
#######################################################
#                                                     #
#                        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 T0335TS556_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS556_5-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          3.199
LGA    K       6      K       6          2.110
LGA    I       7      I       7          1.354
LGA    A       8      A       8          1.370
LGA    R       9      R       9          1.354
LGA    I      10      I      10          0.885
LGA    N      11      N      11          0.959
LGA    E      12      E      12          0.924
LGA    L      13      L      13          1.175
LGA    A      14      A      14          0.354
LGA    A      15      A      15          0.836
LGA    K      16      K      16          1.362
LGA    A      17      A      17          0.960
LGA    K      18      K      18          0.942
LGA    A      19      A      19          2.550
LGA    G      20      G      20          2.421
LGA    V      21      V      21          0.524
LGA    I      22      I      22          1.499
LGA    T      23      T      23          2.603
LGA    E      24      E      24          4.174
LGA    E      25      E      25          4.463
LGA    E      26      E      26          2.648
LGA    K      27      K      27          1.299
LGA    A      28      A      28          1.776
LGA    E      29      E      29          2.302
LGA    Q      30      Q      30          4.337
LGA    Q      31      Q      31          4.432
LGA    K      32      K      32          3.872
LGA    L      33      -       -           -
LGA    R      34      -       -           -
LGA    Q      35      L      33          3.671
LGA    E      36      R      34           -
LGA    Y      37      Q      35           -
LGA    L      38      E      36           -
LGA    K      39      Y      37           -
LGA    G      40      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    2.43    96.55     67.856     1.145

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.747043 * X  +  -0.480194 * Y  +  -0.459718 * Z  +  -0.777717
  Y_new =   0.393164 * X  +   0.876773 * Y  +  -0.276933 * Z  + -11.497463
  Z_new =   0.536049 * X  +   0.026136 * Y  +   0.843782 * Z  + -15.146261 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.030965   -3.110628  [ DEG:     1.7742   -178.2258 ]
  Theta =  -0.565750   -2.575842  [ DEG:   -32.4151   -147.5849 ]
  Phi   =   0.484461   -2.657132  [ DEG:    27.7576   -152.2424 ]
 
# 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: T0335TS556_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS556_5-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   2.43   96.55  67.856
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS556_5-D1
PFRMAT TS
TARGET T0335
MODEL 5
PARENT N/A
ATOM     21  N   ALA     5      -2.044  -9.139  -9.548  1.00 10.00
ATOM     22  CA  ALA     5      -2.030  -9.634  -8.177  1.00 10.00
ATOM     23  C   ALA     5      -1.275  -8.685  -7.255  1.00 10.00
ATOM     24  O   ALA     5      -1.687  -8.447  -6.121  1.00 10.00
ATOM     25  CB  ALA     5      -1.419 -11.026  -8.123  1.00 10.00
ATOM     26  N   LYS     6      -0.167  -8.143  -7.751  1.00 10.00
ATOM     27  CA  LYS     6       0.607  -7.161  -7.002  1.00 10.00
ATOM     28  C   LYS     6      -0.227  -5.925  -6.691  1.00 10.00
ATOM     29  O   LYS     6      -0.237  -5.440  -5.559  1.00 10.00
ATOM     30  CB  LYS     6       1.862  -6.777  -7.771  1.00 10.00
ATOM     31  N   ILE     7      -0.925  -5.418  -7.701  1.00 10.00
ATOM     32  CA  ILE     7      -1.803  -4.267  -7.525  1.00 10.00
ATOM     33  C   ILE     7      -2.892  -4.558  -6.501  1.00 10.00
