soccer pt 2

tyrosine

10.1

cystine

8.2

lysine

10.5

histidine

6

arginine

12.5

glutamic acid

4.2

aspartic acid

3.6

carboxylic group

2.2

amino grup

9.4

6a

overall shape,helices as rods, sheets can be seen but not individual strands

3.5 A

Trace the backbone (3.5 < 5.4 Å for helix and <5Å between strands in sheet ; bulky side chains visible

2-2.5A

Side-chain shapes; similarly shaped side chains assigned using the protein 1 ̊ structure

1.5A

Atom shapes start to separate (C–C bond ≈ 1.5 Å)

1.2A

Individual atom positions

where does the a helix singal in the circular dichroism

two minima 208 and 222 nm peak at 195 nm , range 20 to -15

what B sheets signal in the circular dichromsm

one minimum 216-218 nm, and max at 195nm , 10 to -10

where does unstructed signal in the circular dichroism

mimumunm near 198 nm -5 to -0 , flat at 0 at 210

what amino acids favor helix

• Glu, Met, Ala, Leu

what amino acids favor strand

• Val, Ile, Tyr, Phe, Trp, Thr

what amino acids favor turn

• Gly, Pro, Asn, Asp, Ser

where do you see antiparallel beta sheets in ramchandran diagram

phi=-139, psi=+135

where do you see parallel beta sheets in ramchandran diagram

phi=-119, psi=+113

where do you see left handed alpha helix in ramchandran diagram

phi=+57 , psi=+47

where do you see right handed alpha helix in ramchandran diagram

phi= -57, psi= -47

cofactor

non-protein chemical compound or metallic ion required for a protein—usually an enzyme—to function correctly