Homework #5

1. This is a known protein, and here are some of its descriptions:
HEADER
Cardiotoxin 12-MAR-94 2CRS 2CRS 2
COMPND
Cardiotoxin III (NMR, 13 STRUCTURES) 2CRS 3
SOURCE
Taiwan COBRA (NAJA NAJA ATRA) Venom 2CRS 4
EXPDTA
NMR 2CRS 5
AUTHOR
R.BHASKARAN,C.C.HUANG,K.D.CHANG,C.YU 2CRS 6
REVDAT
1 01-Nov-94 2CRS 0 2CRS 7
JRNL

AUTH R.BHASKARAN,C.C.HUANG,K.D.CHANG,C.YU

SWISS-PROT ANNOTATION:
ID
11557
DE
11557, 60 bases. number of residues: 60; molecular weight: 6.7 kdal
1 LKCNKLVPLF YKTCPAGKNL CYKMFMVATP KVPVKRGCID VCPKSSLLVK YVCCNTDRCN

2. Multiple sequence Alignment for proteins that share homology with Cardiotoxin III 3. Its secondary structure predicted by Garnier method. Osgusthorpe, and Robinson, J. Mol. Biol.,(1978) 120:97-120 Garnier plot of CARDIOTOXIN III (NMR, 13 STRUCTURES) 60 aa; DCH = 0, DCS = 0 . 10 . 20 . 30 . 40 . 50 . 60 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN helix H HHH HHHH sheet EEEEEEEEE EEEEE E E EEEEE EEEEEEEE turns TTT TTTT T T TT TTTT TTTTTT coil C C

4. CHARGE DISTRIBUTIONAL ANALYSIS

1  0+00+00000 0+00000+00 00+0000000 +000++000- 000+00000+ 000000-+00

A. CHARGE CLUSTERS.

Positive charge clusters (cmin = 13/30 or 18/45 or 22/60): none

Negative charge clusters: not evaluated (frequency of - < 5%, too low)

Mixed charge clusters (cmin = 15/30 or 20/45 or 25/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS.

High scoring positive charge segments:

score= 2.00 frequency= 0.183 ( KR )

score= 0.00 frequency= 0.000 ( BZX )

score= -1.00 frequency= 0.783 ( LAGSVTIPNFQYHMCW )

score= -2.00 frequency= 0.033 ( ED )

Minimal length of displayed segments set to: 20

M_0.01= 13.07 (cv= 7.77, lambda= 0.52686, k= 0.16371, x= 5.30;90% confidence interval for segment length: 23 +- 25) M_0.05= 9.97 (x= 2.20)

# of segments (>=20 residues) exceeding M_0.05: none High scoring negative charge segments:

score= 2.00 frequency= 0.033 ( ED )

score= 0.00 frequency= 0.000 ( BZX )

score= -1.00 frequency= 0.783 ( LAGSVTIPNFQYHMCW )

score= -2.00 frequency= 0.183 ( KR )

Minimal length of displayed segments set to: 20

M_0.01= 4.94 (cv= 2.54, lambda= 1.61122, k= 0.47671, x= 2.40;90% confidence interval for segment length: 3 +- 3) M_0.05= 3.92 (x= 1.38)

# of segments (>=20 residues) exceeding M_0.05: none High scoring mixed charge segments:

score= 1.00 frequency= 0.217 ( KEDR )

score= 0.00 frequency= 0.000 ( BZX )

score= -1.00 frequency= 0.783 ( LAGSVTIPNFQYHMCW )

Minimal length of displayed segments set to: 20

M_0.01= 6.07 (cv= 3.19, lambda= 1.28520, k= 0.40993, x= 2.89;90% confidence interval for segment length: 11 +- 9) M_0.05= 4.80 (x= 1.62)

# of segments (>=20 residues) exceeding M_0.05: none High scoring uncharged segments:

score= 1.00 frequency= 0.783 ( LAGSVTIPNFQYHMCW )

score= 0.00 frequency= 0.000 ( BZX )

score= -8.00 frequency= 0.217 ( KEDR )

M_0.01= 32.53 (cv= 20.56, lambda= 0.19916, k= 0.10900, x= 11.97; 90% confidence interval for segment length: 54 +- 44) M_0.05= 24.34 (x= 3.79)

# of segments (>=20 residues) exceeding M_0.05: none

C. CHARGE RUNS AND PATTERNS.

pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)|

lmin0 5 | 3 | 6 | 29 | 10 | 6 | 10 | 11 | 6 | 12 |

lmin1 6 | 4 | 7 | 36 | 12 | 7 | 12 | 14 | 8 | 14 |

lmin2 7 | 4 | 8 | 39 | 13 | 8 | 14 | 15 | 9 | 16 | There are no charge runs or patterns exceeding the given minimal lengths.

Run count statistics:

+ runs >= 3: 0

- runs >= 3: 0

0 runs >= 20: 0