
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0349AL243_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL243_1-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      R       2          1.098
LGA    E       3      E       3          1.033
LGA    L       4      L       4          0.725
LGA    L       5      L       5          0.269
LGA    R       6      R       6          1.232
LGA    T       7      T       7          2.519
LGA    N       8      N       8          4.340
LGA    D       9      D       9          0.956
LGA    A      10      A      10          1.475
LGA    V      11      V      11          1.066
LGA    L      12      L      12          0.480
LGA    L      13      L      13          1.139
LGA    S      14      S      14          1.243
LGA    A      15      A      15          0.871
LGA    V      16      V      16          0.520
LGA    G      17      G      17          0.962
LGA    A      18      A      18          1.072
LGA    L      19      L      19          0.867
LGA    L      20      L      20          0.770
LGA    D      21      D      21          0.972
LGA    G      22      G      22          0.553
LGA    A      23      A      23          1.010
LGA    D      24      D      24          1.804
LGA    I      25      I      25          0.504
LGA    G      26      G      26          1.471
LGA    H      27      H      27          1.194
LGA    L      28      L      28          1.188
LGA    V      29      V      29          1.186
LGA    R      46      P      45          3.915
LGA    -       -      R      46           -
LGA    R      47      R      47          0.877
LGA    V      48      V      48          0.811
LGA    L      49      L      49          0.732
LGA    V      50      V      50          0.590
LGA    H      51      H      51          1.080
LGA    E      52      E      52          1.871
LGA    D      53      D      53          2.335
LGA    D      54      D      54          1.493
LGA    L      55      L      55          0.966
LGA    A      56      A      56          0.352
LGA    G      57      G      57          0.464
LGA    A      58      A      58          0.235
LGA    R      59      R      59          0.592
LGA    R      60      R      60          0.851
LGA    L      61      L      61          0.709
LGA    L      62      L      62          0.418
LGA    T      63      T      63          0.770
LGA    D      64      D      64          1.645
LGA    A      65      A      65          2.088
LGA    G      66      G      66          3.614
LGA    L      67      L      67          2.139
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50   57    5.0     50    1.50    98.00     82.248     3.133

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.704043 * X  +  -0.623691 * Y  +   0.339607 * Z  +   6.517982
  Y_new =   0.664198 * X  +   0.747546 * Y  +  -0.004083 * Z  + -66.810059
  Z_new =  -0.251325 * X  +   0.228441 * Y  +   0.940559 * Z  + -39.900459 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.238264   -2.903328  [ DEG:    13.6515   -166.3485 ]
  Theta =   0.254049    2.887544  [ DEG:    14.5559    165.4441 ]
  Phi   =   0.756285   -2.385308  [ DEG:    43.3319   -136.6681 ]
 
# 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: T0349AL243_1-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL243_1-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50   57   5.0   50   1.50   98.00  82.248
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL243_1-D1
REMARK Aligment from pdb entry: 1yj7A
ATOM      1  N   ARG     2       2.886   8.673  -5.770  1.00  0.00              
ATOM      2  CA  ARG     2       4.068   7.913  -5.404  1.00  0.00              
ATOM      3  C   ARG     2       3.689   6.775  -4.470  1.00  0.00              
ATOM      4  O   ARG     2       3.014   6.995  -3.475  1.00  0.00              
ATOM      5  N   GLU     3       4.122   5.569  -4.818  1.00  0.00              
