
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   82 (   82),  selected   82 , name T0340TS393_1-D1
# Molecule2: number of CA atoms   82 (  626),  selected   82 , name T0340_D1.pdb
# PARAMETERS: T0340TS393_1-D1.T0340_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       4      R       4          1.990
LGA    P       5      P       5          2.889
LGA    R       6      R       6          0.647
LGA    L       7      L       7          1.473
LGA    C       8      C       8          0.771
LGA    H       9      H       9          0.953
LGA    L      10      L      10          0.661
LGA    R      11      R      11          0.567
LGA    K      12      K      12          1.319
LGA    G      13      G      13          2.204
LGA    P      14      P      14          1.600
LGA    Q      15      Q      15          1.366
LGA    G      16      G      16          0.976
LGA    Y      17      Y      17          1.688
LGA    G      18      G      18          1.407
LGA    F      19      F      19          2.116
LGA    N      20      N      20          1.701
LGA    L      21      L      21          1.372
LGA    H      22      H      22          0.515
LGA    S      23      S      23          1.181
LGA    D      24      D      24          4.086
LGA    K      25      K      25          3.753
LGA    S      26      S      26          4.338
LGA    R      27      R      27          3.584
LGA    P      28      P      28          2.049
LGA    G      29      G      29          2.275
LGA    Q      30      Q      30          1.025
LGA    Y      31      Y      31          0.323
LGA    I      32      I      32          0.745
LGA    R      33      R      33          0.836
LGA    S      34      S      34          0.868
LGA    V      35      V      35          1.239
LGA    D      36      D      36          1.812
LGA    P      37      P      37          1.528
LGA    G      38      G      38          1.415
LGA    S      39      S      39          1.654
LGA    P      40      P      40          1.173
LGA    A      41      A      41          0.462
LGA    A      42      A      42          1.412
LGA    R      43      R      43          2.025
LGA    S      44      S      44          2.518
LGA    G      45      G      45          2.075
LGA    L      46      L      46          1.326
LGA    R      47      R      47          1.770
LGA    A      48      A      48          1.199
LGA    Q      49      Q      49          1.853
LGA    D      50      D      50          0.891
LGA    R      51      R      51          1.282
LGA    L      52      L      52          1.021
LGA    I      53      I      53          0.830
LGA    E      54      E      54          1.020
LGA    V      55      V      55          2.833
LGA    N      56      N      56          0.984
LGA    G      57      G      57          4.391
LGA    Q      58      Q      58          3.703
LGA    N      59      N      59          2.967
LGA    V      60      V      60          2.032
LGA    E      61      E      61          0.815
LGA    G      62      G      62          1.471
LGA    L      63      L      63          1.648
LGA    R      64      R      64          2.179
LGA    H      65      H      65          1.605
LGA    A      66      A      66          1.906
LGA    E      67      E      67          1.494
LGA    V      68      V      68          1.058
LGA    V      69      V      69          1.402
LGA    A      70      A      70          1.782
LGA    S      71      S      71          1.376
LGA    I      72      I      72          1.205
LGA    K      73      K      73          1.772
LGA    A      74      A      74          1.905
LGA    R      75      R      75          1.933
LGA    E      76      E      76          2.578
LGA    D      77      D      77          2.791
LGA    E      78      E      78          3.475
LGA    A      79      A      79          0.884
LGA    R      80      R      80          0.841
