
#######################################################
#                                                     #
#                        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   49 (  196),  selected   49 , name T0349TS383_3-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS383_3-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           -
LGA    -       -      E       3           -
LGA    L       4      L       4          3.472
LGA    L       5      L       5          2.315
LGA    R       6      R       6          4.387
LGA    T       7      T       7          5.623
LGA    N       8      N       8           #
LGA    D       9      D       9          3.152
LGA    A      10      A      10          4.548
LGA    V      11      V      11          2.201
LGA    L      12      L      12          1.275
LGA    L      13      L      13          0.617
LGA    S      14      S      14          1.021
LGA    A      15      A      15          1.157
LGA    V      16      V      16          1.240
LGA    G      17      G      17          1.279
LGA    A      18      A      18          1.362
LGA    L      19      L      19          1.403
LGA    L      20      L      20          1.433
LGA    D      21      D      21          1.814
LGA    G      22      G      22          2.091
LGA    A      23      A      23          2.345
LGA    G      26      D      24          1.968
LGA    H      27      I      25          1.783
LGA    L      28      G      26          1.766
LGA    V      29      H      27          2.542
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    P      45      R      47          2.111
LGA    R      46      V      48          2.846
LGA    R      47      L      49          2.869
LGA    V      48      V      50          1.923
LGA    L      49      H      51          1.505
LGA    V      50      E      52           #
LGA    H      51      D      53          3.720
LGA    E      52      -       -           -
LGA    D      53      -       -           -
LGA    D      54      D      54          3.935
LGA    L      55      L      55          3.519
LGA    A      56      A      56          3.117
LGA    G      57      G      57          2.393
LGA    A      58      A      58          1.067
LGA    R      59      R      59          1.960
LGA    R      60      R      60          0.680
LGA    L      61      L      61          1.654
LGA    L      62      L      62          1.397
LGA    T      63      T      63          2.603
LGA    D      64      D      64          4.155
LGA    -       -      A      65           -
LGA    L      67      G      66          2.047
LGA    A      68      L      67          2.971
LGA    H      69      A      68          3.660
LGA    E      70      H      69           -
LGA    L      71      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   49   57    5.0     43    2.60    72.09     57.898     1.591

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.250169 * X  +  -0.840101 * Y  +   0.481297 * Z  +  -9.113544
  Y_new =   0.839221 * X  +  -0.059747 * Y  +  -0.540499 * Z  + -15.533405
  Z_new =   0.482829 * X  +   0.539130 * Y  +   0.690083 * Z  + -62.750717 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.663205   -2.478387  [ DEG:    37.9989   -142.0011 ]
  Theta =  -0.503883   -2.637710  [ DEG:   -28.8704   -151.1296 ]
  Phi   =   1.281087   -1.860506  [ DEG:    73.4009   -106.5991 ]
 