ATOM     34  O   ILE     7      -3.156  -3.747  -5.613  1.00 10.00
ATOM     35  CB  ILE     7      -2.418  -3.861  -8.856  1.00 10.00
ATOM     36  N   ALA     8      -3.525  -5.720  -6.631  1.00 10.00
ATOM     37  CA  ALA     8      -4.591  -6.118  -5.719  1.00 10.00
ATOM     38  C   ALA     8      -4.100  -6.149  -4.278  1.00 10.00
ATOM     39  O   ALA     8      -4.792  -5.694  -3.366  1.00 10.00
ATOM     40  CB  ALA     8      -5.152  -7.474  -6.119  1.00 10.00
ATOM     41  N   ARG     9      -2.902  -6.687  -4.077  1.00 10.00
ATOM     42  CA  ARG     9      -2.307  -6.759  -2.748  1.00 10.00
ATOM     43  C   ARG     9      -2.175  -5.374  -2.128  1.00 10.00
ATOM     44  O   ARG     9      -2.611  -5.143  -1.000  1.00 10.00
ATOM     45  CB  ARG     9      -0.951  -7.446  -2.811  1.00 10.00
ATOM     46  N   ILE    10      -1.570  -4.454  -2.872  1.00 10.00
ATOM     47  CA  ILE    10      -1.378  -3.089  -2.397  1.00 10.00
ATOM     48  C   ILE    10      -2.711  -2.374  -2.220  1.00 10.00
ATOM     49  O   ILE    10      -2.913  -1.649  -1.246  1.00 10.00
ATOM     50  CB  ILE    10      -0.481  -2.316  -3.352  1.00 10.00
ATOM     51  N   ASN    11      -3.618  -2.582  -3.168  1.00 10.00
ATOM     52  CA  ASN    11      -4.942  -1.974  -3.108  1.00 10.00
ATOM     53  C   ASN    11      -5.728  -2.483  -1.906  1.00 10.00
ATOM     54  O   ASN    11      -6.485  -1.735  -1.286  1.00 10.00
ATOM     55  CB  ASN    11      -5.708  -2.242  -4.395  1.00 10.00
ATOM     56  N   GLU    12      -5.542  -3.757  -1.581  1.00 10.00
ATOM     57  CA  GLU    12      -6.232  -4.367  -0.450  1.00 10.00
ATOM     58  C   GLU    12      -5.716  -3.816   0.872  1.00 10.00
ATOM     59  O   GLU    12      -6.484  -3.607   1.811  1.00 10.00
ATOM     60  CB  GLU    12      -6.081  -5.880  -0.490  1.00 10.00
ATOM     61  N   LEU    13      -4.409  -3.581   0.941  1.00 10.00
ATOM     62  CA  LEU    13      -3.791  -3.033   2.142  1.00 10.00
ATOM     63  C   LEU    13      -4.286  -1.620   2.420  1.00 10.00
ATOM     64  O   LEU    13      -4.512  -1.247   3.571  1.00 10.00
ATOM     65  CB  LEU    13      -2.276  -3.052   2.014  1.00 10.00
ATOM     66  N   ALA    14      -4.452  -0.838   1.359  1.00 10.00
ATOM     67  CA  ALA    14      -5.010   0.505   1.477  1.00 10.00
ATOM     68  C   ALA    14      -6.413   0.468   2.066  1.00 10.00
ATOM     69  O   ALA    14      -6.752   1.269   2.938  1.00 10.00
ATOM     70  CB  ALA    14      -5.020   1.196   0.122  1.00 10.00
ATOM     71  N   ALA    15      -7.228  -0.467   1.586  1.00 10.00
ATOM     72  CA  ALA    15      -8.593  -0.618   2.075  1.00 10.00
ATOM     73  C   ALA    15      -8.612  -0.986   3.552  1.00 10.00
ATOM     74  O   ALA    15      -9.364  -0.409   4.337  1.00 10.00
ATOM     75  CB  ALA    15      -9.337  -1.661   1.256  1.00 10.00
ATOM     76  N   LYS    16      -7.779  -1.952   3.927  1.00 10.00
ATOM     77  CA  LYS    16      -7.697  -2.399   5.312  1.00 10.00
ATOM     78  C   LYS    16      -7.272  -1.262   6.233  1.00 10.00
ATOM     79  O   LYS    16      -7.845  -1.072   7.306  1.00 10.00
ATOM     80  CB  LYS    16      -6.736  -3.571   5.435  1.00 10.00
ATOM     81  N   ALA    17      -6.263  -0.509   5.808  1.00 10.00
ATOM     82  CA  ALA    17      -5.755   0.608   6.596  1.00 10.00
ATOM     83  C   ALA    17      -6.832   1.663   6.812  1.00 10.00
ATOM     84  O   ALA    17      -7.005   2.170   7.922  1.00 10.00
ATOM     85  CB  ALA    17      -4.538   1.222   5.923  1.00 10.00
ATOM     86  N   LYS    18      -7.556   1.991   5.747  1.00 10.00
ATOM     87  CA  LYS    18      -8.614   2.991   5.818  1.00 10.00
ATOM     88  C   LYS    18      -9.731   2.546   6.753  1.00 10.00
