
#######################################################
#                                                     #
#                        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 (  216),  selected   36 , name T0335TS015_2u-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS015_2u-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          3.019
LGA    K       6      K       6          2.420
LGA    I       7      I       7          2.318
LGA    A       8      A       8          1.901
LGA    R       9      R       9          1.405
LGA    I      10      I      10          1.521
LGA    N      11      N      11          1.586
LGA    E      12      E      12          0.978
LGA    L      13      L      13          0.749
LGA    A      14      A      14          1.368
LGA    A      15      A      15          1.902
LGA    K      16      K      16          1.689
LGA    A      17      A      17          1.298
LGA    K      18      K      18          1.377
LGA    -       -      A      19           -
LGA    A      19      G      20          0.620
LGA    G      20      V      21          1.566
LGA    V      21      -       -           -
LGA    I      22      I      22          4.001
LGA    T      23      T      23          0.999
LGA    E      24      E      24          2.115
LGA    E      25      E      25          2.874
LGA    E      26      E      26          2.193
LGA    K      27      K      27          0.676
LGA    A      28      A      28          1.850
LGA    E      29      E      29          2.621
LGA    Q      30      Q      30          1.844
LGA    Q      31      Q      31          0.842
LGA    K      32      K      32          2.341
LGA    L      33      L      33          2.917
LGA    R      34      R      34          1.781
LGA    Q      35      Q      35          0.424
LGA    E      36      E      36          1.986
LGA    Y      37      Y      37          2.770
LGA    L      38      L      38          2.125
LGA    K      39      K      39          0.469
LGA    G      40      G      40          1.940

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     35    1.96    94.29     87.232     1.702

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.294436 * X  +  -0.890832 * Y  +   0.346015 * Z  +   3.803459
  Y_new =   0.864771 * X  +   0.094237 * Y  +  -0.493245 * Z  +  -2.615867
  Z_new =   0.406791 * X  +   0.444452 * Y  +   0.798113 * Z  + -10.320996 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.508109   -2.633483  [ DEG:    29.1125   -150.8875 ]
  Theta =  -0.418938   -2.722655  [ DEG:   -24.0034   -155.9966 ]
  Phi   =   1.242629   -1.898964  [ DEG:    71.1974   -108.8026 ]
 
# 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: T0335TS015_2u-D1                              
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS015_2u-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   35   1.96   94.29  87.232
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS015_2u-D1
PFRMAT TS
TARGET T0335
MODEL  2  UNREFINED
PARENT N/A
ATOM     27  N   ALA     5      -2.921 -10.137  -8.940  1.00  1.00           N
ATOM     28  CA  ALA     5      -2.976 -10.585  -7.544  1.00  1.00           C
ATOM     29  C   ALA     5      -2.494  -9.462  -6.631  1.00  1.00           C
ATOM     30  O   ALA     5      -2.995  -9.318  -5.510  1.00  1.00           O
