DSSP will define the secondary structure of proteins given a set of 3D coordinates. The output (with some added annotation) for the TATA-binding protein looks like this:
.-- sequential resnumber, including chain breaks as extra residues
| .-- original PDB resname, not nec. sequential, may contain letters
| | .-- amino acid sequence in one letter code
| | | .-- secondary structure summary based on columns 19-38
| | | | xxxxxxxxxxxxxxxxxxxx recommend columns for secstruc details
| | | | .-- 3-turns/helix
| | | | |.-- 4-turns/helix
| | | | ||.-- 5-turns/helix
| | | | |||.-- geometrical bend
| | | | ||||.-- chirality
| | | | |||||.-- beta bridge label
| | | | ||||||.-- beta bridge label
| | | | ||||||| .-- beta bridge partner resnum
| | | | ||||||| | .-- beta bridge partner resnum
| | | | ||||||| | |.-- beta sheet label
| | | | ||||||| | || .-- solvent accessibility
| | | | ||||||| | || |
....;....1....;....2....;....3....;....4....;....5....;....6....;....7..
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI
1 5 S 0 0 155 0, 0.0 107,-0.1 0, 0.0 106, 0.0 0.000 360.0 360.0 360.0 -26.1
2 6 K + 0 0 134 105,-0.2 2,-0.5 2, 0.0 106,-0.2 0.364 360.0 107.7-106.2 0.4
3 7 V + 0 0 33 104,-0.2 2,-0.3 105,-0.1 104,-0.2 -0.712 45.9 177.0 -86.4 123.8
4 8 K E -A 106 0A 123 102,-2.6 102,-1.3 -2,-0.5 2,-0.3 -0.881 13.8-176.2-123.4 154.0
5 9 L E -A 105 0A 14 -2,-0.3 2,-0.4 100,-0.2 100,-0.3 -0.906 7.6-175.7-151.5 118.2
6 10 R E -A 104 0A 169 98,-3.3 98,-2.6 -2,-0.3 -2, 0.0 -0.978 32.6-109.8-124.4 133.5
7 11 I E +A 103 0A 51 -2,-0.4 96,-0.3 96,-0.2 3,-0.1 -0.358 37.4 171.2 -56.5 133.5
8 12 E E - 0 0 59 94,-3.4 2,-0.3 1,-0.4 95,-0.2 0.590 63.5 -1.8-115.4 -31.3
9 13 N E -A 102 0A 36 93,-1.8 93,-2.9 58,-0.1 -1,-0.4 -0.971 49.9-160.1-165.0 145.0
10 14 I E -AB 101 66A 2 56,-2.3 56,-1.3 -2,-0.3 2,-0.5 -0.997 10.3-167.1-130.8 127.8
11 15 V E -A 100 0A 22 89,-3.3 88,-3.3 -2,-0.4 89,-2.4 -0.980 9.6-168.6-116.0 129.3
12 16 A E -AB 98 63A 0 51,-2.0 51,-2.6 -2,-0.5 2,-0.5 -0.969 19.9-136.3-123.7 138.8
13 17 S E -AB 97 62A 49 84,-2.9 84,-2.1 -2,-0.4 2,-0.4 -0.826 31.5-168.7 -87.7 128.2
14 18 V E -AB 96 61A 4 47,-3.4 47,-3.3 -2,-0.5 2,-0.5 -0.960 18.4-165.9-125.4 141.5
15 19 D E -AB 95 60A 22 80,-1.3 80,-2.4 -2,-0.4 45,-0.3 -0.958 7.4-179.7-126.4 108.1
Column 17 is the secondary structure category for each respective residue. In this case redidues 8 - 19 are considered in the EXTENDED conformation otherwise known as beta strand.
Return to Post-structure Analysis
Revised: Tuesday, 20-Oct-1998 14:50:19 EDT