Table 4.
Results of normal mode analysis for proteins with ‘non-interacting regions with PB change’
| PDBcode | Region of interest | Mobile/Rigid? | Whole/Embedded | Mode |
|---|---|---|---|---|
|
Cases with substantial change in non-interacting residues whereas interacting region has very less change | ||||
| 2HQS:A |
Interface region |
Highly mobile |
Whole |
5 |
| |
NIR_PBc far away (mainly 86-91) |
Highly mobile |
Whole |
3 |
| 1GHQ:A |
Interface region |
Highly mobile |
Whole |
1 |
| |
NIR_PBc far away (264-274) |
Partially mobile |
Embedded |
1 |
| 1OPH:A |
Interface region |
Highly mobile |
Whole |
1 |
| |
NIR_PBc far away (120-123) |
Mobile |
Embedded |
1 |
| |
NIR_PBc near interface (191-194) |
Mobile |
Embedded |
1 |
| 1KXP:D |
Interface region |
Rigid |
- |
- |
| |
NIR_PBc far away (314-325) |
Low mobility |
Embedded |
1 |
| |
NIR_PBc near interface (250-258) |
Rigid |
- |
- |
| 2BTF:A |
Interface region |
Rigid |
- |
- |
| |
NIR_PBc far away (156-158) |
Rigid |
- |
- |
| 1XD3:A |
Interface region |
Partly mobile |
Embedded |
2 |
| |
NIR_PBc near interface (89-93) |
Rigid |
- |
- |
| 1BVK:F |
Interface region |
Partly mobile |
Whole |
1 |
| |
NIR_PBc with interface (100-105) |
Mobile |
Embedded |
2 |
| 1B6C:B |
Interface region |
Rigid |
- |
- |
| |
NIR_PBc near interface (15-22) |
Mobile |
Whole |
3 |
| |
NIR_PBc near interface (152-157) |
Mobile |
Embedded |
4 |
|
Cases with substantial change in non-interacting residues near interacting region as well as in interacting region | ||||
| 1I2M:A |
Interface region |
Rigid |
- |
- |
| |
NIR_PBc far away (145-149) |
Mobile |
Embedded |
4 |
| NIR_PBc near interface (32-29) | Partly mobile | Embedded | 2 | |
*The abbreviations used are: IR - Interface regions, NIR_PBc – Non-interacting regions with PB change.
This table lists the results of the analysis using NMA regarding the intrinsic tendency for regions of interest to be rigid or mobile. The term ‘Embedded’ indicates that the region under consideration possesses intrinsic mobility as part of a segment, whereas the term ‘Whole’ indicates that the region is independent. NIR_PBc which are indicated to be mobile are shown in bold formatting and those indicated to be rigid are italicized. Note that the PDB codes and chains provided are for the bound form whereas the corresponding unbound form structure was used for NMA.