
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0363TS035_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS035_4-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11           -
LGA    -       -      Q      12           -
LGA    Q      12      I      13          4.550
LGA    I      13      N      14          5.672
LGA    N      14      I      15          2.298
LGA    I      15      E      16          2.523
LGA    E      16      I      17          3.250
LGA    I      17      A      18          1.240
LGA    A      18      Y      19          3.505
LGA    Y      19      A      20          2.033
LGA    A      20      F      21          4.112
LGA    F      21      P      22          2.717
LGA    P      22      -       -           -
LGA    E      23      -       -           -
LGA    R      24      -       -           -
LGA    Y      25      E      23          0.852
LGA    Y      26      R      24          1.021
LGA    L      27      Y      25          2.176
LGA    K      28      Y      26          1.539
LGA    S      29      L      27          2.774
LGA    F      30      K      28          2.151
LGA    Q      31      S      29          3.129
LGA    V      32      F      30          4.416
LGA    -       -      Q      31           -
LGA    D      33      V      32          1.919
LGA    -       -      D      33           -
LGA    E      34      E      34          3.140
LGA    G      35      G      35          2.547
LGA    I      36      I      36          1.464
LGA    T      37      T      37          1.975
LGA    V      38      V      38          3.238
LGA    Q      39      Q      39          2.445
LGA    T      40      T      40          1.906
LGA    A      41      A      41          2.810
LGA    I      42      I      42          3.032
LGA    T      43      T      43          2.724
LGA    Q      44      Q      44          2.769
LGA    S      45      S      45          2.734
LGA    G      46      G      46          1.799
LGA    I      47      I      47          1.502
LGA    L      48      L      48          1.805
LGA    S      49      S      49          2.391
LGA    Q      50      Q      50          2.721
LGA    F      51      F      51          2.358
LGA    P      52      P      52          3.398
LGA    E      53      E      53          3.370
LGA    I      54      I      54          2.957
LGA    -       -      D      55           -
LGA    D      55      L      56          5.216
LGA    L      56      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   46    5.0     41    2.88    51.22     59.675     1.376

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.125009 * X  +   0.855637 * Y  +  -0.502253 * Z  +  33.058388
  Y_new =   0.524756 * X  +   0.486643 * Y  +   0.698434 * Z  +  19.114849
  Z_new =   0.842024 * X  +  -0.176250 * Y  +  -0.509835 * Z  +   3.496650 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.808753    0.332840  [ DEG:  -160.9297     19.0703 ]
  Theta =  -1.001024   -2.140569  [ DEG:   -57.3544   -122.6456 ]
  Phi   =   1.804659   -1.336933  [ DEG:   103.3994    -76.6006 ]
 
# 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: T0363TS035_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS035_4-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   46   5.0   41   2.88   51.22  59.675
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS035_4-D1
PFRMAT TS
TARGET T0363
MODEL  4  REFINED
PARENT N/A
ATOM     41  N   ASN    11      16.050   9.100  15.613  1.00  0.00
ATOM     42  CA  ASN    11      15.472   8.030  14.822  1.00  0.00
ATOM     43  C   ASN    11      16.028   8.016  13.408  1.00  0.00
ATOM     44  O   ASN    11      16.009   6.992  12.727  1.00  0.00
ATOM     45  N   GLN    12      16.534   9.152  12.935  1.00  0.00
ATOM     46  CA  GLN    12      17.015   9.219  11.570  1.00  0.00
ATOM     47  C   GLN    12      18.011  10.351  11.381  1.00  0.00
ATOM     48  O   GLN    12      17.917  11.395  12.027  1.00  0.00