# 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: T0349TS383_3-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS383_3-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   49   57   5.0   43   2.60   72.09  57.898
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS383_3-D1
PFRMAT TS
TARGET T0349
MODEL 3
PARENT 1u8sA
ATOM      1  N   LEU     4       4.932   2.095  -1.148  1.00  0.00
ATOM      2  CA  LEU     4       4.816   0.679  -1.414  1.00  0.00
ATOM      3  C   LEU     4       5.132  -0.055  -0.129  1.00  0.00
ATOM      4  O   LEU     4       6.116   0.254   0.541  1.00  0.00
ATOM      5  N   LEU     5       4.285  -1.011   0.235  1.00  0.00
ATOM      6  CA  LEU     5       4.499  -1.762   1.459  1.00  0.00
ATOM      7  C   LEU     5       4.240  -3.244   1.265  1.00  0.00
ATOM      8  O   LEU     5       3.510  -3.638   0.363  1.00  0.00
ATOM      9  N   ARG     6       4.866  -4.058   2.108  1.00  0.00
ATOM     10  CA  ARG     6       4.715  -5.510   2.067  1.00  0.00
ATOM     11  C   ARG     6       4.956  -6.037   3.468  1.00  0.00
ATOM     12  O   ARG     6       6.069  -5.953   3.989  1.00  0.00
ATOM     13  N   THR     7       3.911  -6.571   4.084  1.00  0.00
ATOM     14  CA  THR     7       4.045  -7.107   5.422  1.00  0.00
ATOM     15  C   THR     7       3.184  -8.340   5.579  1.00  0.00
ATOM     16  O   THR     7       2.443  -8.692   4.667  1.00  0.00
ATOM     17  N   ASN     8       3.274  -9.007   6.724  1.00  0.00
ATOM     18  CA  ASN     8       2.463 -10.197   6.938  1.00  0.00
ATOM     19  C   ASN     8       1.010  -9.780   7.031  1.00  0.00
ATOM     20  O   ASN     8       0.650  -8.928   7.841  1.00  0.00
ATOM     21  N   ASP     9       0.170 -10.381   6.202  1.00  0.00
ATOM     22  CA  ASP     9      -1.234 -10.020   6.212  1.00  0.00
ATOM     23  C   ASP     9      -1.917 -10.295   7.548  1.00  0.00
ATOM     24  O   ASP     9      -2.012 -11.435   7.999  1.00  0.00
ATOM     25  N   ALA    10      -5.211  -8.372  10.268  1.00  0.00
ATOM     26  CA  ALA    10      -6.380  -7.494  10.170  1.00  0.00
ATOM     27  C   ALA    10      -6.094  -6.033  10.515  1.00  0.00
ATOM     28  O   ALA    10      -5.292  -5.736  11.404  1.00  0.00
ATOM     29  N   VAL    11      -6.760  -5.131   9.799  1.00  0.00
ATOM     30  CA  VAL    11      -6.579  -3.712  10.041  1.00  0.00
ATOM     31  C   VAL    11      -5.238  -3.156   9.600  1.00  0.00
ATOM     32  O   VAL    11      -4.992  -1.955   9.717  1.00  0.00
ATOM     33  N   LEU    12      -4.364  -4.015   9.087  1.00  0.00
ATOM     34  CA  LEU    12      -3.062  -3.545   8.642  1.00  0.00
ATOM     35  C   LEU    12      -3.241  -2.469   7.566  1.00  0.00
ATOM     36  O   LEU    12      -2.551  -1.453   7.582  1.00  0.00
ATOM     37  N   LEU    13      -4.186  -2.679   6.653  1.00  0.00
ATOM     38  CA  LEU    13      -4.455  -1.698   5.603  1.00  0.00
ATOM     39  C   LEU    13      -5.064  -0.431   6.222  1.00  0.00
ATOM     40  O   LEU    13      -4.740   0.690   5.813  1.00  0.00
ATOM     41  N   SER    14      -5.950  -0.624   7.202  1.00  0.00
ATOM     42  CA  SER    14      -6.594   0.478   7.913  1.00  0.00
ATOM     43  C   SER    14      -5.545   1.445   8.460  1.00  0.00
ATOM     44  O   SER    14      -5.687   2.658   8.357  1.00  0.00
ATOM     45  N   ALA    15      -4.489   0.892   9.045  1.00  0.00
