
#######################################################
#                                                     #
#                        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   52 (  210),  selected   52 , name T0349AL243_2
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349AL243_2.T0349.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    L       4      L       5          3.592
LGA    L       5      R       6          4.529
LGA    R       6      T       7          4.744
LGA    N       8      N       8           #
LGA    D       9      D       9          1.719
LGA    A      10      A      10          2.343
LGA    V      11      V      11          0.668
LGA    L      12      L      12          1.053
LGA    L      13      L      13          0.810
LGA    S      14      S      14          1.146
LGA    A      15      A      15          0.924
LGA    V      16      V      16          0.759
LGA    G      17      G      17          1.085
LGA    A      18      A      18          0.701
LGA    L      19      L      19          0.734
LGA    L      20      L      20          0.616
LGA    D      21      D      21          1.811
LGA    G      22      G      22          2.259
LGA    A      23      A      23          1.862
LGA    D      24      D      24          2.044
LGA    L      28      I      25          1.007
LGA    V      29      G      26          2.117
LGA    L      30      H      27          2.522
LGA    D      31      -       -           -
LGA    S      35      L      28          4.240
LGA    I      36      V      29          4.434
LGA    L      37      L      30          3.882
LGA    E      38      D      31          2.816
LGA    -       -      Q      32           -
LGA    -       -      N      33           -
LGA    -       -      M      34           -
LGA    -       -      S      35           -
LGA    -       -      I      36           -
LGA    -       -      L      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    G      39      I      44           #
LGA    S      40      P      45          1.979
LGA    L      41      -       -           -
LGA    G      42      -       -           -
LGA    V      43      R      46          4.598
LGA    I      44      R      47          1.351
LGA    R      47      V      48          3.706
LGA    V      48      L      49          1.389
LGA    L      49      V      50          3.161
LGA    V      50      H      51          2.384
LGA    -       -      E      52           -
LGA    D      53      D      53          4.162
LGA    D      54      D      54          0.870
LGA    L      55      L      55          0.836
LGA    A      56      A      56          0.800
LGA    G      57      G      57          0.582
LGA    A      58      A      58          0.212
LGA    R      59      R      59          0.618
LGA    R      60      R      60          0.629
LGA    L      61      L      61          0.579
LGA    L      62      L      62          0.888
LGA    T      63      T      63          1.324
LGA    D      64      D      64          2.051
LGA    -       -      A      65           -
LGA    A      65      G      66          1.137
LGA    G      66      L      67          1.404
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      S      73           -
LGA    -       -      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   52   75    5.0     47    2.30    63.83     46.817     1.955

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.889204 * X  +  -0.442868 * Y  +   0.114822 * Z  +   8.709945
  Y_new =  -0.443403 * X  +  -0.896046 * Y  +  -0.022249 * Z  +  36.465347
  Z_new =   0.112739 * X  +  -0.031129 * Y  +  -0.993137 * Z  +  11.517999 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.110259    0.031334  [ DEG:  -178.2047      1.7953 ]
  Theta =  -0.112980   -3.028613  [ DEG:    -6.4732   -173.5267 ]
  Phi   =  -0.462568    2.679024  [ DEG:   -26.5032    153.4968 ]
 
