
#######################################################
#                                                     #
#                        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 T0363AL381_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL381_5-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      Q      12           -
LGA    I      13      -       -           -
LGA    N      14      I      13          4.507
LGA    I      15      N      14          4.040
LGA    E      16      I      15          3.341
LGA    I      17      E      16          4.353
LGA    A      18      -       -           -
LGA    Y      19      -       -           -
LGA    A      20      -       -           -
LGA    F      21      -       -           -
LGA    P      22      -       -           -
LGA    E      23      -       -           -
LGA    R      24      -       -           -
LGA    Y      25      -       -           -
LGA    Y      26      -       -           -
LGA    L      27      -       -           -
LGA    K      28      -       -           -
LGA    S      29      -       -           -
LGA    F      30      -       -           -
LGA    Q      31      -       -           -
LGA    V      32      -       -           -
LGA    D      33      -       -           -
LGA    E      34      -       -           -
LGA    G      35      -       -           -
LGA    I      36      -       -           -
LGA    T      37      -       -           -
LGA    V      38      -       -           -
LGA    Q      39      I      17          2.755
LGA    T      40      A      18          1.757
LGA    A      41      Y      19          1.556
LGA    I      42      A      20          1.776
LGA    T      43      F      21          1.648
LGA    Q      44      P      22          2.326
LGA    S      45      E      23          2.442
LGA    G      46      R      24          2.707
LGA    I      47      Y      25          2.120
LGA    L      48      Y      26          2.787
LGA    S      49      L      27          2.239
LGA    Q      50      K      28          2.813
LGA    F      51      S      29           #
LGA    -       -      F      30           -
LGA    -       -      Q      31           -
LGA    -       -      V      32           -
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    -       -      I      36           -
LGA    -       -      T      37           -
LGA    -       -      V      38           -
LGA    -       -      Q      39           -
LGA    -       -      T      40           -
LGA    P      52      A      41          3.341
LGA    E      53      I      42          1.921
LGA    I      54      T      43          1.424
LGA    -       -      Q      44           -
LGA    D      55      S      45          3.635
LGA    L      56      G      46          2.204
LGA    -       -      I      47           -
LGA    -       -      L      48           -
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   46    5.0     21    2.80     0.00     30.519     0.724

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.943327 * X  +  -0.308681 * Y  +   0.121861 * Z  +  39.990467
  Y_new =   0.148486 * X  +  -0.064191 * Y  +   0.986829 * Z  +  51.264660
  Z_new =  -0.296793 * X  +   0.948997 * Y  +   0.106388 * Z  +  26.882622 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.459157   -1.682436  [ DEG:    83.6035    -96.3965 ]
  Theta =   0.301332    2.840261  [ DEG:    17.2651    162.7349 ]
  Phi   =   2.985467   -0.156126  [ DEG:   171.0547     -8.9453 ]
 
# 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: T0363AL381_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL381_5-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   21   2.80    0.00  30.519
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL381_5-D1