ATOM      6  CA  GLU     3       3.846   4.393  -3.997  1.00  0.00              
ATOM      7  C   GLU     3       4.590   4.557  -2.694  1.00  0.00              
ATOM      8  O   GLU     3       5.715   5.025  -2.687  1.00  0.00              
ATOM      9  N   LEU     4       3.951   4.198  -1.604  1.00  0.00              
ATOM     10  CA  LEU     4       4.648   4.086  -0.306  1.00  0.00              
ATOM     11  C   LEU     4       5.089   2.642  -0.081  1.00  0.00              
ATOM     12  O   LEU     4       6.281   2.337  -0.069  1.00  0.00              
ATOM     13  N   LEU     5       4.118   1.746   0.046  1.00  0.00              
ATOM     14  CA  LEU     5       4.360   0.348   0.355  1.00  0.00              
ATOM     15  C   LEU     5       3.422  -0.572  -0.433  1.00  0.00              
ATOM     16  O   LEU     5       2.256  -0.253  -0.630  1.00  0.00              
ATOM     17  N   ARG     6       3.955  -1.706  -0.866  1.00  0.00              
ATOM     18  CA  ARG     6       3.173  -2.834  -1.379  1.00  0.00              
ATOM     19  C   ARG     6       3.284  -4.043  -0.447  1.00  0.00              
ATOM     20  O   ARG     6       4.059  -4.041   0.529  1.00  0.00              
ATOM     21  N   THR     7       2.516  -5.088  -0.754  1.00  0.00              
ATOM     22  CA  THR     7       2.595  -6.342  -0.026  1.00  0.00              
ATOM     23  C   THR     7       1.969  -6.314   1.352  1.00  0.00              
ATOM     24  O   THR     7       2.263  -7.169   2.193  1.00  0.00              
ATOM     25  N   ASN     8       1.113  -5.325   1.623  1.00  0.00              
ATOM     26  CA  ASN     8       0.535  -5.178   2.959  1.00  0.00              
ATOM     27  C   ASN     8      -0.698  -6.073   3.136  1.00  0.00              
ATOM     28  O   ASN     8      -1.448  -6.310   2.185  1.00  0.00              
ATOM     29  N   ASP     9      -0.921  -6.549   4.362  1.00  0.00              
ATOM     30  CA  ASP     9      -2.203  -7.161   4.709  1.00  0.00              
ATOM     31  C   ASP     9      -3.291  -6.105   4.686  1.00  0.00              
ATOM     32  O   ASP     9      -3.023  -4.904   4.777  1.00  0.00              
ATOM     33  N   ALA    10      -4.534  -6.554   4.576  1.00  0.00              
ATOM     34  CA  ALA    10      -5.648  -5.628   4.600  1.00  0.00              
ATOM     35  C   ALA    10      -5.686  -4.874   5.933  1.00  0.00              
ATOM     36  O   ALA    10      -5.859  -3.658   5.950  1.00  0.00              
ATOM     37  N   VAL    11      -5.470  -5.574   7.046  1.00  0.00              
ATOM     38  CA  VAL    11      -5.534  -4.958   8.376  1.00  0.00              
ATOM     39  C   VAL    11      -4.481  -3.857   8.550  1.00  0.00              
ATOM     40  O   VAL    11      -4.792  -2.763   9.021  1.00  0.00              
ATOM     41  N   LEU    12      -3.239  -4.147   8.170  1.00  0.00              
ATOM     42  CA  LEU    12      -2.170  -3.170   8.343  1.00  0.00              
ATOM     43  C   LEU    12      -2.309  -1.994   7.368  1.00  0.00              
ATOM     44  O   LEU    12      -2.086  -0.853   7.766  1.00  0.00              
ATOM     45  N   LEU    13      -2.673  -2.253   6.113  1.00  0.00              
ATOM     46  CA  LEU    13      -2.912  -1.161   5.177  1.00  0.00              
ATOM     47  C   LEU    13      -4.001  -0.268   5.745  1.00  0.00              
ATOM     48  O   LEU    13      -3.902   0.943   5.651  1.00  0.00              
ATOM     49  N   SER    14      -5.054  -0.856   6.324  1.00  0.00              
ATOM     50  CA  SER    14      -6.102  -0.045   6.933  1.00  0.00              
ATOM     51  C   SER    14      -5.612   0.817   8.087  1.00  0.00              
ATOM     52  O   SER    14      -6.005   1.970   8.207  1.00  0.00              
ATOM     53  N   ALA    15      -4.757   0.255   8.929  1.00  0.00              
ATOM     54  CA  ALA    15      -4.201   1.004  10.044  1.00  0.00              