# 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_2                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL243_2.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   75   5.0   47   2.30   63.83  46.817
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL243_2
REMARK Aligment from pdb entry: 2f06A
ATOM      1  N   LEU     4       4.374  -1.410   1.925  1.00  0.00              
ATOM      2  CA  LEU     4       4.279  -2.873   2.081  1.00  0.00              
ATOM      3  C   LEU     4       3.227  -3.186   3.152  1.00  0.00              
ATOM      4  O   LEU     4       3.355  -2.759   4.281  1.00  0.00              
ATOM      5  N   LEU     5       2.132  -3.831   2.745  1.00  0.00              
ATOM      6  CA  LEU     5       1.001  -4.112   3.647  1.00  0.00              
ATOM      7  C   LEU     5       1.170  -5.594   3.919  1.00  0.00              
ATOM      8  O   LEU     5       0.944  -6.448   3.016  1.00  0.00              
ATOM      9  N   ARG     6       1.592  -5.918   5.122  1.00  0.00              
ATOM     10  CA  ARG     6       1.718  -7.302   5.527  1.00  0.00              
ATOM     11  C   ARG     6       0.349  -7.934   5.883  1.00  0.00              
ATOM     12  O   ARG     6      -0.668  -7.285   5.732  1.00  0.00              
ATOM     13  N   ASN     8       0.281  -9.197   6.292  1.00  0.00              
ATOM     14  CA  ASN     8      -1.022  -9.688   6.870  1.00  0.00              
ATOM     15  C   ASN     8      -2.132  -9.697   5.732  1.00  0.00              
ATOM     16  O   ASN     8      -1.904 -10.352   4.715  1.00  0.00              
ATOM     17  N   ASP     9      -3.276  -8.996   5.864  1.00  0.00              
ATOM     18  CA  ASP     9      -4.292  -8.761   4.742  1.00  0.00              
ATOM     19  C   ASP     9      -5.587  -8.030   5.206  1.00  0.00              
ATOM     20  O   ASP     9      -6.498  -7.841   4.388  1.00  0.00              
ATOM     21  N   ALA    10      -5.635  -7.575   6.476  1.00  0.00              
ATOM     22  CA  ALA    10      -6.836  -7.834   7.331  1.00  0.00              
ATOM     23  C   ALA    10      -7.473  -6.872   8.403  1.00  0.00              
ATOM     24  O   ALA    10      -8.354  -7.361   9.125  1.00  0.00              
ATOM     25  N   VAL    11      -7.001  -5.654   8.693  1.00  0.00              
ATOM     26  CA  VAL    11      -5.629  -5.400   8.994  1.00  0.00              
ATOM     27  C   VAL    11      -5.010  -4.040   8.788  1.00  0.00              
ATOM     28  O   VAL    11      -5.488  -2.988   9.247  1.00  0.00              
ATOM     29  N   LEU    12      -3.896  -4.144   8.103  1.00  0.00              
ATOM     30  CA  LEU    12      -2.872  -3.152   8.022  1.00  0.00              
ATOM     31  C   LEU    12      -3.233  -2.044   7.098  1.00  0.00              
ATOM     32  O   LEU    12      -2.749  -0.943   7.288  1.00  0.00              
ATOM     33  N   LEU    13      -4.076  -2.320   6.100  1.00  0.00              
ATOM     34  CA  LEU    13      -4.467  -1.241   5.182  1.00  0.00              
ATOM     35  C   LEU    13      -5.284  -0.143   5.944  1.00  0.00              
ATOM     36  O   LEU    13      -5.124   1.075   5.697  1.00  0.00              
ATOM     37  N   SER    14      -6.133  -0.589   6.859  1.00  0.00              
ATOM     38  CA  SER    14      -6.912   0.354   7.642  1.00  0.00              
ATOM     39  C   SER    14      -6.015   1.222   8.540  1.00  0.00              
ATOM     40  O   SER    14      -6.105   2.465   8.503  1.00  0.00              
ATOM     41  N   ALA    15      -5.124   0.578   9.276  1.00  0.00              
ATOM     42  CA  ALA    15      -4.098   1.308  10.020  1.00  0.00              
ATOM     43  C   ALA    15      -3.300   2.286   9.180  1.00  0.00              
ATOM     44  O   ALA    15      -3.027   3.346   9.676  1.00  0.00              
ATOM     45  N   VAL    16      -2.917   1.954   7.931  1.00  0.00              
ATOM     46  CA  VAL    16      -2.147   2.889   7.092  1.00  0.00              
ATOM     47  C   VAL    16      -2.992   4.098   6.776  1.00  0.00              
