
#######################################################
#                                                     #
#                        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   36 (  178),  selected   36 , name T0335TS757_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS757_3-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          2.020
LGA    K       6      K       6          0.950
LGA    I       7      I       7          1.433
LGA    A       8      A       8          1.971
LGA    R       9      R       9          1.470
LGA    I      10      I      10          0.658
LGA    N      11      N      11          0.635
LGA    E      12      E      12          1.535
LGA    L      13      L      13          1.988
LGA    A      14      A      14          1.534
LGA    A      15      A      15          1.272
LGA    K      16      K      16          1.036
LGA    A      17      A      17          1.062
LGA    K      18      K      18          1.210
LGA    A      19      A      19          2.478
LGA    G      20      G      20          2.294
LGA    V      21      V      21          0.545
LGA    I      22      I      22          0.613
LGA    T      23      T      23          4.368
LGA    E      24      -       -           -
LGA    E      25      E      24          2.661
LGA    E      26      E      25          3.393
LGA    K      27      E      26          2.998
LGA    A      28      K      27          4.610
LGA    E      29      A      28          4.522
LGA    Q      30      -       -           -
LGA    Q      31      -       -           -
LGA    K      32      -       -           -
LGA    L      33      E      29           #
LGA    R      34      Q      30          4.610
LGA    Q      35      Q      31          2.701
LGA    E      36      K      32          2.817
LGA    Y      37      L      33          2.667
LGA    L      38      -       -           -
LGA    K      39      R      34          1.170
LGA    G      40      Q      35           #
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     29    2.44    75.86     63.679     1.140

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.881334 * X  +  -0.409595 * Y  +  -0.235546 * Z  +   2.872678
  Y_new =   0.220736 * X  +   0.797697 * Y  +  -0.561208 * Z  + -12.043726
  Z_new =   0.417763 * X  +   0.442619 * Y  +   0.793450 * Z  + -10.266014 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.508843   -2.632750  [ DEG:    29.1545   -150.8455 ]
  Theta =  -0.430982   -2.710611  [ DEG:   -24.6934   -155.3066 ]
  Phi   =   0.245409   -2.896184  [ DEG:    14.0609   -165.9391 ]
 
# 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: T0335TS757_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS757_3-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   29   2.44   75.86  63.679
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS757_3-D1
PFRMAT TS
TARGET T0335
MODEL  3
PARENT N/A
ATOM     31  N   ALA     5       0.056  -8.677  -8.005  1.00 10.00    
ATOM     32  CA  ALA     5      -0.476  -9.295  -6.802  1.00 10.00    
ATOM     33  C   ALA     5      -0.332  -8.323  -5.629  1.00 10.00    
ATOM     34  O   ALA     5      -1.148  -8.332  -4.708  1.00 10.00    
ATOM     35  CB  ALA     5       0.243 -10.622  -6.550  1.00 10.00    
ATOM     36  N   LYS     6       0.710  -7.508  -5.701  1.00 10.00    
ATOM     37  CA  LYS     6       0.970  -6.532  -4.656  1.00 10.00    
ATOM     38  C   LYS     6       0.106  -5.292  -4.896  1.00 10.00    
ATOM     39  O   LYS     6      -0.326  -4.639  -3.948  1.00 10.00    
ATOM     40  CB  LYS     6       2.467  -6.229  -4.567  1.00 10.00    
ATOM     45  N   ILE     7      -0.121  -5.006  -6.170  1.00 10.00    
ATOM     46  CA  ILE     7      -0.927  -3.856  -6.547  1.00 10.00    
ATOM     47  C   ILE     7      -2.394  -4.137  -6.217  1.00 10.00    
ATOM     48  O   ILE     7      -3.100  -3.262  -5.717  1.00 10.00    
