
#######################################################
#                                                     #
#                        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 T0351AL243_1
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351AL243_1.T0351.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      L       3           -
LGA    A      44      Y       4           #
LGA    E      45      D       5           #
LGA    L      46      A       6          5.322
LGA    E      47      I       7          2.200
LGA    T      48      M       8          3.690
LGA    -       -      Y       9           -
LGA    -       -      K      10           -
LGA    -       -      Y      11           -
LGA    -       -      P      12           -
LGA    -       -      N      13           -
LGA    W      49      A      14          4.780
LGA    W      50      V      15           -
LGA    E      51      S      16           -
LGA    -       -      R      17           -
LGA    -       -      K      18           -
LGA    -       -      D      19           -
LGA    E      52      F      20          3.218
LGA    L      53      E      21           #
LGA    -       -      L      22           -
LGA    -       -      R      23           -
LGA    -       -      N      24           -
LGA    -       -      D      25           -
LGA    -       -      G      26           -
LGA    -       -      N      27           -
LGA    -       -      G      28           -
LGA    -       -      S      29           -
LGA    -       -      Y      30           -
LGA    Q      54      I      31          2.937
LGA    K      55      E      32          2.342
LGA    N      56      K      33          1.589
LGA    V      65      W      34          1.759
LGA    -       -      N      35           -
LGA    E      66      L      36           #
LGA    L      67      R      37           -
LGA    L      68      A      38           -
LGA    A      69      -       -           -
LGA    Q      70      -       -           -
LGA    E      71      P      39          3.426
LGA    L      72      L      40          3.546
LGA    S      73      -       -           -
LGA    Q      74      P      41          2.994
LGA    E      75      T      42          3.887
LGA    K      76      Q      43          3.045
LGA    L      77      A      44          2.737
LGA    A      78      E      45          1.963
LGA    R      79      L      46          1.374
LGA    K      80      E      47          0.784
LGA    Q      81      T      48          0.314
LGA    L      82      W      49          0.554
LGA    E      83      W      50          0.295
LGA    E      84      E      51          0.375
LGA    L      85      E      52          0.518
LGA    N      86      L      53          1.022
LGA    K      87      Q      54          1.334
LGA    T      88      K      55          0.841
LGA    L      89      N      56          0.777
LGA    G      90      -       -           -
LGA    N      91      -       -           -
LGA    E      92      -       -           -
LGA    L      93      -       -           -
LGA    S      94      -       -           -
LGA    D      95      -       -           -
LGA    I      96      -       -           -
LGA    K      97      -       -           -
LGA    L      98      -       -           -
LGA    S      99      -       -           -
LGA    L     100      -       -           -
LGA    L     101      -       -           -
LGA    S     102      -       -           -
LGA    L     103      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   52   56    5.0     27    2.55     7.41     35.847     1.017