ATOM     48  O   VAL    16      -2.527   5.264   6.749  1.00  0.00              
ATOM     49  N   GLY    17      -4.239   3.855   6.460  1.00  0.00              
ATOM     50  CA  GLY    17      -5.091   5.014   6.119  1.00  0.00              
ATOM     51  C   GLY    17      -5.390   5.844   7.365  1.00  0.00              
ATOM     52  O   GLY    17      -5.592   7.067   7.255  1.00  0.00              
ATOM     53  N   ALA    18      -5.418   5.179   8.503  1.00  0.00              
ATOM     54  CA  ALA    18      -5.490   5.868   9.819  1.00  0.00              
ATOM     55  C   ALA    18      -4.263   6.739  10.194  1.00  0.00              
ATOM     56  O   ALA    18      -4.431   7.865  10.637  1.00  0.00              
ATOM     57  N   LEU    19      -3.053   6.210  10.110  1.00  0.00              
ATOM     58  CA  LEU    19      -1.811   7.040  10.095  1.00  0.00              
ATOM     59  C   LEU    19      -1.882   8.297   9.227  1.00  0.00              
ATOM     60  O   LEU    19      -1.595   9.395   9.702  1.00  0.00              
ATOM     61  N   LEU    20      -2.264   8.151   7.973  1.00  0.00              
ATOM     62  CA  LEU    20      -2.370   9.289   7.084  1.00  0.00              
ATOM     63  C   LEU    20      -3.477  10.268   7.454  1.00  0.00              
ATOM     64  O   LEU    20      -3.233  11.471   7.388  1.00  0.00              
ATOM     65  N   ASP    21      -4.667   9.771   7.846  1.00  0.00              
ATOM     66  CA  ASP    21      -5.761  10.614   8.332  1.00  0.00              
ATOM     67  C   ASP    21      -5.351  11.470   9.524  1.00  0.00              
ATOM     68  O   ASP    21      -5.782  12.637   9.655  1.00  0.00              
ATOM     69  N   GLY    22      -4.597  10.868  10.443  1.00  0.00              
ATOM     70  CA  GLY    22      -4.226  11.554  11.686  1.00  0.00              
ATOM     71  C   GLY    22      -3.314  12.776  11.386  1.00  0.00              
ATOM     72  O   GLY    22      -3.296  13.765  12.158  1.00  0.00              
ATOM     73  N   ALA    23      -2.572  12.705  10.271  1.00  0.00              
ATOM     74  CA  ALA    23      -1.700  13.787   9.894  1.00  0.00              
ATOM     75  C   ALA    23      -2.392  14.852   9.009  1.00  0.00              
ATOM     76  O   ALA    23      -1.728  15.851   8.593  1.00  0.00              
ATOM     77  N   ASP    24      -3.694  14.656   8.741  1.00  0.00              
ATOM     78  CA  ASP    24      -4.495  15.450   7.788  1.00  0.00              
ATOM     79  C   ASP    24      -3.818  15.399   6.419  1.00  0.00              
ATOM     80  O   ASP    24      -3.676  16.422   5.742  1.00  0.00              
ATOM     81  N   LEU    28      -3.380  14.187   6.038  1.00  0.00              
ATOM     82  CA  LEU    28      -2.799  13.938   4.746  1.00  0.00              
ATOM     83  C   LEU    28      -3.893  13.358   3.907  1.00  0.00              
ATOM     84  O   LEU    28      -4.504  12.339   4.256  1.00  0.00              
ATOM     85  N   VAL    29      -4.184  14.056   2.809  1.00  0.00              
ATOM     86  CA  VAL    29      -5.161  13.594   1.813  1.00  0.00              
ATOM     87  C   VAL    29      -4.537  12.628   0.796  1.00  0.00              
ATOM     88  O   VAL    29      -3.427  12.852   0.239  1.00  0.00              
ATOM     89  N   LEU    30      -5.308  11.604   0.475  1.00  0.00              
ATOM     90  CA  LEU    30      -4.979  10.681  -0.596  1.00  0.00              
ATOM     91  C   LEU    30      -5.572  11.202  -1.910  1.00  0.00              
ATOM     92  O   LEU    30      -6.741  11.469  -1.982  1.00  0.00              
ATOM     93  N   ASP    31      -4.768  11.331  -2.953  1.00  0.00              
ATOM     94  CA  ASP    31      -5.220  11.787  -4.284  1.00  0.00              
ATOM     95  C   ASP    31      -5.575  10.668  -5.218  1.00  0.00              
ATOM     96  O   ASP    31      -6.466  10.783  -6.041  1.00  0.00              