ATOM     49  CB  ILE     7      -1.557  -4.419  -8.987  1.00 10.00    
ATOM     53  N   ALA     8      -2.810  -5.361  -6.510  1.00 10.00    
ATOM     54  CA  ALA     8      -4.181  -5.767  -6.251  1.00 10.00    
ATOM     55  C   ALA     8      -4.376  -5.958  -4.746  1.00 10.00    
ATOM     56  O   ALA     8      -5.440  -5.654  -4.210  1.00 10.00    
ATOM     57  CB  ALA     8      -4.496  -7.036  -7.045  1.00 10.00    
ATOM     58  N   ARG     9      -3.331  -6.461  -4.105  1.00 10.00    
ATOM     59  CA  ARG     9      -3.373  -6.697  -2.672  1.00 10.00    
ATOM     60  C   ARG     9      -3.355  -5.367  -1.915  1.00 10.00    
ATOM     61  O   ARG     9      -3.954  -5.248  -0.848  1.00 10.00    
ATOM     62  CB  ARG     9      -2.187  -7.550  -2.218  1.00 10.00    
ATOM     69  N   ILE    10      -2.660  -4.401  -2.498  1.00 10.00    
ATOM     70  CA  ILE    10      -2.556  -3.084  -1.892  1.00 10.00    
ATOM     71  C   ILE    10      -3.954  -2.481  -1.748  1.00 10.00    
ATOM     72  O   ILE    10      -4.239  -1.791  -0.771  1.00 10.00    
ATOM     73  CB  ILE    10      -2.179  -0.730  -2.884  1.00 10.00    
ATOM     77  N   ASN    11      -4.789  -2.763  -2.737  1.00 10.00    
ATOM     78  CA  ASN    11      -6.151  -2.257  -2.734  1.00 10.00    
ATOM     79  C   ASN    11      -7.010  -3.121  -1.808  1.00 10.00    
ATOM     80  O   ASN    11      -7.884  -2.610  -1.110  1.00 10.00    
ATOM     81  CB  ASN    11      -6.763  -2.312  -4.135  1.00 10.00    
ATOM     85  N   GLU    12      -6.729  -4.416  -1.832  1.00 10.00    
ATOM     86  CA  GLU    12      -7.465  -5.355  -1.003  1.00 10.00    
ATOM     87  C   GLU    12      -7.278  -5.017   0.477  1.00 10.00    
ATOM     88  O   GLU    12      -8.242  -4.704   1.173  1.00 10.00    
ATOM     89  CB  GLU    12      -7.038  -6.795  -1.296  1.00 10.00    
ATOM     94  N   LEU    13      -6.030  -5.092   0.916  1.00 10.00    
ATOM     95  CA  LEU    13      -5.703  -4.798   2.301  1.00 10.00    
ATOM     96  C   LEU    13      -5.820  -3.292   2.539  1.00 10.00    
ATOM     97  O   LEU    13      -6.014  -2.852   3.671  1.00 10.00    
ATOM     98  CB  LEU    13      -4.333  -5.373   2.662  1.00 10.00    
ATOM    102  N   ALA    14      -5.698  -2.542   1.453  1.00 10.00    
ATOM    103  CA  ALA    14      -5.787  -1.094   1.530  1.00 10.00    
ATOM    104  C   ALA    14      -7.182  -0.698   2.018  1.00 10.00    
ATOM    105  O   ALA    14      -7.316   0.121   2.927  1.00 10.00    
ATOM    106  CB  ALA    14      -5.454  -0.488   0.164  1.00 10.00    
ATOM    107  N   ALA    15      -8.185  -1.298   1.394  1.00 10.00    
ATOM    108  CA  ALA    15      -9.564  -1.018   1.754  1.00 10.00    
ATOM    109  C   ALA    15      -9.764  -1.294   3.245  1.00 10.00    
ATOM    110  O   ALA    15     -10.428  -0.526   3.939  1.00 10.00    
ATOM    111  CB  ALA    15     -10.500  -1.852   0.876  1.00 10.00    
ATOM    112  N   LYS    16      -9.176  -2.394   3.695  1.00 10.00    
ATOM    113  CA  LYS    16      -9.282  -2.782   5.091  1.00 10.00    
ATOM    114  C   LYS    16      -8.568  -1.742   5.959  1.00 10.00    
ATOM    115  O   LYS    16      -9.029  -1.419   7.052  1.00 10.00    
ATOM    116  CB  LYS    16      -8.766  -4.208   5.292  1.00 10.00    
ATOM    121  N   ALA    17      -7.455  -1.248   5.438  1.00 10.00    
ATOM    122  CA  ALA    17      -6.673  -0.252   6.152  1.00 10.00    
ATOM    123  C   ALA    17      -7.496   1.030   6.295  1.00 10.00    
ATOM    124  O   ALA    17      -7.305   1.792   7.240  1.00 10.00    
ATOM    125  CB  ALA    17      -5.352  -0.016   5.415  1.00 10.00    
ATOM    126  N   LYS    18      -8.395   1.228   5.342  1.00 10.00    
ATOM    127  CA  LYS    18      -9.249   2.404   5.351  1.00 10.00    
ATOM    128  C   LYS    18     -10.243   2.299   6.509  1.00 10.00    
ATOM    129  O   LYS    18     -10.506   3.284   7.197  1.00 10.00    
