
#######################################################
#                                                     #
#                        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 T0349TS383_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS383_5-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    R       2      M       1          2.566
LGA    E       3      R       2          3.894
LGA    L       4      E       3          3.046
LGA    L       5      L       4           #
LGA    -       -      L       5           -
LGA    R       6      R       6           #
LGA    T       7      -       -           -
LGA    N       8      -       -           -
LGA    D       9      -       -           -
LGA    A      10      -       -           -
LGA    V      11      -       -           -
LGA    L      12      -       -           -
LGA    L      13      -       -           -
LGA    S      14      -       -           -
LGA    A      15      -       -           -
LGA    V      16      -       -           -
LGA    G      17      -       -           -
LGA    A      18      -       -           -
LGA    L      19      -       -           -
LGA    L      20      -       -           -
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      -       -           -
LGA    I      25      T       7          3.094
LGA    G      26      N       8          3.557
LGA    H      27      D       9          3.605
LGA    L      28      A      10          3.244
LGA    V      29      V      11           #
LGA    P      45      L      12          1.674
LGA    R      46      L      13           -
LGA    R      47      S      14           -
LGA    V      48      -       -           -
LGA    L      49      A      15          5.478
LGA    V      50      V      16           #
LGA    -       -      G      17           -
LGA    H      51      A      18          5.114
LGA    -       -      L      19           -
LGA    -       -      L      20           -
LGA    -       -      D      21           -
LGA    -       -      G      22           -
LGA    -       -      A      23           -
LGA    -       -      D      24           -
LGA    -       -      I      25           -
LGA    E      52      G      26           #
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    -       -      L      49           -
LGA    -       -      V      50           -
LGA    -       -      H      51           -
LGA    -       -      E      52           -
LGA    D      53      D      53          3.252
LGA    D      54      D      54          3.776
LGA    L      55      L      55          2.741
LGA    A      56      A      56          1.833
LGA    G      57      G      57          1.593
LGA    A      58      A      58          2.065
LGA    R      59      R      59          2.052
LGA    R      60      R      60          0.997
LGA    L      61      L      61          0.883
LGA    L      62      L      62          0.952
LGA    T      63      T      63          1.407
LGA    D      64      D      64          1.812
LGA    A      65      A      65          1.473
LGA    -       -      G      66           -
LGA    G      66      L      67          2.466
LGA    L      67      A      68          4.026
LGA    A      68      H      69          3.893
LGA    H      69      E      70           #
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   54   57    5.0     26    2.97    50.00     32.596     0.846

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.574571 * X  +   0.499829 * Y  +  -0.648105 * Z  +  -6.360747
  Y_new =  -0.770799 * X  +   0.064196 * Y  +  -0.633835 * Z  +  20.051615
  Z_new =  -0.275204 * X  +   0.863742 * Y  +   0.422153 * Z  +  14.060347 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.116190   -2.025403  [ DEG:    63.9530   -116.0470 ]