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.733166 * X  +   0.667577 * Y  +  -0.129647 * Z  + -27.252348
  Y_new =  -0.602477 * X  +  -0.549199 * Y  +   0.579139 * Z  +  25.937841
  Z_new =   0.315418 * X  +   0.502715 * Y  +   0.804854 * Z  + -43.254101 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.558314   -2.583278  [ DEG:    31.9890   -148.0110 ]
  Theta =  -0.320897   -2.820696  [ DEG:   -18.3860   -161.6140 ]
  Phi   =  -2.453731    0.687862  [ DEG:  -140.5884     39.4116 ]
 
# 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: T0351AL243_1                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351AL243_1.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   56   5.0   27   2.55    7.41  35.847
REMARK  ---------------------------------------------------------- 
MOLECULE T0351AL243_1
REMARK Aligment from pdb entry: 1uurA
ATOM      1  N   ALA    44       5.748  -1.865   5.699  1.00  0.00              
ATOM      2  CA  ALA    44       4.778  -0.966   6.356  1.00  0.00              
ATOM      3  C   ALA    44       4.696   0.419   5.679  1.00  0.00              
ATOM      4  O   ALA    44       3.609   1.003   5.564  1.00  0.00              
ATOM      5  N   GLU    45       5.839   0.944   5.233  1.00  0.00              
ATOM      6  CA  GLU    45       5.857   2.237   4.558  1.00  0.00              
ATOM      7  C   GLU    45       5.032   2.128   3.293  1.00  0.00              
ATOM      8  O   GLU    45       4.244   3.015   2.964  1.00  0.00              
ATOM      9  N   LEU    46       5.238   1.028   2.585  1.00  0.00              
ATOM     10  CA  LEU    46       4.521   0.756   1.354  1.00  0.00              
ATOM     11  C   LEU    46       3.013   0.765   1.580  1.00  0.00              
ATOM     12  O   LEU    46       2.276   1.462   0.872  1.00  0.00              
ATOM     13  N   GLU    47       2.552   0.002   2.567  1.00  0.00              
ATOM     14  CA  GLU    47       1.127  -0.063   2.848  1.00  0.00              
ATOM     15  C   GLU    47       0.541   1.327   3.083  1.00  0.00              
ATOM     16  O   GLU    47      -0.481   1.682   2.495  1.00  0.00              
ATOM     17  N   THR    48       1.191   2.115   3.935  1.00  0.00              
ATOM     18  CA  THR    48       0.713   3.468   4.214  1.00  0.00              
ATOM     19  C   THR    48       0.684   4.292   2.926  1.00  0.00              
ATOM     20  O   THR    48      -0.298   4.981   2.647  1.00  0.00              
ATOM     21  N   TRP    49       1.759   4.206   2.143  1.00  0.00              
ATOM     22  CA  TRP    49       1.859   4.926   0.879  1.00  0.00              
ATOM     23  C   TRP    49       0.662   4.616  -0.008  1.00  0.00              
ATOM     24  O   TRP    49       0.057   5.524  -0.582  1.00  0.00              
ATOM     25  N   TRP    50       0.327   3.332  -0.127  1.00  0.00              
ATOM     26  CA  TRP    50      -0.813   2.911  -0.933  1.00  0.00              
ATOM     27  C   TRP    50      -2.105   3.398  -0.302  1.00  0.00              
ATOM     28  O   TRP    50      -2.942   3.999  -0.977  1.00  0.00              
ATOM     29  N   GLU    51      -2.265   3.134   0.994  1.00  0.00              
ATOM     30  CA  GLU    51      -3.471   3.539   1.716  1.00  0.00              
ATOM     31  C   GLU    51      -3.739   5.025   1.663  1.00  0.00              
ATOM     32  O   GLU    51      -4.883   5.462   1.775  1.00  0.00              
