|
|
| Home | Wednesday, May 22, 2013 02:07 |
Definitions
Hydrogen bonds
| Parameter | Description | Unit |
|---|---|---|
| Hydrogen bond | Hydrogen bond XV - YW: a hydrogen bond between XV atom of base 1 (on the left, chain 1) and YW atom of base 2 (on the right, chain 2). For example, N1 - N3 of the base pair C-G is a hydrogen bond between the N1 atom of base C and the N3 atom of base G | |
| Bond distance | Length of the hydrogen bond XV - YW. | Angstrom |
Sugar conformation
| Parameter | Description | Unit |
|---|---|---|
| &nu0 | Torsion angle in the five-membered sugar ring: C4'-O4'-C1'-C2' | Degree |
| v1 | Torsion angle in the five-membered sugar ring: O4'-C1'-C2'-C3' | Degree |
| v2 | Torsion angle in the five-membered sugar ring: C1'-C2'-C3'-C4' | Degree |
| v3 | Torsion angle in the five-membered sugar ring: C3'-C4'-O4'-C1' | Degree |
| v4 | Torsion angle in the five-membered sugar ring: C4'-O4'-C1-C2' | Degree |
| P | The torsion angles v0-v4 can be combined, following the method of Altona and Sundaralingam, to yield two pseudorotation parameters, the phase angle P angle and the amplitude of sugar pseudorotation tm, which specify the location of the puckered atoms and the magnitude of puckering of the five-membered ring (see following formula)' | Degree |
| tm | See description under parameter P.' | Degree |
| Reference | C. Altona and M. Sundaralingam. Conformational analysis of the sugar ring in nucleoside and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc., 94(23):8205-8212, 1972. |
Backbone and sugar-base side-group torsion angles
| Parameter | Description | Unit |
|---|---|---|
| alpha | Backbone torsion angle: O3' (i-1)-P-O5'-C5' | Degree |
| beta | Backbone torsion angle: -P-O5'-C5'-C4' | Degree |
| gamma | Backbone torsion angle: O5'-C5'-C4'-C3' | Degree |
| delta | Backbone torsion angle: C5'-C4'-C3'-O3' | Degree |
| epsilon | Backbone torsion angle: C4'-C3'-O3'-P(i+1) | Degree |
| zeta | Backbone torsion angle: C3'-O3'-P(i+1)-O5'(i+1) | Degree |
| chi | Backbone torsion (1) for pyrimidine (Y): O4'-C1'-N1'-C2 (2) for purines*(R) O4'-C1'-Ni-C4 | Degree |
Base-pair virtual parameters
| Parameter | Description | Unit |
|---|---|---|
| Lambda (I) | Virtual angle N9-C1'-C1' | Degree |
| Lambda (II) | Virtual angle N1-C1'-C1' | Degree |
| C1'-C1' | Virtual bond length C1'-C1' in a Watson-Crick base pair. | Degree |
| RN9-YN1 | Virtual bond length connecting the R(N9)-Y(N1) atom pair in a Watson-Crick base pair (Y for pyrimidine, R for purine). | Angstrom |
| RC8-YC6 | Virtual bond length connecting the R(C9)-Y(C6) atom pair in a Watson-Crick base pair (Y for pyrimidine, R for purine) | Angstrom |
Base-pair rigid-body parameters
| Parameter | Description | Unit |
|---|---|---|
| Shear | Translation along x-axis in the base-pair reference frame. | Angstrom |
| Stretch | Translation along y-axis in the base-pair reference frame. | Angstrom |
| Stagger | Translation along z-axis in the base-pair reference frame. | Angstrom |
| Buckle | Rotation along x-axis in the base-pair reference frame. | Degree |
| Propeller | Rotation along y-axis in the base-pair reference frame. | Degree |
| Opening | Rotation along z-axis in the base-pair reference frame. | Degree |
