
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS556_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          1.595
LGA    K       6      K       6          1.409
LGA    I       7      I       7          0.818
LGA    A       8      A       8          0.704
LGA    R       9      R       9          1.031
LGA    I      10      I      10          0.852
LGA    N      11      N      11          0.227
LGA    E      12      E      12          0.390
LGA    L      13      L      13          0.909
LGA    A      14      A      14          0.893
LGA    A      15      A      15          1.133
LGA    K      16      K      16          1.061
LGA    A      17      A      17          0.236
LGA    K      18      K      18          1.547
LGA    A      19      A      19          2.702
LGA    G      20      G      20          2.091
LGA    V      21      V      21          1.824
LGA    I      22      -       -           -
LGA    T      23      -       -           -
LGA    E      24      -       -           -
LGA    E      25      -       -           -
LGA    E      26      -       -           -
LGA    K      27      -       -           -
LGA    A      28      -       -           -
LGA    E      29      -       -           -
LGA    Q      30      I      22          1.921
LGA    Q      31      T      23          4.832
LGA    K      32      E      24          2.055
LGA    L      33      E      25          2.632
LGA    R      34      E      26          2.704
LGA    Q      35      K      27          2.624
LGA    E      36      A      28          2.744
LGA    Y      37      E      29          2.907
LGA    L      38      Q      30          2.216
LGA    -       -      Q      31           -
LGA    K      39      K      32          3.739
LGA    G      40      L      33           #
LGA    -       -      R      34           -
LGA    -       -      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     27    2.08    66.67     66.823     1.241

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.680729 * X  +  -0.100489 * Y  +  -0.725610 * Z  +   2.657369
  Y_new =   0.526584 * X  +   0.755719 * Y  +   0.389355 * Z  + -13.844390
  Z_new =   0.509231 * X  +  -0.647140 * Y  +   0.567356 * Z  + -11.209120 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.850997    2.290596  [ DEG:   -48.7585    131.2415 ]
  Theta =  -0.534291   -2.607301  [ DEG:   -30.6126   -149.3874 ]
  Phi   =   0.658409   -2.483184  [ DEG:    37.7241   -142.2759 ]
 
# 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_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS556_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   27   2.08   66.67  66.823
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS556_3-D1
PFRMAT TS
TARGET T0335
MODEL 3
PARENT N/A
ATOM     21  N   ALA     5       0.192  -9.441  -7.508  1.00 10.00
ATOM     22  CA  ALA     5       0.039  -9.557  -6.063  1.00 10.00
ATOM     23  C   ALA     5       0.265  -8.217  -5.376  1.00 10.00
ATOM     24  O   ALA     5      -0.431  -7.873  -4.420  1.00 10.00
ATOM     25  CB  ALA     5       0.993 -10.605  -5.511  1.00 10.00
ATOM     26  N   LYS     6       1.241  -7.462  -5.868  1.00 10.00
ATOM     27  CA  LYS     6       1.573  -6.166  -5.289  1.00 10.00
ATOM     28  C   LYS     6       0.403  -5.198  -5.399  1.00 10.00
ATOM     29  O   LYS     6       0.125  -4.437  -4.472  1.00 10.00
ATOM     30  CB  LYS     6       2.809  -5.586  -5.962  1.00 10.00
ATOM     31  N   ILE     7      -0.281  -5.231  -6.538  1.00 10.00
ATOM     32  CA  ILE     7      -1.437  -4.370  -6.763  1.00 10.00
ATOM     33  C   ILE     7      -2.592  -4.749  -5.846  1.00 10.00
ATOM     34  O   ILE     7      -3.215  -3.886  -5.228  1.00 10.00