ATOM     31  H   ALA     5      -2.329 -10.609  -9.593  1.00  1.00           N
ATOM     32  HA  ALA     5      -4.004 -10.845  -7.287  1.00  1.00           N
ATOM     33  N   LYS     6      -1.552  -8.652  -7.082  1.00  1.00           N
ATOM     34  CA  LYS     6      -0.958  -7.558  -6.305  1.00  1.00           C
ATOM     35  C   LYS     6      -1.977  -6.431  -6.153  1.00  1.00           C
ATOM     36  O   LYS     6      -1.934  -5.689  -5.166  1.00  1.00           O
ATOM     37  H   LYS     6      -1.227  -8.840  -8.008  1.00  1.00           N
ATOM     38  HA  LYS     6      -0.673  -7.926  -5.319  1.00  1.00           N
ATOM     39  N   ILE     7      -2.843  -6.252  -7.089  1.00  1.00           N
ATOM     40  CA  ILE     7      -3.837  -5.182  -6.952  1.00  1.00           C
ATOM     41  C   ILE     7      -4.867  -5.576  -5.897  1.00  1.00           C
ATOM     42  O   ILE     7      -5.431  -4.703  -5.227  1.00  1.00           O
ATOM     43  H   ILE     7      -2.855  -6.845  -7.894  1.00  1.00           N
ATOM     44  HA  ILE     7      -3.340  -4.261  -6.648  1.00  1.00           N
ATOM     45  N   ALA     8      -5.200  -6.870  -5.862  1.00  1.00           N
ATOM     46  CA  ALA     8      -6.217  -7.325  -4.908  1.00  1.00           C
ATOM     47  C   ALA     8      -5.669  -7.214  -3.488  1.00  1.00           C
ATOM     48  O   ALA     8      -6.397  -6.815  -2.573  1.00  1.00           O
ATOM     49  H   ALA     8      -4.771  -7.525  -6.485  1.00  1.00           N
ATOM     50  HA  ALA     8      -7.108  -6.704  -5.002  1.00  1.00           N
ATOM     51  N   ARG     9      -4.445  -7.599  -3.298  1.00  1.00           N
ATOM     52  CA  ARG     9      -3.791  -7.487  -1.990  1.00  1.00           C
ATOM     53  C   ARG     9      -3.659  -6.014  -1.613  1.00  1.00           C
ATOM     54  O   ARG     9      -3.959  -5.639  -0.473  1.00  1.00           O
ATOM     55  H   ARG     9      -3.943  -7.975  -4.078  1.00  1.00           N
ATOM     56  HA  ARG     9      -4.389  -8.003  -1.239  1.00  1.00           N
ATOM     57  N   ILE    10      -3.392  -5.132  -2.542  1.00  1.00           N
ATOM     58  CA  ILE    10      -3.274  -3.696  -2.264  1.00  1.00           C
ATOM     59  C   ILE    10      -4.639  -3.141  -1.869  1.00  1.00           C
ATOM     60  O   ILE    10      -4.748  -2.412  -0.877  1.00  1.00           O
ATOM     61  H   ILE    10      -3.253  -5.475  -3.472  1.00  1.00           N
ATOM     62  HA  ILE    10      -2.569  -3.541  -1.448  1.00  1.00           N
ATOM     63  N   ASN    11      -5.604  -3.575  -2.644  1.00  1.00           N
ATOM     64  CA  ASN    11      -6.981  -3.125  -2.412  1.00  1.00           C
ATOM     65  C   ASN    11      -7.415  -3.525  -1.005  1.00  1.00           C
ATOM     66  O   ASN    11      -8.079  -2.742  -0.317  1.00  1.00           O
ATOM     67  H   ASN    11      -5.402  -4.190  -3.406  1.00  1.00           N
ATOM     68  HA  ASN    11      -7.030  -2.041  -2.512  1.00  1.00           N
ATOM     69  N   GLU    12      -7.088  -4.733  -0.606  1.00  1.00           N
ATOM     70  CA  GLU    12      -7.461  -5.126   0.757  1.00  1.00           C
ATOM     71  C   GLU    12      -6.752  -4.219   1.759  1.00  1.00           C
ATOM     72  O   GLU    12      -7.350  -3.821   2.765  1.00  1.00           O
ATOM     73  H   GLU    12      -6.573  -5.366  -1.186  1.00  1.00           N