  Theta =   0.278801    2.862791  [ DEG:    15.9741    164.0258 ]
  Phi   =  -0.930232    2.211361  [ DEG:   -53.2984    126.7016 ]
 
# 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: T0349TS383_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS383_5-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   54   57   5.0   26   2.97   50.00  32.596
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS383_5-D1
PFRMAT TS
TARGET T0349
MODEL 5
PARENT 1pvmA
ATOM      1  N   MET     1       9.172  14.669  -4.742  1.00  0.00
ATOM      2  CA  MET     1       8.352  13.655  -5.398  1.00  0.00
ATOM      3  C   MET     1       7.087  13.458  -4.567  1.00  0.00
ATOM      4  O   MET     1       7.170  13.009  -3.426  1.00  0.00
ATOM      5  N   ARG     2       1.326  10.680  -4.569  1.00  0.00
ATOM      6  CA  ARG     2       0.308  10.283  -5.529  1.00  0.00
ATOM      7  C   ARG     2       0.934   9.567  -6.720  1.00  0.00
ATOM      8  O   ARG     2       0.368   8.613  -7.251  1.00  0.00
ATOM      9  N   GLU     3       2.118  10.019  -7.119  1.00  0.00
ATOM     10  CA  GLU     3       2.818   9.436  -8.259  1.00  0.00
ATOM     11  C   GLU     3       3.316   8.014  -8.041  1.00  0.00
ATOM     12  O   GLU     3       3.348   7.222  -8.984  1.00  0.00
ATOM     13  N   LEU     4       3.701   7.683  -6.811  1.00  0.00
ATOM     14  CA  LEU     4       4.230   6.350  -6.529  1.00  0.00
ATOM     15  C   LEU     4       3.311   5.396  -5.770  1.00  0.00
ATOM     16  O   LEU     4       3.593   4.204  -5.683  1.00  0.00
ATOM     17  N   LEU     5       2.220   5.909  -5.220  1.00  0.00
ATOM     18  CA  LEU     5       1.300   5.059  -4.476  1.00  0.00
ATOM     19  C   LEU     5       0.697   3.993  -5.382  1.00  0.00
ATOM     20  O   LEU     5       0.837   4.046  -6.603  1.00  0.00
ATOM     21  N   ARG     6       0.023   3.029  -4.766  1.00  0.00
ATOM     22  CA  ARG     6      -0.629   1.944  -5.482  1.00  0.00
ATOM     23  C   ARG     6      -2.127   2.187  -5.353  1.00  0.00
ATOM     24  O   ARG     6      -2.698   2.028  -4.277  1.00  0.00
ATOM     25  N   THR     7      -2.753   2.594  -6.454  1.00  0.00
ATOM     26  CA  THR     7      -4.184   2.881  -6.472  1.00  0.00
ATOM     27  C   THR     7      -4.978   1.604  -6.695  1.00  0.00
ATOM     28  O   THR     7      -6.208   1.617  -6.711  1.00  0.00
ATOM     29  N   ASN     8     -14.310  -5.703   4.286  1.00  0.00
ATOM     30  CA  ASN     8     -15.285  -5.245   5.268  1.00  0.00
ATOM     31  C   ASN     8     -14.744  -5.396   6.686  1.00  0.00
ATOM     32  O   ASN     8     -14.065  -6.378   7.003  1.00  0.00
ATOM     33  N   ASP     9     -15.062  -4.435   7.547  1.00  0.00
ATOM     34  CA  ASP     9     -14.565  -4.466   8.915  1.00  0.00
ATOM     35  C   ASP     9     -15.009  -5.644   9.780  1.00  0.00
ATOM     36  O   ASP     9     -14.497  -5.828  10.887  1.00  0.00
ATOM     37  N   ALA    10     -15.950  -6.443   9.287  1.00  0.00
ATOM     38  CA  ALA    10     -16.407  -7.610  10.031  1.00  0.00
ATOM     39  C   ALA    10     -15.783  -8.900   9.496  1.00  0.00
ATOM     40  O   ALA    10     -16.099  -9.999   9.952  1.00  0.00
ATOM     41  N   VAL    11     -14.893  -8.752   8.523  1.00  0.00
ATOM     42  CA  VAL    11     -14.188  -9.889   7.950  1.00  0.00
ATOM     43  C   VAL    11     -13.342 -10.452   9.091  1.00  0.00
ATOM     44  O   VAL    11     -12.746  -9.692   9.854  1.00  0.00
ATOM     45  N   LEU    12     -13.293 -11.773   9.226  1.00  0.00
ATOM     46  CA  LEU    12     -12.499 -12.371  10.295  1.00  0.00
ATOM     47  C   LEU    12     -11.015 -12.282   9.948  1.00  0.00
ATOM     48  O   LEU    12     -10.645 -12.120   8.785  1.00  0.00