ATOM     33  N   GLU    52      -2.678   5.799   1.503  1.00  0.00              
ATOM     34  CA  GLU    52      -2.810   7.239   1.441  1.00  0.00              
ATOM     35  C   GLU    52      -3.179   7.664   0.026  1.00  0.00              
ATOM     36  O   GLU    52      -3.919   8.627  -0.162  1.00  0.00              
ATOM     37  N   LEU    53      -2.667   6.950  -0.971  1.00  0.00              
ATOM     38  CA  LEU    53      -2.972   7.290  -2.353  1.00  0.00              
ATOM     39  C   LEU    53      -4.461   7.106  -2.633  1.00  0.00              
ATOM     40  O   LEU    53      -5.111   8.013  -3.158  1.00  0.00              
ATOM     41  N   GLN    54      -4.995   5.940  -2.270  1.00  0.00              
ATOM     42  CA  GLN    54      -6.411   5.643  -2.488  1.00  0.00              
ATOM     43  C   GLN    54      -7.270   6.691  -1.793  1.00  0.00              
ATOM     44  O   GLN    54      -8.340   7.064  -2.277  1.00  0.00              
ATOM     45  N   LYS    55      -6.779   7.171  -0.658  1.00  0.00              
ATOM     46  CA  LYS    55      -7.482   8.166   0.145  1.00  0.00              
ATOM     47  C   LYS    55      -7.274   9.621  -0.310  1.00  0.00              
ATOM     48  O   LYS    55      -8.087  10.491  -0.004  1.00  0.00              
ATOM     49  N   ASN    56      -6.207   9.884  -1.061  1.00  0.00              
ATOM     50  CA  ASN    56      -5.950  11.248  -1.487  1.00  0.00              
ATOM     51  C   ASN    56      -5.761  11.544  -2.961  1.00  0.00              
ATOM     52  O   ASN    56      -5.430  12.670  -3.319  1.00  0.00              
ATOM     53  N   VAL    65      -5.955  10.562  -3.826  1.00  0.00              
ATOM     54  CA  VAL    65      -5.805  10.821  -5.250  1.00  0.00              
ATOM     55  C   VAL    65      -6.903  10.162  -6.052  1.00  0.00              
ATOM     56  O   VAL    65      -7.265   9.019  -5.786  1.00  0.00              
ATOM     57  N   GLU    66      -7.454  10.890  -7.016  1.00  0.00              
ATOM     58  CA  GLU    66      -8.468  10.306  -7.875  1.00  0.00              
ATOM     59  C   GLU    66      -7.656   9.466  -8.853  1.00  0.00              
ATOM     60  O   GLU    66      -6.862   9.992  -9.638  1.00  0.00              
ATOM     61  N   LEU    67      -7.842   8.158  -8.791  1.00  0.00              
ATOM     62  CA  LEU    67      -7.101   7.262  -9.656  1.00  0.00              
ATOM     63  C   LEU    67      -7.890   6.881 -10.892  1.00  0.00              
ATOM     64  O   LEU    67      -9.083   6.629 -10.811  1.00  0.00              
ATOM     65  N   LEU    68      -7.214   6.840 -12.033  1.00  0.00              
ATOM     66  CA  LEU    68      -7.854   6.450 -13.277  1.00  0.00              
ATOM     67  C   LEU    68      -7.957   4.924 -13.299  1.00  0.00              
ATOM     68  O   LEU    68      -7.124   4.228 -12.715  1.00  0.00              
ATOM     69  N   ALA    69      -8.991   4.388 -13.967  1.00  0.00              
ATOM     70  CA  ALA    69      -9.231   2.949 -14.081  1.00  0.00              
ATOM     71  C   ALA    69      -8.002   2.050 -13.928  1.00  0.00              
ATOM     72  O   ALA    69      -7.947   1.226 -13.016  1.00  0.00              
ATOM     73  N   GLN    70      -7.014   2.208 -14.803  1.00  0.00              
ATOM     74  CA  GLN    70      -5.814   1.378 -14.727  1.00  0.00              
ATOM     75  C   GLN    70      -5.086   1.470 -13.391  1.00  0.00              
ATOM     76  O   GLN    70      -4.817   0.447 -12.760  1.00  0.00              