ATOM     74  HA  GLU    12      -8.539  -5.030   0.882  1.00  1.00           N
ATOM     75  N   LEU    13      -5.505  -3.835   1.425  1.00  1.00           N
ATOM     76  CA  LEU    13      -4.728  -2.988   2.337  1.00  1.00           C
ATOM     77  C   LEU    13      -5.417  -1.634   2.484  1.00  1.00           C
ATOM     78  O   LEU    13      -5.653  -1.180   3.609  1.00  1.00           O
ATOM     79  H   LEU    13      -5.097  -4.153   0.568  1.00  1.00           N
ATOM     80  HA  LEU    13      -4.663  -3.470   3.313  1.00  1.00           N
ATOM     81  N   ALA    14      -5.699  -0.992   1.386  1.00  1.00           N
ATOM     82  CA  ALA    14      -6.365   0.315   1.421  1.00  1.00           C
ATOM     83  C   ALA    14      -7.611   0.227   2.296  1.00  1.00           C
ATOM     84  O   ALA    14      -7.892   1.151   3.067  1.00  1.00           O
ATOM     85  H   ALA    14      -5.459  -1.408   0.508  1.00  1.00           N
ATOM     86  HA  ALA    14      -5.683   1.059   1.834  1.00  1.00           N
ATOM     87  N   ALA    15      -8.340  -0.870   2.143  1.00  1.00           N
ATOM     88  CA  ALA    15      -9.551  -1.088   2.942  1.00  1.00           C
ATOM     89  C   ALA    15      -9.198  -1.039   4.426  1.00  1.00           C
ATOM     90  O   ALA    15      -9.788  -0.253   5.176  1.00  1.00           O
ATOM     91  H   ALA    15      -8.049  -1.557   1.476  1.00  1.00           N
ATOM     92  HA  ALA    15     -10.281  -0.312   2.716  1.00  1.00           N
ATOM     93  N   LYS    16      -8.235  -1.860   4.782  1.00  1.00           N
ATOM     94  CA  LYS    16      -7.780  -1.927   6.176  1.00  1.00           C
ATOM     95  C   LYS    16      -7.304  -0.547   6.621  1.00  1.00           C
ATOM     96  O   LYS    16      -7.500  -0.171   7.782  1.00  1.00           O
ATOM     97  H   LYS    16      -7.821  -2.455   4.093  1.00  1.00           N
ATOM     98  HA  LYS    16      -8.604  -2.250   6.812  1.00  1.00           N
ATOM     99  N   ALA    17      -6.690   0.198   5.723  1.00  1.00           N
ATOM    100  CA  ALA    17      -6.218   1.539   6.082  1.00  1.00           C
ATOM    101  C   ALA    17      -7.416   2.457   6.311  1.00  1.00           C
ATOM    102  O   ALA    17      -7.355   3.353   7.159  1.00  1.00           O
ATOM    103  H   ALA    17      -6.550  -0.150   4.795  1.00  1.00           N
ATOM    104  HA  ALA    17      -5.624   1.483   6.995  1.00  1.00           N
ATOM    105  N   LYS    18      -8.482   2.208   5.597  1.00  1.00           N
ATOM    106  CA  LYS    18      -9.669   3.064   5.706  1.00  1.00           C
ATOM    107  C   LYS    18     -10.383   2.780   7.024  1.00  1.00           C
ATOM    108  O   LYS    18     -10.883   3.709   7.668  1.00  1.00           O
ATOM    109  H   LYS    18      -8.476   1.441   4.956  1.00  1.00           N
ATOM    110  HA  LYS    18      -9.365   4.111   5.675  1.00  1.00           N
ATOM    111  N   ALA    19     -10.473   1.552   7.452  1.00  1.00           N
ATOM    112  CA  ALA    19     -11.172   1.239   8.703  1.00  1.00           C
ATOM    113  C   ALA    19     -10.334   1.716   9.886  1.00  1.00           C
ATOM    114  O   ALA    19     -10.823   1.738  11.021  1.00  1.00           O
ATOM    115  H   ALA    19     -10.054   0.818   6.917  1.00  1.00           N
