
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0349AL586_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL586_1-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    R       2      M       1          5.669
LGA    E       3      R       2          4.267
LGA    L       4      E       3          5.510
LGA    L       5      L       4          3.111
LGA    -       -      L       5           -
LGA    R       6      R       6          2.136
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    D       9      D       9          1.972
LGA    -       -      A      10           -
LGA    A      10      V      11          1.544
LGA    V      11      L      12          2.182
LGA    L      12      L      13          2.662
LGA    L      13      S      14          1.765
LGA    S      14      A      15          0.874
LGA    A      15      V      16          0.871
LGA    V      16      G      17          0.694
LGA    G      17      A      18          1.340
LGA    A      18      L      19          1.445
LGA    L      19      L      20          1.481
LGA    L      20      D      21          1.401
LGA    D      21      G      22          1.377
LGA    G      22      A      23          1.086
LGA    A      23      D      24          1.122
LGA    -       -      I      25           -
LGA    -       -      G      26           -
LGA    G      26      H      27          1.828
LGA    H      27      L      28          2.237
LGA    L      28      V      29          3.361
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    V      29      R      47          2.966
LGA    P      45      V      48           #
LGA    R      46      -       -           -
LGA    R      47      L      49           #
LGA    V      48      V      50           #
LGA    -       -      H      51           -
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    L      49      L      55          1.058
LGA    D      53      A      56          3.238
LGA    -       -      G      57           -
LGA    -       -      A      58           -
LGA    D      54      R      59          3.342
LGA    L      55      R      60          3.146
LGA    -       -      L      61           -
LGA    -       -      L      62           -
LGA    A      56      T      63          2.857
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    G      57      L      67          2.449
LGA    T      63      A      68           -
LGA    D      64      H      69           -
LGA    A      65      E      70           -
LGA    G      66      L      71           -
LGA    L      67      R      72           -
LGA    A      68      -       -           -
LGA    H      69      -       -           -
LGA    E      70      -       -           -
LGA    L      71      -       -           -
LGA    R      72      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   57    5.0     30    2.62    20.00     39.487     1.103

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.403571 * X  +  -0.142148 * Y  +   0.903839 * Z  + -23.825136
  Y_new =   0.494788 * X  +   0.864856 * Y  +  -0.084909 * Z  + -28.508347
  Z_new =  -0.769620 * X  +   0.481476 * Y  +   0.419364 * Z  + -15.086745 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.854238   -2.287354  [ DEG:    48.9442   -131.0558 ]
  Theta =   0.878246    2.263346  [ DEG:    50.3198    129.6802 ]
  Phi   =   0.886589   -2.255004  [ DEG:    50.7978   -129.2022 ]
 
# 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: T0349AL586_1-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL586_1-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   57   5.0   30   2.62   20.00  39.487
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL586_1-D1
REMARK Aligment from pdb entry: 1ttz_A
ATOM      1  N   ARG     2       0.397  11.736  -1.982  1.00  0.00              
ATOM      2  CA  ARG     2       1.364  10.859  -1.334  1.00  0.00              
ATOM      3  C   ARG     2       1.312   9.488  -1.995  1.00  0.00              
ATOM      4  O   ARG     2       0.374   9.184  -2.726  1.00  0.00              
ATOM      5  N   GLU     3       2.332   8.673  -1.750  1.00  0.00              
ATOM      6  CA  GLU     3       2.364   7.322  -2.283  1.00  0.00              
ATOM      7  C   GLU     3       2.429   6.417  -1.066  1.00  0.00              
ATOM      8  O   GLU     3       3.344   6.532  -0.251  1.00  0.00              
ATOM      9  N   LEU     4       1.449   5.536  -0.923  1.00  0.00              
ATOM     10  CA  LEU     4       1.449   4.613   0.197  1.00  0.00              