ATOM     46  CA  ALA    15      -3.407   1.693   9.612  1.00  0.00
ATOM     47  C   ALA    15      -2.860   2.678   8.596  1.00  0.00
ATOM     48  O   ALA    15      -2.788   3.880   8.850  1.00  0.00
ATOM     49  N   VAL    16      -2.460   2.144   7.447  1.00  0.00
ATOM     50  CA  VAL    16      -1.898   2.942   6.376  1.00  0.00
ATOM     51  C   VAL    16      -2.810   4.078   5.962  1.00  0.00
ATOM     52  O   VAL    16      -2.390   5.235   5.898  1.00  0.00
ATOM     53  N   GLY    17      -4.061   3.736   5.673  1.00  0.00
ATOM     54  CA  GLY    17      -5.055   4.708   5.254  1.00  0.00
ATOM     55  C   GLY    17      -5.311   5.736   6.345  1.00  0.00
ATOM     56  O   GLY    17      -5.610   6.897   6.057  1.00  0.00
ATOM     57  N   ALA    18      -5.198   5.311   7.600  1.00  0.00
ATOM     58  CA  ALA    18      -5.428   6.213   8.720  1.00  0.00
ATOM     59  C   ALA    18      -4.282   7.209   8.828  1.00  0.00
ATOM     60  O   ALA    18      -4.491   8.429   8.911  1.00  0.00
ATOM     61  N   LEU    19      -3.063   6.683   8.815  1.00  0.00
ATOM     62  CA  LEU    19      -1.884   7.520   8.923  1.00  0.00
ATOM     63  C   LEU    19      -1.830   8.565   7.817  1.00  0.00
ATOM     64  O   LEU    19      -1.564   9.741   8.079  1.00  0.00
ATOM     65  N   LEU    20      -2.109   8.150   6.586  1.00  0.00
ATOM     66  CA  LEU    20      -2.065   9.071   5.456  1.00  0.00
ATOM     67  C   LEU    20      -3.150  10.145   5.498  1.00  0.00
ATOM     68  O   LEU    20      -2.867  11.337   5.284  1.00  0.00
ATOM     69  N   ASP    21      -4.389   9.731   5.770  1.00  0.00
ATOM     70  CA  ASP    21      -5.510  10.672   5.833  1.00  0.00
ATOM     71  C   ASP    21      -5.418  11.643   7.019  1.00  0.00
ATOM     72  O   ASP    21      -5.775  12.808   6.895  1.00  0.00
ATOM     73  N   GLY    22      -4.943  11.165   8.167  1.00  0.00
ATOM     74  CA  GLY    22      -4.802  12.032   9.332  1.00  0.00
ATOM     75  C   GLY    22      -3.681  13.041   9.119  1.00  0.00
ATOM     76  O   GLY    22      -3.635  14.079   9.788  1.00  0.00
ATOM     77  N   ALA    23      -2.765  12.734   8.205  1.00  0.00
ATOM     78  CA  ALA    23      -1.659  13.643   7.915  1.00  0.00
ATOM     79  C   ALA    23      -2.151  14.709   6.934  1.00  0.00
ATOM     80  O   ALA    23      -1.380  15.557   6.479  1.00  0.00
ATOM     81  N   GLY    26      -3.443  14.643   6.612  1.00  0.00
ATOM     82  CA  GLY    26      -4.050  15.603   5.706  1.00  0.00
ATOM     83  C   GLY    26      -3.810  15.338   4.233  1.00  0.00
ATOM     84  O   GLY    26      -4.007  16.225   3.401  1.00  0.00
ATOM     85  N   HIS    27      -3.393  14.123   3.895  1.00  0.00
ATOM     86  CA  HIS    27      -3.132  13.802   2.498  1.00  0.00
ATOM     87  C   HIS    27      -4.298  13.105   1.814  1.00  0.00
ATOM     88  O   HIS    27      -5.197  12.568   2.461  1.00  0.00
ATOM     89  N   LEU    28      -4.272  13.138   0.490  1.00  0.00
ATOM     90  CA  LEU    28      -5.291  12.508  -0.323  1.00  0.00
ATOM     91  C   LEU    28      -4.712  11.234  -0.913  1.00  0.00
ATOM     92  O   LEU    28      -3.521  11.172  -1.223  1.00  0.00
ATOM     93  N   VAL    29      -5.549  10.213  -1.042  1.00  0.00
ATOM     94  CA  VAL    29      -5.125   8.958  -1.638  1.00  0.00
ATOM     95  C   VAL    29      -5.756   8.995  -3.028  1.00  0.00