ATOM     35  CB  ILE     7      -1.871  -4.436  -8.219  1.00 10.00
ATOM     36  N   ALA     8      -2.874  -6.046  -5.760  1.00 10.00
ATOM     37  CA  ALA     8      -3.960  -6.541  -4.924  1.00 10.00
ATOM     38  C   ALA     8      -3.667  -6.311  -3.448  1.00 10.00
ATOM     39  O   ALA     8      -4.577  -6.059  -2.657  1.00 10.00
ATOM     40  CB  ALA     8      -4.207  -8.017  -5.194  1.00 10.00
ATOM     41  N   ARG     9      -2.392  -6.397  -3.082  1.00 10.00
ATOM     42  CA  ARG     9      -1.976  -6.186  -1.700  1.00 10.00
ATOM     43  C   ARG     9      -2.167  -4.733  -1.284  1.00 10.00
ATOM     44  O   ARG     9      -2.635  -4.449  -0.181  1.00 10.00
ATOM     45  CB  ARG     9      -0.527  -6.607  -1.513  1.00 10.00
ATOM     46  N   ILE    10      -1.803  -3.815  -2.173  1.00 10.00
ATOM     47  CA  ILE    10      -1.937  -2.389  -1.901  1.00 10.00
ATOM     48  C   ILE    10      -3.401  -1.984  -1.794  1.00 10.00
ATOM     49  O   ILE    10      -3.773  -1.185  -0.935  1.00 10.00
ATOM     50  CB  ILE    10      -1.237  -1.575  -2.980  1.00 10.00
ATOM     51  N   ASN    11      -4.229  -2.541  -2.671  1.00 10.00
ATOM     52  CA  ASN    11      -5.659  -2.252  -2.665  1.00 10.00
ATOM     53  C   ASN    11      -6.311  -2.724  -1.373  1.00 10.00
ATOM     54  O   ASN    11      -7.135  -2.020  -0.790  1.00 10.00
ATOM     55  CB  ASN    11      -6.334  -2.895  -3.867  1.00 10.00
ATOM     56  N   GLU    12      -5.936  -3.918  -0.929  1.00 10.00
ATOM     57  CA  GLU    12      -6.483  -4.486   0.298  1.00 10.00
ATOM     58  C   GLU    12      -5.989  -3.727   1.524  1.00 10.00
ATOM     59  O   GLU    12      -6.749  -3.478   2.460  1.00 10.00
ATOM     60  CB  GLU    12      -6.126  -5.960   0.407  1.00 10.00
ATOM     61  N   LEU    13      -4.711  -3.362   1.512  1.00 10.00
ATOM     62  CA  LEU    13      -4.117  -2.620   2.617  1.00 10.00
ATOM     63  C   LEU    13      -4.846  -1.304   2.852  1.00 10.00
ATOM     64  O   LEU    13      -5.219  -0.981   3.980  1.00 10.00
ATOM     65  CB  LEU    13      -2.640  -2.370   2.353  1.00 10.00
ATOM     66  N   ALA    14      -5.047  -0.544   1.779  1.00 10.00
ATOM     67  CA  ALA    14      -5.743   0.734   1.864  1.00 10.00
ATOM     68  C   ALA    14      -7.162   0.556   2.388  1.00 10.00
ATOM     69  O   ALA    14      -7.633   1.340   3.210  1.00 10.00
ATOM     70  CB  ALA    14      -5.757   1.421   0.507  1.00 10.00
ATOM     71  N   ALA    15      -7.839  -0.482   1.906  1.00 10.00
ATOM     72  CA  ALA    15      -9.212  -0.755   2.311  1.00 10.00
ATOM     73  C   ALA    15      -9.289  -1.111   3.790  1.00 10.00
ATOM     74  O   ALA    15     -10.170  -0.637   4.508  1.00 10.00
ATOM     75  CB  ALA    15      -9.802  -1.872   1.463  1.00 10.00
ATOM     76  N   LYS    16      -8.362  -1.948   4.241  1.00 10.00
ATOM     77  CA  LYS    16      -8.335  -2.387   5.631  1.00 10.00
ATOM     78  C   LYS    16      -7.932  -1.249   6.560  1.00 10.00
ATOM     79  O   LYS    16      -8.476  -1.105   7.655  1.00 10.00
ATOM     80  CB  LYS    16      -7.393  -3.569   5.797  1.00 10.00
ATOM     81  N   ALA    17      -6.973  -0.442   6.117  1.00 10.00
ATOM     82  CA  ALA    17      -6.502   0.692   6.903  1.00 10.00
ATOM     83  C   ALA    17      -7.608   1.719   7.107  1.00 10.00
ATOM     84  O   ALA    17      -7.772   2.261   8.200  1.00 10.00
ATOM     85  CB  ALA    17      -5.295   1.335   6.236  1.00 10.00
ATOM     86  N   LYS    18      -8.366   1.983   6.048  1.00 10.00
ATOM     87  CA  LYS    18      -9.476   2.927   6.115  1.00 10.00
ATOM     88  C   LYS    18     -10.576   2.417   7.038  1.00 10.00
