Amino acids, substitutions and variant impact

This site provides insights into the nature of the amino acids and how they substitute for each other. It is an update on a series of pages first developed in 1999 to aid geneticists who used to ask Rob a lot of questions about amino acids and what did it mean to change from one to another. Since then, the pages have remained the most accessed tools we've ever developed and the Book Chapter describing them has been cited more than 1000 times. We thought it was high time to update them. If you love the 1990s style old pages, you can still see them at aasold.russelllab.org.

There are pages with information on each amino acid, in addition to others talking more generally about concepts. You can access these easily by using this clickable Venn diagram:

AA Venn diagram Hydrophillc Negative Charged Positive Hydrophobic C-beta branched Aromatic Aliphatic Tiny Small The main-chain Asparagine (Asn,N) Glutamine (Gln,Q) Aspartate (Asp,D) Glutamate (Glu,E) Phosphoserine (pSer,pS) Phosphothreonine (pThr,pT) Phosphotyrosine (pTyr,pY) Phosphohistidine (pHis,pH) Sulfotyrosine (sTyr,sY) Histidine (His,H) Phenylalanine (Phe,F) Tryptophan (Trp,W) Tyrosine (Tyr,Y) Arginine (Arg,R) Methylarginine (meArg,meR) Dimethylarginine (idmeArg,dimeR) Dimethylarginine (idmeArg,dimeR) Lysine (Lys,K) Methyllysine (meLys,meK) Dimethyllysine (dimeLys,dimeK) Trimethyllysine (trimeLys,trimeK) Threonine (Thr,T) Serine (Ser,S) Glycine (Gly,G) Cystine (Cys,C) Alanine (Ala,A) Proline (Pro,P) Valine (Val,V) Isoleucine (Ile,I) Methionine (Met,M) Leucine (Leu,L) Acetyllysine (acLys,acK)

In case the above fails, here are links to the amino acids and groups, in addition to some other pages.

Standard 20 amino acids

Ala Cys Asp Glu Phe Gly His Ile Lys Leu
Met Asn Pro Gln Arg Ser Thr Val Trp Tyr

Common post-translational modifications
pSer pThr pTyr pHis sTyr acLys meLys dimeLys triemeLys meArg dimeArg trimeArg

Property groups
Hydrophobic Aliphatic Aromatic Polar/Hydrophilic Charged Small Tiny C-beta branched The main chain

Other pages
Functional site tendencies
Evolutionary conservation
Substituation matrices

And new for the AA site, here are some guides to what happens when you change one amino acid to another. Upper case pairs are those accessible by a single codon change.

A C D E F G H I K L M N P Q R S T V W Y
A - ac AD AE af AG ah ai ak al am an AP aq ar AS AT AV aw ay
C ca - cd ce CF CG ch ci ck cl cm cn cp cq CR CS ct cv CW CY
D DA dc - DE df DG DH di dk dl dm DN dp dq dr ds dt DV dw DY
E EA ec ED - ef EG eh ei EK el em en ep EQ er es et EV ew ey
F fa FC fd fe - fg fh FI fk FL fm fn fp fq fr FS ft FV fw FY
G GA GC GD GE gf - gh gi gk gl gm gn gp gq GR GS gt GV GW gy
H ha hc HD he hf hg - hi hk HL hm HN HP HQ HR hs ht hv hw HY
I ia ic id ie IF ig ih - IK IL IM IN ip iq IR IS IT IV iw iy
K ka kc kd KE kf kg kh KI - kl KM KN kp KQ KR ks KT kv kw ky
L la lc ld le LF lg LH LI lk - LM ln LP LQ LR LS lt LV LW ly
M ma mc md me mf mg mh MI MK ML - mn mp mq MR ms MT MV mw my
N na nc ND ne nf ng NH NI NK nl nm - np nq nr NS NT nv nw NY
P PA pc pd pe pf pg PH pi pk PL pm pn - PQ PR PS PT pv pw py
Q qa qc qd QE qf qg QH qi QK QL qm qn QP - QR qs qt qv qw qy
R ra RC rd re rf RG RH RI RK RL RM rn RP RQ - RS RT rv RW ry
S SA SC sd se SF SG sh SI sk SL sm SN SP sq SR - ST sv SW SY
T TA tc td te tf tg th TI TK tl TM TN TP tq TR TS - tv tw ty
V VA vc VD VE VF VG vh VI vk VL VM vn vp vq vr vs vt - vw vy
W wa WC wd we wf WG wh wi wk WL wm wn wp wq WR WS wt wv - wy
Y ya YC YD ye YF yg YH yi yk yl ym YN yp yq yr YS yt yv yw -

And also new and very beta, you can now see individual (i.e. specific protein/position/change) variants and the data we have precomputed based on Schmenger et al, npj Genomic Med, 2022 (PubMed). These are accessible either by using aas.russelllab.org/variant/uniprot-accesssion/modificiation (e.g. aas.russelllab.org/variant/TP53/M160V). You can see thousands of links to these in the pages above (i.e. about amino acid changes).

Citation: M.J. Betts, R.B. Russell. Amino acid properties and consequences of subsitutions.
In Bioinformatics for Geneticists, M.R. Barnes, I.C. Gray eds, Wiley, 2003. Buy it at Wiley or Amazon.
Author: Rob Russell, Heidelberg University