ATOM     55  C   ALA    15      -3.359   2.181   9.531  1.00  0.00              
ATOM     56  O   ALA    15      -3.481   3.304  10.013  1.00  0.00              
ATOM     57  N   VAL    16      -2.548   1.921   8.523  1.00  0.00              
ATOM     58  CA  VAL    16      -1.681   2.949   7.937  1.00  0.00              
ATOM     59  C   VAL    16      -2.486   4.038   7.215  1.00  0.00              
ATOM     60  O   VAL    16      -2.179   5.235   7.337  1.00  0.00              
ATOM     61  N   GLY    17      -3.512   3.624   6.460  1.00  0.00              
ATOM     62  CA  GLY    17      -4.376   4.542   5.733  1.00  0.00              
ATOM     63  C   GLY    17      -5.145   5.434   6.697  1.00  0.00              
ATOM     64  O   GLY    17      -5.189   6.652   6.537  1.00  0.00              
ATOM     65  N   ALA    18      -5.707   4.849   7.751  1.00  0.00              
ATOM     66  CA  ALA    18      -6.428   5.645   8.733  1.00  0.00              
ATOM     67  C   ALA    18      -5.498   6.597   9.482  1.00  0.00              
ATOM     68  O   ALA    18      -5.862   7.737   9.736  1.00  0.00              
ATOM     69  N   LEU    19      -4.289   6.149   9.811  1.00  0.00              
ATOM     70  CA  LEU    19      -3.309   7.003  10.463  1.00  0.00              
ATOM     71  C   LEU    19      -2.960   8.237   9.613  1.00  0.00              
ATOM     72  O   LEU    19      -2.917   9.364  10.103  1.00  0.00              
ATOM     73  N   LEU    20      -2.716   8.011   8.330  1.00  0.00              
ATOM     74  CA  LEU    20      -2.376   9.106   7.416  1.00  0.00              
ATOM     75  C   LEU    20      -3.547  10.052   7.266  1.00  0.00              
ATOM     76  O   LEU    20      -3.389  11.268   7.414  1.00  0.00              
ATOM     77  N   ASP    21      -4.739   9.522   6.997  1.00  0.00              
ATOM     78  CA  ASP    21      -5.888  10.396   6.810  1.00  0.00              
ATOM     79  C   ASP    21      -6.142  11.232   8.062  1.00  0.00              
ATOM     80  O   ASP    21      -6.459  12.416   7.974  1.00  0.00              
ATOM     81  N   GLY    22      -5.977  10.631   9.234  1.00  0.00              
ATOM     82  CA  GLY    22      -6.289  11.348  10.471  1.00  0.00              
ATOM     83  C   GLY    22      -5.218  12.379  10.831  1.00  0.00              
ATOM     84  O   GLY    22      -5.456  13.267  11.658  1.00  0.00              
ATOM     85  N   ALA    23      -4.063  12.279  10.175  1.00  0.00              
ATOM     86  CA  ALA    23      -2.973  13.227  10.280  1.00  0.00              
ATOM     87  C   ALA    23      -2.863  14.113   9.017  1.00  0.00              
ATOM     88  O   ALA    23      -1.792  14.628   8.668  1.00  0.00              
ATOM     89  N   ASP    24      -3.990  14.259   8.333  1.00  0.00              
ATOM     90  CA  ASP    24      -4.151  15.212   7.241  1.00  0.00              
ATOM     91  C   ASP    24      -3.193  14.981   6.079  1.00  0.00              
ATOM     92  O   ASP    24      -2.655  15.913   5.468  1.00  0.00              
ATOM     93  N   ILE    25      -3.041  13.708   5.740  1.00  0.00              
ATOM     94  CA  ILE    25      -2.395  13.292   4.510  1.00  0.00              
ATOM     95  C   ILE    25      -3.335  12.396   3.715  1.00  0.00              
ATOM     96  O   ILE    25      -3.769  11.343   4.195  1.00  0.00              
ATOM     97  N   GLY    26      -3.643  12.813   2.489  1.00  0.00              
ATOM     98  CA  GLY    26      -4.439  12.012   1.572  1.00  0.00              
ATOM     99  C   GLY    26      -3.719  10.725   1.218  1.00  0.00              
ATOM    100  O   GLY    26      -2.498  10.697   1.165  1.00  0.00              
ATOM    101  N   HIS    27      -4.473   9.662   0.984  1.00  0.00              
ATOM    102  CA  HIS    27      -3.873   8.399   0.583  1.00  0.00              
ATOM    103  C   HIS    27      -4.831   7.619  -0.315  1.00  0.00              