REMARK Aligment from pdb entry: 2d04B
ATOM     41  N   ASN    11      24.633  19.967   9.972  1.00  0.00              
ATOM     42  CA  ASN    11      24.925  18.696  10.616  1.00  0.00              
ATOM     43  C   ASN    11      23.741  17.818  10.777  1.00  0.00              
ATOM     44  O   ASN    11      22.612  18.208  10.498  1.00  0.00              
ATOM     45  N   GLN    12      18.676  14.328   7.710  1.00  0.00              
ATOM     46  CA  GLN    12      18.560  13.404   8.806  1.00  0.00              
ATOM     47  C   GLN    12      19.831  12.668   9.084  1.00  0.00              
ATOM     48  O   GLN    12      20.662  12.463   8.207  1.00  0.00              
ATOM     49  N   ILE    13      19.966  12.228  10.318  1.00  0.00              
ATOM     50  CA  ILE    13      21.164  11.533  10.700  1.00  0.00              
ATOM     51  C   ILE    13      21.501  10.296   9.870  1.00  0.00              
ATOM     52  O   ILE    13      22.671  10.008   9.620  1.00  0.00              
ATOM     53  N   ASN    14      20.476   9.571   9.440  1.00  0.00              
ATOM     54  CA  ASN    14      20.685   8.390   8.630  1.00  0.00              
ATOM     55  C   ASN    14      20.746   8.670   7.130  1.00  0.00              
ATOM     56  O   ASN    14      20.529   7.767   6.325  1.00  0.00              
ATOM     57  N   ILE    15      20.987   9.933   6.765  1.00  0.00              
ATOM     58  CA  ILE    15      21.240  10.296   5.376  1.00  0.00              
ATOM     59  C   ILE    15      20.137  10.750   4.423  1.00  0.00              
ATOM     60  O   ILE    15      20.422  11.157   3.302  1.00  0.00              
ATOM     61  N   GLU    16      18.879  10.685   4.824  1.00  0.00              
ATOM     62  CA  GLU    16      17.842  11.156   3.920  1.00  0.00              
ATOM     63  C   GLU    16      17.541  12.642   4.189  1.00  0.00              
ATOM     64  O   GLU    16      17.238  13.019   5.327  1.00  0.00              
ATOM     65  N   ILE    17      17.645  13.480   3.148  1.00  0.00              
ATOM     66  CA  ILE    17      17.333  14.915   3.253  1.00  0.00              
ATOM     67  C   ILE    17      15.822  15.009   3.064  1.00  0.00              
ATOM     68  O   ILE    17      15.309  14.655   1.993  1.00  0.00              
ATOM     69  N   ALA    18      15.104  15.489   4.081  1.00  0.00              
ATOM     70  CA  ALA    18      13.653  15.551   3.978  1.00  0.00              
ATOM     71  C   ALA    18      13.023  16.948   4.143  1.00  0.00              
ATOM     72  O   ALA    18      13.387  17.696   5.048  1.00  0.00              
ATOM     73  N   TYR    19      12.115  17.308   3.226  1.00  0.00              
ATOM     74  CA  TYR    19      11.421  18.599   3.257  1.00  0.00              
ATOM     75  C   TYR    19      10.052  18.367   3.795  1.00  0.00              
ATOM     76  O   TYR    19       9.311  17.489   3.347  1.00  0.00              
ATOM     77  N   ALA    20       9.732  19.145   4.810  1.00  0.00              
ATOM     78  CA  ALA    20       8.426  19.048   5.367  1.00  0.00              
ATOM     79  C   ALA    20       7.766  20.363   5.122  1.00  0.00              
ATOM     80  O   ALA    20       8.370  21.329   4.690  1.00  0.00              
ATOM     81  N   PHE    21       6.481  20.349   5.395  1.00  0.00              
ATOM     82  CA  PHE    21       5.632  21.489   5.224  1.00  0.00              
ATOM     83  C   PHE    21       4.824  21.393   6.495  1.00  0.00              
ATOM     84  O   PHE    21       4.084  20.447   6.664  1.00  0.00              
ATOM     85  N   PRO    22       4.923  22.319   7.433  1.00  0.00              
