
#######################################################
#                                                     #
#                        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   54 (  216),  selected   54 , name T0335AL243_1
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335AL243_1.T0335.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    N       4      S       3          3.116
LGA    A       5      N       4          3.486
LGA    -       -      A       5           -
LGA    K       6      K       6          3.048
LGA    I       7      I       7          2.365
LGA    A       8      A       8          2.955
LGA    R       9      R       9          2.721
LGA    I      10      I      10          1.063
LGA    N      11      N      11          0.381
LGA    E      12      E      12          1.314
LGA    L      13      L      13          2.144
LGA    A      14      A      14          1.993
LGA    A      15      A      15          2.755
LGA    K      16      K      16          3.355
LGA    A      17      A      17          3.326
LGA    K      18      K      18          4.324
LGA    -       -      A      19           -
LGA    A      19      G      20          4.113
LGA    G      20      V      21           #
LGA    V      21      -       -           -
LGA    I      22      -       -           -
LGA    E      24      -       -           -
LGA    E      25      -       -           -
LGA    E      26      I      22          3.299
LGA    K      27      T      23          3.564
LGA    A      28      E      24          2.452
LGA    E      29      E      25          2.484
LGA    Q      30      E      26          2.595
LGA    Q      31      K      27          2.457
LGA    K      32      A      28          2.151
LGA    L      33      E      29          2.127
LGA    R      34      Q      30          2.271
LGA    Q      35      Q      31          2.319
LGA    E      36      K      32          2.736
LGA    L      38      L      33          2.888
LGA    K      39      R      34          3.702
LGA    G      40      Q      35          3.658
LGA    F      41      E      36          2.032
LGA    R      42      Y      37          1.590
LGA    S      43      L      38          1.987
LGA    S      44      K      39          4.322
LGA    M      45      G      40          4.722
LGA    K      46      F      41          2.062
LGA    N      47      R      42          2.263
LGA    T      48      -       -           -
LGA    E      58      -       -           -
LGA    E      65      -       -           -
LGA    K      66      -       -           -
LGA    L      67      -       -           -
LGA    K      68      -       -           -
LGA    R      69      -       -           -
LGA    E      70      -       -           -
LGA    Q      71      -       -           -
LGA    R      72      -       -           -
LGA    N      73      -       -           -
LGA    N      74      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   54   42    5.0     37    2.86    43.24     61.445     1.251

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.720167 * X  +   0.628696 * Y  +   0.293428 * Z  + -48.235565
  Y_new =   0.670088 * X  +   0.739910 * Y  +   0.059290 * Z  +  -1.567701
  Z_new =  -0.179834 * X  +   0.239322 * Y  +  -0.954141 * Z  +  98.516602 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.895838   -0.245754  [ DEG:   165.9193    -14.0807 ]
  Theta =   0.180818    2.960774  [ DEG:    10.3601    169.6399 ]
  Phi   =   2.392200   -0.749392  [ DEG:   137.0630    -42.9370 ]
 
