Amino Acid and Peptide Structure Workbench

Draw the 20 standard amino acids from memory and check yourself, convert any one between Fischer, wedge-dash and ionization-state drawings, build peptides to see their names, charge and pI, and turn φ and ψ in a 3D peptide to see which backbone shapes are sterically allowed.

Task

Amino acid

Series

Your drawing

Sketch it, then reveal the answer and compare.

Answer

Covered until you reveal it.

Greek letters Peptide planes

Try this

Draw L-alanine as a wedge-dash structure, then reveal it. Which group is on the wedge, and which is hashed?
Switch to D and draw it again. Which two bonds changed, and what happened to the R/S label?
Pick glycine. Why is there no wedge or hash at all?
Set the task to "At a pH" and draw aspartate at pH 1, 3, 7 and 12. How many groups carry a charge each time?
Draw L-cysteine and L-serine side by side. They have the same spatial arrangement, so why is Cys R and Ser S?
Pick proline. Which extra bond makes it a secondary amine, and what does that do to the N-terminal charge drawing?
Choose Peptide, press Clear, then build Ala-Gly with the residue buttons. Mark the peptide bond and the six atoms that lie in one plane.

Show the drawing rules

Wedge-dash: as drawn here, with N on the left, C′ on the right and both in the plane of the page, the side chain R is on a wedge (toward you) and H is on a hash (away) for an L-amino acid. A D-amino acid swaps them. Turn the molecule and the wedge and hash change places, so always check the orientation.
Fischer: the carboxyl group at the top (COO⁻ at pH 7), R at the bottom, NH₃⁺ on the left for L and on the right for D. Horizontal bonds come toward you, vertical bonds go away.
L and D: almost every L-amino acid is S. Cysteine is R because its CH₂SH outranks COOH in the CIP rules; its shape in space is the same as the others. Glycine has no stereocentre. Isoleucine and threonine have a second stereocentre at Cβ: L-isoleucine is (2S,3S) and L-threonine is (2S,3R).
Ionization: each group is drawn in its majority form at the chosen pH: below its pK₌ it is protonated, above it deprotonated.
Peptides: written N to C. The peptide bond is C′–N, planar and usually trans. Side chains alternate up and down along the zigzag; for L-residues the ones pointing up are on wedges and the ones pointing down are on hashes.

Pick a task, draw on the pad, then reveal the answer.

Series

Show

Greek letters

Fischer projection

Click the α-carbon to flip L and D.

Wedge-dash, as it exists at this pH

Click α (or β for Ile and Thr) to flip it.

Ionization ladder

Every protonation state from low to high pH. The bar shows how much of each is present at the pH above.

Titration curve

pH against equivalents of OH⁻ added to the fully protonated form. Shaded bands: pK₌ ± 1 (buffering).

Try this

Drag the pH slider for glutamate from 1 to 12. List each species and its net charge. At what pH is the net charge zero?
Click the α-carbon in either drawing. What does the name become, and what changed in the Fischer view?
Pick isoleucine and click the β-carbon in either drawing. Why are there four stereoisomers, and which ones are allo-isoleucine?
Compare the pI of aspartate, glycine and lysine. How does the side chain move it?
Pick histidine and set pH 6.0. What fraction of the side chain is protonated? Why does His buffer near physiological pH?
Compare the titration curves of glycine and lysine: how many buffering regions does each have?
Hover over the carboxyl group in one drawing. Where is it in the others?

Show the definitions

Zwitterion: a molecule with both a positive and a negative charge and a net charge of zero.
pI: the pH at which the net charge is zero. For a molecule with two relevant pK_a values it is their average. This app finds it by solving for net charge = 0.
Net charge: sum over groups of the fraction ionized, from the Henderson–Hasselbalch equation, treating each group independently.
Titration curve: the ideal curve from the same equation. It leaves out the OH⁻ that water itself takes up, so a measured curve flattens more below pH 2 and above pH 12.
Ionization ladder: groups lose their protons in order of pK_a. The few molecules that ionize out of that order are not drawn.
Source of pK_a values: the table on the CochranLearning page for ionizable amino acid side chains.

Sequence (N to C, up to 6)

Examples

Add a residue

Show

Peptide planes Greek letters

Structure

Ionizable groups

Termini use the end residue’s free amino acid α values.

Titration curve

Equivalents of OH⁻ added to the fully protonated peptide.

Try this

Build Gly-Ala. Count the peptide bonds and the ionizable groups. Which two groups carry the charges at pH 7?
Add Lys to the end. How do the net charge at pH 7 and the pI change?
Turn on the peptide planes. Which six atoms lie in each plane, and which bonds can rotate?
Slide the pH from 1 to 13 and watch the group table. At what pH does each group switch from protonated to deprotonated, and how does the net charge change?
Build Tyr-Gly-Gly-Phe-Leu (Leu-enkephalin). Predict its pI, then check.
Build Glu-Glu, then Glu. How many buffering regions does each titration curve have?
Build Ala-Ser and Ser-Ala. What is the same, and what differs?
Why does the peptide bond not rotate freely? Use the resonance idea and the planes.

Show the definitions

Residue: an amino acid after losing water to form a peptide bond. Mass of the peptide = sum of residue masses + one water.
N to C: peptides are written from the free amino end (N-terminus) to the free carboxyl end (C-terminus).
Charge and pI: the N-terminus uses the first residue’s α-NH₃⁺ pK_a, the C-terminus the last residue’s α-COOH pK_a, plus each ionizable side chain. Values come from the free amino acid table. In a real peptide the two ends are farther apart, so they shift toward each other (α-NH₃⁺ to about 8 and α-COOH to about 3.5), and side-chain values also move with their surroundings.