LGA    L      81      L      81          1.322
LGA    L      82      L      82          1.253
LGA    V      83      V      83          1.172
LGA    V      84      V      84          1.998
LGA    G      85      G      85          1.620

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   82   82    5.0     82    1.91   100.00     89.789     4.086

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.465734 * X  +   0.859013 * Y  +   0.212576 * Z  +   9.982052
  Y_new =  -0.689616 * X  +   0.502851 * Y  +  -0.521123 * Z  +  25.922203
  Z_new =  -0.554546 * X  +   0.096109 * Y  +   0.826584 * Z  +   9.148646 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.115752   -3.025840  [ DEG:     6.6321   -173.3679 ]
  Theta =   0.587817    2.553775  [ DEG:    33.6795    146.3205 ]
  Phi   =  -0.976805    2.164788  [ DEG:   -55.9668    124.0332 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0340TS393_1-D1                               
REMARK     2: T0340_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS393_1-D1.T0340_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   82   82   5.0   82   1.91  100.00  89.789
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS393_1-D1
PFRMAT TS
TARGET T0340
MODEL 1
PARENT N/A
ATOM      4  CA  ARG     4      16.291  39.425   8.796  1.00 25.00           C
ATOM      5  CA  PRO     5      14.106  37.946  11.594  1.00 25.00           C
ATOM      6  CA  ARG     6      10.566  36.551  11.160  1.00 25.00           C
ATOM      7  CA  LEU     7       8.838  34.467  13.894  1.00 25.00           C
ATOM      8  CA  CYS     8       6.395  31.589  13.809  1.00 25.00           C
ATOM      9  CA  HIS     9       5.538  31.049  17.533  1.00 25.00           C
ATOM     10  CA  LEU    10       3.692  27.827  16.571  1.00 25.00           C
ATOM     11  CA  ARG    11       1.556  26.300  19.246  1.00 25.00           C
ATOM     12  CA  LYS    12       1.498  22.485  19.740  1.00 25.00           C
ATOM     13  CA  GLY    13      -2.137  21.394  19.959  1.00 25.00           C
ATOM     14  CA  PRO    14      -2.778  17.713  19.244  1.00 25.00           C
ATOM     15  CA  GLN    15      -2.230  16.369  15.790  1.00 25.00           C
ATOM     16  CA  GLY    16       0.612  18.854  15.506  1.00 25.00           C
ATOM     17  CA  TYR    17       3.065  20.587  13.129  1.00 25.00           C
ATOM     18  CA  GLY    18       1.401  20.721   9.692  1.00 25.00           C
ATOM     19  CA  PHE    19       4.838  21.791   8.296  1.00 25.00           C
ATOM     20  CA  ASN    20       5.867  18.776   6.201  1.00 25.00           C
ATOM     21  CA  LEU    21       9.498  18.918   5.069  1.00 25.00           C
ATOM     22  CA  HIS    22      10.860  19.417   1.576  1.00 25.00           C
ATOM     23  CA  SER    23      14.215  19.564  -0.241  1.00 25.00           C
ATOM     24  CA  ASP    24      17.965  19.035  -0.102  1.00 25.00           C
ATOM     25  CA  LYS    25      19.121  17.001  -3.122  1.00 25.00           C
ATOM     26  CA  SER    26      21.470  19.962  -3.866  1.00 25.00           C
ATOM     27  CA  ARG    27      22.193  22.984  -1.612  1.00 25.00           C
ATOM     28  CA  PRO    28      20.937  23.435   1.960  1.00 25.00           C
ATOM     29  CA  GLY    29      17.485  24.768   0.925  1.00 25.00           C
ATOM     30  CA  GLN    30      15.246  23.493   3.724  1.00 25.00           C
ATOM     31  CA  TYR    31      11.576  24.398   3.242  1.00 25.00           C
ATOM     32  CA  ILE    32       7.874  25.133   3.157  1.00 25.00           C
ATOM     33  CA  ARG    33       5.758  22.630   1.308  1.00 25.00           C
ATOM     34  CA  SER    34       2.302  23.269   2.725  1.00 25.00           C
ATOM     35  CA  VAL    35       0.266  24.038   5.804  1.00 25.00           C
ATOM     36  CA  ASP    36      -2.682  21.573   5.871  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.215  24.453   5.728  1.00 25.00           C