# 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: T0335AL243_1                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL243_1.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   54   42   5.0   37   2.86   43.24  61.445
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL243_1
REMARK Aligment from pdb entry: 1dg3A
ATOM      1  N   ASN     4      -1.039  -4.955 -12.442  1.00  0.00              
ATOM      2  CA  ASN     4      -2.446  -4.904 -12.078  1.00  0.00              
ATOM      3  C   ASN     4      -2.864  -5.898 -10.998  1.00  0.00              
ATOM      4  O   ASN     4      -3.819  -5.648 -10.258  1.00  0.00              
ATOM      5  N   ALA     5      -2.156  -7.019 -10.899  1.00  0.00              
ATOM      6  CA  ALA     5      -2.468  -8.003  -9.873  1.00  0.00              
ATOM      7  C   ALA     5      -1.891  -7.510  -8.548  1.00  0.00              
ATOM      8  O   ALA     5      -2.403  -7.826  -7.474  1.00  0.00              
ATOM      9  N   LYS     6      -0.820  -6.730  -8.634  1.00  0.00              
ATOM     10  CA  LYS     6      -0.189  -6.180  -7.446  1.00  0.00              
ATOM     11  C   LYS     6      -1.059  -5.071  -6.875  1.00  0.00              
ATOM     12  O   LYS     6      -1.348  -5.053  -5.681  1.00  0.00              
ATOM     13  N   ILE     7      -1.467  -4.138  -7.731  1.00  0.00              
ATOM     14  CA  ILE     7      -2.304  -3.031  -7.287  1.00  0.00              
ATOM     15  C   ILE     7      -3.589  -3.519  -6.628  1.00  0.00              
ATOM     16  O   ILE     7      -4.012  -2.969  -5.612  1.00  0.00              
ATOM     17  N   ALA     8      -4.208  -4.550  -7.195  1.00  0.00              
ATOM     18  CA  ALA     8      -5.448  -5.066  -6.627  1.00  0.00              
ATOM     19  C   ALA     8      -5.203  -5.730  -5.278  1.00  0.00              
ATOM     20  O   ALA     8      -6.014  -5.608  -4.363  1.00  0.00              
ATOM     21  N   ARG     9      -4.085  -6.438  -5.165  1.00  0.00              
ATOM     22  CA  ARG     9      -3.729  -7.105  -3.919  1.00  0.00              
ATOM     23  C   ARG     9      -3.496  -6.028  -2.864  1.00  0.00              
ATOM     24  O   ARG     9      -3.970  -6.126  -1.729  1.00  0.00              
ATOM     25  N   ILE    10      -2.758  -4.997  -3.261  1.00  0.00              
ATOM     26  CA  ILE    10      -2.443  -3.886  -2.378  1.00  0.00              
ATOM     27  C   ILE    10      -3.706  -3.215  -1.854  1.00  0.00              
ATOM     28  O   ILE    10      -3.855  -3.013  -0.647  1.00  0.00              
ATOM     29  N   ASN    11      -4.611  -2.863  -2.764  1.00  0.00              
ATOM     30  CA  ASN    11      -5.862  -2.217  -2.380  1.00  0.00              
ATOM     31  C   ASN    11      -6.638  -3.087  -1.399  1.00  0.00              
ATOM     32  O   ASN    11      -7.195  -2.588  -0.425  1.00  0.00              
ATOM     33  N   GLU    12      -6.667  -4.390  -1.658  1.00  0.00              
ATOM     34  CA  GLU    12      -7.369  -5.330  -0.791  1.00  0.00              
ATOM     35  C   GLU    12      -6.774  -5.350   0.617  1.00  0.00              
ATOM     36  O   GLU    12      -7.501  -5.499   1.602  1.00  0.00              
ATOM     37  N   LEU    13      -5.456  -5.207   0.710  1.00  0.00              
ATOM     38  CA  LEU    13      -4.791  -5.220   2.012  1.00  0.00              
ATOM     39  C   LEU    13      -5.021  -3.910   2.756  1.00  0.00              
ATOM     40  O   LEU    13      -5.144  -3.905   3.983  1.00  0.00              