ATOM     89  O   LYS    18     -11.167   3.186   7.796  1.00 10.00
ATOM     90  CB  LYS    18     -10.029   3.195   4.723  1.00 10.00
ATOM     91  N   ALA    19     -10.847   1.118   6.967  1.00 10.00
ATOM     92  CA  ALA    19     -11.877   0.505   7.796  1.00 10.00
ATOM     93  C   ALA    19     -11.529   0.610   9.274  1.00 10.00
ATOM     94  O   ALA    19     -12.414   0.628  10.130  1.00 10.00
ATOM     95  CB  ALA    19     -12.081  -0.949   7.398  1.00 10.00
ATOM     96  N   GLY    20     -10.235   0.677   9.570  1.00 10.00
ATOM     97  CA  GLY    20      -9.769   0.801  10.945  1.00 10.00
ATOM     98  C   GLY    20      -9.695   2.262  11.372  1.00 10.00
ATOM     99  O   GLY    20      -9.073   2.593  12.381  1.00 10.00
ATOM    100  N   VAL    21     -10.334   3.132  10.598  1.00 10.00
ATOM    101  CA  VAL    21     -10.385   4.553  10.921  1.00 10.00
ATOM    102  C   VAL    21     -11.584   4.876  11.802  1.00 10.00
ATOM    103  O   VAL    21     -12.675   4.343  11.601  1.00 10.00
ATOM    104  CB  VAL    21     -10.419   5.386   9.648  1.00 10.00
ATOM    105  N   ILE    22     -11.376   5.753  12.778  1.00 10.00
ATOM    106  CA  ILE    22     -12.453   6.189  13.659  1.00 10.00
ATOM    107  C   ILE    22     -12.796   7.654  13.425  1.00 10.00
ATOM    108  O   ILE    22     -13.960   8.003  13.222  1.00 10.00
ATOM    109  CB  ILE    22     -12.075   5.957  15.114  1.00 10.00
ATOM    110  N   THR    23     -11.778   8.508  13.452  1.00 10.00
ATOM    111  CA  THR    23     -11.970   9.935  13.228  1.00 10.00
ATOM    112  C   THR    23     -10.894  10.497  12.308  1.00 10.00
ATOM    113  O   THR    23      -9.993   9.776  11.878  1.00 10.00
ATOM    114  CB  THR    23     -11.981  10.684  14.553  1.00 10.00
ATOM    115  N   GLU    24     -10.992  11.788  12.010  1.00 10.00
ATOM    116  CA  GLU    24     -10.020  12.452  11.150  1.00 10.00
ATOM    117  C   GLU    24      -8.607  12.307  11.701  1.00 10.00
ATOM    118  O   GLU    24      -7.652  12.125  10.946  1.00 10.00
ATOM    119  CB  GLU    24     -10.376  13.921  10.982  1.00 10.00
ATOM    120  N   GLU    25      -8.481  12.387  13.022  1.00 10.00
ATOM    121  CA  GLU    25      -7.193  12.207  13.680  1.00 10.00
ATOM    122  C   GLU    25      -6.668  10.790  13.485  1.00 10.00
ATOM    123  O   GLU    25      -5.499  10.591  13.156  1.00 10.00
ATOM    124  CB  GLU    25      -7.306  12.532  15.162  1.00 10.00
ATOM    125  N   GLU    26      -7.540   9.808  13.688  1.00 10.00
ATOM    126  CA  GLU    26      -7.178   8.409  13.489  1.00 10.00
ATOM    127  C   GLU    26      -6.937   8.108  12.016  1.00 10.00
ATOM    128  O   GLU    26      -6.134   7.240  11.674  1.00 10.00
ATOM    129  CB  GLU    26      -8.259   7.497  14.049  1.00 10.00
ATOM    130  N   LYS    27      -7.637   8.829  11.147  1.00 10.00
ATOM    131  CA  LYS    27      -7.468   8.672   9.708  1.00 10.00
ATOM    132  C   LYS    27      -6.065   9.074   9.271  1.00 10.00
ATOM    133  O   LYS    27      -5.439   8.395   8.457  1.00 10.00
ATOM    134  CB  LYS    27      -8.512   9.484   8.958  1.00 10.00
ATOM    135  N   ALA    28      -5.576  10.184   9.817  1.00 10.00
ATOM    136  CA  ALA    28      -4.240  10.670   9.496  1.00 10.00
ATOM    137  C   ALA    28      -3.171   9.681   9.941  1.00 10.00
ATOM    138  O   ALA    28      -2.212   9.420   9.214  1.00 10.00
ATOM    139  CB  ALA    28      -4.005  12.031  10.134  1.00 10.00
ATOM    140  N   GLU    29      -3.342   9.132  11.140  1.00 10.00
ATOM    141  CA  GLU    29      -2.408   8.147  11.671  1.00 10.00
ATOM    142  C   GLU    29      -2.531   6.819  10.936  1.00 10.00
ATOM    143  O   GLU    29      -1.540   6.119  10.729  1.00 10.00