ATOM     49  N   ILE    13      18.986  10.170  10.495  1.00  0.00
ATOM     50  CA  ILE    13      19.972  11.212  10.279  1.00  0.00
ATOM     51  C   ILE    13      19.939  11.727   8.850  1.00  0.00
ATOM     52  O   ILE    13      19.927  10.951   7.896  1.00  0.00
ATOM     53  N   ASN    14      19.923  13.045   8.672  1.00  0.00
ATOM     54  CA  ASN    14      19.973  13.597   7.332  1.00  0.00
ATOM     55  C   ASN    14      21.091  14.614   7.186  1.00  0.00
ATOM     56  O   ASN    14      21.186  15.569   7.956  1.00  0.00
ATOM     57  N   ILE    15      21.962  14.433   6.197  1.00  0.00
ATOM     58  CA  ILE    15      23.083  15.340   6.042  1.00  0.00
ATOM     59  C   ILE    15      22.981  16.141   4.754  1.00  0.00
ATOM     60  O   ILE    15      22.992  15.583   3.657  1.00  0.00
ATOM     61  N   GLU    16      22.880  17.462   4.859  1.00  0.00
ATOM     62  CA  GLU    16      22.781  18.279   3.665  1.00  0.00
ATOM     63  C   GLU    16      24.118  18.903   3.300  1.00  0.00
ATOM     64  O   GLU    16      24.749  19.575   4.115  1.00  0.00
ATOM     65  N   ILE    17      24.578  18.696   2.070  1.00  0.00
ATOM     66  CA  ILE    17      25.872  19.222   1.681  1.00  0.00
ATOM     67  C   ILE    17      25.749  20.229   0.550  1.00  0.00
ATOM     68  O   ILE    17      25.179  19.938  -0.502  1.00  0.00
ATOM     69  N   ALA    18      26.279  21.433   0.739  1.00  0.00
ATOM     70  CA  ALA    18      26.180  22.441  -0.298  1.00  0.00
ATOM     71  C   ALA    18      27.498  23.173  -0.497  1.00  0.00
ATOM     72  O   ALA    18      28.124  23.625   0.461  1.00  0.00
ATOM     73  N   TYR    19      27.945  23.304  -1.742  1.00  0.00
ATOM     74  CA  TYR    19      29.169  24.038  -1.999  1.00  0.00
ATOM     75  C   TYR    19      28.882  25.441  -2.510  1.00  0.00
ATOM     76  O   TYR    19      28.032  25.641  -3.375  1.00  0.00
ATOM     77  N   ALA    20      29.587  26.441  -1.987  1.00  0.00
ATOM     78  CA  ALA    20      29.341  27.803  -2.417  1.00  0.00
ATOM     79  C   ALA    20      30.639  28.547  -2.687  1.00  0.00
ATOM     80  O   ALA    20      31.661  28.294  -2.052  1.00  0.00
ATOM     81  N   PHE    21      30.625  29.480  -3.636  1.00  0.00
ATOM     82  CA  PHE    21      31.827  30.236  -3.927  1.00  0.00
ATOM     83  C   PHE    21      31.509  31.550  -4.619  1.00  0.00
ATOM     84  O   PHE    21      30.564  31.644  -5.401  1.00  0.00
ATOM     85  N   PRO    22      32.290  32.592  -4.349  1.00  0.00
ATOM     86  CA  PRO    22      32.007  33.884  -4.944  1.00  0.00
ATOM     87  C   PRO    22      31.935  33.798  -6.461  1.00  0.00
ATOM     88  O   PRO    22      31.159  34.505  -7.100  1.00  0.00
ATOM     89  N   GLU    23      32.741  32.931  -7.066  1.00  0.00
ATOM     90  CA  GLU    23      32.745  32.831  -8.512  1.00  0.00
ATOM     91  C   GLU    23      32.277  31.462  -8.981  1.00  0.00
ATOM     92  O   GLU    23      31.932  31.274 -10.146  1.00  0.00
ATOM     93  N   ARG    24      32.254  30.482  -8.083  1.00  0.00
ATOM     94  CA  ARG    24      31.826  29.152  -8.473  1.00  0.00
ATOM     95  C   ARG    24      30.705  28.641  -7.584  1.00  0.00
ATOM     96  O   ARG    24      30.527  29.103  -6.457  1.00  0.00
ATOM     97  N   TYR    25      29.924  27.680  -8.070  1.00  0.00
ATOM     98  CA  TYR    25      28.849  27.141  -7.261  1.00  0.00
ATOM     99  C   TYR    25      28.777  25.626  -7.364  1.00  0.00
ATOM    100  O   TYR    25      28.923  25.055  -8.444  1.00  0.00
ATOM    101  N   TYR    26      28.549  24.943  -6.244  1.00  0.00
ATOM    102  CA  TYR    26      28.453  23.498  -6.284  1.00  0.00
ATOM    103  C   TYR    26      27.273  22.993  -5.468  1.00  0.00
ATOM    104  O   TYR    26      26.855  23.624  -4.498  1.00  0.00
ATOM    105  N   LEU    27      26.712  21.848  -5.843  1.00  0.00
ATOM    106  CA  LEU    27      25.746  21.196  -4.980  1.00  0.00
ATOM    107  C   LEU    27      26.180  19.785  -4.619  1.00  0.00
