BIOC 450- Bond length and stuff MT1

energies, pkas, and all the values you need to know

barrier for peptide isomerization

-20kcal/mol

C-N bond length in peptide bond

1.32 A

C-N bond length (normal)

1.47 A

Aspartic acid pka

3.9

Glutamic acid pka

4.3

Histidine pka

6.0

Cysteine pka

8.3

tyrosine pka

10.1

lysine pka

10.5

amine pka backbone

8

COOH pka backbone

3

Aspartate pka (burried in peptide)

2

glutamate pka (in peptide)

6

C-O bond length backbone

1.24 A

Calpha-C bond length backbone

1.51 A

N-C alpha bond length, backbone

1.45A

N-H bond length backbone

1.0 A

bond lenght range, electronegative atoms

2.4 to 4.0 A

typical energy, ionic interaction

3 kal/mol (between 1-5)

H bonding, typical bond length

2.6 to 3.2 A

typical energy, H bonding

1-3 kcal/mol

SIE

-3.7 kcal/mol

Phi

look along N-Calpha bond

Psi

look along Calpha- C’ bond

alpha helix angle values

• PHi = -57

• Psi= -47

alpha helix turn length / size

3.6 residues per turn/ 5.4 A pitch

alpha helix diameter

5 A

rise , alpha helix

1.5 A rise/ residue

charges, alpha helix

• +0.5 charge at N-term

• - 0.5 at C term

helix capping

• 4H unsatisfied

• polar residues at helix termini

strands size beta helix

• 5-12 residues

length, beta helix

3.3 A / residue

turn, beta helix

2.0 residue

turns, length

4 residues (usually)

stabilisation energy typical proteins

-5kcal/mol to -15kcal/mol