ATOM     86  CA  PRO    22       4.081  22.101   8.611  1.00  0.00              
ATOM     87  C   PRO    22       4.237  20.750   9.328  1.00  0.00              
ATOM     88  O   PRO    22       3.383  20.371  10.134  1.00  0.00              
ATOM     89  N   GLU    23       5.323  20.032   9.049  1.00  0.00              
ATOM     90  CA  GLU    23       5.558  18.779   9.746  1.00  0.00              
ATOM     91  C   GLU    23       5.374  17.511   8.932  1.00  0.00              
ATOM     92  O   GLU    23       5.990  16.485   9.243  1.00  0.00              
ATOM     93  N   ARG    24       4.535  17.553   7.896  1.00  0.00              
ATOM     94  CA  ARG    24       4.307  16.366   7.058  1.00  0.00              
ATOM     95  C   ARG    24       5.342  16.293   5.949  1.00  0.00              
ATOM     96  O   ARG    24       5.538  17.250   5.202  1.00  0.00              
ATOM     97  N   TYR    25       6.009  15.154   5.830  1.00  0.00              
ATOM     98  CA  TYR    25       7.015  15.016   4.783  1.00  0.00              
ATOM     99  C   TYR    25       6.390  15.247   3.392  1.00  0.00              
ATOM    100  O   TYR    25       5.251  14.863   3.170  1.00  0.00              
ATOM    101  N   TYR    26       7.122  15.880   2.464  1.00  0.00              
ATOM    102  CA  TYR    26       6.605  16.130   1.100  1.00  0.00              
ATOM    103  C   TYR    26       7.627  15.849  -0.004  1.00  0.00              
ATOM    104  O   TYR    26       7.299  15.734  -1.173  1.00  0.00              
ATOM    105  N   LEU    27       8.895  15.770   0.366  1.00  0.00              
ATOM    106  CA  LEU    27       9.911  15.450  -0.614  1.00  0.00              
ATOM    107  C   LEU    27      11.028  14.846   0.195  1.00  0.00              
ATOM    108  O   LEU    27      11.012  14.885   1.424  1.00  0.00              
ATOM    109  N   LYS    28      12.015  14.288  -0.482  1.00  0.00              
ATOM    110  CA  LYS    28      13.113  13.677   0.247  1.00  0.00              
ATOM    111  C   LYS    28      14.086  13.181  -0.785  1.00  0.00              
ATOM    112  O   LYS    28      13.691  12.815  -1.883  1.00  0.00              
ATOM    113  N   SER    29      15.368  13.160  -0.453  1.00  0.00              
ATOM    114  CA  SER    29      16.361  12.694  -1.423  1.00  0.00              
ATOM    115  C   SER    29      16.298  11.181  -1.681  1.00  0.00              
ATOM    116  O   SER    29      16.853  10.691  -2.668  1.00  0.00              
ATOM    117  N   PHE    30      15.615  10.470  -0.776  1.00  0.00              
ATOM    118  CA  PHE    30      15.446   9.008  -0.778  1.00  0.00              
ATOM    119  C   PHE    30      16.761   8.312  -0.719  1.00  0.00              
ATOM    120  O   PHE    30      17.162   7.540  -1.579  1.00  0.00              
ATOM    121  N   GLN    31      17.451   8.652   0.348  1.00  0.00              
ATOM    122  CA  GLN    31      18.735   8.111   0.618  1.00  0.00              
ATOM    123  C   GLN    31      18.727   7.730   2.065  1.00  0.00              
ATOM    124  O   GLN    31      19.750   7.672   2.730  1.00  0.00              
ATOM    125  N   VAL    32      17.536   7.467   2.556  1.00  0.00              
ATOM    126  CA  VAL    32      17.481   7.024   3.898  1.00  0.00              
ATOM    127  C   VAL    32      18.325   5.746   3.979  1.00  0.00              
ATOM    128  O   VAL    32      18.275   4.916   3.071  1.00  0.00              
ATOM    129  N   ASP    33      19.098   5.596   5.058  1.00  0.00              
ATOM    130  CA  ASP    33      19.923   4.406   5.290  1.00  0.00              
ATOM    131  C   ASP    33      21.172   4.333   4.469  1.00  0.00              
ATOM    132  O   ASP    33      21.920   3.356   4.552  1.00  0.00              