ATOM     38  CA  GLY    38      -6.324  25.497   9.215  1.00 25.00           C
ATOM     39  CA  SER    39      -3.848  23.343  11.193  1.00 25.00           C
ATOM     40  CA  PRO    40      -1.190  24.809  13.497  1.00 25.00           C
ATOM     41  CA  ALA    41       1.263  26.210  10.912  1.00 25.00           C
ATOM     42  CA  ALA    42      -1.622  27.926   9.067  1.00 25.00           C
ATOM     43  CA  ARG    43      -2.856  29.443  12.360  1.00 25.00           C
ATOM     44  CA  SER    44      -0.112  31.920  13.128  1.00 25.00           C
ATOM     45  CA  GLY    45       1.001  33.090   9.629  1.00 25.00           C
ATOM     46  CA  LEU    46       3.866  31.283   7.911  1.00 25.00           C
ATOM     47  CA  ARG    47       3.338  31.787   4.174  1.00 25.00           C
ATOM     48  CA  ALA    48       4.066  28.618   2.102  1.00 25.00           C
ATOM     49  CA  GLN    49       7.158  29.828   0.232  1.00 25.00           C
ATOM     50  CA  ASP    50       9.074  30.227   3.474  1.00 25.00           C
ATOM     51  CA  ARG    51      12.799  29.597   3.762  1.00 25.00           C
ATOM     52  CA  LEU    52      13.467  27.508   6.854  1.00 25.00           C
ATOM     53  CA  ILE    53      16.602  28.545   8.695  1.00 25.00           C
ATOM     54  CA  GLU    54      17.108  28.770  12.468  1.00 25.00           C
ATOM     55  CA  VAL    55      16.485  27.549  15.987  1.00 25.00           C
ATOM     56  CA  ASN    56      15.001  25.906  19.140  1.00 25.00           C
ATOM     57  CA  GLY    57      18.578  24.959  19.960  1.00 25.00           C
ATOM     58  CA  GLN    58      18.449  22.970  16.676  1.00 25.00           C
ATOM     59  CA  ASN    59      19.578  24.236  13.226  1.00 25.00           C
ATOM     60  CA  VAL    60      18.527  23.949   9.616  1.00 25.00           C
ATOM     61  CA  GLU    61      21.334  25.597   7.593  1.00 25.00           C
ATOM     62  CA  GLY    62      22.959  22.217   7.195  1.00 25.00           C
ATOM     63  CA  LEU    63      20.899  19.061   7.563  1.00 25.00           C
ATOM     64  CA  ARG    64      19.451  16.619   5.006  1.00 25.00           C
ATOM     65  CA  HIS    65      15.729  17.360   5.561  1.00 25.00           C
ATOM     66  CA  ALA    66      15.066  14.222   7.655  1.00 25.00           C
ATOM     67  CA  GLU    67      17.094  15.695  10.549  1.00 25.00           C
ATOM     68  CA  VAL    68      15.106  18.959  10.314  1.00 25.00           C
ATOM     69  CA  VAL    69      11.821  16.990  10.364  1.00 25.00           C
ATOM     70  CA  ALA    70      13.004  15.049  13.446  1.00 25.00           C
ATOM     71  CA  SER    71      13.931  18.331  15.188  1.00 25.00           C
ATOM     72  CA  ILE    72      10.479  19.771  14.365  1.00 25.00           C
ATOM     73  CA  LYS    73       8.804  16.627  15.771  1.00 25.00           C
ATOM     74  CA  ALA    74      10.891  16.917  18.970  1.00 25.00           C
ATOM     75  CA  ARG    75      10.013  20.264  20.611  1.00 25.00           C
ATOM     76  CA  GLU    76       6.507  20.720  22.026  1.00 25.00           C
ATOM     77  CA  ASP    77       5.419  24.202  23.161  1.00 25.00           C
ATOM     78  CA  GLU    78       6.872  27.183  21.184  1.00 25.00           C
ATOM     79  CA  ALA    79       8.494  25.658  18.080  1.00 25.00           C
ATOM     80  CA  ARG    80      10.533  28.759  17.165  1.00 25.00           C
ATOM     81  CA  LEU    81      11.537  29.519  13.576  1.00 25.00           C
ATOM     82  CA  LEU    82      13.487  32.351  11.951  1.00 25.00           C
ATOM     83  CA  VAL    83      12.460  32.611   8.329  1.00 25.00           C
ATOM     84  CA  VAL    84      14.585  34.658   5.999  1.00 25.00           C
ATOM     85  CA  GLY    85      11.859  34.803   3.281  1.00 25.00           C
TER
END