ATOM     96  O   VAL    29      -6.966   8.814  -3.177  1.00  0.00
ATOM    153  N   PRO    45       0.423  -0.697  -3.194  1.00  0.00
ATOM    154  CA  PRO    45       0.983   0.300  -4.083  1.00  0.00
ATOM    155  C   PRO    45       0.019   1.442  -3.841  1.00  0.00
ATOM    156  O   PRO    45      -1.188   1.237  -3.903  1.00  0.00
ATOM    157  N   ARG    46       0.535   2.632  -3.557  1.00  0.00
ATOM    158  CA  ARG    46      -0.329   3.759  -3.293  1.00  0.00
ATOM    159  C   ARG    46       0.312   5.064  -3.713  1.00  0.00
ATOM    160  O   ARG    46       1.511   5.282  -3.512  1.00  0.00
ATOM    161  N   ARG    47      -0.503   5.921  -4.322  1.00  0.00
ATOM    162  CA  ARG    47      -0.073   7.234  -4.770  1.00  0.00
ATOM    163  C   ARG    47      -0.913   8.246  -4.006  1.00  0.00
ATOM    164  O   ARG    47      -2.130   8.311  -4.181  1.00  0.00
ATOM    165  N   VAL    48      -0.256   9.021  -3.149  1.00  0.00
ATOM    166  CA  VAL    48      -0.929  10.034  -2.344  1.00  0.00
ATOM    167  C   VAL    48      -0.370  11.383  -2.758  1.00  0.00
ATOM    168  O   VAL    48       0.615  11.449  -3.492  1.00  0.00
ATOM    169  N   LEU    49      -0.993  12.452  -2.276  1.00  0.00
ATOM    170  CA  LEU    49      -0.561  13.805  -2.582  1.00  0.00
ATOM    171  C   LEU    49      -1.020  14.697  -1.447  1.00  0.00
ATOM    172  O   LEU    49      -1.959  14.362  -0.720  1.00  0.00
ATOM    173  N   VAL    50      -0.360  15.836  -1.297  1.00  0.00
ATOM    174  CA  VAL    50      -0.724  16.761  -0.246  1.00  0.00
ATOM    175  C   VAL    50       0.257  17.898  -0.283  1.00  0.00
ATOM    176  O   VAL    50       1.059  17.986  -1.209  1.00  0.00
ATOM    177  N   HIS    51       0.196  18.780   0.701  1.00  0.00
ATOM    178  CA  HIS    51       1.128  19.894   0.734  1.00  0.00
ATOM    179  C   HIS    51       2.490  19.335   1.142  1.00  0.00
ATOM    180  O   HIS    51       2.585  18.208   1.641  1.00  0.00
ATOM    181  N   GLU    52       3.570  20.103   0.921  1.00  0.00
ATOM    182  CA  GLU    52       4.897  19.601   1.308  1.00  0.00
ATOM    183  C   GLU    52       4.965  19.246   2.798  1.00  0.00
ATOM    184  O   GLU    52       5.592  18.260   3.193  1.00  0.00
ATOM    185  N   ASP    53       4.289  20.030   3.623  1.00  0.00
ATOM    186  CA  ASP    53       4.290  19.756   5.049  1.00  0.00
ATOM    187  C   ASP    53       3.665  18.401   5.362  1.00  0.00
ATOM    188  O   ASP    53       4.210  17.624   6.142  1.00  0.00
ATOM    189  N   ASP    54       2.521  18.119   4.746  1.00  0.00
ATOM    190  CA  ASP    54       1.820  16.857   4.983  1.00  0.00
ATOM    191  C   ASP    54       2.551  15.651   4.389  1.00  0.00
ATOM    192  O   ASP    54       2.650  14.595   5.023  1.00  0.00
ATOM    193  N   LEU    55       3.051  15.802   3.169  1.00  0.00
ATOM    194  CA  LEU    55       3.779  14.721   2.545  1.00  0.00
ATOM    195  C   LEU    55       5.025  14.441   3.387  1.00  0.00
ATOM    196  O   LEU    55       5.371  13.281   3.632  1.00  0.00
ATOM    197  N   ALA    56       5.696  15.497   3.835  1.00  0.00
ATOM    198  CA  ALA    56       6.890  15.305   4.648  1.00  0.00
ATOM    199  C   ALA    56       6.499  14.595   5.931  1.00  0.00
ATOM    200  O   ALA    56       7.251  13.771   6.446  1.00  0.00
ATOM    201  N   GLY    57       5.318  14.920   6.445  1.00  0.00
ATOM    202  CA  GLY    57       4.840  14.299   7.671  1.00  0.00