ATOM     89  O   LYS    18     -10.260   3.346   7.526  1.00 10.00
ATOM     90  CB  LYS    18      -9.165   3.278   4.430  1.00 10.00
ATOM     91  N   ALA    19     -10.085   1.268   6.679  1.00 10.00
ATOM     92  CA  ALA    19     -11.134   0.713   7.525  1.00 10.00
ATOM     93  C   ALA    19     -10.756   0.797   8.998  1.00 10.00
ATOM     94  O   ALA    19     -11.605   1.048   9.853  1.00 10.00
ATOM     95  CB  ALA    19     -11.426  -0.728   7.132  1.00 10.00
ATOM     96  N   GLY    20      -9.476   0.586   9.288  1.00 10.00
ATOM     97  CA  GLY    20      -8.979   0.655  10.657  1.00 10.00
ATOM     98  C   GLY    20      -8.790   2.100  11.102  1.00 10.00
ATOM     99  O   GLY    20      -8.416   2.363  12.245  1.00 10.00
ATOM    100  N   VAL    21      -9.050   3.033  10.192  1.00 10.00
ATOM    101  CA  VAL    21      -8.792   4.445  10.448  1.00 10.00
ATOM    102  C   VAL    21      -7.328   4.684  10.793  1.00 10.00
ATOM    103  O   VAL    21      -7.006   5.538  11.618  1.00 10.00
ATOM    104  CB  VAL    21      -9.692   4.954  11.563  1.00 10.00
ATOM    105  N   ILE    22      -6.444   3.924  10.156  1.00 10.00
ATOM    106  CA  ILE    22      -5.013   4.034  10.414  1.00 10.00
ATOM    107  C   ILE    22      -4.485   5.405  10.012  1.00 10.00
ATOM    108  O   ILE    22      -5.091   6.099   9.197  1.00 10.00
ATOM    109  CB  ILE    22      -4.256   2.936   9.680  1.00 10.00
ATOM    110  N   THR    23      -3.350   5.789  10.589  1.00 10.00
ATOM    111  CA  THR    23      -2.739   7.080  10.293  1.00 10.00
ATOM    112  C   THR    23      -2.077   7.074   8.922  1.00 10.00
ATOM    113  O   THR    23      -1.886   6.018   8.319  1.00 10.00
ATOM    114  CB  THR    23      -1.730   7.448  11.370  1.00 10.00
ATOM    115  N   GLU    24      -1.729   8.259   8.433  1.00 10.00
ATOM    116  CA  GLU    24      -0.982   8.386   7.187  1.00 10.00
ATOM    117  C   GLU    24       0.336   7.624   7.255  1.00 10.00
ATOM    118  O   GLU    24       0.754   7.002   6.280  1.00 10.00
ATOM    119  CB  GLU    24      -0.733   9.851   6.865  1.00 10.00
ATOM    120  N   GLU    25       0.985   7.678   8.413  1.00 10.00
ATOM    121  CA  GLU    25       2.266   7.008   8.604  1.00 10.00
ATOM    122  C   GLU    25       2.103   5.494   8.592  1.00 10.00
ATOM    123  O   GLU    25       2.949   4.774   8.060  1.00 10.00
ATOM    124  CB  GLU    25       2.913   7.464   9.904  1.00 10.00
ATOM    125  N   GLU    26       1.012   5.016   9.180  1.00 10.00
ATOM    126  CA  GLU    26       0.723   3.587   9.214  1.00 10.00
ATOM    127  C   GLU    26       0.500   3.038   7.811  1.00 10.00
ATOM    128  O   GLU    26       0.981   1.957   7.473  1.00 10.00
ATOM    129  CB  GLU    26      -0.488   3.313  10.092  1.00 10.00
ATOM    130  N   LYS    27      -0.234   3.790   6.996  1.00 10.00
ATOM    131  CA  LYS    27      -0.484   3.401   5.613  1.00 10.00
ATOM    132  C   LYS    27       0.816   3.308   4.824  1.00 10.00
ATOM    133  O   LYS    27       1.029   2.359   4.071  1.00 10.00
ATOM    134  CB  LYS    27      -1.439   4.383   4.951  1.00 10.00
ATOM    135  N   ALA    28       1.683   4.299   5.002  1.00 10.00
ATOM    136  CA  ALA    28       2.970   4.325   4.318  1.00 10.00
ATOM    137  C   ALA    28       3.815   3.113   4.688  1.00 10.00
ATOM    138  O   ALA    28       4.464   2.512   3.832  1.00 10.00
ATOM    139  CB  ALA    28       3.716   5.611   4.637  1.00 10.00
ATOM    140  N   GLU    29       3.801   2.758   5.968  1.00 10.00
ATOM    141  CA  GLU    29       4.560   1.612   6.453  1.00 10.00
ATOM    142  C   GLU    29       4.026   0.310   5.868  1.00 10.00
ATOM    143  O   GLU    29       4.796  -0.571   5.484  1.00 10.00