ATOM     11  C   LEU     4       1.839   3.225  -0.284  1.00  0.00              
ATOM     12  O   LEU     4       1.066   2.555  -0.970  1.00  0.00              
ATOM     13  N   LEU     5       3.050   2.802   0.052  1.00  0.00              
ATOM     14  CA  LEU     5       3.480   1.476  -0.330  1.00  0.00              
ATOM     15  C   LEU     5       2.923   0.520   0.719  1.00  0.00              
ATOM     16  O   LEU     5       3.132   0.703   1.921  1.00  0.00              
ATOM     17  N   ARG     6       2.184  -0.480   0.262  1.00  0.00              
ATOM     18  CA  ARG     6       1.616  -1.466   1.163  1.00  0.00              
ATOM     19  C   ARG     6       1.524  -2.823   0.487  1.00  0.00              
ATOM     20  O   ARG     6       1.858  -2.967  -0.687  1.00  0.00              
ATOM     21  N   ASP     9      -2.911  -7.039   5.212  1.00  0.00              
ATOM     22  CA  ASP     9      -2.016  -6.574   6.267  1.00  0.00              
ATOM     23  C   ASP     9      -2.727  -5.554   7.146  1.00  0.00              
ATOM     24  O   ASP     9      -3.110  -4.478   6.686  1.00  0.00              
ATOM     25  N   ALA    10      -2.902  -5.904   8.415  1.00  0.00              
ATOM     26  CA  ALA    10      -3.559  -5.029   9.375  1.00  0.00              
ATOM     27  C   ALA    10      -2.803  -3.708   9.559  1.00  0.00              
ATOM     28  O   ALA    10      -3.418  -2.658   9.744  1.00  0.00              
ATOM     29  N   VAL    11      -1.476  -3.760   9.515  1.00  0.00              
ATOM     30  CA  VAL    11      -0.673  -2.545   9.681  1.00  0.00              
ATOM     31  C   VAL    11      -0.933  -1.578   8.535  1.00  0.00              
ATOM     32  O   VAL    11      -1.005  -0.366   8.737  1.00  0.00              
ATOM     33  N   LEU    12      -1.076  -2.125   7.331  1.00  0.00              
ATOM     34  CA  LEU    12      -1.344  -1.311   6.156  1.00  0.00              
ATOM     35  C   LEU    12      -2.732  -0.685   6.244  1.00  0.00              
ATOM     36  O   LEU    12      -2.921   0.469   5.872  1.00  0.00              
ATOM     37  N   LEU    13      -3.704  -1.443   6.739  1.00  0.00              
ATOM     38  CA  LEU    13      -5.052  -0.909   6.876  1.00  0.00              
ATOM     39  C   LEU    13      -5.033   0.235   7.871  1.00  0.00              
ATOM     40  O   LEU    13      -5.768   1.203   7.720  1.00  0.00              
ATOM     41  N   SER    14      -4.187   0.117   8.891  1.00  0.00              
ATOM     42  CA  SER    14      -4.076   1.159   9.908  1.00  0.00              
ATOM     43  C   SER    14      -3.449   2.427   9.336  1.00  0.00              
ATOM     44  O   SER    14      -3.785   3.534   9.755  1.00  0.00              
ATOM     45  N   ALA    15      -2.526   2.264   8.389  1.00  0.00              
ATOM     46  CA  ALA    15      -1.885   3.418   7.765  1.00  0.00              
ATOM     47  C   ALA    15      -2.968   4.175   7.002  1.00  0.00              
ATOM     48  O   ALA    15      -3.016   5.401   7.015  1.00  0.00              
ATOM     49  N   VAL    16      -3.844   3.432   6.342  1.00  0.00              
ATOM     50  CA  VAL    16      -4.925   4.047   5.591  1.00  0.00              
ATOM     51  C   VAL    16      -5.773   4.933   6.512  1.00  0.00              
ATOM     52  O   VAL    16      -6.155   6.041   6.135  1.00  0.00              
ATOM     53  N   GLY    17      -6.056   4.449   7.721  1.00  0.00              
ATOM     54  CA  GLY    17      -6.854   5.215   8.673  1.00  0.00              
ATOM     55  C   GLY    17      -6.076   6.421   9.187  1.00  0.00              
ATOM     56  O   GLY    17      -6.661   7.472   9.460  1.00  0.00              
ATOM     57  N   ALA    18      -4.761   6.270   9.324  1.00  0.00              
ATOM     58  CA  ALA    18      -3.922   7.365   9.794  1.00  0.00              
ATOM     59  C   ALA    18      -3.977   8.501   8.771  1.00  0.00              
ATOM     60  O   ALA    18      -3.983   9.673   9.135  1.00  0.00              
ATOM     61  N   LEU    19      -4.009   8.143   7.488  1.00  0.00              
ATOM     62  CA  LEU    19      -4.084   9.140   6.429  1.00  0.00              
ATOM     63  C   LEU    19      -5.388   9.918   6.511  1.00  0.00              
ATOM     64  O   LEU    19      -5.421  11.111   6.238  1.00  0.00              
ATOM     65  N   LEU    20      -6.461   9.233   6.890  1.00  0.00              