ATOM    116  HA  ALA    19     -12.138   1.744   8.716  1.00  1.00           N
ATOM    117  N   GLY    20      -9.075   2.007   9.640  1.00  1.00           N
ATOM    118  CA  GLY    20      -8.230   2.527  10.720  1.00  1.00           C
ATOM    119  C   GLY    20      -7.394   1.392  11.304  1.00  1.00           C
ATOM    120  O   GLY    20      -6.662   1.601  12.279  1.00  1.00           O
ATOM    121  H   GLY    20      -8.706   1.921   8.714  1.00  1.00           N
ATOM    122  HA  GLY    20      -7.569   3.299  10.324  1.00  1.00           N
ATOM    123  N   VAL    21      -7.441   0.232  10.787  1.00  1.00           N
ATOM    124  CA  VAL    21      -6.639  -0.879  11.308  1.00  1.00           C
ATOM    125  C   VAL    21      -5.162  -0.620  11.017  1.00  1.00           C
ATOM    126  O   VAL    21      -4.292  -1.243  11.636  1.00  1.00           O
ATOM    127  H   VAL    21      -8.052   0.084  10.008  1.00  1.00           N
ATOM    128  HA  VAL    21      -6.787  -0.960  12.385  1.00  1.00           N
ATOM    129  N   ILE    22      -4.925   0.204  10.002  1.00  1.00           N
ATOM    130  CA  ILE    22      -3.569   0.547   9.558  1.00  1.00           C
ATOM    131  C   ILE    22      -3.282   2.009   9.884  1.00  1.00           C
ATOM    132  O   ILE    22      -4.098   2.884   9.573  1.00  1.00           O
ATOM    133  H   ILE    22      -5.718   0.610   9.547  1.00  1.00           N
ATOM    134  HA  ILE    22      -2.848  -0.088  10.072  1.00  1.00           N
ATOM    135  N   THR    23      -2.165   2.297  10.471  1.00  1.00           N
ATOM    136  CA  THR    23      -1.864   3.657  10.929  1.00  1.00           C
ATOM    137  C   THR    23      -1.203   4.439   9.799  1.00  1.00           C
ATOM    138  O   THR    23      -0.662   3.838   8.865  1.00  1.00           O
ATOM    139  H   THR    23      -1.513   1.557  10.635  1.00  1.00           N
ATOM    140  HA  THR    23      -2.788   4.154  11.224  1.00  1.00           N
ATOM    141  N   GLU    24      -1.190   5.792  10.061  1.00  1.00           N
ATOM    142  CA  GLU    24      -0.592   6.754   9.129  1.00  1.00           C
ATOM    143  C   GLU    24       0.886   6.427   8.939  1.00  1.00           C
ATOM    144  O   GLU    24       1.381   6.438   7.807  1.00  1.00           O
ATOM    145  H   GLU    24      -1.620   6.113  10.904  1.00  1.00           N
ATOM    146  HA  GLU    24      -1.104   6.696   8.169  1.00  1.00           N
ATOM    147  N   GLU    25       1.566   6.114  10.016  1.00  1.00           N
ATOM    148  CA  GLU    25       2.998   5.804   9.950  1.00  1.00           C
ATOM    149  C   GLU    25       3.214   4.584   9.058  1.00  1.00           C
ATOM    150  O   GLU    25       4.217   4.513   8.340  1.00  1.00           O
ATOM    151  H   GLU    25       1.091   6.100  10.896  1.00  1.00           N
ATOM    152  HA  GLU    25       3.535   6.656   9.536  1.00  1.00           N
ATOM    153  N   GLU    26       2.273   3.701   9.064  1.00  1.00           N
ATOM    154  CA  GLU    26       2.385   2.456   8.296  1.00  1.00           C
ATOM    155  C   GLU    26       2.030   2.726   6.836  1.00  1.00           C
ATOM    156  O   GLU    26       2.769   2.315   5.935  1.00  1.00           O
ATOM    157  H   GLU    26       1.464   3.869   9.629  1.00  1.00           N