ATOM    144  CB  GLU    29       4.533   1.562   7.973  1.00 10.00
ATOM    145  N   GLN    30       2.704   0.195   5.803  1.00 10.00
ATOM    146  CA  GLN    30       2.065  -0.962   5.188  1.00 10.00
ATOM    147  C   GLN    30       2.444  -1.084   3.718  1.00 10.00
ATOM    148  O   GLN    30       2.645  -2.186   3.208  1.00 10.00
ATOM    149  CB  GLN    30       0.555  -0.878   5.343  1.00 10.00
ATOM    150  N   GLN    31       2.540   0.055   3.040  1.00 10.00
ATOM    151  CA  GLN    31       2.924   0.080   1.634  1.00 10.00
ATOM    152  C   GLN    31       4.336  -0.457   1.439  1.00 10.00
ATOM    153  O   GLN    31       4.608  -1.184   0.484  1.00 10.00
ATOM    154  CB  GLN    31       2.809   1.490   1.078  1.00 10.00
ATOM    155  N   LYS    32       5.232  -0.093   2.351  1.00 10.00
ATOM    156  CA  LYS    32       6.616  -0.547   2.287  1.00 10.00
ATOM    157  C   LYS    32       6.720  -2.042   2.563  1.00 10.00
ATOM    158  O   LYS    32       7.499  -2.748   1.922  1.00 10.00
ATOM    159  CB  LYS    32       7.476   0.236   3.268  1.00 10.00
ATOM    160  N   LEU    33       5.929  -2.518   3.519  1.00 10.00
ATOM    161  CA  LEU    33       5.919  -3.933   3.869  1.00 10.00
ATOM    162  C   LEU    33       5.367  -4.780   2.730  1.00 10.00
ATOM    163  O   LEU    33       5.899  -5.846   2.422  1.00 10.00
ATOM    164  CB  LEU    33       5.114  -4.159   5.139  1.00 10.00
ATOM    165  N   ARG    34       4.296  -4.299   2.107  1.00 10.00
ATOM    166  CA  ARG    34       3.676  -5.004   0.992  1.00 10.00
ATOM    167  C   ARG    34       4.607  -5.053  -0.213  1.00 10.00
ATOM    168  O   ARG    34       4.695  -6.070  -0.901  1.00 10.00
ATOM    169  CB  ARG    34       2.355  -4.351   0.619  1.00 10.00
ATOM    170  N   GLN    35       5.299  -3.947  -0.465  1.00 10.00
ATOM    171  CA  GLN    35       6.237  -3.867  -1.579  1.00 10.00
ATOM    172  C   GLN    35       7.354  -4.892  -1.432  1.00 10.00
ATOM    173  O   GLN    35       7.697  -5.592  -2.386  1.00 10.00
ATOM    174  CB  GLN    35       6.813  -2.464  -1.687  1.00 10.00
ATOM    175  N   GLU    36       7.919  -4.977  -0.233  1.00 10.00
ATOM    176  CA  GLU    36       8.993  -5.924   0.044  1.00 10.00
ATOM    177  C   GLU    36       8.472  -7.355   0.064  1.00 10.00
ATOM    178  O   GLU    36       9.081  -8.256  -0.512  1.00 10.00
ATOM    179  CB  GLU    36       9.672  -5.585   1.362  1.00 10.00
ATOM    180  N   TYR    37       7.341  -7.559   0.732  1.00 10.00
ATOM    181  CA  TYR    37       6.775  -8.893   0.893  1.00 10.00
ATOM    182  C   TYR    37       5.944  -9.288  -0.321  1.00 10.00
ATOM    183  O   TYR    37       5.532 -10.440  -0.455  1.00 10.00
ATOM    184  CB  TYR    37       5.936  -8.964   2.159  1.00 10.00
ATOM    185  N   LEU    38       5.698  -8.325  -1.204  1.00 10.00
ATOM    186  CA  LEU    38       4.926  -8.574  -2.415  1.00 10.00
ATOM    187  C   LEU    38       5.646  -9.548  -3.336  1.00 10.00
ATOM    188  O   LEU    38       5.014 -10.284  -4.095  1.00 10.00
ATOM    189  CB  LEU    38       4.640  -7.267  -3.139  1.00 10.00
ATOM    190  N   LYS    39       6.973  -9.551  -3.266  1.00 10.00
ATOM    191  CA  LYS    39       7.783 -10.441  -4.090  1.00 10.00
ATOM    192  C   LYS    39       7.529 -11.901  -3.738  1.00 10.00
ATOM    193  O   LYS    39       7.276 -12.726  -4.616  1.00 10.00
ATOM    194  CB  LYS    39       9.259 -10.105  -3.940  1.00 10.00
ATOM    195  N   GLY    40       7.598 -12.214  -2.449  1.00 10.00
ATOM    196  CA  GLY    40       7.378 -13.576  -1.979  1.00 10.00
ATOM    197  C   GLY    40       5.944 -14.022  -2.235  1.00 10.00
ATOM    198  O   GLY    40       5.704 -15.149  -2.669  1.00 10.00
TER
END
