Amino Acid Properties and Structure

Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen. R stands for 20 possible different side chains. The R group may be as simple as a hydrogen atom or as complex as a carbon chain with functional groups. The physical and chemical properties of the R side chains determine the unique characteristics and functions of each particular amino acid and thus the entire protein.

• Amino Acid Structure
• Amino Acid Chart
• Amino Acid Properties
• Fluorophores

Amino Acid Properties and Amino Acid Structure Chart Name Abbreviation M.W. pI CAS Registry Number Structure / formula 3D Structure Alanine 89.09 6 56-41-7 CH3-CH(NH2)-COOH Ala A Arginine 174.2 11.15 74-79-3 HN=C(NH2)-NH-(CH2)3-CH(NH2)-COOH Arg R Asparagine 132.12 5.41 5794-13-8 H2N-CO-CH2-CH(NH2)-COOH Asn N Aspartic acid 133.1 2.77 56-84-8 HOOC-CH2-CH(NH2)-COOH Asp D Cysteine 121.15 5.02 52-90-4 HS-CH2-CH(NH2)-COOH Cys C Glutamine 146.15 5.65 56-85-9 H2N-CO-(CH2)2-CH(NH2)-COOH Gln Q Glutamic acid 147.13 3.22 56-86-0 HOOC-(CH2)2-CH(NH2)-COOH Glu E Glycine 75.07 5.97 56-40-6 NH2-CH2-COOH Gly G Histidine 155.16 7.47 71-00-1 N=C-NH-C=C-CH2-CH(NH2)-COOH |________| His H Isoleucine 131.17 5.94 73-32-5 CH3-CH2-CH(CH3)-CH(NH2)-COOH Ile I Leucine 131.17 5.98 61-90-5 (CH3)2-CH-CH2-CH(NH2)-COOH Leu L Lysine 146.19 9.59 39665-12-8 H2N-(CH2)4-CH(NH2)-COOH Lys K Methionine 149.21 5.74 63-68-3 CH3-S-(CH2)2-CH(NH2)-COOH Met M Phenylalanine 165.19 5.48 63-91-2 Ph-CH2-CH(NH2)-COOH Phe F Proline 115.13 6.3 147-85-3 NH-(CH2)3-CH-COOH |_________| Pro P Serine 105.09 5.68 56-45-1 HO-CH2-CH(NH2)-COOH Ser S Threonine 119.12 5.64 72-19-5 CH3-CH(OH)-CH(NH2)-COOH Thr T Tryptophan 204.23 5.89 73-22-3 Ph-NH-CH-C-CH2-CH(NH2)-COOH |_______| Trp W Tyrosine 181.19 5.66 60-18-4 HO-p-Ph-CH2-CH(NH2)-COOH Tyr Y Valine 117.15 5.96 72-18-4 CH3-CH(CH2)-CH(NH2)-COOH Val V

Amino Acid Chart

Amino Acid Properties Amino Acid Code Hydropathy Charge pKa, NH2 pKa, COOH pK(R) Solubility Arginine R hydrophilic + 9.09 2.18 13.2 71.8 Asparagine N hydrophilic N 8.8 2.02   2.4 Aspartate D hydrophilic - 9.6 1.88 3.65 0.42 Glutamate E hydrophilic - 9.67 2.19 4.25 0.72 Glutamine Q hydrophilic N 9.13 2.17   2.6 Lysine K hydrophilic + 10.28 8.9 2.2   Serine S hydrophilic N 9.15 2.21   36.2 Threonine T hydrophilic N 9.12 2.15   freely Cysteine C moderate N 10.78 1.71 8.33 freely Histidine H moderate + 8.97 1.78 6 4.19 Methionine M moderate N 9.21 2.28   5.14 Alanine A hydrophobic N 9.87 2.35   15.8 Valine V hydrophobic N 9.72 2.29   5.6 Glycine G hydrophobic N 9.6 2.34   22.5 Isoleucine I hydrophobic N 9.76 2.32   3.36 Leucine L hydrophobic N 9.6 2.36   2.37 Phenylalanine F hydrophobic N 9.24 2.58   2.7 Proline P hydrophobic N 10.6 1.99   1.54 Tryptophan W hydrophobic N 9.39 2.38   1.06 Tyrosine Y hydrophobic N 9.11 2.2 10.1 0.038

