 -1.3598122 G 0.26597436 1.3010656 H 0.26597436 -0.7377888 I 1.37420084 -0.5995614 K -1.58106978 -0.4613340 L 1.30031907 -1.1870280 M 1.00479201 -1.2215848 N -1.21166095 1.4047361 P -0.62060683 1.5775204 Q -1.50718802 -0.5650046 R -0.39896153 1.2319519 S -0.25119800 1.2665087 T -0.25119800 0.1952462 V 0.56150142 -0.4958909 W 0.56150142 -0.3576634 Y -0.25119800 1.3010656 AA composition of total proteins Average non-bonded energy per atom A 1.42335002 -0.713698364 C -1.51708224 -1.418585637 D 0.06732543 1.184462365 E 0.52409161 1.098868910 F -0.55597008 -0.557616182 G 0.90948807 -0.728803091 H -1.34579493 -0.008811091 I 0.22909678 -0.995653273 K 0.48126978 1.909489274 L 1.98003379 -1.071176910 M -1.18878155 -1.056072183 N -0.31807103 0.972996183 P -0.02307621 0.273143818 Q -0.48460036 1.169357637 R 0.40990006 1.400963456 S 0.87618220 0.001258727 T 0.36707823 -0.069230000 V 0.78578056 -1.146700546 W -1.74070735 -0.582790728 Y -0.87951279 0.338597637 Long range non-bonded energy per atom Average non-bonded energy per residue A 0.405879599 -1.8494691 C -0.766879855 0.3870543 D 1.290362986 0.3870543 E 1.192087054 0.3870543 F -1.153431854 0.3870543 G 0.124155261 0.3870543 H 0.084844888 0.3870543 I -1.369638904 0.3870543 K 1.657259798 0.3870543 L -0.635845279 -3.3254565 M -0.694810838 0.3870543 N 1.120018037 0.3870543 P 0.589328005 0.3870543 Q 0.969328275 0.3870543 R -0.006879315 -1.4049969 S 0.641741835 0.3870543 T 0.248638108 0.3870543 V -1.146880125 0.3870543 W -1.874122021 0.3870543 Y -0.675155652 0.3870543 Optimized propensity to form reverse turn Relative frequency in alpha-helix A 0.21362379 0.97327489 C 0.03989360 0.29817092 D 1.48764517 0.03563049 E 0.76698661 1.53586152 F -0.13383659 0.14814781 G 0.68333874 -1.76464676 H 0.16858263 0.71073445 I -0.22391891 -0.22690994 K -0.25609117 0.74824023 L -0.30113233 1.01078066 M -0.19818110 1.64837885 N 0.95358570 -0.48945038 P 0.71551100 -1.91466986 Q 0.31014056 0.89826333 R -0.03731982 -0.26441572 S -0.04375427 -0.78949658 T 0.05276250 -0.78949658 V 0.20075488 -0.45194460 W -3.64061261 -0.15189839 Y -0.75797838 -1.16455434 Information measure for pleated-sheet Information measure for loop A -0.5833681 -1.26048124 C 0.8750522 0.96757895 D -0.9707610 0.79233826 E -1.8139102 -1.28551562 F 0.7155374 -0.58455287 G -0.8568219 1.41819786 H -0.6517316 -0.20903711 I 1.7865648 -1.11027494 K -0.6289437 0.26661619 L 0.8750522 -1.33558439 M 0.8750522 -1.31055001 N -0.9251854 1.19288840 P -1.4720930 0.89247579 Q 0.2142055 0.06634112 R 0.1230542 0.66716634 S -0.5150047 0.81737264 T 0.4192958 0.01627235 V 1.6498379 -1.56089385 W 0.1002664 0.74226949 Y 0.7839009 0.81737264 Normalized frequency of extended structure A -0.93587460 C 0.94137282 D -1.95697153 E -1.51318710 F 0.09307691 G -1.19114884 H -0.64525471 I 1.30661133 K -1.15187588 L 0.32478737 M 0.25016875 N -0.77092818 P 0.86675420 Q 0.03809477 R 0.23053227 S |
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and