
#######################################################
#                                                     #
#                        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   52 (  208),  selected   52 , name T0349TS125_3u-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS125_3u-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    R       2      M       1          4.589
LGA    E       3      R       2          2.282
LGA    L       4      E       3          1.504
LGA    L       5      L       4          1.035
LGA    R       6      L       5          1.757
LGA    -       -      R       6           -
LGA    T       7      T       7           #
LGA    N       8      N       8           -
LGA    D       9      D       9          3.007
LGA    A      10      A      10          4.289
LGA    V      11      V      11          1.565
LGA    L      12      L      12          1.605
LGA    L      13      L      13          1.117
LGA    S      14      S      14          0.640
LGA    A      15      A      15          0.910
LGA    V      16      V      16          0.611
LGA    G      17      G      17          0.214
LGA    A      18      A      18          0.430
LGA    L      19      L      19          0.574
LGA    L      20      L      20          0.321
LGA    D      21      D      21          0.898
LGA    G      22      G      22          1.564
LGA    A      23      A      23          1.424
LGA    D      24      D      24          0.717
LGA    I      25      I      25          0.550
LGA    G      26      G      26          1.631
LGA    H      27      H      27          1.941
LGA    L      28      L      28          3.927
LGA    V      29      V      29           #
LGA    -       -      P      45           -
LGA    R      46      R      46          4.352
LGA    R      47      R      47          2.241
LGA    V      48      V      48          2.556
LGA    L      49      L      49          2.643
LGA    V      50      V      50          1.287
LGA    D      53      H      51          2.261
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    D      54      D      54          1.776
LGA    L      55      L      55          1.490
LGA    A      56      A      56          0.846
LGA    G      57      G      57          0.587
LGA    A      58      A      58          0.660
LGA    R      59      R      59          0.385
LGA    R      60      R      60          0.712
LGA    L      61      L      61          0.581
LGA    L      62      L      62          0.564
LGA    T      63      T      63          0.741
LGA    D      64      D      64          1.606
LGA    A      65      A      65          3.136
LGA    -       -      G      66           -
LGA    G      66      L      67          1.400
LGA    L      67      A      68          2.788
LGA    A      68      H      69          1.553
LGA    -       -      E      70           -
LGA    L      71      L      71          1.207
LGA    R      72      R      72          1.867

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   52   57    5.0     48    1.93    83.33     72.974     2.363

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.897146 * X  +  -0.408993 * Y  +   0.166895 * Z  +   1.256714
  Y_new =  -0.383479 * X  +  -0.908635 * Y  +  -0.165309 * Z  +   3.387770
  Z_new =   0.219257 * X  +   0.084306 * Y  +  -0.972018 * Z  +   2.852433 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.055077   -0.086516  [ DEG:   175.0430     -4.9570 ]
  Theta =  -0.221053   -2.920539  [ DEG:   -12.6654   -167.3346 ]
  Phi   =  -0.403938    2.737654  [ DEG:   -23.1440    156.8560 ]
 