ATOM     41  N   ALA    14      -5.072  -2.800   2.020  1.00  0.00              
ATOM     42  CA  ALA    14      -5.321  -1.503   2.639  1.00  0.00              
ATOM     43  C   ALA    14      -6.703  -1.594   3.266  1.00  0.00              
ATOM     44  O   ALA    14      -6.922  -1.150   4.397  1.00  0.00              
ATOM     45  N   ALA    15      -7.640  -2.173   2.518  1.00  0.00              
ATOM     46  CA  ALA    15      -9.001  -2.336   3.013  1.00  0.00              
ATOM     47  C   ALA    15      -8.986  -3.143   4.311  1.00  0.00              
ATOM     48  O   ALA    15      -9.646  -2.781   5.285  1.00  0.00              
ATOM     49  N   LYS    16      -8.231  -4.237   4.323  1.00  0.00              
ATOM     50  CA  LYS    16      -8.144  -5.067   5.518  1.00  0.00              
ATOM     51  C   LYS    16      -7.594  -4.266   6.699  1.00  0.00              
ATOM     52  O   LYS    16      -8.074  -4.392   7.825  1.00  0.00              
ATOM     53  N   ALA    17      -6.588  -3.440   6.433  1.00  0.00              
ATOM     54  CA  ALA    17      -5.975  -2.606   7.463  1.00  0.00              
ATOM     55  C   ALA    17      -7.019  -1.672   8.074  1.00  0.00              
ATOM     56  O   ALA    17      -7.157  -1.588   9.298  1.00  0.00              
ATOM     57  N   LYS    18      -7.751  -0.971   7.213  1.00  0.00              
ATOM     58  CA  LYS    18      -8.780  -0.039   7.666  1.00  0.00              
ATOM     59  C   LYS    18      -9.899  -0.733   8.430  1.00  0.00              
ATOM     60  O   LYS    18     -10.582  -0.111   9.248  1.00  0.00              
ATOM     61  N   ALA    19     -10.080  -2.024   8.170  1.00  0.00              
ATOM     62  CA  ALA    19     -11.125  -2.787   8.837  1.00  0.00              
ATOM     63  C   ALA    19     -10.736  -3.248  10.240  1.00  0.00              
ATOM     64  O   ALA    19     -11.598  -3.656  11.020  1.00  0.00              
ATOM     65  N   GLY    20     -10.204  -0.266  16.452  1.00  0.00              
ATOM     66  CA  GLY    20      -9.519   0.615  17.396  1.00  0.00              
ATOM     67  C   GLY    20      -8.014   0.712  17.150  1.00  0.00              
ATOM     68  O   GLY    20      -7.208   0.360  18.014  1.00  0.00              
ATOM     69  N   VAL    21      -7.634   1.180  15.966  1.00  0.00              
ATOM     70  CA  VAL    21      -6.217   1.322  15.650  1.00  0.00              
ATOM     71  C   VAL    21      -5.666   2.592  16.293  1.00  0.00              
ATOM     72  O   VAL    21      -4.473   2.690  16.570  1.00  0.00              
ATOM     73  N   ILE    22      -6.538   3.566  16.532  1.00  0.00              
ATOM     74  CA  ILE    22      -6.088   4.798  17.157  1.00  0.00              
ATOM     75  C   ILE    22      -5.776   5.935  16.202  1.00  0.00              
ATOM     76  O   ILE    22      -5.838   5.776  14.983  1.00  0.00              
ATOM     77  N   GLU    24      -5.411   7.081  16.773  1.00  0.00              
ATOM     78  CA  GLU    24      -5.112   8.291  16.008  1.00  0.00              
ATOM     79  C   GLU    24      -3.961   8.241  14.998  1.00  0.00              
ATOM     80  O   GLU    24      -3.887   9.093  14.114  1.00  0.00              
ATOM     81  N   GLU    25      -3.068   7.260  15.109  1.00  0.00              
ATOM     82  CA  GLU    25      -1.928   7.178  14.195  1.00  0.00              
ATOM     83  C   GLU    25      -2.160   6.289  12.970  1.00  0.00              
ATOM     84  O   GLU    25      -1.261   6.110  12.155  1.00  0.00              