LifeTein® Modifications: Fluorophores list including absorption and emission peak values Fluorophore Absorption Emission Indo-1, Ca saturated 331 nm 404 nm DyLight 350 332 nm 435 nm LysoSensor Yellow pH 9.0 335 nm 530 nm Dansyl Cadaverine, MeOH 335 nm 526 nm Dansyl Cadaverine 335 nm 524 nm Fura-2 Ca2+ 336 nm 505 nm SBFI-Na+ 336 nm 527 nm Fura-2, high Ca 336 nm 504 nm Alexa 350 343 nm 441 nm Amino Coumarin 345 nm 442 nm 7-Amino-4-methylcoumarin pH 7.0 346 nm 442 nm Indo-1, Ca free 346 nm 479 nm Indo-1 Ca2+ 346 nm 404 nm AMCA conjugate 347 nm 444 nm Hoechst 33342 352 nm 455 nm Hoechst 33258 352 nm 455 nm Hoechst 33258-DNA 352 nm 455 nm 6,8-Difluoro-7-hydroxy-4-methylcoumarin pH 9.0 358 nm 450 nm DAPI 358 nm 463 nm DAPI-DNA 359 nm 461 nm Coumarin 360 nm 447 nm 7-Hydroxy-4-methylcoumarin 360 nm 447 nm 7-Hydroxy-4-methylcoumarin pH 9.0 361 nm 448 nm Marina Blue 362 nm 464 nm Fura-2, no Ca 367 nm 515 nm Dapoxyl (2-aminoethyl) sulfonamide 372 nm 582 nm LysoTracker Blue 373 nm 421 nm LysoSensor Blue pH 5.0 374 nm 424 nm LysoSensor Blue 374 nm 424 nm 1-Anilinonaphthalene-8-sulfonic acid (1,8-ANS) 375 nm 479 nm 1,8-ANS (1-Anilinonaphthalene-8-sulfonic acid) 375 nm 480 nm BFP (Blue Fluorescent Protein) 380 nm 439 nm LysoSensor Yellow pH 3.0 389 nm 542 nm Sapphire 396 nm 511 nm Cascade Blue 398 nm 420 nm Cascade Yellow antibody conjugate pH 8.0 399 nm 549 nm Cascade Yellow 399 nm 549 nm DyLight 405 399 nm 434 nm Cascade Blue BSA pH 7.0 401 nm 419 nm Alexa 405 401 nm 421 nm Pacific Blue 404 nm 455 nm Pacific Blue antibody conjugate pH 8.0 404 nm 455 nm Lucifer Yellow, CH 428 nm 542 nm Auramine O 431 nm 501 nm Alexa 430 431 nm 540 nm Acridine Orange 431 nm 520 nm Alexa Fluor 430 antibody conjugate pH 7.2 431 nm 540 nm POPO-1 433 nm 457 nm POPO-1-DNA 433 nm 458 nm PO-PRO-1 434 nm 457 nm CFP (Cyan Fluorescent Protein) 434 nm 474 nm Fura Red, high Ca 434 nm 659 nm Fura Red Ca2+ 435 nm 670 nm PO-PRO-1-DNA 435 nm 457 nm eCFP (Enhanced Cyan Fluorescent Protein) 437 nm 476 nm SYTOX Blue-DNA 445 nm 470 nm LysoSensor Green pH 5.0 447 nm 502 nm LysoSensor Green 447 nm 504 nm evoglow-Pp1 448 nm 495 nm evoglow-Bs1 448 nm 496 nm evoglow-Bs2 448 nm 496 nm SYTO 45-DNA 451 nm 486 nm BOBO-1-DNA 461 nm 484 nm BO-PRO-1-DNA 462 nm 482 nm BOPRO-1 462 nm 482 nm NBD-X 466 nm 534 nm NBD-X, MeOH 467 nm 538 nm SYPRO Ruby 467 nm 618 nm Di-8-ANEPPS-lipid 469 nm 631 nm Di-8 ANEPPS 469 nm 630 nm FM 1-43 472 nm 578 nm Fura Red, low Ca 472 nm 673 nm FM 1-43 lipid 473 nm 579 nm mHoneydew 478 nm 562 nm BCECF pH 5.5 485 nm 521 nm DiO 487 nm 501 nm SYTO 13-DNA 488 nm 506 nm eGFP (Enhanced Green Fluorescent Protein) 488 nm 509 nm GFP (S65T) 489 nm 509 nm Cy 2 489 nm 503 nm Fluorescein pH 9.0 490 nm 514 nm MitoTracker Green 490 nm 512 nm MitoTracker Green FM, MeOH 490 nm 512 nm YOYO-1-DNA 491 nm 509 