# 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: T0349TS125_3u-D1                              
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS125_3u-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   57   5.0   48   1.93   83.33  72.974
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS125_3u-D1
PFRMAT   TS
TARGET   T0349
MODEL    3  UNREFINED
PARENT   2f06a1   
ATOM     20  N   MET     1       8.635  12.475 -12.543    1.00  0.50
ATOM     21  CA  MET     1       8.898  11.302 -11.718    1.00  0.50
ATOM     22  C   MET     1       8.295  11.485 -10.328    1.00  0.50
ATOM     23  O   MET     1       8.615  12.417  -9.572    1.00  0.50
ATOM     27  N   ARG     2       7.393  10.571  -9.998    1.00  0.50
ATOM     28  CA  ARG     2       6.666  10.605  -8.764    1.00  0.50
ATOM     29  C   ARG     2       7.175   9.581  -7.749    1.00  0.50
ATOM     30  O   ARG     2       7.754   8.567  -8.079    1.00  0.50
ATOM     32  N   GLU     3       6.929   9.880  -6.484    1.00  0.50
ATOM     33  CA  GLU     3       7.259   8.990  -5.399    1.00  0.50
ATOM     34  C   GLU     3       6.030   8.128  -5.111    1.00  0.50
ATOM     35  O   GLU     3       4.918   8.634  -4.861    1.00  0.50
ATOM     41  N   LEU     4       6.228   6.818  -5.215    1.00  0.50
ATOM     42  CA  LEU     4       5.243   5.878  -4.772    1.00  0.50
ATOM     43  C   LEU     4       5.668   5.266  -3.442    1.00  0.50
ATOM     44  O   LEU     4       6.809   4.849  -3.264    1.00  0.50
ATOM     50  N   LEU     5       4.766   5.197  -2.491    1.00  0.50
ATOM     51  CA  LEU     5       5.071   4.452  -1.270    1.00  0.50
ATOM     52  C   LEU     5       4.780   2.966  -1.472    1.00  0.50
ATOM     53  O   LEU     5       3.734   2.563  -2.002    1.00  0.50
ATOM     58  N   ARG     6       5.720   2.154  -1.022    1.00  0.50
ATOM     59  CA  ARG     6       5.494   0.740  -0.864    1.00  0.50
ATOM     60  C   ARG     6       5.547   0.393   0.597    1.00  0.50
ATOM     61  O   ARG     6       6.611   0.496   1.198    1.00  0.50
ATOM     91  N   THR     7       2.110  -6.536   7.347    1.00  0.50
ATOM     92  CA  THR     7       2.263  -7.838   7.962    1.00  0.50
ATOM     93  C   THR     7       0.901  -8.467   8.346    1.00  0.50
ATOM     94  O   THR     7      -0.129  -7.892   8.052    1.00  0.50
ATOM    100  N   ASN     8       0.855  -9.656   8.938    1.00  0.50
ATOM    101  CA  ASN     8      -0.457 -10.110   9.522    1.00  0.50
ATOM    102  C   ASN     8      -1.506 -10.336   8.350    1.00  0.50
ATOM    103  O   ASN     8      -1.203 -11.125   7.455    1.00  0.50
ATOM    108  N   ASP     9      -2.680  -9.672   8.321    1.00  0.50
ATOM    109  CA  ASP     9      -3.643  -9.651   7.131    1.00  0.50
ATOM    110  C   ASP     9      -4.985  -8.914   7.419    1.00  0.50
ATOM    111  O   ASP     9      -5.859  -8.889   6.541    1.00  0.50
ATOM    117  N   ALA    10      -5.115  -8.277   8.602    1.00  0.50
ATOM    118  CA  ALA    10      -6.349  -8.456   9.430    1.00  0.50
ATOM    119  C   ALA    10      -7.074  -7.373  10.314    1.00  0.50
ATOM    120  O   ALA    10      -7.973  -7.786  11.061    1.00  0.50
ATOM    123  N   VAL    11      -6.661  -6.107  10.438    1.00  0.50
ATOM    124  CA  VAL    11      -5.316  -5.752  10.760    1.00  0.50
ATOM    125  C   VAL    11      -4.735  -4.414  10.380    1.00  0.50
ATOM    126  O   VAL    11      -5.273  -3.327  10.652    1.00  0.50
ATOM    127  N   LEU    12      -3.584  -4.571   9.770    1.00  0.50
ATOM    128  CA  LEU    12      -2.593  -3.560   9.587    1.00  0.50
ATOM    129  C   LEU    12      -2.944  -2.619   8.491    1.00  0.50
ATOM    130  O   LEU    12      -2.509  -1.482   8.534    1.00  0.50
ATOM    138  N   LEU    13      -3.724  -3.076   7.508    1.00  0.50
