Probe atom types

a. Engh & Huber atom types

Atom types in X-SITE are first classified according to the Engh & Huber (1991) atom types shown below, with van der Waals radii taken from Pauling.

          van der
            Waals
No Type    radius  Description
-- ----    ------  ------------------------------------------------------
 1 NH1      1.65   Backbone NH, Arg NE, His ND1, NE1, Trp NE1
 2 C        1.76   Backbone C, Arg CZ, Asn CG, Asp CG, Gln CD, Glu CD
 3 CH1E     1.87   Backbone CA (exc. Gly), Ile CB, Leu CG, Thr CB, Val CB
 4 O        1.40   Backbone O, Asn OD1, Gln OE1
 5 CH2E     1.87   Tetrahedral CH2 (except CH2P,CH2G) All CB
 6 CH3E     1.87   Tetrahedral CH3
 7 CR1E     1.76   Aromatic CH (except CR1W, CRHH, CR1H)
 8 OH1      1.40   Alcohol OH (Ser OG, Thr OG1, Tyr OH)
 9 OC       1.40   Carboxyl O (Asp OD1, OD2, Glu OE1, OE2)
10 CH2G     1.87   Gly CA
11 CH2P     1.87   Pro CG, CD
12 NC2      1.65   Arg NH1, NH2
13 NH2      1.65   Asn ND2, Gln NE2
14 CR1W     1.76   Trp CZ2, CH2
15 CY2      1.76   Tyr CZ
16 SH1E     1.85   Cys S
17 CF       1.76   Phe CG
18 SM       1.85   Met S
19 CY       1.76   Tyr CG
20 CW       1.76   Trp CD2, CE2
21 CRHH     1.76   His CE1
22 NH3      1.50   Lys NZ
23 CR1H     1.76   His CD2
24 C5       1.76   His CG
25 N        1.65   Pro N
26 C5W      1.76   Trp CG
27 HOH      1.40   Water
-------------------------------------------------------------------------

b. Probe types

The above atom types are grouped into different "probe" types which are used for the X-SITE predictions. The default groupings are shown below. It is possible to change these, and indeed the atom definitions above, but requires regenerating all the X-SITE distributions.

Probe  Name                  Atom types
-----  --------------------  --------------------------------
  1    Backbone N             1
  2    Charged N             12 22
  3    Uncharged N           13 25
  4    Backbone O             4
  5    Carboxyl O             9
  6    Hydroxyl O             8
  7    Backbone C             2
  8    Aromatic C             7 14 21 23
  9    Aliphatic C            3  5  6 10 11 15 17 19 20 24 26
 10    All sulphurs          16 18
 11    Waters                27
-------------------------------------------------------------

The above combination of 11 different probe atom-types gives 36 different 3-atom fragment types in the 20 standard amino acids found in proteins.

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