ATOM    158  HA  GLU    26       3.407   2.082   8.359  1.00  1.00           N
ATOM    159  N   LYS    27       0.912   3.410   6.620  1.00  1.00           N
ATOM    160  CA  LYS    27       0.495   3.731   5.250  1.00  1.00           C
ATOM    161  C   LYS    27       1.636   4.437   4.524  1.00  1.00           C
ATOM    162  O   LYS    27       1.851   4.200   3.329  1.00  1.00           O
ATOM    163  H   LYS    27       0.355   3.708   7.394  1.00  1.00           N
ATOM    164  HA  LYS    27       0.242   2.811   4.722  1.00  1.00           N
ATOM    165  N   ALA    28       2.474   5.156   5.355  1.00  1.00           N
ATOM    166  CA  ALA    28       3.620   5.897   4.818  1.00  1.00           C
ATOM    167  C   ALA    28       4.668   4.911   4.308  1.00  1.00           C
ATOM    168  O   ALA    28       5.295   5.158   3.271  1.00  1.00           O
ATOM    169  H   ALA    28       2.259   5.204   6.330  1.00  1.00           N
ATOM    170  HA  ALA    28       3.289   6.533   3.997  1.00  1.00           N
ATOM    171  N   GLU    29       4.834   3.830   5.018  1.00  1.00           N
ATOM    172  CA  GLU    29       5.837   2.835   4.623  1.00  1.00           C
ATOM    173  C   GLU    29       5.417   2.182   3.309  1.00  1.00           C
ATOM    174  O   GLU    29       6.236   2.055   2.393  1.00  1.00           O
ATOM    175  H   GLU    29       4.281   3.685   5.838  1.00  1.00           N
ATOM    176  HA  GLU    29       6.802   3.323   4.494  1.00  1.00           N
ATOM    177  N   GLN    30       4.184   1.793   3.208  1.00  1.00           N
ATOM    178  CA  GLN    30       3.661   1.100   2.027  1.00  1.00           C
ATOM    179  C   GLN    30       3.677   2.049   0.831  1.00  1.00           C
ATOM    180  O   GLN    30       3.923   1.614  -0.300  1.00  1.00           O
ATOM    181  H   GLN    30       3.586   1.967   3.991  1.00  1.00           N
ATOM    182  HA  GLN    30       4.283   0.231   1.809  1.00  1.00           N
ATOM    183  N   GLN    31       3.405   3.332   1.125  1.00  1.00           N
ATOM    184  CA  GLN    31       3.446   4.360   0.079  1.00  1.00           C
ATOM    185  C   GLN    31       4.851   4.428  -0.513  1.00  1.00           C
ATOM    186  O   GLN    31       5.005   4.434  -1.739  1.00  1.00           O
ATOM    187  H   GLN    31       3.179   3.585   2.065  1.00  1.00           N
ATOM    188  HA  GLN    31       2.733   4.107  -0.707  1.00  1.00           N
ATOM    189  N   LYS    32       5.873   4.468   0.360  1.00  1.00           N
ATOM    190  CA  LYS    32       7.269   4.511  -0.089  1.00  1.00           C
ATOM    191  C   LYS    32       7.582   3.256  -0.897  1.00  1.00           C
ATOM    192  O   LYS    32       8.289   3.331  -1.908  1.00  1.00           O
ATOM    193  H   LYS    32       5.661   4.483   1.337  1.00  1.00           N
ATOM    194  HA  LYS    32       7.423   5.392  -0.712  1.00  1.00           N
ATOM    195  N   LEU    33       7.196   2.126  -0.438  1.00  1.00           N
ATOM    196  CA  LEU    33       7.450   0.873  -1.156  1.00  1.00           C
ATOM    197  C   LEU    33       6.755   0.917  -2.515  1.00  1.00           C
ATOM    198  O   LEU    33       7.399   0.694  -3.546  1.00  1.00           O
ATOM    199  H   LEU    33       6.707   2.112   0.435  1.00  1.00           N
ATOM    200  HA  LEU    33       8.523   0.747  -1.301  1.00  1.00           N