ATOM    139  CA  LEU    13      -4.104  -2.163   6.421    1.00  0.50
ATOM    140  C   LEU    13      -4.998  -1.000   6.970    1.00  0.50
ATOM    141  O   LEU    13      -4.867   0.173   6.549    1.00  0.50
ATOM    146  N   SER    14      -5.877  -1.340   7.902    1.00  0.50
ATOM    147  CA  SER    14      -6.727  -0.324   8.496    1.00  0.50
ATOM    148  C   SER    14      -5.910   0.705   9.293    1.00  0.50
ATOM    149  O   SER    14      -6.041   1.923   9.064    1.00  0.50
ATOM    153  N   ALA    15      -5.035   0.216  10.158    1.00  0.50
ATOM    154  CA  ALA    15      -4.076   1.092  10.830    1.00  0.50
ATOM    155  C   ALA    15      -3.270   1.967   9.890    1.00  0.50
ATOM    156  O   ALA    15      -3.061   3.099  10.231    1.00  0.50
ATOM    162  N   VAL    16      -2.812   1.469   8.724    1.00  0.50
ATOM    163  CA  VAL    16      -2.032   2.300   7.790    1.00  0.50
ATOM    164  C   VAL    16      -2.902   3.411   7.256    1.00  0.50
ATOM    165  O   VAL    16      -2.477   4.579   7.074    1.00  0.50
ATOM    169  N   GLY    17      -4.121   3.072   6.923    1.00  0.50
ATOM    170  CA  GLY    17      -4.995   4.129   6.372    1.00  0.50
ATOM    171  C   GLY    17      -5.386   5.122   7.463    1.00  0.50
ATOM    172  O   GLY    17      -5.626   6.305   7.160    1.00  0.50
ATOM    176  N   ALA    18      -5.451   4.634   8.686    1.00  0.50
ATOM    177  CA  ALA    18      -5.614   5.508   9.878    1.00  0.50
ATOM    178  C   ALA    18      -4.440   6.476  10.173    1.00  0.50
ATOM    179  O   ALA    18      -4.671   7.647  10.433    1.00  0.50
ATOM    185  N   LEU    19      -3.209   5.993  10.226    1.00  0.50
ATOM    186  CA  LEU    19      -1.999   6.863  10.143    1.00  0.50
ATOM    187  C   LEU    19      -2.068   7.973   9.092    1.00  0.50
ATOM    188  O   LEU    19      -1.845   9.140   9.408    1.00  0.50
ATOM    192  N   LEU    20      -2.379   7.625   7.858    1.00  0.50
ATOM    193  CA  LEU    20      -2.479   8.612   6.804    1.00  0.50
ATOM    194  C   LEU    20      -3.637   9.587   6.970    1.00  0.50
ATOM    195  O   LEU    20      -3.433  10.776   6.735    1.00  0.50
ATOM    200  N   ASP    21      -4.827   9.104   7.378    1.00  0.50
ATOM    201  CA  ASP    21      -5.974   9.963   7.680    1.00  0.50
ATOM    202  C   ASP    21      -5.657  11.004   8.746    1.00  0.50
ATOM    203  O   ASP    21      -6.135  12.159   8.680    1.00  0.50
ATOM    205  N   GLY    22      -4.931  10.579   9.780    1.00  0.50
ATOM    206  CA  GLY    22      -4.649  11.458  10.921    1.00  0.50
ATOM    207  C   GLY    22      -3.767  12.659  10.482    1.00  0.50
ATOM    208  O   GLY    22      -3.823  13.751  11.095    1.00  0.50
ATOM    214  N   ALA    23      -2.965  12.453   9.425    1.00  0.50
ATOM    215  CA  ALA    23      -2.114  13.503   8.930    1.00  0.50
ATOM    216  C   ALA    23      -2.795  14.394   7.863    1.00  0.50
ATOM    217  O   ALA    23      -2.146  15.347   7.332    1.00  0.50
ATOM    223  N   ASP    24      -4.074  14.105   7.568    1.00  0.50
ATOM    224  CA  ASP    24      -4.852  14.713   6.470    1.00  0.50
ATOM    225  C   ASP    24      -4.103  14.488   5.157    1.00  0.50
ATOM    226  O   ASP    24      -3.963  15.403   4.341    1.00  0.50
ATOM    231  N   ILE    25      -3.604  13.252   4.984    1.00  0.50
ATOM    232  CA  ILE    25      -2.949  12.838   3.773    1.00  0.50
ATOM    233  C   ILE    25      -3.977  12.092   2.982    1.00  0.50
ATOM    234  O   ILE    25      -4.569  11.113   3.452    1.00  0.50
ATOM    239  N   GLY    26      -4.235  12.606   1.779    1.00  0.50
ATOM    240  CA  GLY    26      -5.142  11.959   0.820    1.00  0.50