ATOM     77  N   GLU    71      -4.754   2.689 -12.973  1.00  0.00              
ATOM     78  CA  GLU    71      -4.060   2.907 -11.707  1.00  0.00              
ATOM     79  C   GLU    71      -4.889   2.372 -10.547  1.00  0.00              
ATOM     80  O   GLU    71      -4.350   1.913  -9.540  1.00  0.00              
ATOM     81  N   LEU    72      -6.205   2.434 -10.687  1.00  0.00              
ATOM     82  CA  LEU    72      -7.094   1.970  -9.633  1.00  0.00              
ATOM     83  C   LEU    72      -7.020   0.465  -9.439  1.00  0.00              
ATOM     84  O   LEU    72      -6.841  -0.036  -8.326  1.00  0.00              
ATOM     85  N   SER    73      -7.158  -0.248 -10.545  1.00  0.00              
ATOM     86  CA  SER    73      -7.117  -1.693 -10.537  1.00  0.00              
ATOM     87  C   SER    73      -5.772  -2.172 -10.009  1.00  0.00              
ATOM     88  O   SER    73      -5.678  -3.225  -9.372  1.00  0.00              
ATOM     89  N   GLN    74      -4.737  -1.382 -10.283  1.00  0.00              
ATOM     90  CA  GLN    74      -3.378  -1.687  -9.861  1.00  0.00              
ATOM     91  C   GLN    74      -3.183  -1.484  -8.368  1.00  0.00              
ATOM     92  O   GLN    74      -2.576  -2.325  -7.710  1.00  0.00              
ATOM     93  N   GLU    75      -3.679  -0.372  -7.827  1.00  0.00              
ATOM     94  CA  GLU    75      -3.534  -0.130  -6.393  1.00  0.00              
ATOM     95  C   GLU    75      -4.173  -1.297  -5.645  1.00  0.00              
ATOM     96  O   GLU    75      -3.632  -1.802  -4.660  1.00  0.00              
ATOM     97  N   LYS    76      -5.330  -1.729  -6.121  1.00  0.00              
ATOM     98  CA  LYS    76      -6.006  -2.830  -5.475  1.00  0.00              
ATOM     99  C   LYS    76      -5.191  -4.112  -5.538  1.00  0.00              
ATOM    100  O   LYS    76      -5.136  -4.865  -4.566  1.00  0.00              
ATOM    101  N   LEU    77      -4.553  -4.344  -6.681  1.00  0.00              
ATOM    102  CA  LEU    77      -3.740  -5.535  -6.887  1.00  0.00              
ATOM    103  C   LEU    77      -2.486  -5.510  -6.032  1.00  0.00              
ATOM    104  O   LEU    77      -2.093  -6.528  -5.469  1.00  0.00              
ATOM    105  N   ALA    78      -1.854  -4.345  -5.942  1.00  0.00              
ATOM    106  CA  ALA    78      -0.646  -4.204  -5.152  1.00  0.00              
ATOM    107  C   ALA    78      -0.956  -4.355  -3.680  1.00  0.00              
ATOM    108  O   ALA    78      -0.190  -4.971  -2.939  1.00  0.00              
ATOM    109  N   ARG    79      -2.080  -3.777  -3.263  1.00  0.00              
ATOM    110  CA  ARG    79      -2.503  -3.825  -1.872  1.00  0.00              
ATOM    111  C   ARG    79      -2.649  -5.255  -1.404  1.00  0.00              
ATOM    112  O   ARG    79      -2.142  -5.610  -0.343  1.00  0.00              
ATOM    113  N   LYS    80      -3.337  -6.064  -2.210  1.00  0.00              
ATOM    114  CA  LYS    80      -3.575  -7.471  -1.904  1.00  0.00              
ATOM    115  C   LYS    80      -2.287  -8.275  -1.822  1.00  0.00              
ATOM    116  O   LYS    80      -2.109  -9.065  -0.893  1.00  0.00              
ATOM    117  N   GLN    81      -1.386  -8.076  -2.781  1.00  0.00              
ATOM    118  CA  GLN    81      -0.125  -8.811  -2.771  1.00  0.00              
ATOM    119  C   GLN    81       0.797  -8.389  -1.638  1.00  0.00              
ATOM    120  O   GLN    81       1.429  -9.228  -1.004  1.00  0.00              