ATOM    201  N   ARG    34       5.448   1.141  -2.574  1.00  1.00           N
ATOM    202  CA  ARG    34       4.710   1.213  -3.840  1.00  1.00           C
ATOM    203  C   ARG    34       5.415   2.181  -4.785  1.00  1.00           C
ATOM    204  O   ARG    34       5.494   1.920  -5.990  1.00  1.00           O
ATOM    205  H   ARG    34       4.971   1.289  -1.708  1.00  1.00           N
ATOM    206  HA  ARG    34       4.671   0.223  -4.295  1.00  1.00           N
ATOM    207  N   GLN    35       5.811   3.287  -4.201  1.00  1.00           N
ATOM    208  CA  GLN    35       6.531   4.273  -5.013  1.00  1.00           C
ATOM    209  C   GLN    35       7.821   3.655  -5.541  1.00  1.00           C
ATOM    210  O   GLN    35       8.115   3.764  -6.738  1.00  1.00           O
ATOM    211  H   GLN    35       5.633   3.468  -3.234  1.00  1.00           N
ATOM    212  HA  GLN    35       5.905   4.580  -5.851  1.00  1.00           N
ATOM    213  N   GLU    36       8.543   2.901  -4.725  1.00  1.00           N
ATOM    214  CA  GLU    36       9.827   2.302  -5.102  1.00  1.00           C
ATOM    215  C   GLU    36       9.607   1.282  -6.214  1.00  1.00           C
ATOM    216  O   GLU    36      10.385   1.235  -7.173  1.00  1.00           O
ATOM    217  H   GLU    36       8.182   2.771  -3.801  1.00  1.00           N
ATOM    218  HA  GLU    36      10.504   3.083  -5.453  1.00  1.00           N
ATOM    219  N   TYR    37       8.525   0.522  -6.066  1.00  1.00           N
ATOM    220  CA  TYR    37       8.117  -0.577  -6.948  1.00  1.00           C
ATOM    221  C   TYR    37       7.738  -0.018  -8.316  1.00  1.00           C
ATOM    222  O   TYR    37       8.264  -0.474  -9.337  1.00  1.00           O
ATOM    223  H   TYR    37       7.985   0.736  -5.252  1.00  1.00           N
ATOM    224  HA  TYR    37       8.943  -1.280  -7.058  1.00  1.00           N
ATOM    225  N   LEU    38       6.857   0.907  -8.277  1.00  1.00           N
ATOM    226  CA  LEU    38       6.288   1.579  -9.451  1.00  1.00           C
ATOM    227  C   LEU    38       7.401   2.283 -10.222  1.00  1.00           C
ATOM    228  O   LEU    38       7.359   2.335 -11.457  1.00  1.00           O
ATOM    229  H   LEU    38       6.549   1.158  -7.360  1.00  1.00           N
ATOM    230  HA  LEU    38       5.810   0.842 -10.095  1.00  1.00           N
ATOM    231  N   LYS    39       8.390   2.865  -9.646  1.00  1.00           N
ATOM    232  CA  LYS    39       9.488   3.479 -10.400  1.00  1.00           C
ATOM    233  C   LYS    39      10.168   2.418 -11.260  1.00  1.00           C
ATOM    234  O   LYS    39      10.479   2.675 -12.428  1.00  1.00           O
ATOM    235  H   LYS    39       8.407   2.869  -8.645  1.00  1.00           N
ATOM    236  HA  LYS    39       9.093   4.267 -11.040  1.00  1.00           N
ATOM    237  N   GLY    40      10.323   1.248 -10.714  1.00  1.00           N
ATOM    238  CA  GLY    40      11.050   0.166 -11.386  1.00  1.00           C
ATOM    239  C   GLY    40      10.130  -0.514 -12.396  1.00  1.00           C
ATOM    240  O   GLY    40      10.560  -0.825 -13.513  1.00  1.00           O
ATOM    241  H   GLY    40       9.961   1.111  -9.792  1.00  1.00           N
ATOM    242  HA  GLY    40      11.917   0.578 -11.904  1.00  1.00           N
TER
END