ATOM    241  C   GLY    26      -4.432  10.880  -0.010    1.00  0.50
ATOM    242  O   GLY    26      -3.303  11.065  -0.542    1.00  0.50
ATOM    247  N   HIS    27      -5.149   9.787  -0.207    1.00  0.50
ATOM    248  CA  HIS    27      -4.733   8.730  -1.110    1.00  0.50
ATOM    249  C   HIS    27      -5.275   9.024  -2.514    1.00  0.50
ATOM    250  O   HIS    27      -6.448   9.227  -2.678    1.00  0.50
ATOM    255  N   LEU    28      -4.423   9.029  -3.525    1.00  0.50
ATOM    256  CA  LEU    28      -4.821   9.262  -4.930    1.00  0.50
ATOM    257  C   LEU    28      -5.087   8.002  -5.699    1.00  0.50
ATOM    258  O   LEU    28      -5.939   7.956  -6.570    1.00  0.50
ATOM    261  N   VAL    29      -4.278   7.012  -5.391    1.00  0.50
ATOM    262  CA  VAL    29      -4.194   5.764  -6.153    1.00  0.50
ATOM    263  C   VAL    29      -3.479   4.765  -5.277    1.00  0.50
ATOM    264  O   VAL    29      -2.424   5.066  -4.671    1.00  0.50
ATOM    346  N   ARG    46       1.163  -2.648   0.140    1.00  0.50
ATOM    347  CA  ARG    46       0.419  -1.523  -0.342    1.00  0.50
ATOM    348  C   ARG    46       1.317  -0.606  -1.157    1.00  0.50
ATOM    349  O   ARG    46       2.202   0.053  -0.615    1.00  0.50
ATOM    354  N   ARG    47       1.021  -0.531  -2.434    1.00  0.50
ATOM    355  CA  ARG    47       1.590   0.475  -3.292    1.00  0.50
ATOM    356  C   ARG    47       0.647   1.662  -3.371    1.00  0.50
ATOM    357  O   ARG    47      -0.555   1.489  -3.596    1.00  0.50
ATOM    365  N   VAL    48       1.182   2.859  -3.211    1.00  0.50
ATOM    366  CA  VAL    48       0.353   3.968  -2.842    1.00  0.50
ATOM    367  C   VAL    48       0.867   5.255  -3.455    1.00  0.50
ATOM    368  O   VAL    48       2.038   5.584  -3.324    1.00  0.50
ATOM    369  N   LEU    49      -0.035   5.963  -4.120    1.00  0.50
ATOM    370  CA  LEU    49       0.162   7.383  -4.472    1.00  0.50
ATOM    371  C   LEU    49      -0.596   8.266  -3.471    1.00  0.50
ATOM    372  O   LEU    49      -1.814   8.155  -3.357    1.00  0.50
ATOM    377  N   VAL    50       0.125   9.104  -2.712    1.00  0.50
ATOM    378  CA  VAL    50      -0.512   9.958  -1.713    1.00  0.50
ATOM    379  C   VAL    50      -0.291  11.478  -2.014    1.00  0.50
ATOM    380  O   VAL    50       0.524  11.815  -2.893    1.00  0.50
ATOM    384  N   ASP    53      -0.977  12.352  -1.266    1.00  0.50
ATOM    385  CA  ASP    53      -0.907  13.825  -1.501    1.00  0.50
ATOM    386  C   ASP    53       0.409  14.504  -1.058    1.00  0.50
ATOM    387  O   ASP    53       0.790  15.557  -1.599    1.00  0.50
ATOM    390  N   ASP    54       1.087  13.893  -0.085    1.00  0.50
ATOM    391  CA  ASP    54       2.363  14.372   0.429    1.00  0.50
ATOM    392  C   ASP    54       3.251  13.156   0.786    1.00  0.50
ATOM    393  O   ASP    54       3.222  12.676   1.929    1.00  0.50
ATOM    398  N   LEU    55       4.007  12.621  -0.202    1.00  0.50
ATOM    399  CA  LEU    55       4.758  11.377   0.096    1.00  0.50
ATOM    400  C   LEU    55       5.818  11.462   1.218    1.00  0.50
ATOM    401  O   LEU    55       5.961  10.509   1.975    1.00  0.50
ATOM    405  N   ALA    56       6.482  12.602   1.373    1.00  0.50
ATOM    406  CA  ALA    56       7.522  12.766   2.399    1.00  0.50
ATOM    407  C   ALA    56       6.930  12.798   3.822    1.00  0.50
ATOM    408  O   ALA    56       7.469  12.159   4.734    1.00  0.50
ATOM    413  N   GLY    57       5.833  13.531   3.981    1.00  0.50
ATOM    414  CA  GLY    57       5.120  13.587   5.269    1.00  0.50
ATOM    415  C   GLY    57       4.557  12.191   5.593    1.00  0.50