ATOM     97  N   SER    35      -4.795   9.615  -5.103  1.00  0.00              
ATOM     98  CA  SER    35      -4.799   8.494  -6.046  1.00  0.00              
ATOM     99  C   SER    35      -4.087   7.350  -5.367  1.00  0.00              
ATOM    100  O   SER    35      -2.994   7.519  -4.779  1.00  0.00              
ATOM    101  N   ILE    36      -4.683   6.183  -5.464  1.00  0.00              
ATOM    102  CA  ILE    36      -3.995   5.032  -5.007  1.00  0.00              
ATOM    103  C   ILE    36      -4.397   3.801  -5.809  1.00  0.00              
ATOM    104  O   ILE    36      -5.385   3.814  -6.558  1.00  0.00              
ATOM    105  N   LEU    37      -3.642   2.732  -5.632  1.00  0.00              
ATOM    106  CA  LEU    37      -3.816   1.575  -6.444  1.00  0.00              
ATOM    107  C   LEU    37      -3.091   0.548  -5.600  1.00  0.00              
ATOM    108  O   LEU    37      -1.985   0.780  -5.084  1.00  0.00              
ATOM    109  N   GLU    38      -3.718  -0.577  -5.366  1.00  0.00              
ATOM    110  CA  GLU    38      -2.990  -1.603  -4.669  1.00  0.00              
ATOM    111  C   GLU    38      -2.467  -2.600  -5.696  1.00  0.00              
ATOM    112  O   GLU    38      -3.231  -3.146  -6.487  1.00  0.00              
ATOM    113  N   GLY    39      -1.164  -2.873  -5.664  1.00  0.00              
ATOM    114  CA  GLY    39      -0.666  -4.023  -6.454  1.00  0.00              
ATOM    115  C   GLY    39      -0.525  -5.228  -5.504  1.00  0.00              
ATOM    116  O   GLY    39       0.406  -5.264  -4.723  1.00  0.00              
ATOM    117  N   SER    40      -1.426  -6.219  -5.586  1.00  0.00              
ATOM    118  CA ASER    40      -1.537  -7.281  -4.570  1.00  0.00              
ATOM    119  CA BSER    40      -1.458  -7.270  -4.557  1.00  0.00              
ATOM    120  C   SER    40      -1.056  -8.664  -5.013  1.00  0.00              
ATOM    121  O   SER    40      -1.108  -9.009  -6.200  1.00  0.00              
ATOM    122  N   LEU    41      -0.026 -10.503   0.477  1.00  0.00              
ATOM    123  CA ALEU    41       0.227  -9.134   0.890  1.00  0.00              
ATOM    124  CA BLEU    41      -0.019  -9.106   0.922  1.00  0.00              
ATOM    125  C   LEU    41      -0.143  -8.212  -0.242  1.00  0.00              
ATOM    126  O   LEU    41      -0.262  -8.674  -1.383  1.00  0.00              
ATOM    127  N   GLY    42      -0.230  -6.921   0.074  1.00  0.00              
ATOM    128  CA  GLY    42      -0.317  -5.925  -0.972  1.00  0.00              
ATOM    129  C   GLY    42       0.765  -4.902  -0.950  1.00  0.00              
ATOM    130  O   GLY    42       1.479  -4.740   0.035  1.00  0.00              
ATOM    131  N   VAL    43       0.900  -4.225  -2.057  1.00  0.00              
ATOM    132  CA  VAL    43       1.602  -3.005  -1.977  1.00  0.00              
ATOM    133  C   VAL    43       0.665  -1.844  -2.338  1.00  0.00              
ATOM    134  O   VAL    43       0.166  -1.763  -3.509  1.00  0.00              
ATOM    135  N   ILE    44       0.480  -0.955  -1.366  1.00  0.00              
ATOM    136  CA  ILE    44      -0.237   0.255  -1.635  1.00  0.00              
ATOM    137  C   ILE    44       0.660   1.253  -2.349  1.00  0.00              
ATOM    138  O   ILE    44       1.597   1.791  -1.761  1.00  0.00              
ATOM    139  N   ARG    47       0.309   1.530  -3.584  1.00  0.00              
ATOM    140  CA  ARG    47       0.881   2.634  -4.311  1.00  0.00              
ATOM    141  C   ARG    47      -0.014   3.852  -4.163  1.00  0.00              
ATOM    142  O   ARG    47      -1.231   3.757  -4.349  1.00  0.00              
ATOM    143  N   VAL    48       0.578   4.991  -3.854  1.00  0.00              
ATOM    144  CA  VAL    48      -0.185   6.060  -3.280  1.00  0.00              
ATOM    145  C   VAL    48       0.354   7.406  -3.720  1.00  0.00              
ATOM    146  O   VAL    48       1.543   7.671  -3.603  1.00  0.00              