ATOM     49  N   LEU    13     -10.169 -12.387  10.965  1.00  0.00
ATOM     50  CA  LEU    13      -8.731 -12.351  10.750  1.00  0.00
ATOM     51  C   LEU    13      -8.351 -13.473   9.784  1.00  0.00
ATOM     52  O   LEU    13      -7.506 -13.293   8.912  1.00  0.00
ATOM     53  N   SER    14      -8.996 -14.628   9.940  1.00  0.00
ATOM     54  CA  SER    14      -8.739 -15.790   9.091  1.00  0.00
ATOM     55  C   SER    14      -8.974 -15.455   7.620  1.00  0.00
ATOM     56  O   SER    14      -8.099 -15.659   6.781  1.00  0.00
ATOM     57  N   ALA    15     -10.154 -14.931   7.309  1.00  0.00
ATOM     58  CA  ALA    15     -10.470 -14.589   5.931  1.00  0.00
ATOM     59  C   ALA    15      -9.600 -13.466   5.387  1.00  0.00
ATOM     60  O   ALA    15      -9.207 -13.487   4.221  1.00  0.00
ATOM     61  N   VAL    16      -9.297 -12.483   6.226  1.00  0.00
ATOM     62  CA  VAL    16      -8.463 -11.371   5.789  1.00  0.00
ATOM     63  C   VAL    16      -7.049 -11.836   5.456  1.00  0.00
ATOM     64  O   VAL    16      -6.467 -11.409   4.459  1.00  0.00
ATOM     65  N   GLY    17      -6.492 -12.710   6.288  1.00  0.00
ATOM     66  CA  GLY    17      -5.141 -13.207   6.058  1.00  0.00
ATOM     67  C   GLY    17      -5.087 -14.109   4.833  1.00  0.00
ATOM     68  O   GLY    17      -4.075 -14.141   4.127  1.00  0.00
ATOM     69  N   ALA    18      -6.168 -14.837   4.567  1.00  0.00
ATOM     70  CA  ALA    18      -6.187 -15.684   3.383  1.00  0.00
ATOM     71  C   ALA    18      -6.076 -14.782   2.155  1.00  0.00
ATOM     72  O   ALA    18      -5.386 -15.117   1.190  1.00  0.00
ATOM     73  N   LEU    19      -6.747 -13.635   2.198  1.00  0.00
ATOM     74  CA  LEU    19      -6.697 -12.675   1.097  1.00  0.00
ATOM     75  C   LEU    19      -5.270 -12.138   0.947  1.00  0.00
ATOM     76  O   LEU    19      -4.751 -12.034  -0.164  1.00  0.00
ATOM     77  N   LEU    20      -4.635 -11.802   2.068  1.00  0.00
ATOM     78  CA  LEU    20      -3.264 -11.297   2.044  1.00  0.00
ATOM     79  C   LEU    20      -2.311 -12.331   1.458  1.00  0.00
ATOM     80  O   LEU    20      -1.486 -12.018   0.593  1.00  0.00
ATOM     81  N   ASP    21      -2.417 -13.567   1.938  1.00  0.00
ATOM     82  CA  ASP    21      -1.550 -14.634   1.458  1.00  0.00
ATOM     83  C   ASP    21      -1.757 -14.972  -0.011  1.00  0.00
ATOM     84  O   ASP    21      -0.793 -15.215  -0.725  1.00  0.00
ATOM     85  N   GLY    22      -3.002 -14.975  -0.473  1.00  0.00
ATOM     86  CA  GLY    22      -3.267 -15.310  -1.868  1.00  0.00
ATOM     87  C   GLY    22      -2.843 -14.213  -2.839  1.00  0.00
ATOM     88  O   GLY    22      -2.463 -14.499  -3.973  1.00  0.00
ATOM     89  N   ALA    23      -2.883 -12.962  -2.391  1.00  0.00
ATOM     90  CA  ALA    23      -2.499 -11.835  -3.239  1.00  0.00
ATOM     91  C   ALA    23      -1.068 -11.350  -3.016  1.00  0.00
ATOM     92  O   ALA    23      -0.559 -10.540  -3.793  1.00  0.00
ATOM     93  N   ASP    24      -0.424 -11.840  -1.963  1.00  0.00
ATOM     94  CA  ASP    24       0.933 -11.411  -1.633  1.00  0.00
ATOM     95  C   ASP    24       0.934  -9.903  -1.369  1.00  0.00
ATOM     96  O   ASP    24       1.848  -9.189  -1.775  1.00  0.00
ATOM     97  N   ILE    25      -0.119  -9.433  -0.711  1.00  0.00
ATOM     98  CA  ILE    25      -0.267  -8.024  -0.345  1.00  0.00
ATOM     99  C   ILE    25      -0.564  -8.043   1.142  1.00  0.00
ATOM    100  O   ILE    25      -1.632  -8.486   1.563  1.00  0.00
ATOM    101  N   GLY    26       0.381  -7.561   1.940  1.00  0.00
ATOM    102  CA  GLY    26       0.222  -7.599   3.380  1.00  0.00
ATOM    103  C   GLY    26      -0.249  -6.307   4.014  1.00  0.00
ATOM    104  O   GLY    26       0.225  -5.882   5.066  1.00  0.00