ATOM    104  O   HIS    27      -6.065   7.721  -0.193  1.00  0.00              
ATOM    105  N   LEU    28      -4.250   6.881  -1.262  1.00  0.00              
ATOM    106  CA  LEU    28      -4.995   6.007  -2.131  1.00  0.00              
ATOM    107  C   LEU    28      -4.519   4.574  -1.933  1.00  0.00              
ATOM    108  O   LEU    28      -3.377   4.331  -1.563  1.00  0.00              
ATOM    109  N   VAL    29      -5.414   3.626  -2.173  1.00  0.00              
ATOM    110  CA  VAL    29      -5.158   2.228  -1.915  1.00  0.00              
ATOM    111  C   VAL    29      -5.596   1.389  -3.101  1.00  0.00              
ATOM    112  O   VAL    29      -6.611   1.694  -3.732  1.00  0.00              
ATOM    141  N   ARG    46      -2.114  -5.376  -0.473  1.00  0.00              
ATOM    142  CA  ARG    46      -2.527  -3.986  -0.571  1.00  0.00              
ATOM    143  C   ARG    46      -1.341  -3.065  -0.798  1.00  0.00              
ATOM    144  O   ARG    46      -0.272  -3.271  -0.233  1.00  0.00              
ATOM    145  N   ARG    47      -1.561  -2.061  -1.640  1.00  0.00              
ATOM    146  CA  ARG    47      -0.589  -1.018  -1.932  1.00  0.00              
ATOM    147  C   ARG    47      -1.166   0.329  -1.519  1.00  0.00              
ATOM    148  O   ARG    47      -2.311   0.640  -1.842  1.00  0.00              
ATOM    149  N   VAL    48      -0.378   1.125  -0.798  1.00  0.00              
ATOM    150  CA  VAL    48      -0.755   2.481  -0.425  1.00  0.00              
ATOM    151  C   VAL    48       0.148   3.449  -1.160  1.00  0.00              
ATOM    152  O   VAL    48       1.354   3.222  -1.261  1.00  0.00              
ATOM    153  N   LEU    49      -0.453   4.511  -1.688  1.00  0.00              
ATOM    154  CA  LEU    49       0.237   5.598  -2.387  1.00  0.00              
ATOM    155  C   LEU    49      -0.217   6.950  -1.860  1.00  0.00              
ATOM    156  O   LEU    49      -1.280   7.060  -1.254  1.00  0.00              
ATOM    157  N   VAL    50       0.577   7.981  -2.115  1.00  0.00              
ATOM    158  CA  VAL    50       0.218   9.353  -1.792  1.00  0.00              
ATOM    159  C   VAL    50       0.528  10.254  -2.984  1.00  0.00              
ATOM    160  O   VAL    50       1.250   9.869  -3.899  1.00  0.00              
ATOM    161  N   HIS    51      -0.008  11.463  -2.959  1.00  0.00              
ATOM    162  CA  HIS    51       0.411  12.482  -3.916  1.00  0.00              
ATOM    163  C   HIS    51       1.890  12.710  -3.685  1.00  0.00              
ATOM    164  O   HIS    51       2.358  12.700  -2.534  1.00  0.00              
ATOM    165  N   GLU    52       2.663  12.878  -4.760  1.00  0.00              
ATOM    166  CA  GLU    52       4.119  12.952  -4.609  1.00  0.00              
ATOM    167  C   GLU    52       4.596  14.029  -3.650  1.00  0.00              
ATOM    168  O   GLU    52       5.583  13.826  -2.945  1.00  0.00              
ATOM    169  N   ASP    53       3.897  15.164  -3.602  1.00  0.00              
ATOM    170  CA  ASP    53       4.289  16.285  -2.777  1.00  0.00              
ATOM    171  C   ASP    53       4.168  15.955  -1.300  1.00  0.00              
ATOM    172  O   ASP    53       4.809  16.596  -0.474  1.00  0.00              
ATOM    173  N   ASP    54       3.363  14.946  -0.989  1.00  0.00              
ATOM    174  CA  ASP    54       3.096  14.546   0.388  1.00  0.00              
ATOM    175  C   ASP    54       4.011  13.420   0.882  1.00  0.00              
ATOM    176  O   ASP    54       3.857  12.940   2.023  1.00  0.00              
ATOM    177  N   LEU    55       4.958  12.987   0.049  1.00  0.00              
ATOM    178  CA  LEU    55       5.732  11.804   0.370  1.00  0.00              
ATOM    179  C   LEU    55       6.515  11.946   1.691  1.00  0.00              