ATOM    121  N   LEU    82       0.879  -7.094  -1.371  1.00  0.00              
ATOM    122  CA  LEU    82       1.713  -6.638  -0.276  1.00  0.00              
ATOM    123  C   LEU    82       1.193  -7.218   1.054  1.00  0.00              
ATOM    124  O   LEU    82       1.984  -7.574   1.933  1.00  0.00              
ATOM    125  N   GLU    83      -0.129  -7.312   1.205  1.00  0.00              
ATOM    126  CA  GLU    83      -0.702  -7.866   2.434  1.00  0.00              
ATOM    127  C   GLU    83      -0.221  -9.288   2.659  1.00  0.00              
ATOM    128  O   GLU    83       0.101  -9.684   3.787  1.00  0.00              
ATOM    129  N   GLU    84      -0.199 -10.055   1.574  1.00  0.00              
ATOM    130  CA  GLU    84       0.216 -11.441   1.617  1.00  0.00              
ATOM    131  C   GLU    84       1.694 -11.516   1.951  1.00  0.00              
ATOM    132  O   GLU    84       2.098 -12.301   2.807  1.00  0.00              
ATOM    133  N   LEU    85       2.497 -10.687   1.289  1.00  0.00              
ATOM    134  CA  LEU    85       3.937 -10.664   1.545  1.00  0.00              
ATOM    135  C   LEU    85       4.181 -10.368   3.007  1.00  0.00              
ATOM    136  O   LEU    85       5.014 -11.000   3.654  1.00  0.00              
ATOM    137  N   ASN    86       3.454  -9.389   3.522  1.00  0.00              
ATOM    138  CA  ASN    86       3.588  -9.013   4.912  1.00  0.00              
ATOM    139  C   ASN    86       3.283 -10.205   5.841  1.00  0.00              
ATOM    140  O   ASN    86       4.050 -10.474   6.768  1.00  0.00              
ATOM    141  N   LYS    87       2.187 -10.926   5.597  1.00  0.00              
ATOM    142  CA  LYS    87       1.855 -12.076   6.443  1.00  0.00              
ATOM    143  C   LYS    87       2.891 -13.172   6.346  1.00  0.00              
ATOM    144  O   LYS    87       3.250 -13.790   7.346  1.00  0.00              
ATOM    145  N   THR    88       3.362 -13.424   5.133  1.00  0.00              
ATOM    146  CA  THR    88       4.381 -14.440   4.918  1.00  0.00              
ATOM    147  C   THR    88       5.576 -14.098   5.796  1.00  0.00              
ATOM    148  O   THR    88       5.943 -14.863   6.683  1.00  0.00              
ATOM    149  N   LEU    89       6.168 -12.932   5.551  1.00  0.00              
ATOM    150  CA  LEU    89       7.326 -12.486   6.311  1.00  0.00              
ATOM    151  C   LEU    89       7.077 -12.599   7.805  1.00  0.00              
ATOM    152  O   LEU    89       7.956 -13.005   8.560  1.00  0.00              
ATOM    153  N   GLY    90       5.874 -12.241   8.232  1.00  0.00              
ATOM    154  CA  GLY    90       5.536 -12.311   9.643  1.00  0.00              
ATOM    155  C   GLY    90       5.689 -13.707  10.240  1.00  0.00              
ATOM    156  O   GLY    90       6.233 -13.840  11.325  1.00  0.00              
ATOM    157  N   ASN    91       5.213 -14.738   9.541  1.00  0.00              
ATOM    158  CA  ASN    91       5.318 -16.118  10.023  1.00  0.00              
ATOM    159  C   ASN    91       6.778 -16.595  10.075  1.00  0.00              
ATOM    160  O   ASN    91       7.147 -17.396  10.934  1.00  0.00              
ATOM    161  N   GLU    92       7.610 -16.112   9.157  1.00  0.00              
ATOM    162  CA  GLU    92       9.017 -16.499   9.157  1.00  0.00              
ATOM    163  C   GLU    92       9.705 -15.891  10.366  1.00  0.00              
ATOM    164  O   GLU    92      10.511 -16.541  11.031  1.00  0.00              