ATOM    105  N   HIS    27      -1.221  -5.698   3.354  1.00  0.00
ATOM    106  CA  HIS    27      -1.809  -4.468   3.838  1.00  0.00
ATOM    107  C   HIS    27      -3.156  -4.323   3.158  1.00  0.00
ATOM    108  O   HIS    27      -3.225  -4.315   1.929  1.00  0.00
ATOM    109  N   LEU    28      -4.221  -4.234   3.948  1.00  0.00
ATOM    110  CA  LEU    28      -5.566  -4.086   3.410  1.00  0.00
ATOM    111  C   LEU    28      -6.278  -2.885   4.006  1.00  0.00
ATOM    112  O   LEU    28      -6.201  -2.640   5.212  1.00  0.00
ATOM    113  N   VAL    29      -9.557  -1.183   5.249  1.00  0.00
ATOM    114  CA  VAL    29     -10.798  -1.713   5.797  1.00  0.00
ATOM    115  C   VAL    29     -11.907  -0.668   5.763  1.00  0.00
ATOM    116  O   VAL    29     -11.692   0.485   6.139  1.00  0.00
ATOM    161  N   PRO    45      -2.543  -4.669   8.926  1.00  0.00
ATOM    162  CA  PRO    45      -1.156  -4.948   8.574  1.00  0.00
ATOM    163  C   PRO    45      -0.694  -6.193   9.315  1.00  0.00
ATOM    164  O   PRO    45      -1.362  -6.654  10.241  1.00  0.00
ATOM    165  N   ARG    46       0.458  -6.723   8.914  1.00  0.00
ATOM    166  CA  ARG    46       1.018  -7.898   9.563  1.00  0.00
ATOM    167  C   ARG    46       1.273  -7.634  11.036  1.00  0.00
ATOM    168  O   ARG    46       0.923  -8.443  11.883  1.00  0.00
ATOM    169  N   ARG    47       1.895  -6.495  11.334  1.00  0.00
ATOM    170  CA  ARG    47       2.212  -6.145  12.711  1.00  0.00
ATOM    171  C   ARG    47       0.963  -6.017  13.568  1.00  0.00
ATOM    172  O   ARG    47       0.961  -6.421  14.729  1.00  0.00
ATOM    173  N   VAL    48      -8.676  -5.456  15.307  1.00  0.00
ATOM    174  CA  VAL    48      -7.251  -5.707  15.130  1.00  0.00
ATOM    175  C   VAL    48      -6.529  -4.624  14.319  1.00  0.00
ATOM    176  O   VAL    48      -5.425  -4.201  14.670  1.00  0.00
ATOM    177  N   LEU    49      -7.166  -4.188  13.239  1.00  0.00
ATOM    178  CA  LEU    49      -6.621  -3.179  12.330  1.00  0.00
ATOM    179  C   LEU    49      -6.162  -1.887  12.994  1.00  0.00
ATOM    180  O   LEU    49      -6.642  -1.521  14.075  1.00  0.00
ATOM    181  N   VAL    50      -5.236  -1.198  12.327  1.00  0.00
ATOM    182  CA  VAL    50      -4.760   0.092  12.810  1.00  0.00
ATOM    183  C   VAL    50      -5.939   1.041  12.639  1.00  0.00
ATOM    184  O   VAL    50      -6.514   1.140  11.549  1.00  0.00
ATOM    185  N   HIS    51      -6.291   1.724  13.722  1.00  0.00
ATOM    186  CA  HIS    51      -7.406   2.661  13.740  1.00  0.00
ATOM    187  C   HIS    51      -7.103   3.739  14.780  1.00  0.00
ATOM    188  O   HIS    51      -6.646   3.426  15.874  1.00  0.00
ATOM    189  N   GLU    52      -0.877  14.838  -1.852  1.00  0.00
ATOM    190  CA  GLU    52       0.082  15.865  -2.253  1.00  0.00
ATOM    191  C   GLU    52       1.337  15.904  -1.372  1.00  0.00
ATOM    192  O   GLU    52       2.221  16.743  -1.569  1.00  0.00
ATOM    193  N   ASP    53       1.412  14.999  -0.400  1.00  0.00
ATOM    194  CA  ASP    53       2.571  14.921   0.487  1.00  0.00
ATOM    195  C   ASP    53       3.813  14.532  -0.304  1.00  0.00
ATOM    196  O   ASP    53       3.741  13.711  -1.220  1.00  0.00
ATOM    197  N   ASP    54       4.953  15.112   0.056  1.00  0.00
ATOM    198  CA  ASP    54       6.204  14.765  -0.599  1.00  0.00
ATOM    199  C   ASP    54       6.637  13.454   0.058  1.00  0.00
ATOM    200  O   ASP    54       6.328  13.217   1.229  1.00  0.00
ATOM    201  N   LEU    55       7.344  12.606  -0.680  1.00  0.00
ATOM    202  CA  LEU    55       7.785  11.331  -0.123  1.00  0.00
ATOM    203  C   LEU    55       8.532  11.495   1.191  1.00  0.00
ATOM    204  O   LEU    55       8.474  10.616   2.050  1.00  0.00