ATOM     85  N   GLU    26      -3.364   5.748  12.842  1.00  0.00              
ATOM     86  CA  GLU    26      -3.692   4.856  11.734  1.00  0.00              
ATOM     87  C   GLU    26      -3.266   5.371  10.358  1.00  0.00              
ATOM     88  O   GLU    26      -2.566   4.675   9.620  1.00  0.00              
ATOM     89  N   LYS    27      -3.684   6.587  10.018  1.00  0.00              
ATOM     90  CA  LYS    27      -3.354   7.176   8.727  1.00  0.00              
ATOM     91  C   LYS    27      -1.883   7.454   8.508  1.00  0.00              
ATOM     92  O   LYS    27      -1.326   7.100   7.471  1.00  0.00              
ATOM     93  N   ALA    28      -1.259   8.104   9.480  1.00  0.00              
ATOM     94  CA  ALA    28       0.154   8.441   9.396  1.00  0.00              
ATOM     95  C   ALA    28       1.012   7.187   9.213  1.00  0.00              
ATOM     96  O   ALA    28       1.921   7.163   8.384  1.00  0.00              
ATOM     97  N   GLU    29       0.711   6.148   9.989  1.00  0.00              
ATOM     98  CA  GLU    29       1.448   4.888   9.920  1.00  0.00              
ATOM     99  C   GLU    29       1.354   4.237   8.530  1.00  0.00              
ATOM    100  O   GLU    29       2.369   3.869   7.944  1.00  0.00              
ATOM    101  N   GLN    30       0.141   4.113   8.001  1.00  0.00              
ATOM    102  CA  GLN    30      -0.046   3.502   6.683  1.00  0.00              
ATOM    103  C   GLN    30       0.581   4.308   5.543  1.00  0.00              
ATOM    104  O   GLN    30       1.271   3.751   4.691  1.00  0.00              
ATOM    105  N   GLN    31       0.342   5.616   5.525  1.00  0.00              
ATOM    106  CA  GLN    31       0.887   6.451   4.462  1.00  0.00              
ATOM    107  C   GLN    31       2.406   6.466   4.471  1.00  0.00              
ATOM    108  O   GLN    31       3.036   6.489   3.416  1.00  0.00              
ATOM    109  N   LYS    32       3.001   6.458   5.656  1.00  0.00              
ATOM    110  CA  LYS    32       4.453   6.450   5.740  1.00  0.00              
ATOM    111  C   LYS    32       4.952   5.124   5.169  1.00  0.00              
ATOM    112  O   LYS    32       6.010   5.062   4.538  1.00  0.00              
ATOM    113  N   LEU    33       4.184   4.064   5.400  1.00  0.00              
ATOM    114  CA  LEU    33       4.549   2.749   4.892  1.00  0.00              
ATOM    115  C   LEU    33       4.445   2.746   3.373  1.00  0.00              
ATOM    116  O   LEU    33       5.385   2.374   2.673  1.00  0.00              
ATOM    117  N   ARG    34       3.288   3.162   2.875  1.00  0.00              
ATOM    118  CA  ARG    34       3.049   3.203   1.437  1.00  0.00              
ATOM    119  C   ARG    34       4.063   4.100   0.733  1.00  0.00              
ATOM    120  O   ARG    34       4.532   3.783  -0.359  1.00  0.00              
ATOM    121  N   GLN    35       4.407   5.215   1.369  1.00  0.00              
ATOM    122  CA  GLN    35       5.377   6.145   0.804  1.00  0.00              
ATOM    123  C   GLN    35       6.707   5.439   0.566  1.00  0.00              
ATOM    124  O   GLN    35       7.352   5.641  -0.461  1.00  0.00              
ATOM    125  N   GLU    36       7.108   4.604   1.519  1.00  0.00              
ATOM    126  CA  GLU    36       8.367   3.873   1.428  1.00  0.00              
ATOM    127  C   GLU    36       8.368   2.744   0.394  1.00  0.00              
ATOM    128  O   GLU    36       9.426   2.223   0.048  1.00  0.00              