ATOM    133  N   GLU    34      21.419   5.333   3.656  1.00  0.00              
ATOM    134  CA  GLU    34      22.586   5.191   2.836  1.00  0.00              
ATOM    135  C   GLU    34      23.888   5.475   3.513  1.00  0.00              
ATOM    136  O   GLU    34      24.948   5.505   2.907  1.00  0.00              
ATOM    137  N   GLY    35      23.801   5.672   4.809  1.00  0.00              
ATOM    138  CA  GLY    35      25.000   5.944   5.548  1.00  0.00              
ATOM    139  C   GLY    35      24.532   6.485   6.865  1.00  0.00              
ATOM    140  O   GLY    35      23.333   6.496   7.138  1.00  0.00              
ATOM    141  N   ILE    36      25.451   6.943   7.697  1.00  0.00              
ATOM    142  CA  ILE    36      25.012   7.487   8.979  1.00  0.00              
ATOM    143  C   ILE    36      25.867   8.681   9.454  1.00  0.00              
ATOM    144  O   ILE    36      26.947   8.893   8.917  1.00  0.00              
ATOM    145  N   THR    37      25.371   9.442  10.446  1.00  0.00              
ATOM    146  CA  THR    37      26.040  10.647  10.947  1.00  0.00              
ATOM    147  C   THR    37      26.206  11.549   9.735  1.00  0.00              
ATOM    148  O   THR    37      27.280  12.101   9.464  1.00  0.00              
ATOM    149  N   VAL    38      25.111  11.702   8.996  1.00  0.00              
ATOM    150  CA  VAL    38      25.110  12.433   7.734  1.00  0.00              
ATOM    151  C   VAL    38      25.072  13.955   7.828  1.00  0.00              
ATOM    152  O   VAL    38      24.605  14.504   8.817  1.00  0.00              
ATOM    153  N   GLN    39      25.532  14.652   6.794  1.00  0.00              
ATOM    154  CA  GLN    39      25.570  16.106   6.867  1.00  0.00              
ATOM    155  C   GLN    39      25.385  16.693   5.495  1.00  0.00              
ATOM    156  O   GLN    39      25.773  16.078   4.512  1.00  0.00              
ATOM    157  N   THR    40      24.795  17.876   5.395  1.00  0.00              
ATOM    158  CA  THR    40      24.615  18.442   4.065  1.00  0.00              
ATOM    159  C   THR    40      25.585  19.604   3.880  1.00  0.00              
ATOM    160  O   THR    40      25.843  20.361   4.814  1.00  0.00              
ATOM    161  N   ALA    41      26.163  19.749   2.699  1.00  0.00              
ATOM    162  CA  ALA    41      27.124  20.834   2.531  1.00  0.00              
ATOM    163  C   ALA    41      27.034  21.430   1.152  1.00  0.00              
ATOM    164  O   ALA    41      26.727  20.725   0.190  1.00  0.00              
ATOM    165  N   ILE    42      27.305  22.723   1.031  1.00  0.00              
ATOM    166  CA  ILE    42      27.237  23.338  -0.282  1.00  0.00              
ATOM    167  C   ILE    42      28.652  23.541  -0.785  1.00  0.00              
ATOM    168  O   ILE    42      29.439  24.267  -0.187  1.00  0.00              
ATOM    169  N   THR    43      29.005  22.903  -1.884  1.00  0.00              
ATOM    170  CA  THR    43      30.375  23.056  -2.313  1.00  0.00              
ATOM    171  C   THR    43      30.709  24.425  -2.867  1.00  0.00              
ATOM    172  O   THR    43      29.822  25.212  -3.208  1.00  0.00              
ATOM    173  N   GLN    44      31.988  24.744  -2.936  1.00  0.00              
ATOM    174  CA  GLN    44      32.301  26.045  -3.455  1.00  0.00              
ATOM    175  C   GLN    44      31.946  26.201  -4.952  1.00  0.00              
ATOM    176  O   GLN    44      32.031  27.305  -5.465  1.00  0.00              
ATOM    177  N   SER    45      31.540  25.138  -5.657  1.00  0.00              
ATOM    178  CA  SER    45      31.161  25.302  -7.072  1.00  0.00              