ATOM    205  N   ALA    56       9.233  12.613   1.360  1.00  0.00
ATOM    206  CA  ALA    56       9.963  12.844   2.606  1.00  0.00
ATOM    207  C   ALA    56       8.988  13.076   3.757  1.00  0.00
ATOM    208  O   ALA    56       9.273  12.738   4.908  1.00  0.00
ATOM    209  N   GLY    57       7.836  13.658   3.443  1.00  0.00
ATOM    210  CA  GLY    57       6.827  13.921   4.458  1.00  0.00
ATOM    211  C   GLY    57       6.186  12.604   4.874  1.00  0.00
ATOM    212  O   GLY    57       5.881  12.390   6.048  1.00  0.00
ATOM    213  N   ALA    58       5.983  11.722   3.903  1.00  0.00
ATOM    214  CA  ALA    58       5.397  10.418   4.183  1.00  0.00
ATOM    215  C   ALA    58       6.358   9.617   5.057  1.00  0.00
ATOM    216  O   ALA    58       5.936   8.966   6.012  1.00  0.00
ATOM    217  N   ARG    59       7.648   9.672   4.734  1.00  0.00
ATOM    218  CA  ARG    59       8.651   8.956   5.514  1.00  0.00
ATOM    219  C   ARG    59       8.601   9.407   6.973  1.00  0.00
ATOM    220  O   ARG    59       8.647   8.586   7.889  1.00  0.00
ATOM    221  N   ARG    60       8.506  10.717   7.185  1.00  0.00
ATOM    222  CA  ARG    60       8.450  11.270   8.533  1.00  0.00
ATOM    223  C   ARG    60       7.197  10.785   9.259  1.00  0.00
ATOM    224  O   ARG    60       7.231  10.485  10.457  1.00  0.00
ATOM    225  N   LEU    61       6.092  10.711   8.525  1.00  0.00
ATOM    226  CA  LEU    61       4.832  10.255   9.092  1.00  0.00
ATOM    227  C   LEU    61       4.919   8.781   9.487  1.00  0.00
ATOM    228  O   LEU    61       4.518   8.399  10.590  1.00  0.00
ATOM    229  N   LEU    62       5.427   7.950   8.583  1.00  0.00
ATOM    230  CA  LEU    62       5.540   6.527   8.877  1.00  0.00
ATOM    231  C   LEU    62       6.438   6.311  10.085  1.00  0.00
ATOM    232  O   LEU    62       6.066   5.609  11.022  1.00  0.00
ATOM    233  N   THR    63       7.617   6.924  10.056  1.00  0.00
ATOM    234  CA  THR    63       8.581   6.787  11.142  1.00  0.00
ATOM    235  C   THR    63       8.034   7.262  12.489  1.00  0.00
ATOM    236  O   THR    63       8.243   6.620  13.516  1.00  0.00
ATOM    237  N   ASP    64       7.342   8.393  12.483  1.00  0.00
ATOM    238  CA  ASP    64       6.773   8.942  13.706  1.00  0.00
ATOM    239  C   ASP    64       5.761   7.968  14.318  1.00  0.00
ATOM    240  O   ASP    64       5.599   7.897  15.541  1.00  0.00
ATOM    241  N   ALA    65       5.098   7.206  13.454  1.00  0.00
ATOM    242  CA  ALA    65       4.066   6.265  13.878  1.00  0.00
ATOM    243  C   ALA    65       4.462   4.797  13.929  1.00  0.00
ATOM    244  O   ALA    65       3.617   3.948  14.221  1.00  0.00
ATOM    245  N   GLY    66       5.730   4.504  13.651  1.00  0.00
ATOM    246  CA  GLY    66       6.207   3.129  13.663  1.00  0.00
ATOM    247  C   GLY    66       5.561   2.260  12.596  1.00  0.00
ATOM    248  O   GLY    66       5.414   1.049  12.772  1.00  0.00
ATOM    249  N   LEU    67       5.193   2.878  11.480  1.00  0.00
ATOM    250  CA  LEU    67       4.537   2.184  10.374  1.00  0.00
ATOM    251  C   LEU    67       5.468   1.892   9.198  1.00  0.00
ATOM    252  O   LEU    67       6.506   2.537   9.046  1.00  0.00
ATOM    253  N   ALA    68       5.095   0.917   8.369  1.00  0.00
ATOM    254  CA  ALA    68       5.868   0.617   7.168  1.00  0.00
ATOM    255  C   ALA    68       4.981   0.800   5.927  1.00  0.00
ATOM    256  O   ALA    68       5.402   0.564   4.796  1.00  0.00
ATOM    257  N   HIS    69       3.752   1.256   6.160  1.00  0.00
ATOM    258  CA  HIS    69       2.807   1.534   5.085  1.00  0.00
ATOM    259  C   HIS    69       1.611   2.299   5.640  1.00  0.00
ATOM    260  O   HIS    69       1.323   2.244   6.838  1.00  0.00
TER
END
