| GRID manual | ||
|---|---|---|
| <<< Previous | Next >>> | |
Appendix C. Table of probe types
This is a table of JTYPE values which may be used in order to describe the hydrogen bonding geometry of the probe
JTYPE General Description Number of H-bonds Optimal angle
Value of Probe Donated Accepted between bonds
2 Planar NH2 2 120
3 sp3 NH3 etc. 3 109
4 sp3 hydroxyl. 1 2 109
8 sp2 carbonyl. 2 120
22 sp3 NH2 piperidine 2 109
28 Ether oxygen 2 109
34 Phenol hydroxy OH 1 1 120
34 OH in carboxy COOH 1 1 120
51 sp3 NH: 1 1 109
64 Phosphate oxygen 2 109
74 Flat fluorine 2 120
82 sp3 NH2 ethylamine 2 1 109
83 sp3 NH3 etc. 3 109
84 sp3 hydroxyl. 1 2 109
88 Phenolate O 2 120
91 The Hydrophobic Probe
92 The Amphipathic Probe
95 Water 2 2 109
96 Water 2 2 109
110-114 These Probes are metal cations |
Note that more than one JTYPE value may be provided for the same chemical group. Thus types 3 and 83 define the same Probe type, and so do types 4 and 84, and types 95 and 96.
Note also that the same value of JTYPE may be used for different chemical groups. In the above table type 34 is shown twice as an example of this. Type 34 can be either a phenolic or a carboxy OH group, and these two Probes would be distinguished by their other properties. The JTYPE value only defines the hydrogen-bonding geometry of the Probe.
Note that the oxygen with JTYPE=64 is not an sp3 ester oxygen joining a phosphate group to the remainder of its molecule, but an oxygen which is bonded to only one atom (e.g.: to the phosphorus of phosphate; arsenic of arsenate).
Note finally that 91, 92 and 110-119 are special Types.
| <<< Previous | Home | Next >>> |
| Table of types of target ATOMS/HETATMS | Up | GRUB table of recognized molecules |