ATOM     66  CA  LEU    20      -7.771   9.870   7.008  1.00  0.00              
ATOM     67  C   LEU    20      -7.841  10.763   8.237  1.00  0.00              
ATOM     68  O   LEU    20      -8.311  11.900   8.165  1.00  0.00              
ATOM     69  N   ASP    21      -7.365  10.251   9.369  1.00  0.00              
ATOM     70  CA  ASP    21      -7.408  11.010  10.613  1.00  0.00              
ATOM     71  C   ASP    21      -6.475  12.213  10.638  1.00  0.00              
ATOM     72  O   ASP    21      -6.815  13.248  11.206  1.00  0.00              
ATOM     73  N   GLY    22      -5.299  12.077  10.034  1.00  0.00              
ATOM     74  CA  GLY    22      -4.350  13.182   9.980  1.00  0.00              
ATOM     75  C   GLY    22      -4.791  14.130   8.868  1.00  0.00              
ATOM     76  O   GLY    22      -4.210  15.197   8.675  1.00  0.00              
ATOM     77  N   ALA    23      -5.830  13.726   8.142  1.00  0.00              
ATOM     78  CA  ALA    23      -6.358  14.513   7.038  1.00  0.00              
ATOM     79  C   ALA    23      -5.254  14.818   6.035  1.00  0.00              
ATOM     80  O   ALA    23      -5.102  15.951   5.569  1.00  0.00              
ATOM     81  N   GLY    26      -3.751  10.554  -1.797  1.00  0.00              
ATOM     82  CA  GLY    26      -2.669   9.587  -1.764  1.00  0.00              
ATOM     83  C   GLY    26      -3.057   8.425  -2.662  1.00  0.00              
ATOM     84  O   GLY    26      -4.246   8.161  -2.860  1.00  0.00              
ATOM     85  N   HIS    27      -2.058   7.745  -3.214  1.00  0.00              
ATOM     86  CA  HIS    27      -2.318   6.599  -4.074  1.00  0.00              
ATOM     87  C   HIS    27      -1.527   5.411  -3.561  1.00  0.00              
ATOM     88  O   HIS    27      -0.359   5.541  -3.201  1.00  0.00              
ATOM     89  N   LEU    28      -2.171   4.254  -3.528  1.00  0.00              
ATOM     90  CA  LEU    28      -1.533   3.040  -3.056  1.00  0.00              
ATOM     91  C   LEU    28      -0.782   2.306  -4.155  1.00  0.00              
ATOM     92  O   LEU    28      -1.225   2.249  -5.297  1.00  0.00              
ATOM     93  N   VAL    29       0.368   1.758  -3.791  1.00  0.00              
ATOM     94  CA  VAL    29       1.174   0.963  -4.697  1.00  0.00              
ATOM     95  C   VAL    29       1.425  -0.316  -3.914  1.00  0.00              
ATOM     96  O   VAL    29       2.064  -0.290  -2.867  1.00  0.00              
ATOM    129  N   PRO    45       3.565  -0.709   6.183  1.00  0.00              
ATOM    130  CA  PRO    45       3.297   0.417   5.285  1.00  0.00              
ATOM    131  C   PRO    45       4.329   1.542   5.361  1.00  0.00              
ATOM    132  O   PRO    45       4.818   1.886   6.440  1.00  0.00              
ATOM    133  N   ARG    46       4.640   2.115   4.202  1.00  0.00              
ATOM    134  CA  ARG    46       5.597   3.212   4.103  1.00  0.00              
ATOM    135  C   ARG    46       4.997   4.330   3.256  1.00  0.00              
ATOM    136  O   ARG    46       4.461   4.078   2.180  1.00  0.00              
ATOM    137  N   ARG    47       5.075   5.559   3.751  1.00  0.00              
ATOM    138  CA  ARG    47       4.551   6.714   3.028  1.00  0.00              
ATOM    139  C   ARG    47       5.695   7.479   2.369  1.00  0.00              
ATOM    140  O   ARG    47       6.741   7.688   2.982  1.00  0.00              
ATOM    141  N   VAL    48       5.500   7.897   1.124  1.00  0.00              
ATOM    142  CA  VAL    48       6.535   8.641   0.417  1.00  0.00              
ATOM    143  C   VAL    48       5.897   9.883  -0.203  1.00  0.00              
ATOM    144  O   VAL    48       4.834   9.791  -0.816  1.00  0.00              
ATOM    145  N   LEU    49       6.521  11.047  -0.035  1.00  0.00              
ATOM    146  CA  LEU    49       5.954  12.253  -0.620  1.00  0.00              
ATOM    147  C   LEU    49       6.654  12.626  -1.922  1.00  0.00              
ATOM    148  O   LEU    49       7.645  12.007  -2.302  1.00  0.00              
ATOM    149  N   ASP    53      10.767  12.027   0.406  1.00  0.00              
ATOM    150  CA  ASP    53      10.907  11.725   1.828  1.00  0.00              
ATOM    151  C   ASP    53      10.032  10.529   2.136  1.00  0.00              
ATOM    152  O   ASP    53       9.003  10.332   1.494  1.00  0.00              
ATOM    153  N   ASP    54      10.431   9.731   3.115  1.00  0.00              