ATOM    130  CB  LYS    18      -9.913   2.593   3.986  1.00 10.00    
ATOM    135  N   ALA    19     -10.767   1.096   6.690  1.00 10.00    
ATOM    136  CA  ALA    19     -11.726   0.849   7.753  1.00 10.00    
ATOM    137  C   ALA    19     -11.009   0.902   9.103  1.00 10.00    
ATOM    138  O   ALA    19     -11.606   1.268  10.114  1.00 10.00    
ATOM    139  CB  ALA    19     -12.421  -0.493   7.514  1.00 10.00    
ATOM    140  N   GLY    20      -9.737   0.531   9.076  1.00 10.00    
ATOM    141  CA  GLY    20      -8.932   0.532  10.286  1.00 10.00    
ATOM    142  C   GLY    20      -8.751   1.952  10.824  1.00 10.00    
ATOM    143  O   GLY    20      -8.421   2.139  11.994  1.00 10.00    
ATOM    144  N   VAL    21      -8.976   2.917   9.945  1.00 10.00    
ATOM    145  CA  VAL    21      -8.842   4.315  10.317  1.00 10.00    
ATOM    146  C   VAL    21      -7.358   4.669  10.427  1.00 10.00    
ATOM    147  O   VAL    21      -6.956   5.399  11.332  1.00 10.00    
ATOM    148  CB  VAL    21      -9.392   6.097  12.103  1.00 10.00    
ATOM    151  N   ILE    22      -6.584   4.137   9.492  1.00 10.00    
ATOM    152  CA  ILE    22      -5.153   4.388   9.472  1.00 10.00    
ATOM    153  C   ILE    22      -4.859   5.563   8.538  1.00 10.00    
ATOM    154  O   ILE    22      -5.273   5.559   7.380  1.00 10.00    
ATOM    155  CB  ILE    22      -4.723   1.933  10.148  1.00 10.00    
ATOM    159  N   THR    23      -4.146   6.541   9.076  1.00 10.00    
ATOM    160  CA  THR    23      -3.791   7.720   8.305  1.00 10.00    
ATOM    161  C   THR    23      -2.451   7.510   7.597  1.00 10.00    
ATOM    162  O   THR    23      -1.785   6.498   7.807  1.00 10.00    
ATOM    163  CB  THR    23      -5.099   8.963  10.183  1.00 10.00    
ATOM    166  N   GLU    24      -2.095   8.484   6.772  1.00 10.00    
ATOM    167  CA  GLU    24      -0.846   8.420   6.032  1.00 10.00    
ATOM    168  C   GLU    24       0.340   8.351   6.995  1.00 10.00    
ATOM    169  O   GLU    24       1.401   7.839   6.644  1.00 10.00    
ATOM    170  CB  GLU    24      -0.711   9.610   5.080  1.00 10.00    
ATOM    175  N   GLU    25       0.119   8.874   8.193  1.00 10.00    
ATOM    176  CA  GLU    25       1.156   8.877   9.211  1.00 10.00    
ATOM    177  C   GLU    25       1.436   7.451   9.689  1.00 10.00    
ATOM    178  O   GLU    25       2.581   7.100   9.972  1.00 10.00    
ATOM    179  CB  GLU    25       0.772   9.784  10.382  1.00 10.00    
ATOM    184  N   GLU    26       0.371   6.667   9.764  1.00 10.00    
ATOM    185  CA  GLU    26       0.487   5.287  10.204  1.00 10.00    
ATOM    186  C   GLU    26       1.196   4.448   9.138  1.00 10.00    
ATOM    187  O   GLU    26       2.062   3.635   9.457  1.00 10.00    
ATOM    188  CB  GLU    26      -0.885   4.700  10.540  1.00 10.00    
ATOM    193  N   LYS    27       0.801   4.675   7.894  1.00 10.00    
ATOM    194  CA  LYS    27       1.388   3.951   6.778  1.00 10.00    
ATOM    195  C   LYS    27       2.847   4.380   6.609  1.00 10.00    
ATOM    196  O   LYS    27       3.678   3.600   6.146  1.00 10.00    
ATOM    197  CB  LYS    27       0.543   4.134   5.517  1.00 10.00    
ATOM    202  N   ALA    28       3.114   5.620   6.991  1.00 10.00    
ATOM    203  CA  ALA    28       4.458   6.163   6.887  1.00 10.00    
ATOM    204  C   ALA    28       5.373   5.441   7.877  1.00 10.00    
ATOM    205  O   ALA    28       6.593   5.452   7.723  1.00 10.00    
ATOM    206  CB  ALA    28       4.418   7.674   7.125  1.00 10.00    
ATOM    207  N   GLU    29       4.749   4.829   8.873  1.00 10.00    
ATOM    208  CA  GLU    29       5.492   4.103   9.889  1.00 10.00    
ATOM    209  C   GLU    29       6.443   3.099   9.234  1.00 10.00    
ATOM    210  O   GLU    29       7.612   3.012   9.608  1.00 10.00    