Residue to turn

φ (phi), about N–Cα

ψ (psi), about Cα–C′

Auto-rotate

Speed40°/s

Go to

Molecular model

Steric clashes Hydrogen bonds Peptide planes Labels View

Side-chain rotamer, χ₁ (N–Cα–Cβ–Oγ)

Series (both residues)

Animation Animate the rotation

Try this

Select Ser 2. Click α-helix, then β-strand (antiparallel). By how many degrees did φ and ψ turn, and in which direction? Find the same turn in the model.
With Ser 2 selected, press Down N→Cα (φ). The model now matches the φ Newman projection. Which atoms are in front and which are behind? Drag the φ slider and watch both.
With Ser 2 selected, set φ = 0°. Which atoms collide? Switch to Space-filling to see how far they overlap.
Select Ser 1 and set Auto-rotate to φ. Which atoms move? Why does the steric map repeat three times across the plot?
Select Ser 2 and set Auto-rotate to ψ. Which atoms move, and why does the map now repeat twice from bottom to top?
Which two bonds of this dipeptide turn whole parts of the backbone, and which two only spin an end group? What would have to be added to each end to give both serines a full φ and ψ?
Set φ to 170, then type −170. Which way does the arrow go, and why is the turn only 20° and not 340°?
Select Ser 1 and set ψ = 0°. Proteins often have ψ near 0°. Which contact does this model flag, and what does that tell you about hard-sphere models?
Select Ser 1, set ψ = −75° and the rotamer to +60°. Which hydrogen bond appears?
Turn on Compare with glycine under the Ramachandran plot. Why can glycine reach regions that serine cannot?
Turn on Peptide planes and drag ψ of Ser 1 and φ of Ser 2. Which six atoms stay together as one flat unit, and where are the hinges?
Switch between L and D. What happens to the steric map, and which two atoms change places in the Newman projections?

Show the definitions

φ (phi): the dihedral angle C′_i−1–N–Cα–C′, about the N–Cα bond. ψ (psi): N–Cα–C′–N_i+1, about the Cα–C′ bond. ω (omega): about the peptide bond C′–N, held near 180° (trans) by its partial double-bond character.
The model: the dipeptide Ser-Ser in its majority form at pH 7, ⁺H₃N–Ser–Ser–COO⁻. The amino end is protonated (NH₃⁺), the carboxyl end is ionized (COO⁻, drawn with two equal C–O bonds), and the two side-chain OH groups are neutral.
φ and ψ at the two ends: a dipeptide has one peptide bond, so only ψ of Ser 1 and φ of Ser 2 are full backbone angles. Ser 1 has no C′_i−1, so its φ is measured to one ammonium hydrogen, marked H¹; turning it only spins the NH₃⁺ group, and every 120° gives the same shape. Ser 2 has no N_i+1, so its ψ is measured to one carboxylate oxygen, marked O″; turning it only spins the COO⁻ group, and every 180° gives the same shape.
What can move: only φ, ψ and χ₁. Bond lengths, bond angles and the flat trans peptide unit are fixed at standard values (N–Cα–C′ = 110°). The peptide unit stays still on screen.
Newman projection: you look straight down one bond. The atom nearest you is the front atom (black bonds from the centre) and the atom behind it is the back atom (teal bonds from the circle).
Sign convention: the angle is the turn from the front reference bond to the back reference bond. Clockwise is positive, counterclockwise is negative, and the range is −180° to +180°.
Rotation arrow: drawn the short way round, so going from +170° to −170° is a 20° turn through 180°.
Auto-rotate: turns φ, ψ or both of the chosen residue steadily in the positive (clockwise) direction, passing from +180° to −180° and round again. With both on, the two angles turn at the same speed, so the point on the Ramachandran plot runs along a diagonal. A preset, a typed value, a click on the plot or taking hold of a moving slider switches it off.
Steric test: atoms are treated as hard spheres. Every pair of atoms whose distance changes when a bond rotates is compared with two limits, in Å (normal limit, then outer limit): H···H 2.0, 1.9; H···C, H···N, H···O 2.4, 2.2; N···N, N···O, O···O 2.7, 2.6; C···O 2.8, 2.7; C···N 2.9, 2.8; C···C 3.0, 2.9 (after Ramachandran, Ramakrishnan and Sasisekharan, 1963). Distances are rounded to 0.1 Å first. A hydrogen on N or O may come within 1.8 Å of an oxygen, because that is a hydrogen bond and not a clash.
Close contact and clash: a pair inside its normal limit is a close contact (orange). A pair inside its outer limit is a steric clash (pink).
Ramachandran plot: the shading is the same test run at every φ and ψ of the residue you are turning. Fully allowed: no close contacts. Outer limit: close contacts but no clash. Not allowed: at least one clash. Because each serine is at an end of the chain, these maps are not the textbook Ramachandran plot, which is for a residue with a peptide bond on both sides. Gold dots mark the typical values of such a residue in each secondary structure.
What the model leaves out: the attraction between the NH₃⁺ and COO⁻ charges, attraction between atoms in general, the energy of hydrogen bonds, water, and the small changes in bond angles that real molecules use.

Molecular model

Ser-Ser at pH 7. Drag to turn it; point at an atom to name it.

CNOHφ and ψ bondsclose contactsteric clashhydrogen bond

Looking down the bonds

Back atoms (teal) turn from the dashed start position to the new one. The red arrow shows the turn: clockwise is a positive angle.

Ramachandran plot

Click or drag to set φ and ψ of the residue you are turning. The shading is the steric map worked out from the model above.

Compare with glycine

Filled point: the residue you are turning. Ring: the other residue. Gold dots: typical values for a residue inside a protein (α, 3₁₀, β, PPII, α_L).