ATOM    129  N   LEU    38       7.193   2.356  -0.090  1.00  0.00              
ATOM    130  CA  LEU    38       7.111   1.280  -1.078  1.00  0.00              
ATOM    131  C   LEU    38       6.873   1.834  -2.480  1.00  0.00              
ATOM    132  O   LEU    38       6.920   1.103  -3.468  1.00  0.00              
ATOM    133  N   LYS    39       6.620   3.135  -2.543  1.00  0.00              
ATOM    134  CA  LYS    39       6.356   3.845  -3.789  1.00  0.00              
ATOM    135  C   LYS    39       7.354   3.496  -4.893  1.00  0.00              
ATOM    136  O   LYS    39       6.967   3.201  -6.025  1.00  0.00              
ATOM    137  N   GLY    40       8.636   3.526  -4.557  1.00  0.00              
ATOM    138  CA  GLY    40       9.679   3.210  -5.522  1.00  0.00              
ATOM    139  C   GLY    40       9.542   1.767  -6.001  1.00  0.00              
ATOM    140  O   GLY    40       9.581   1.493  -7.200  1.00  0.00              
ATOM    141  N   PHE    41       9.377   0.848  -5.056  1.00  0.00              
ATOM    142  CA  PHE    41       9.232  -0.569  -5.372  1.00  0.00              
ATOM    143  C   PHE    41       8.017  -0.826  -6.259  1.00  0.00              
ATOM    144  O   PHE    41       8.043  -1.689  -7.136  1.00  0.00              
ATOM    145  N   ARG    42       6.951  -0.074  -6.020  1.00  0.00              
ATOM    146  CA  ARG    42       5.723  -0.224  -6.785  1.00  0.00              
ATOM    147  C   ARG    42       5.891   0.281  -8.212  1.00  0.00              
ATOM    148  O   ARG    42       5.440  -0.355  -9.164  1.00  0.00              
ATOM    149  N   SER    43       6.546   1.426  -8.358  1.00  0.00              
ATOM    150  CA  SER    43       6.776   2.005  -9.676  1.00  0.00              
ATOM    151  C   SER    43       7.581   1.030 -10.535  1.00  0.00              
ATOM    152  O   SER    43       7.323   0.883 -11.732  1.00  0.00              
ATOM    153  N   SER    44       8.549   0.362  -9.914  1.00  0.00              
ATOM    154  CA  SER    44       9.395  -0.599 -10.613  1.00  0.00              
ATOM    155  C   SER    44       8.557  -1.675 -11.290  1.00  0.00              
ATOM    156  O   SER    44       8.770  -1.993 -12.461  1.00  0.00              
ATOM    157  N   MET    45       7.611  -2.239 -10.549  1.00  0.00              
ATOM    158  CA  MET    45       6.744  -3.277 -11.089  1.00  0.00              
ATOM    159  C   MET    45       5.959  -2.723 -12.275  1.00  0.00              
ATOM    160  O   MET    45       5.727  -3.422 -13.257  1.00  0.00              
ATOM    161  N   LYS    46       5.555  -1.461 -12.173  1.00  0.00              
ATOM    162  CA  LYS    46       4.800  -0.805 -13.236  1.00  0.00              
ATOM    163  C   LYS    46       5.646  -0.652 -14.494  1.00  0.00              
ATOM    164  O   LYS    46       5.291  -1.146 -15.569  1.00  0.00              
ATOM    165  N   ASN    47       6.765   0.045 -14.349  1.00  0.00              
ATOM    166  CA  ASN    47       7.670   0.288 -15.462  1.00  0.00              
ATOM    167  C   ASN    47       8.210  -1.012 -16.060  1.00  0.00              
ATOM    168  O   ASN    47       8.708  -1.024 -17.184  1.00  0.00              
ATOM    169  N   THR    48       8.102  -2.103 -15.311  1.00  0.00              
ATOM    170  CA  THR    48       8.592  -3.398 -15.772  1.00  0.00              
ATOM    171  C   THR    48       7.521  -4.216 -16.491  1.00  0.00              
ATOM    172  O   THR    48       7.840  -5.115 -17.269  1.00  0.00              