ATOM    180  O   LEU    55       6.471  11.052   2.541  1.00  0.00              
ATOM    181  N   ALA    56       7.202  13.056   1.875  1.00  0.00              
ATOM    182  CA  ALA    56       8.019  13.222   3.093  1.00  0.00              
ATOM    183  C   ALA    56       7.139  13.256   4.352  1.00  0.00              
ATOM    184  O   ALA    56       7.423  12.565   5.323  1.00  0.00              
ATOM    185  N   GLY    57       6.056  14.022   4.326  1.00  0.00              
ATOM    186  CA  GLY    57       5.105  14.084   5.435  1.00  0.00              
ATOM    187  C   GLY    57       4.560  12.706   5.765  1.00  0.00              
ATOM    188  O   GLY    57       4.472  12.321   6.935  1.00  0.00              
ATOM    189  N   ALA    58       4.200  11.946   4.726  1.00  0.00              
ATOM    190  CA  ALA    58       3.663  10.599   4.905  1.00  0.00              
ATOM    191  C   ALA    58       4.643   9.624   5.540  1.00  0.00              
ATOM    192  O   ALA    58       4.294   8.920   6.493  1.00  0.00              
ATOM    193  N   ARG    59       5.868   9.575   5.027  1.00  0.00              
ATOM    194  CA  ARG    59       6.877   8.687   5.579  1.00  0.00              
ATOM    195  C   ARG    59       7.206   9.101   7.022  1.00  0.00              
ATOM    196  O   ARG    59       7.421   8.231   7.860  1.00  0.00              
ATOM    197  N   ARG    60       7.205  10.391   7.296  1.00  0.00              
ATOM    198  CA  ARG    60       7.443  10.899   8.655  1.00  0.00              
ATOM    199  C   ARG    60       6.411  10.359   9.641  1.00  0.00              
ATOM    200  O   ARG    60       6.771   9.788  10.681  1.00  0.00              
ATOM    201  N   LEU    61       5.128  10.488   9.287  1.00  0.00              
ATOM    202  CA  LEU    61       4.036   9.995  10.094  1.00  0.00              
ATOM    203  C   LEU    61       4.128   8.476  10.289  1.00  0.00              
ATOM    204  O   LEU    61       3.940   7.973  11.400  1.00  0.00              
ATOM    205  N   LEU    62       4.394   7.746   9.209  1.00  0.00              
ATOM    206  CA  LEU    62       4.485   6.301   9.299  1.00  0.00              
ATOM    207  C   LEU    62       5.667   5.891  10.193  1.00  0.00              
ATOM    208  O   LEU    62       5.486   5.031  11.077  1.00  0.00              
ATOM    209  N   THR    63       6.831   6.494   9.963  1.00  0.00              
ATOM    210  CA  THR    63       8.045   6.220  10.749  1.00  0.00              
ATOM    211  C   THR    63       7.780   6.476  12.235  1.00  0.00              
ATOM    212  O   THR    63       8.168   5.662  13.100  1.00  0.00              
ATOM    213  N   ASP    64       7.115   7.593  12.523  1.00  0.00              
ATOM    214  CA  ASP    64       6.804   7.994  13.904  1.00  0.00              
ATOM    215  C   ASP    64       5.834   7.073  14.602  1.00  0.00              
ATOM    216  O   ASP    64       5.693   7.149  15.828  1.00  0.00              
ATOM    217  N   ALA    65       5.128   6.228  13.847  1.00  0.00              
ATOM    218  CA  ALA    65       4.205   5.264  14.406  1.00  0.00              
ATOM    219  C   ALA    65       4.642   3.818  14.220  1.00  0.00              
ATOM    220  O   ALA    65       3.882   2.893  14.492  1.00  0.00              
ATOM    221  N   GLY    66       5.877   3.624  13.760  1.00  0.00              
ATOM    222  CA  GLY    66       6.455   2.303  13.607  1.00  0.00              
ATOM    223  C   GLY    66       5.917   1.454  12.467  1.00  0.00              
ATOM    224  O   GLY    66       5.940   0.238  12.554  1.00  0.00              
ATOM    225  N   LEU    67       5.396   2.095  11.418  1.00  0.00              
ATOM    226  CA  LEU    67       4.862   1.379  10.257  1.00  0.00              
ATOM    227  C   LEU    67       5.848   1.457   9.103  1.00  0.00              
ATOM    228  O   LEU    67       6.503   2.490   8.923  1.00  0.00              
END