ATOM    108  O   LEU    27      26.647  19.028  -5.467  1.00  0.00
ATOM    109  N   LYS    28      26.035  19.403  -3.353  1.00  0.00
ATOM    110  CA  LYS    28      26.406  18.059  -2.954  1.00  0.00
ATOM    111  C   LYS    28      25.226  17.305  -2.361  1.00  0.00
ATOM    112  O   LYS    28      24.549  17.795  -1.458  1.00  0.00
ATOM    113  N   SER    29      24.955  16.101  -2.857  1.00  0.00
ATOM    114  CA  SER    29      23.901  15.297  -2.269  1.00  0.00
ATOM    115  C   SER    29      24.466  14.194  -1.387  1.00  0.00
ATOM    116  O   SER    29      25.312  13.410  -1.813  1.00  0.00
ATOM    117  N   PHE    30      24.009  14.111  -0.141  1.00  0.00
ATOM    118  CA  PHE    30      24.544  13.111   0.763  1.00  0.00
ATOM    119  C   PHE    30      23.481  12.595   1.718  1.00  0.00
ATOM    120  O   PHE    30      22.398  13.166   1.833  1.00  0.00
ATOM    121  N   GLN    31      23.768  11.504   2.423  1.00  0.00
ATOM    122  CA  GLN    31      22.783  10.948   3.331  1.00  0.00
ATOM    123  C   GLN    31      23.430  10.068   4.388  1.00  0.00
ATOM    124  O   GLN    31      24.568   9.626   4.238  1.00  0.00
ATOM    125  N   VAL    32      22.720   9.797   5.479  1.00  0.00
ATOM    126  CA  VAL    32      23.258   8.911   6.493  1.00  0.00
ATOM    127  C   VAL    32      22.193   7.979   7.046  1.00  0.00
ATOM    128  O   VAL    32      20.998   8.264   6.970  1.00  0.00
ATOM    129  N   ASP    33      22.600   6.847   7.613  1.00  0.00
ATOM    130  CA  ASP    33      21.630   5.926   8.172  1.00  0.00
ATOM    131  C   ASP    33      21.150   6.382   9.540  1.00  0.00
ATOM    132  O   ASP    33      21.883   7.028  10.288  1.00  0.00
ATOM    133  N   GLU    34      19.910   6.056   9.897  1.00  0.00
ATOM    134  CA  GLU    34      19.390   6.483  11.182  1.00  0.00
ATOM    135  C   GLU    34      20.227   5.947  12.331  1.00  0.00
ATOM    136  O   GLU    34      20.188   6.470  13.444  1.00  0.00
ATOM    137  N   GLY    35      21.002   4.893  12.087  1.00  0.00
ATOM    138  CA  GLY    35      21.804   4.322  13.152  1.00  0.00
ATOM    139  C   GLY    35      23.289   4.402  12.836  1.00  0.00
ATOM    140  O   GLY    35      24.084   3.591  13.310  1.00  0.00
ATOM    141  N   ILE    36      23.695   5.381  12.032  1.00  0.00
ATOM    142  CA  ILE    36      25.112   5.611  11.829  1.00  0.00
ATOM    143  C   ILE    36      25.478   7.071  12.047  1.00  0.00
ATOM    144  O   ILE    36      24.732   7.976  11.676  1.00  0.00
ATOM    145  N   THR    37      26.634   7.330  12.652  1.00  0.00
ATOM    146  CA  THR    37      27.116   8.695  12.739  1.00  0.00
ATOM    147  C   THR    37      27.448   9.260  11.367  1.00  0.00
ATOM    148  O   THR    37      27.888   8.539  10.473  1.00  0.00
ATOM    149  N   VAL    38      27.243  10.559  11.172  1.00  0.00
ATOM    150  CA  VAL    38      27.547  11.156   9.886  1.00  0.00
ATOM    151  C   VAL    38      29.008  10.964   9.512  1.00  0.00
ATOM    152  O   VAL    38      29.332  10.598   8.383  1.00  0.00
ATOM    153  N   GLN    39      29.919  11.209  10.449  1.00  0.00
ATOM    154  CA  GLN    39      31.328  11.044  10.151  1.00  0.00
ATOM    155  C   GLN    39      31.619   9.672   9.562  1.00  0.00
ATOM    156  O   GLN    39      32.373   9.541   8.599  1.00  0.00
ATOM    157  N   THR    40      31.027   8.624  10.128  1.00  0.00
ATOM    158  CA  THR    40      31.262   7.291   9.606  1.00  0.00
ATOM    159  C   THR    40      30.773   7.156   8.173  1.00  0.00
ATOM    160  O   THR    40      31.450   6.581   7.322  1.00  0.00
ATOM    161  N   ALA    41      29.589   7.684   7.876  1.00  0.00
ATOM    162  CA  ALA    41      29.074   7.593   6.524  1.00  0.00
ATOM    163  C   ALA    41      29.945   8.356   5.540  1.00  0.00
ATOM    164  O   ALA    41      30.274   7.857   4.465  1.00  0.00
ATOM    165  N   ILE    42      30.336   9.580   5.885  1.00  0.00