ATOM    154  CA  ASP    54       9.653   8.561   3.480  1.00  0.00              
ATOM    155  C   ASP    54       9.442   8.422   4.986  1.00  0.00              
ATOM    156  O   ASP    54      10.308   8.770   5.791  1.00  0.00              
ATOM    157  N   LEU    55       8.258   7.935   5.347  1.00  0.00              
ATOM    158  CA  LEU    55       7.873   7.730   6.737  1.00  0.00              
ATOM    159  C   LEU    55       7.509   6.257   6.865  1.00  0.00              
ATOM    160  O   LEU    55       6.575   5.790   6.207  1.00  0.00              
ATOM    161  N   ALA    56       8.246   5.529   7.698  1.00  0.00              
ATOM    162  CA  ALA    56       7.998   4.103   7.888  1.00  0.00              
ATOM    163  C   ALA    56       7.101   3.820   9.082  1.00  0.00              
ATOM    164  O   ALA    56       7.143   4.534  10.076  1.00  0.00              
ATOM    165  N   GLY    57       6.289   2.772   8.974  1.00  0.00              
ATOM    166  CA  GLY    57       5.417   2.371  10.063  1.00  0.00              
ATOM    167  C   GLY    57       6.335   2.044  11.246  1.00  0.00              
ATOM    168  O   GLY    57       7.465   1.591  11.050  1.00  0.00              
ATOM    169  N   THR    63       1.207   7.286  14.010  1.00  0.00              
ATOM    170  CA  THR    63      -0.171   7.616  14.348  1.00  0.00              
ATOM    171  C   THR    63      -0.511   8.957  13.701  1.00  0.00              
ATOM    172  O   THR    63       0.348   9.574  13.060  1.00  0.00              
ATOM    173  N   ASP    64      -1.750   9.410  13.872  1.00  0.00              
ATOM    174  CA  ASP    64      -2.194  10.669  13.284  1.00  0.00              
ATOM    175  C   ASP    64      -1.273  11.853  13.570  1.00  0.00              
ATOM    176  O   ASP    64      -0.909  12.595  12.657  1.00  0.00              
ATOM    177  N   ALA    65      -0.887  12.059  14.842  1.00  0.00              
ATOM    178  CA  ALA    65      -0.003  13.198  15.102  1.00  0.00              
ATOM    179  C   ALA    65       1.386  13.120  14.453  1.00  0.00              
ATOM    180  O   ALA    65       1.934  14.138  14.028  1.00  0.00              
ATOM    181  N   GLY    66       1.957  11.922  14.375  1.00  0.00              
ATOM    182  CA  GLY    66       3.274  11.772  13.773  1.00  0.00              
ATOM    183  C   GLY    66       3.172  12.015  12.276  1.00  0.00              
ATOM    184  O   GLY    66       4.030  12.655  11.669  1.00  0.00              
ATOM    185  N   LEU    67       2.106  11.497  11.684  1.00  0.00              
ATOM    186  CA  LEU    67       1.886  11.660  10.261  1.00  0.00              
ATOM    187  C   LEU    67       1.670  13.131   9.916  1.00  0.00              
ATOM    188  O   LEU    67       2.338  13.677   9.040  1.00  0.00              
ATOM    189  N   ALA    68       0.733  13.768  10.610  1.00  0.00              
ATOM    190  CA  ALA    68       0.438  15.175  10.374  1.00  0.00              
ATOM    191  C   ALA    68       1.687  16.032  10.570  1.00  0.00              
ATOM    192  O   ALA    68       1.919  16.978   9.817  1.00  0.00              
ATOM    193  N   HIS    69       2.502  15.694  11.565  1.00  0.00              
ATOM    194  CA  HIS    69       3.729  16.447  11.818  1.00  0.00              
ATOM    195  C   HIS    69       4.741  16.218  10.690  1.00  0.00              
ATOM    196  O   HIS    69       5.418  17.145  10.249  1.00  0.00              
ATOM    197  N   GLU    70       4.845  14.978  10.227  1.00  0.00              
ATOM    198  CA  GLU    70       5.774  14.658   9.155  1.00  0.00              
ATOM    199  C   GLU    70       5.418  15.485   7.927  1.00  0.00              
ATOM    200  O   GLU    70       6.285  16.085   7.297  1.00  0.00              
ATOM    201  N   LEU    71       4.133  15.520   7.601  1.00  0.00              
ATOM    202  CA  LEU    71       3.659  16.291   6.457  1.00  0.00              
ATOM    203  C   LEU    71       3.993  17.779   6.607  1.00  0.00              
ATOM    204  O   LEU    71       4.500  18.409   5.677  1.00  0.00              
ATOM    205  N   ARG    72       3.708  18.333   7.780  1.00  0.00              
ATOM    206  CA  ARG    72       3.960  19.749   8.024  1.00  0.00              
ATOM    207  C   ARG    72       5.431  20.095   8.142  1.00  0.00              
ATOM    208  O   ARG    72       5.794  21.267   8.127  1.00  0.00              
END