ATOM    179  C   SER    45      29.645  25.210  -7.262  1.00  0.00              
ATOM    180  O   SER    45      29.132  24.999  -8.368  1.00  0.00              
ATOM    181  N   GLY    46      28.957  25.408  -6.142  1.00  0.00              
ATOM    182  CA  GLY    46      27.519  25.397  -6.104  1.00  0.00              
ATOM    183  C   GLY    46      26.950  24.011  -5.941  1.00  0.00              
ATOM    184  O   GLY    46      25.759  23.880  -5.723  1.00  0.00              
ATOM    185  N   ILE    47      27.764  22.966  -6.013  1.00  0.00              
ATOM    186  CA  ILE    47      27.193  21.624  -5.904  1.00  0.00              
ATOM    187  C   ILE    47      26.664  21.311  -4.506  1.00  0.00              
ATOM    188  O   ILE    47      27.262  21.708  -3.511  1.00  0.00              
ATOM    189  N   LEU    48      25.550  20.600  -4.405  1.00  0.00              
ATOM    190  CA  LEU    48      25.051  20.299  -3.077  1.00  0.00              
ATOM    191  C   LEU    48      25.203  18.849  -2.736  1.00  0.00              
ATOM    192  O   LEU    48      24.651  17.989  -3.411  1.00  0.00              
ATOM    193  N   SER    49      25.920  18.522  -1.678  1.00  0.00              
ATOM    194  CA  SER    49      26.048  17.113  -1.484  1.00  0.00              
ATOM    195  C   SER    49      25.845  16.652  -0.065  1.00  0.00              
ATOM    196  O   SER    49      26.198  17.334   0.902  1.00  0.00              
ATOM    197  N   GLN    50      25.235  15.483   0.056  1.00  0.00              
ATOM    198  CA  GLN    50      25.033  14.911   1.369  1.00  0.00              
ATOM    199  C   GLN    50      26.256  14.043   1.651  1.00  0.00              
ATOM    200  O   GLN    50      26.655  13.220   0.809  1.00  0.00              
ATOM    201  N   PHE    51      26.831  14.231   2.831  1.00  0.00              
ATOM    202  CA  PHE    51      27.990  13.472   3.252  1.00  0.00              
ATOM    203  C   PHE    51      27.795  12.615   4.472  1.00  0.00              
ATOM    204  O   PHE    51      27.240  12.976   5.502  1.00  0.00              
ATOM    205  N   PRO    52      28.330  11.443   4.275  1.00  0.00              
ATOM    206  CA  PRO    52      28.444  10.356   5.201  1.00  0.00              
ATOM    207  C   PRO    52      29.325  10.836   6.359  1.00  0.00              
ATOM    208  O   PRO    52      29.934  11.894   6.268  1.00  0.00              
ATOM    209  N   GLU    53      29.409  10.092   7.453  1.00  0.00              
ATOM    210  CA  GLU    53      30.353  10.560   8.458  1.00  0.00              
ATOM    211  C   GLU    53      31.732  10.069   8.008  1.00  0.00              
ATOM    212  O   GLU    53      32.732  10.379   8.646  1.00  0.00              
ATOM    213  N   ILE    54      31.794   9.293   6.928  1.00  0.00              
ATOM    214  CA  ILE    54      33.101   8.904   6.411  1.00  0.00              
ATOM    215  C   ILE    54      33.320   9.698   5.097  1.00  0.00              
ATOM    216  O   ILE    54      34.106   9.303   4.234  1.00  0.00              
ATOM    217  N   ASP    55      32.611  10.826   4.970  1.00  0.00              
ATOM    218  CA  ASP    55      32.706  11.704   3.807  1.00  0.00              
ATOM    219  C   ASP    55      32.433  11.057   2.491  1.00  0.00              
ATOM    220  O   ASP    55      32.957  11.461   1.457  1.00  0.00              
ATOM    221  N   LEU    56      31.631  10.000   2.504  1.00  0.00              
ATOM    222  CA  LEU    56      31.289   9.479   1.209  1.00  0.00              
ATOM    223  C   LEU    56      30.166  10.368   0.763  1.00  0.00              
ATOM    224  O   LEU    56      29.375  10.887   1.557  1.00  0.00              
END