ATOM    165  N   LEU    93       9.378 -14.634  10.635  1.00  0.00              
ATOM    166  CA  LEU    93       9.950 -13.914  11.754  1.00  0.00              
ATOM    167  C   LEU    93       9.498 -14.496  13.092  1.00  0.00              
ATOM    168  O   LEU    93      10.319 -14.686  13.990  1.00  0.00              
ATOM    169  N   SER    94       8.198 -14.759  13.237  1.00  0.00              
ATOM    170  CA  SER    94       7.694 -15.342  14.476  1.00  0.00              
ATOM    171  C   SER    94       8.448 -16.630  14.710  1.00  0.00              
ATOM    172  O   SER    94       8.740 -16.985  15.846  1.00  0.00              
ATOM    173  N   ASP    95       8.766 -17.333  13.632  1.00  0.00              
ATOM    174  CA  ASP    95       9.463 -18.596  13.774  1.00  0.00              
ATOM    175  C   ASP    95      10.871 -18.432  14.299  1.00  0.00              
ATOM    176  O   ASP    95      11.264 -19.107  15.244  1.00  0.00              
ATOM    177  N   ILE    96      11.628 -17.536  13.680  1.00  0.00              
ATOM    178  CA  ILE    96      12.997 -17.270  14.095  1.00  0.00              
ATOM    179  C   ILE    96      13.017 -16.663  15.493  1.00  0.00              
ATOM    180  O   ILE    96      14.019 -16.746  16.198  1.00  0.00              
ATOM    181  N   LYS    97      11.903 -16.063  15.891  1.00  0.00              
ATOM    182  CA  LYS    97      11.805 -15.448  17.204  1.00  0.00              
ATOM    183  C   LYS    97      11.505 -16.491  18.281  1.00  0.00              
ATOM    184  O   LYS    97      11.979 -16.369  19.408  1.00  0.00              
ATOM    185  N   LEU    98      10.725 -17.513  17.927  1.00  0.00              
ATOM    186  CA  LEU    98      10.365 -18.592  18.854  1.00  0.00              
ATOM    187  C   LEU    98      11.615 -19.339  19.266  1.00  0.00              
ATOM    188  O   LEU    98      11.576 -20.246  20.102  1.00  0.00              
ATOM    189  N   SER    99      12.721 -18.942  18.649  1.00  0.00              
ATOM    190  CA  SER    99      14.026 -19.529  18.890  1.00  0.00              
ATOM    191  C   SER    99      14.878 -18.583  19.736  1.00  0.00              
ATOM    192  O   SER    99      15.225 -18.892  20.880  1.00  0.00              
ATOM    193  N   LEU   100      15.197 -17.428  19.166  1.00  0.00              
ATOM    194  CA  LEU   100      16.004 -16.427  19.846  1.00  0.00              
ATOM    195  C   LEU   100      15.428 -15.981  21.192  1.00  0.00              
ATOM    196  O   LEU   100      16.143 -15.944  22.196  1.00  0.00              
ATOM    197  N   LEU   101      14.146 -15.635  21.216  1.00  0.00              
ATOM    198  CA  LEU   101      13.527 -15.184  22.452  1.00  0.00              
ATOM    199  C   LEU   101      12.282 -15.956  22.862  1.00  0.00              
ATOM    200  O   LEU   101      11.192 -15.392  22.929  1.00  0.00              
ATOM    201  N   SER   102      12.417 -17.262  23.134  1.00  0.00              
ATOM    202  CA  SER   102      11.209 -17.985  23.537  1.00  0.00              
ATOM    203  C   SER   102      10.720 -17.393  24.852  1.00  0.00              
ATOM    204  O   SER   102      11.277 -16.402  25.336  1.00  0.00              
ATOM    205  N   LEU   103       9.694 -17.994  25.443  1.00  0.00              
ATOM    206  CA  LEU   103       9.175 -17.453  26.682  1.00  0.00              
ATOM    207  C   LEU   103       8.299 -16.278  26.311  1.00  0.00              
ATOM    208  O   LEU   103       7.436 -15.868  27.082  1.00  0.00              
END