ATOM    144  CB  GLU    29      -2.633   7.954  13.162  1.00 10.00
ATOM    145  N   GLN    30      -3.754   6.477  10.544  1.00 10.00
ATOM    146  CA  GLN    30      -3.991   5.303   9.712  1.00 10.00
ATOM    147  C   GLN    30      -3.211   5.386   8.407  1.00 10.00
ATOM    148  O   GLN    30      -2.609   4.406   7.970  1.00 10.00
ATOM    149  CB  GLN    30      -5.478   5.142   9.435  1.00 10.00
ATOM    150  N   GLN    31      -3.225   6.563   7.789  1.00 10.00
ATOM    151  CA  GLN    31      -2.491   6.785   6.550  1.00 10.00
ATOM    152  C   GLN    31      -0.988   6.676   6.773  1.00 10.00
ATOM    153  O   GLN    31      -0.280   6.042   5.990  1.00 10.00
ATOM    154  CB  GLN    31      -2.844   8.143   5.960  1.00 10.00
ATOM    155  N   LYS    32      -0.507   7.297   7.844  1.00 10.00
ATOM    156  CA  LYS    32       0.897   7.197   8.222  1.00 10.00
ATOM    157  C   LYS    32       1.316   5.743   8.402  1.00 10.00
ATOM    158  O   LYS    32       2.439   5.366   8.068  1.00 10.00
ATOM    159  CB  LYS    32       1.162   7.988   9.494  1.00 10.00
ATOM    160  N   LEU    33       0.407   4.931   8.931  1.00 10.00
ATOM    161  CA  LEU    33       0.679   3.516   9.150  1.00 10.00
ATOM    162  C   LEU    33       0.579   2.729   7.851  1.00 10.00
ATOM    163  O   LEU    33       1.369   1.817   7.603  1.00 10.00
ATOM    164  CB  LEU    33      -0.274   2.948  10.191  1.00 10.00
ATOM    165  N   ARG    34      -0.398   3.083   7.023  1.00 10.00
ATOM    166  CA  ARG    34      -0.586   2.430   5.733  1.00 10.00
ATOM    167  C   ARG    34       0.687   2.484   4.899  1.00 10.00
ATOM    168  O   ARG    34       1.067   1.501   4.263  1.00 10.00
ATOM    169  CB  ARG    34      -1.743   3.067   4.980  1.00 10.00
ATOM    170  N   GLN    35       1.345   3.639   4.905  1.00 10.00
ATOM    171  CA  GLN    35       2.580   3.822   4.152  1.00 10.00
ATOM    172  C   GLN    35       3.660   2.856   4.622  1.00 10.00
ATOM    173  O   GLN    35       4.350   2.239   3.810  1.00 10.00
ATOM    174  CB  GLN    35       3.065   5.259   4.269  1.00 10.00
ATOM    175  N   GLU    36       3.802   2.728   5.937  1.00 10.00
ATOM    176  CA  GLU    36       4.767   1.802   6.517  1.00 10.00
ATOM    177  C   GLU    36       4.481   0.369   6.090  1.00 10.00
ATOM    178  O   GLU    36       5.397  -0.382   5.751  1.00 10.00
ATOM    179  CB  GLU    36       4.764   1.915   8.034  1.00 10.00
ATOM    180  N   TYR    37       3.207  -0.006   6.106  1.00 10.00
ATOM    181  CA  TYR    37       2.798  -1.350   5.718  1.00 10.00
ATOM    182  C   TYR    37       3.031  -1.589   4.232  1.00 10.00
ATOM    183  O   TYR    37       3.487  -2.658   3.828  1.00 10.00
ATOM    184  CB  TYR    37       1.338  -1.584   6.071  1.00 10.00
ATOM    185  N   LEU    38       2.715  -0.585   3.420  1.00 10.00
ATOM    186  CA  LEU    38       2.898  -0.679   1.976  1.00 10.00
ATOM    187  C   LEU    38       4.363  -0.905   1.621  1.00 10.00
ATOM    188  O   LEU    38       4.678  -1.606   0.660  1.00 10.00
ATOM    189  CB  LEU    38       2.371   0.572   1.291  1.00 10.00
ATOM    190  N   LYS    39       5.255  -0.307   2.404  1.00 10.00
ATOM    191  CA  LYS    39       6.689  -0.467   2.192  1.00 10.00
ATOM    192  C   LYS    39       7.148  -1.867   2.576  1.00 10.00
ATOM    193  O   LYS    39       8.012  -2.449   1.919  1.00 10.00
ATOM    194  CB  LYS    39       7.460   0.581   2.980  1.00 10.00
ATOM    195  N   GLY    40       6.566  -2.404   3.644  1.00 10.00
ATOM    196  CA  GLY    40       6.901  -3.746   4.104  1.00 10.00
ATOM    197  C   GLY    40       6.217  -4.807   3.251  1.00 10.00
ATOM    198  O   GLY    40       6.647  -5.961   3.216  1.00 10.00
TER
END