nm YO-PRO-1-DNA 491 nm 507 nm 5-FAM pH 9.0 492 nm 518 nm 025025')Alexa 488 493 nm 520 nm DM-NERF pH 4.0 493 nm 530 nm Calcein 493 nm 514 nm Fluorescein 0.1 M NaOH 493 nm 513 nm Alexa Fluor 488 hydrazide-water 493 nm 518 nm DyLight 488 493 nm 518 nm Fluorescein antibody conjugate pH 8.0 493 nm 517 nm Calcein pH 9.0 494 nm 514 nm Fluo-4 494 nm 516 nm FDA 495 nm 517 nm DTAF 495 nm 517 nm Fluorescein 495 nm 517 nm FITC antibody conjugate pH 8.0 495 nm 519 nm Fluoro-Emerald 495 nm 524 nm CFDA 495 nm 517 nm FITC 495 nm 517 nm Rhodamine Green 497 nm 524 nm NeuroTrace 500/525, green fluorescent Nissl stain-RNA 497 nm 524 nm Rhodaminen Green pH 7.0 497 nm 523 nm Rhodamine 110 497 nm 520 nm Rhodamine 110 pH 7.0 497 nm 520 nm Nissl 497 nm 524 nm Oregon Green 488 498 nm 526 nm Oregon Green 488 antibody conjugate pH 8.0 498 nm 526 nm SYBR Green I 498 nm 522 nm Rhodol Green antibody conjugate pH 8.0 499 nm 524 nm Alexa Fluor 488 antibody conjugate pH 8.0 499 nm 520 nm Fluorescein dextran pH 8.0 501 nm 524 nm BCECF pH 9.0 501 nm 527 nm BODIPY FL, MeOH 502 nm 511 nm PicoGreen dsDNA quantitation reagent 502 nm 522 nm CyQUANT GR-DNA 502 nm 523 nm BODIPY FL conjugate 503 nm 512 nm LysoTracker Green 503 nm 509 nm 5-(and-6)-Carboxy-2', 7'-dichlorofluorescein pH 9.0 504 nm 525 nm CI-NERF pH 2.5 504 nm 541 nm FM 4-64, 2% CHAPS 506 nm 751 nm Fluo-3 506 nm 527 nm Calcium Green 506 nm 530 nm Calcium Green-1 Ca2+ 506 nm 529 nm Fluo-3 Ca2+ 506 nm 527 nm Magnesium Green 507 nm 530 nm Rhodamine 123, MeOH 507 nm 529 nm Magnesium Green Mg2+ 507 nm 531 nm Sodium Green Na+ 507 nm 531 nm FM 4-64 508 nm 751 nm FlAsH 509 nm 529 nm DM-NERF pH 7.0 509 nm 537 nm Oregon Green 514 512 nm 532 nm Oregon Green 514 antibody conjugate pH 8.0 513 nm 533 nm CI-NERF pH 6.0 513 nm 538 nm eYFP (Enhanced Yellow Fluorescent Protein) 514 nm 526 nm TOTO-1-DNA 514 nm 531 nm TO-PRO-1-DNA 515 nm 531 nm Citrine 515 nm 530 nm 6 JOE 520 nm 548 nm 6-TET, SE pH 9.0 521 nm 542 nm Eosin 524 nm 546 nm Ethidium Bromide 524 nm 605 nm Eosin antibody conjugate pH 8.0 525 nm 546 nm 6-Carboxyrhodamine 6G, hydrochloride 525 nm 547 nm 6-Carboxyrhodamine 6G pH 7.0 526 nm 547 nm Ethidium homodimer-1-DNA 528 nm 617 nm Alexa Fluor 532 antibody conjugate pH 7.2 528 nm 553 nm Bodipy R6G SE 528 nm 547 nm Ethidium homodimer 528 nm 617 nm Alexa 532 528 nm 553 nm BODIPY R6G, MeOH 528 nm 547 nm POPO-3 533 nm 573 nm Erythrosin-5-isothiocyanate pH 9.0 533 nm 554 nm 6-HEX, SE pH 9.0 534 nm 559 nm Propidium Iodide-DNA 538 nm 619 nm Propidium Iodide 538 nm 617 nm PO-PRO-3-DNA 539 nm 571 nm PO-PRO-3 539 nm 571 nm mBanana 540 nm 553 nm Rhodamine B 543 nm 565 nm 5-TAMRA-MeOH 543 nm 567 nm BODIPY TMR-X, SE 544 nm 570 nm BODIPY TMR-X, MeOH 544 nm 570 nm Bodipy TMR-X conjugate 544 nm 573 nm BODIPY TMR-X antibody conjugate pH 7.2 544 nm 573 nm mOrange 