ATOM    416  O   GLY    57       4.654  11.737   6.737    1.00  0.50
ATOM    422  N   ALA    58       3.969  11.533   4.586    1.00  0.50
ATOM    423  CA  ALA    58       3.440  10.181   4.731    1.00  0.50
ATOM    424  C   ALA    58       4.491   9.171   5.117    1.00  0.50
ATOM    425  O   ALA    58       4.282   8.403   6.093    1.00  0.50
ATOM    427  N   ARG    59       5.602   9.176   4.393    1.00  0.50
ATOM    428  CA  ARG    59       6.738   8.331   4.759    1.00  0.50
ATOM    429  C   ARG    59       7.214   8.498   6.216    1.00  0.50
ATOM    430  O   ARG    59       7.462   7.522   6.925    1.00  0.50
ATOM    439  N   ARG    60       7.374   9.725   6.673    1.00  0.50
ATOM    440  CA  ARG    60       7.901   9.895   8.036    1.00  0.50
ATOM    441  C   ARG    60       6.875   9.470   9.118    1.00  0.50
ATOM    442  O   ARG    60       7.268   8.901  10.148    1.00  0.50
ATOM    448  N   LEU    61       5.586   9.744   8.878    1.00  0.50
ATOM    449  CA  LEU    61       4.497   9.288   9.744    1.00  0.50
ATOM    450  C   LEU    61       4.453   7.733   9.878    1.00  0.50
ATOM    451  O   LEU    61       4.386   7.149  10.999    1.00  0.50
ATOM    453  N   LEU    62       4.536   7.068   8.740    1.00  0.50
ATOM    454  CA  LEU    62       4.614   5.630   8.708    1.00  0.50
ATOM    455  C   LEU    62       5.831   5.056   9.435    1.00  0.50
ATOM    456  O   LEU    62       5.644   4.151  10.236    1.00  0.50
ATOM    461  N   THR    63       7.050   5.554   9.171    1.00  0.50
ATOM    462  CA  THR    63       8.265   5.142   9.939    1.00  0.50
ATOM    463  C   THR    63       8.121   5.364  11.450    1.00  0.50
ATOM    464  O   THR    63       8.583   4.549  12.262    1.00  0.50
ATOM    470  N   ASP    64       7.528   6.504  11.814    1.00  0.50
ATOM    471  CA  ASP    64       7.242   6.872  13.198    1.00  0.50
ATOM    472  C   ASP    64       6.305   5.863  13.864    1.00  0.50
ATOM    473  O   ASP    64       6.409   5.636  15.076    1.00  0.50
ATOM    478  N   ALA    65       5.339   5.349  13.098    1.00  0.50
ATOM    479  CA  ALA    65       4.416   4.319  13.559    1.00  0.50
ATOM    480  C   ALA    65       4.908   2.887  13.321    1.00  0.50
ATOM    481  O   ALA    65       4.124   1.937  13.442    1.00  0.50
ATOM    486  N   GLY    66       6.193   2.758  12.953    1.00  0.50
ATOM    487  CA  GLY    66       6.935   1.487  12.904    1.00  0.50
ATOM    488  C   GLY    66       6.532   0.626  11.719    1.00  0.50
ATOM    489  O   GLY    66       6.726  -0.606  11.764    1.00  0.50
ATOM    496  N   LEU    67       6.035   1.262  10.644    1.00  0.50
ATOM    497  CA  LEU    67       5.823   0.564   9.381    1.00  0.50
ATOM    498  C   LEU    67       7.110   0.481   8.594    1.00  0.50
ATOM    499  O   LEU    67       7.956   1.365   8.713    1.00  0.50
ATOM    507  N   ALA    68       7.270  -0.604   7.821    1.00  0.50
ATOM    508  CA  ALA    68       8.321  -0.700   6.846    1.00  0.50
ATOM    509  C   ALA    68       7.802  -0.097   5.513    1.00  0.50
ATOM    510  O   ALA    68       6.870  -0.606   4.932    1.00  0.50
ATOM    512  N   LEU    71       8.407   0.996   5.048    1.00  0.50
ATOM    513  CA  LEU    71       7.997   1.725   3.833    1.00  0.50
ATOM    514  C   LEU    71       9.200   2.031   2.997    1.00  0.50
ATOM    515  O   LEU    71      10.237   2.451   3.501    1.00  0.50
ATOM    519  N   ARG    72       9.037   1.941   1.699    1.00  0.50
ATOM    520  CA  ARG    72      10.109   2.259   0.759    1.00  0.50
ATOM    521  C   ARG    72       9.475   3.186  -0.238    1.00  0.50
ATOM    522  O   ARG    72       8.263   3.128  -0.410    1.00  0.50
TER
END