ATOM    211  CB  GLU    29       4.546   3.405  10.867  1.00 10.00    
ATOM    216  N   GLN    30       5.908   2.366   8.269  1.00 10.00    
ATOM    217  CA  GLN    30       6.694   1.372   7.560  1.00 10.00    
ATOM    218  C   GLN    30       6.818   1.750   6.082  1.00 10.00    
ATOM    219  O   GLN    30       5.869   1.593   5.317  1.00 10.00    
ATOM    220  CB  GLN    30       6.088  -0.024   7.722  1.00 10.00    
ATOM    225  N   GLN    31       7.997   2.239   5.727  1.00 10.00    
ATOM    226  CA  GLN    31       8.258   2.640   4.355  1.00 10.00    
ATOM    227  C   GLN    31       9.079   1.568   3.635  1.00 10.00    
ATOM    228  O   GLN    31       9.327   0.497   4.188  1.00 10.00    
ATOM    229  CB  GLN    31       8.963   3.998   4.305  1.00 10.00    
ATOM    234  N   LYS    32       9.477   1.893   2.414  1.00 10.00    
ATOM    235  CA  LYS    32      10.265   0.972   1.614  1.00 10.00    
ATOM    236  C   LYS    32       9.389  -0.211   1.196  1.00 10.00    
ATOM    237  O   LYS    32       8.695  -0.147   0.182  1.00 10.00    
ATOM    238  CB  LYS    32      11.533   0.561   2.363  1.00 10.00    
ATOM    243  N   LEU    33       9.448  -1.264   1.998  1.00 10.00    
ATOM    244  CA  LEU    33       8.669  -2.459   1.724  1.00 10.00    
ATOM    245  C   LEU    33       7.180  -2.128   1.835  1.00 10.00    
ATOM    246  O   LEU    33       6.408  -2.408   0.919  1.00 10.00    
ATOM    247  CB  LEU    33       9.112  -3.608   2.632  1.00 10.00    
ATOM    251  N   ARG    34       6.820  -1.536   2.965  1.00 10.00    
ATOM    252  CA  ARG    34       5.437  -1.164   3.208  1.00 10.00    
ATOM    253  C   ARG    34       5.007  -0.059   2.241  1.00 10.00    
ATOM    254  O   ARG    34       3.925  -0.123   1.659  1.00 10.00    
ATOM    255  CB  ARG    34       5.241  -0.680   4.645  1.00 10.00    
ATOM    262  N   GLN    35       5.877   0.931   2.100  1.00 10.00    
ATOM    263  CA  GLN    35       5.601   2.050   1.216  1.00 10.00    
ATOM    264  C   GLN    35       5.448   1.560  -0.226  1.00 10.00    
ATOM    265  O   GLN    35       4.603   2.059  -0.969  1.00 10.00    
ATOM    266  CB  GLN    35       6.695   3.115   1.321  1.00 10.00    
ATOM    271  N   GLU    36       6.278   0.590  -0.579  1.00 10.00    
ATOM    272  CA  GLU    36       6.245   0.028  -1.919  1.00 10.00    
ATOM    273  C   GLU    36       4.990  -0.826  -2.106  1.00 10.00    
ATOM    274  O   GLU    36       4.375  -0.809  -3.171  1.00 10.00    
ATOM    275  CB  GLU    36       7.510  -0.786  -2.203  1.00 10.00    
ATOM    280  N   TYR    37       4.645  -1.554  -1.052  1.00 10.00    
ATOM    281  CA  TYR    37       3.474  -2.413  -1.086  1.00 10.00    
ATOM    282  C   TYR    37       2.243  -1.537  -1.330  1.00 10.00    
ATOM    283  O   TYR    37       1.362  -1.903  -2.106  1.00 10.00    
ATOM    284  CB  TYR    37       3.391  -3.067   0.294  1.00 10.00    
ATOM    292  N   LEU    38       2.223  -0.399  -0.653  1.00 10.00    
ATOM    293  CA  LEU    38       1.115   0.532  -0.787  1.00 10.00    
ATOM    294  C   LEU    38       0.956   0.921  -2.257  1.00 10.00    
ATOM    295  O   LEU    38      -0.155   0.927  -2.786  1.00 10.00    
ATOM    296  CB  LEU    38       1.304   1.728   0.149  1.00 10.00    
ATOM    300  N   LYS    39       2.083   1.239  -2.878  1.00 10.00    
ATOM    301  CA  LYS    39       2.084   1.629  -4.276  1.00 10.00    
ATOM    302  C   LYS    39       1.639   0.442  -5.133  1.00 10.00    
ATOM    303  O   LYS    39       0.962   0.620  -6.144  1.00 10.00    
ATOM    304  CB  LYS    39       3.448   2.197  -4.675  1.00 10.00    
ATOM    309  N   GLY    40       2.038  -0.745  -4.697  1.00 10.00    
ATOM    310  CA  GLY    40       1.689  -1.960  -5.411  1.00 10.00    
ATOM    311  C   GLY    40       2.827  -2.399  -6.336  1.00 10.00    
ATOM    312  O   GLY    40       2.757  -3.461  -6.952  1.00 10.00    
TER
END