548 nm 562 nm Calcium Orange 549 nm 574 nm Calcium Orange Ca2+ 549 nm 573 nm 5-TAMRA 549 nm 577 nm Cy 3 549 nm 562 nm TRITC 550 nm 573 nm Magnesium Orange 550 nm 575 nm Rhodamine 551 nm 573 nm MitoTracker Orange 551 nm 575 nm MitoTracker Orange, MeOH 551 nm 575 nm DiI 551 nm 565 nm Tetramethylrhodamine antibody conjugate pH 8.0 552 nm 578 nm Rhod-2 552 nm 577 nm Nile Red-lipid 553 nm 636 nm 5-TAMRA pH 7.0 553 nm 576 nm Alexa 555 553 nm 568 nm Rhod-2 Ca2+ 553 nm 578 nm Alexa Fluor 555 antibody conjugate pH 7.2 553 nm 568 nm Fluor-Ruby 554 nm 582 nm dTomato 554 nm 581 nm DyLight 549 555 nm 569 nm Tetramethylrhodamine dextran pH 7.0 555 nm 582 nm Rhodamine phalloidin pH 7.0 558 nm 575 nm Nile Red 559 nm 637 nm Alexa 546 562 nm 573 nm DsRed 563 nm 581 nm R-Phycoerythrin pH 7.5 565 nm 576 nm Phycoerythrin 565 nm 575 nm Alexa Fluor 610 R-phycoerythrin streptavidin pH 7.2 567 nm 627 nm mTangerine 568 nm 585 nm LOLO-1-DNA 568 nm 580 nm Alexa Fluor 647 R-phycoerythrin streptavidin pH 7.2 569 nm 666 nm BOBO-3-DNA 570 nm 605 nm Resorufin 571 nm 584 nm Resorufin pH 9.0 571 nm 584 nm Lissamine rhodamine 572 nm 590 nm Rhodamine Red-X antibody conjugate pH 8.0 573 nm 591 nm BOPRO-3 574 nm 604 nm BO-PRO-3-DNA 574 nm 604 nm mStrawberry 575 nm 596 nm Alexa 568 576 nm 603 nm Sulforhodamine 101, EtOH 578 nm 593 nm 5-ROX pH 7.0 578 nm 604 nm MitoTracker Red 578 nm 599 nm MitoTracker Red, MeOH 578 nm 599 nm LysoTracker Red 578 nm 589 nm 5-ROX (5-Carboxy-X-rhodamine, triethylammonium salt) 578 nm 604 nm Cy 3.5 578 nm 591 nm Alexa Fluor 568 antibody conjugate pH 7.2 579 nm 603 nm X-Rhod-1 Ca2+ 580 nm 602 nm mRFP 585 nm 608 nm mCherry 587 nm 610 nm mPlum 587 nm 649 nm BODIPY TR-X, SE 588 nm 621 nm BODIPY TR-X, MeOH 588 nm 621 nm Calcium Crimson 589 nm 608 nm BODIPY TR-X phallacidin pH 7.0 590 nm 621 nm Alexa 594 590 nm 619 nm HcRed 590 nm 614 nm Calcium Crimson Ca2+ 590 nm 608 nm DyLight 594 592 nm 616 nm JC-1 592 nm 595 nm JC-1 pH 8.2 593 nm 595 nm Texas Red-X antibody conjugate pH 7.2 596 nm 613 nm ReAsH 597 nm 608 nm Carboxynaphthofluorescein pH 10.0 600 nm 674 nm YOYO-3-DNA 612 nm 631 nm YO-PRO-3-DNA 613 nm 629 nm DyLight 633 624 nm 646 nm Nile Blue, EtOH 631 nm 660 nm TO-PRO-3-DNA 642 nm 657 nm TOTO-3-DNA 642 nm 661 nm Atto 647 644 nm 670 nm Cy 5 646 nm 664 nm BODIPY 650/665-X, MeOH 646 nm 664 nm DDAO pH 9.0 648 nm 657 nm APC (allophycocyanin) 650 nm 660 nm Allophycocyanin pH 7.5 651 nm 660 nm DyLight 649 652 nm 668 nm Alexa 647 653 nm 669 nm Alexa Fluor 647 antibody conjugate pH 7.2 653 nm 668 nm Alexa Fluor 660 antibody conjugate pH 7.2 663 nm 691 nm Alexa 660 664 nm 691 nm Cy 5.5 673 nm 692 nm yLight 680 678 nm 706 nm Alexa 680 679 nm 703 nm Alexa Fluor 680 antibody conjugate pH 7.2 679 nm 702 nm Alexa 700 696 nm 720 nm Alexa Fluor 700 antibody conjugate pH 7.2 696 nm 719 nm