ATOM    203  C   GLY    57       4.674  12.803   7.454  1.00  0.00
ATOM    204  O   GLY    57       5.114  12.004   8.274  1.00  0.00
ATOM    205  N   ALA    58       4.043  12.432   6.344  1.00  0.00
ATOM    206  CA  ALA    58       3.837  11.030   6.031  1.00  0.00
ATOM    207  C   ALA    58       5.183  10.357   5.793  1.00  0.00
ATOM    208  O   ALA    58       5.431   9.263   6.298  1.00  0.00
ATOM    209  N   ARG    59       6.053  11.001   5.018  1.00  0.00
ATOM    210  CA  ARG    59       7.370  10.426   4.756  1.00  0.00
ATOM    211  C   ARG    59       8.059  10.157   6.092  1.00  0.00
ATOM    212  O   ARG    59       8.763   9.168   6.256  1.00  0.00
ATOM    213  N   ARG    60       7.816  11.024   7.062  1.00  0.00
ATOM    214  CA  ARG    60       8.421  10.882   8.379  1.00  0.00
ATOM    215  C   ARG    60       7.844   9.774   9.254  1.00  0.00
ATOM    216  O   ARG    60       8.583   9.003   9.864  1.00  0.00
ATOM    217  N   LEU    61       6.521   9.692   9.308  1.00  0.00
ATOM    218  CA  LEU    61       5.868   8.726  10.179  1.00  0.00
ATOM    219  C   LEU    61       5.477   7.366   9.601  1.00  0.00
ATOM    220  O   LEU    61       5.163   6.440  10.353  1.00  0.00
ATOM    221  N   LEU    62       5.498   7.232   8.278  1.00  0.00
ATOM    222  CA  LEU    62       5.142   5.952   7.673  1.00  0.00
ATOM    223  C   LEU    62       6.131   4.858   8.050  1.00  0.00
ATOM    224  O   LEU    62       5.729   3.791   8.491  1.00  0.00
ATOM    225  N   THR    63       7.440   5.105   7.876  1.00  0.00
ATOM    226  CA  THR    63       8.430   4.077   8.227  1.00  0.00
ATOM    227  C   THR    63       8.218   3.561   9.653  1.00  0.00
ATOM    228  O   THR    63       8.280   2.364   9.913  1.00  0.00
ATOM    229  N   ASP    64       7.953   4.487  10.565  1.00  0.00
ATOM    230  CA  ASP    64       7.716   4.165  11.968  1.00  0.00
ATOM    231  C   ASP    64       6.532   3.204  12.118  1.00  0.00
ATOM    232  O   ASP    64       6.629   2.202  12.832  1.00  0.00
ATOM    233  N   LEU    67       5.422   3.514  11.443  1.00  0.00
ATOM    234  CA  LEU    67       4.237   2.665  11.484  1.00  0.00
ATOM    235  C   LEU    67       4.666   1.275  11.068  1.00  0.00
ATOM    236  O   LEU    67       4.294   0.287  11.687  1.00  0.00
ATOM    237  N   ALA    68       5.456   1.212  10.001  1.00  0.00
ATOM    238  CA  ALA    68       5.936  -0.061   9.504  1.00  0.00
ATOM    239  C   ALA    68       6.720  -0.810  10.556  1.00  0.00
ATOM    240  O   ALA    68       6.507  -1.999  10.764  1.00  0.00
ATOM    241  N   HIS    69       7.626  -0.108  11.224  1.00  0.00
ATOM    242  CA  HIS    69       8.447  -0.717  12.264  1.00  0.00
ATOM    243  C   HIS    69       7.533  -1.335  13.320  1.00  0.00
ATOM    244  O   HIS    69       7.863  -2.353  13.929  1.00  0.00
ATOM    245  N   GLU    70       6.375  -0.716  13.515  1.00  0.00
ATOM    246  CA  GLU    70       5.385  -1.188  14.477  1.00  0.00
ATOM    247  C   GLU    70       4.734  -2.515  14.053  1.00  0.00
ATOM    248  O   GLU    70       4.726  -3.482  14.824  1.00  0.00
ATOM    249  N   LEU    71       4.205  -2.555  12.827  1.00  0.00
ATOM    250  CA  LEU    71       3.524  -3.740  12.294  1.00  0.00
ATOM    251  C   LEU    71       4.379  -4.684  11.459  1.00  0.00
ATOM    252  O   LEU    71       3.848  -5.488  10.696  1.00  0.00
TER
END