ATOM    166  CA  ILE    42      31.170  10.355   4.988  1.00  0.00
ATOM    167  C   ILE    42      32.443   9.609   4.623  1.00  0.00
ATOM    168  O   ILE    42      32.894   9.642   3.480  1.00  0.00
ATOM    169  N   THR    43      33.050   8.922   5.588  1.00  0.00
ATOM    170  CA  THR    43      34.213   8.113   5.280  1.00  0.00
ATOM    171  C   THR    43      33.916   7.095   4.191  1.00  0.00
ATOM    172  O   THR    43      34.686   6.931   3.246  1.00  0.00
ATOM    173  N   GLN    44      32.793   6.390   4.301  1.00  0.00
ATOM    174  CA  GLN    44      32.458   5.401   3.295  1.00  0.00
ATOM    175  C   GLN    44      32.163   6.047   1.951  1.00  0.00
ATOM    176  O   GLN    44      32.347   5.436   0.899  1.00  0.00
ATOM    177  N   SER    45      31.703   7.294   1.957  1.00  0.00
ATOM    178  CA  SER    45      31.427   7.970   0.704  1.00  0.00
ATOM    179  C   SER    45      32.657   8.689   0.173  1.00  0.00
ATOM    180  O   SER    45      32.623   9.308  -0.889  1.00  0.00
ATOM    181  N   GLY    46      33.768   8.625   0.902  1.00  0.00
ATOM    182  CA  GLY    46      34.956   9.340   0.478  1.00  0.00
ATOM    183  C   GLY    46      34.778  10.845   0.609  1.00  0.00
ATOM    184  O   GLY    46      35.506  11.626  -0.002  1.00  0.00
ATOM    185  N   ILE    47      33.809  11.282   1.408  1.00  0.00
ATOM    186  CA  ILE    47      33.680  12.700   1.682  1.00  0.00
ATOM    187  C   ILE    47      34.874  13.230   2.461  1.00  0.00
ATOM    188  O   ILE    47      35.438  14.270   2.126  1.00  0.00
ATOM    189  N   LEU    48      35.281  12.527   3.514  1.00  0.00
ATOM    190  CA  LEU    48      36.425  12.975   4.284  1.00  0.00
ATOM    191  C   LEU    48      37.709  12.902   3.473  1.00  0.00
ATOM    192  O   LEU    48      38.610  13.724   3.635  1.00  0.00
ATOM    193  N   SER    49      37.819  11.918   2.585  1.00  0.00
ATOM    194  CA  SER    49      39.023  11.795   1.786  1.00  0.00
ATOM    195  C   SER    49      39.152  12.935   0.788  1.00  0.00
ATOM    196  O   SER    49      40.249  13.417   0.512  1.00  0.00
ATOM    197  N   GLN    50      38.034  13.388   0.226  1.00  0.00
ATOM    198  CA  GLN    50      38.093  14.482  -0.723  1.00  0.00
ATOM    199  C   GLN    50      38.018  15.831  -0.027  1.00  0.00
ATOM    200  O   GLN    50      38.524  16.834  -0.528  1.00  0.00
ATOM    201  N   PHE    51      37.387  15.885   1.143  1.00  0.00
ATOM    202  CA  PHE    51      37.190  17.161   1.803  1.00  0.00
ATOM    203  C   PHE    51      37.687  17.132   3.238  1.00  0.00
ATOM    204  O   PHE    51      36.900  17.093   4.183  1.00  0.00
ATOM    205  N   PRO    52      39.003  17.148   3.433  1.00  0.00
ATOM    206  CA  PRO    52      39.536  17.134   4.782  1.00  0.00
ATOM    207  C   PRO    52      39.077  18.345   5.577  1.00  0.00
ATOM    208  O   PRO    52      38.948  18.291   6.799  1.00  0.00
ATOM    209  N   GLU    53      38.821  19.463   4.903  1.00  0.00
ATOM    210  CA  GLU    53      38.171  20.576   5.564  1.00  0.00
ATOM    211  C   GLU    53      36.657  20.479   5.467  1.00  0.00
ATOM    212  O   GLU    53      36.037  21.081   4.591  1.00  0.00
ATOM    213  N   ILE    54      36.031  19.721   6.363  1.00  0.00
ATOM    214  CA  ILE    54      34.583  19.638   6.358  1.00  0.00
ATOM    215  C   ILE    54      34.016  19.675   7.767  1.00  0.00
ATOM    216  O   ILE    54      34.437  18.919   8.641  1.00  0.00
ATOM    217  N   ASP    55      33.049  20.553   8.017  1.00  0.00
ATOM    218  CA  ASP    55      32.419  20.585   9.322  1.00  0.00
ATOM    219  C   ASP    55      31.085  19.858   9.319  1.00  0.00
ATOM    220  O   ASP    55      30.049  20.433   8.991  1.00  0.00
ATOM    221  N   LEU    56      31.082  18.578   9.682  1.00  0.00
ATOM    222  CA  LEU    56      29.852  17.813   9.632  1.00  0.00
ATOM    223  C   LEU    56      28.777  18.424  10.517  1.00  0.00
ATOM    224  O   LEU    56      27.593  18.402  10.184  1.00  0.00
TER
END
