example
Distribution of the nucleosides in CSD

PROSIT Result:

Pseudorotational Phase Angle (P), Puckering Amplitude(νmax), χ, and γ for Nucleosides/Nucleotides

Input_File= E:\webpages\BDLB84.pdb


ENGINEERED: YES
In the complex, 2 strands are identified.
The following table prints each strand in the order of 5'->3'.
Strand 1
No.ν0ν1ν2ν3ν4PνmaxχγTYPE
1, {1'=8}
-17.40
32.11
-33.99
24.76
-4.81
169.21
34.61
-103.92
-71.20
 Cyt, C2'-endo
2, {1'=27}
-21.57
32.14
-30.34
18.52
1.77
158.41
32.63
-89.21
48.74
 Gua, C2'-endo
3, {1'=49}
-13.06
-10.95
29.06
-37.29
31.53
38.41
37.09
-143.30
59.88
 Cyt, C4'-exo
4, {1'=68}
-19.96
32.93
-32.80
22.07
-1.50
163.81
34.16
-100.91
44.87
 Gua, C2'-endo
5, {1'=90}
-19.66
30.35
-29.10
18.43
0.73
160.16
30.94
-110.31
43.61
 Ade, C2'-endo
6, {1'=111}
-24.33
29.92
-24.14
10.59
8.55
144.89
29.50
-111.47
52.96
 Ade, C2'-endo
7, {1'=132}
-39.45
29.76
-8.82
-14.09
33.53
103.09
38.97
-133.37
56.68
 PYR, O4'-endo
8, {1'=152}
-40.99
28.80
-5.91
-17.84
36.07
98.36
40.62
-128.42
60.61
 PYR, O4'-endo
9, {1'=172}
-25.20
34.57
-31.32
17.17
4.90
153.77
34.91
-115.80
49.43
 Cyt, C2'-endo
10, {1'=191}
-35.23
45.18
-36.98
18.66
9.79
147.85
43.68
-79.85
38.79
 Gua, C2'-endo
11, {1'=213}
-20.01
32.39
-32.56
21.48
-1.05
163.40
33.97
-110.18
51.00
 Cyt, C2'-endo
12, {1'=232}
-30.03
11.62
9.88
-27.85
35.93
73.91
35.65
-106.53
48.49
 PUR, O4'-endo
Strand 2
No.ν0ν1ν2ν3ν4PνmaxχγTYPE
13, {1'=254}
-22.13
36.04
-36.77
24.63
-1.78
164.33
38.19
-108.02
64.57
 Cyt, C2'-endo
14, {1'=273}
-10.70
-6.73
20.16
-26.73
23.52
41.14
26.77
-138.05
42.10
 PUR, C4'-exo
15, {1'=295}
-8.44
-14.34
30.04
-35.79
27.75
31.94
35.40
-143.54
70.92
 Cyt, C3'-endo
16, {1'=314}
-14.68
29.78
-32.69
24.82
-6.57
172.60
32.96
-97.74
57.65
 Gua, C2'-endo
17, {1'=336}
-15.03
28.85
-31.40
22.87
-5.01
170.60
31.83
-106.19
45.81
 Ade, C2'-endo
18, {1'=357}
-25.79
33.26
-28.24
13.76
7.45
148.75
33.04
-109.25
51.53
 Ade, C2'-endo
19, {1'=378}
-35.93
25.88
-7.50
-12.82
30.32
102.40
34.91
-123.84
67.07
 PYR, O4'-endo
20, {1'=398}
-44.80
30.03
-4.44
-21.45
40.27
95.72
44.59
-127.92
55.75
 PYR, O4'-endo
21, {1'=418}
-34.43
27.80
-11.97
-7.53
26.44
110.96
33.47
-117.81
49.46
 Cyt, C1'-exo
22, {1'=437}
-29.40
41.68
-37.28
21.72
4.35
154.92
41.16
-91.66
44.54
 Gua, C2'-endo
23, {1'=459}
-1.42
-18.65
30.15
-31.62
20.88
20.81
32.25
-139.32
36.81
 Cyt, C3'-endo
24, {1'=478}
0.57
-22.66
34.79
-35.35
21.78
17.56
36.49
-141.92
52.44
 Gua, C3'-endo








Definition of Parameters:



ν0-ν4 : dihedral angles
PUR : purine type base (χ: O4'-C1'-N9-C4)


P : pseudorotation phase angle
PYR : pyrimidine type base (χ: O4'-C1'-N1-C2)


γ : O5'-C5'-C4'-C3'



Ade, Gua, Cyt, Thy refer to the bases in deoxyribonucleosides(tides), whilst ade, gua, cyt, ura refer to the bases in ribonucleosides(tides).


Alpha and Beta refer to alpha- or beta-nucleosides(tides).






Summary:


Number of Compounds read in: 1.

  • Compounds w/o 3D coordinates: 0.

  • Compounds w/ 3D coordinates: 1.

There are 24 nucleosides(tides) identified, of which

  • 12 have purine base and 

  • 12 have pyrimidine base.

    

  • # of nucleosides(tides) with Alpha-sugar: 0,

  • # of nucleosides(tides) with Beta-sugar: 22,

  • and # of nucleosides(tides) whose sugar configuration can't be determined: 2.



Normal termination of prosit.tcl at Tue Mar 23 09:13:23 EST 2004.