ATOM    173  N   GLU    58       6.254  -3.897 -16.233  1.00  0.00              
ATOM    174  CA  GLU    58       5.142  -4.616 -16.849  1.00  0.00              
ATOM    175  C   GLU    58       5.068  -4.292 -18.341  1.00  0.00              
ATOM    176  O   GLU    58       4.603  -3.223 -18.734  1.00  0.00              
ATOM    177  N   GLU    65       5.519  -5.231 -19.166  1.00  0.00              
ATOM    178  CA  GLU    65       5.535  -5.048 -20.614  1.00  0.00              
ATOM    179  C   GLU    65       4.166  -5.110 -21.300  1.00  0.00              
ATOM    180  O   GLU    65       4.074  -4.956 -22.521  1.00  0.00              
ATOM    181  N   LYS    66       3.108  -5.327 -20.524  1.00  0.00              
ATOM    182  CA  LYS    66       1.759  -5.402 -21.088  1.00  0.00              
ATOM    183  C   LYS    66       1.052  -4.054 -21.064  1.00  0.00              
ATOM    184  O   LYS    66      -0.068  -3.929 -21.559  1.00  0.00              
ATOM    185  N   LEU    67       1.693  -3.048 -20.481  1.00  0.00              
ATOM    186  CA  LEU    67       1.089  -1.722 -20.401  1.00  0.00              
ATOM    187  C   LEU    67       1.723  -0.743 -21.380  1.00  0.00              
ATOM    188  O   LEU    67       2.941  -0.721 -21.549  1.00  0.00              
ATOM    189  N   LYS    68       0.890   0.071 -22.020  1.00  0.00              
ATOM    190  CA  LYS    68       1.389   1.057 -22.970  1.00  0.00              
ATOM    191  C   LYS    68       2.069   2.173 -22.191  1.00  0.00              
ATOM    192  O   LYS    68       1.848   2.328 -20.987  1.00  0.00              
ATOM    193  N   ARG    69       2.898   2.946 -22.879  1.00  0.00              
ATOM    194  CA  ARG    69       3.605   4.048 -22.245  1.00  0.00              
ATOM    195  C   ARG    69       2.641   5.083 -21.671  1.00  0.00              
ATOM    196  O   ARG    69       2.891   5.647 -20.605  1.00  0.00              
ATOM    197  N   GLU    70       1.541   5.332 -22.379  1.00  0.00              
ATOM    198  CA  GLU    70       0.562   6.313 -21.923  1.00  0.00              
ATOM    199  C   GLU    70      -0.127   5.826 -20.658  1.00  0.00              
ATOM    200  O   GLU    70      -0.332   6.598 -19.724  1.00  0.00              
ATOM    201  N   GLN    71      -0.484   4.545 -20.628  1.00  0.00              
ATOM    202  CA  GLN    71      -1.135   3.969 -19.457  1.00  0.00              
ATOM    203  C   GLN    71      -0.241   4.100 -18.225  1.00  0.00              
ATOM    204  O   GLN    71      -0.724   4.419 -17.138  1.00  0.00              
ATOM    205  N   ARG    72       1.057   3.855 -18.394  1.00  0.00              
ATOM    206  CA  ARG    72       1.998   3.965 -17.282  1.00  0.00              
ATOM    207  C   ARG    72       2.049   5.413 -16.827  1.00  0.00              
ATOM    208  O   ARG    72       2.036   5.704 -15.631  1.00  0.00              
ATOM    209  N   ASN    73       2.106   6.319 -17.796  1.00  0.00              
ATOM    210  CA  ASN    73       2.145   7.749 -17.521  1.00  0.00              
ATOM    211  C   ASN    73       0.935   8.133 -16.676  1.00  0.00              
ATOM    212  O   ASN    73       1.051   8.904 -15.724  1.00  0.00              
ATOM    213  N   ASN    74      -0.222   7.582 -17.031  1.00  0.00              
ATOM    214  CA  ASN    74      -1.462   7.853 -16.313  1.00  0.00              
ATOM    215  C   ASN    74      -1.404   7.270 -14.903  1.00  0.00              
ATOM    216  O   ASN    74      -1.787   7.929 -13.933  1.00  0.00              
END
