UCSC BME 205 Fall 2008
Intro to Bioinformatics
CA and CB spacing
(Last Update:
13:31 PST 3 November 2008
)
Spacing of CA and CB atoms
I gathered some statistics from a large number of PDB files about CA
and CB spacing. The measurement of the peaks was not as cleanly
defined as I would like along the strands, so probably needs to be redone.
For helices
| Separation | CA-CA-distance | CB-CB distance |
| 1 | 3.8 | 5.3 |
| 2 | 5.43 | 7.3 |
| 3 | 5.13 | 5.7 |
| 4 | 6.16 | 6.3 |
| 5 | 8.67 | 9.7 |
| 6 | 9.93 | 10.9 |
| 7 | 10.49 | 10.6 |
| 8 | 12.3 | 12.7 |
| 9 | 14.2 | 15 |
| 10 | 15.3 | 15.7 |
For strands
| Separation | CA-CA-distance | CB-CB distance |
| 1 | 3.8 | 5.3 |
| 2 | 6.55 | 7.3 |
| 3 | 10 | 10.4 |
| 4 | 13.1 | 13 |
| 5 | 16 | 16 |
| 6 | 19.2 | 19 |
| 7 | 21.1 | 22 |
Between strands:
| type | CA-CA-distance | CB-CB distance |
| antiparallel bonded | 5.25 | 5.02 |
| antiparallel unbonded | 4.43 | 5.58 |
| parallel | 4.84 | 5.14 |
Questions about page content should be directed to
Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250
318 Physical Sciences Building