ATOM    147  N   LEU    49      -0.546   8.237  -4.225  1.00  0.00              
ATOM    148  CA  LEU    49      -0.305   9.687  -4.370  1.00  0.00              
ATOM    149  C   LEU    49      -0.978  10.434  -3.211  1.00  0.00              
ATOM    150  O   LEU    49      -2.193  10.350  -3.052  1.00  0.00              
ATOM    151  N   VAL    50      -0.188  11.122  -2.374  1.00  0.00              
ATOM    152  CA  VAL    50      -0.741  11.838  -1.227  1.00  0.00              
ATOM    153  C   VAL    50      -0.471  13.376  -1.309  1.00  0.00              
ATOM    154  O   VAL    50       0.316  13.814  -2.169  1.00  0.00              
ATOM    155  N   ASP    53      -1.084  14.151  -0.404  1.00  0.00              
ATOM    156  CA  ASP    53      -0.962  15.639  -0.420  1.00  0.00              
ATOM    157  C   ASP    53       0.400  16.197   0.050  1.00  0.00              
ATOM    158  O   ASP    53       0.801  17.306  -0.346  1.00  0.00              
ATOM    159  N   ASP    54       1.095  15.422   0.885  1.00  0.00              
ATOM    160  CA  ASP    54       2.413  15.773   1.398  1.00  0.00              
ATOM    161  C   ASP    54       3.264  14.487   1.522  1.00  0.00              
ATOM    162  O   ASP    54       3.268  13.841   2.581  1.00  0.00              
ATOM    163  N   LEU    55       3.951  14.081   0.427  1.00  0.00              
ATOM    164  CA  LEU    55       4.661  12.781   0.497  1.00  0.00              
ATOM    165  C   LEU    55       5.775  12.658   1.563  1.00  0.00              
ATOM    166  O   LEU    55       5.911  11.597   2.161  1.00  0.00              
ATOM    167  N   ALA    56       6.493  13.738   1.852  1.00  0.00              
ATOM    168  CA  ALA    56       7.585  13.708   2.836  1.00  0.00              
ATOM    169  C   ALA    56       7.061  13.545   4.276  1.00  0.00              
ATOM    170  O   ALA    56       7.613  12.758   5.053  1.00  0.00              
ATOM    171  N   GLY    57       6.004  14.284   4.599  1.00  0.00              
ATOM    172  CA  GLY    57       5.354  14.170   5.916  1.00  0.00              
ATOM    173  C   GLY    57       4.748  12.762   6.057  1.00  0.00              
ATOM    174  O   GLY    57       4.878  12.136   7.114  1.00  0.00              
ATOM    175  N   ALA    58       4.087  12.284   4.995  1.00  0.00              
ATOM    176  CA  ALA    58       3.509  10.945   4.964  1.00  0.00              
ATOM    177  C   ALA    58       4.532   9.853   5.141  1.00  0.00              
ATOM    178  O   ALA    58       4.336   8.953   6.000  1.00  0.00              
ATOM    179  N   ARG    59       5.608   9.928   4.368  1.00  0.00              
ATOM    180  CA  ARG    59       6.723   8.998   4.545  1.00  0.00              
ATOM    181  C   ARG    59       7.272   8.925   5.984  1.00  0.00              
ATOM    182  O   ARG    59       7.511   7.846   6.525  1.00  0.00              
ATOM    183  N   ARG    60       7.505  10.063   6.609  1.00  0.00              
ATOM    184  CA  ARG    60       8.100  10.007   7.953  1.00  0.00              
ATOM    185  C   ARG    60       7.108   9.459   9.012  1.00  0.00              
ATOM    186  O   ARG    60       7.523   8.728   9.924  1.00  0.00              
ATOM    187  N   LEU    61       5.823   9.811   8.882  1.00  0.00              
ATOM    188  CA  LEU    61       4.756   9.268   9.726  1.00  0.00              
ATOM    189  C   LEU    61       4.653   7.713   9.629  1.00  0.00              
ATOM    190  O   LEU    61       4.612   6.969  10.652  1.00  0.00              
ATOM    191  N   LEU    62       4.654   7.226   8.401  1.00  0.00              
ATOM    192  CA  LEU    62       4.670   5.807   8.151  1.00  0.00              
ATOM    193  C   LEU    62       5.893   5.088   8.721  1.00  0.00              
ATOM    194  O   LEU    62       5.705   4.079   9.386  1.00  0.00              
ATOM    195  N   THR    63       7.119   5.577   8.471  1.00  0.00              
ATOM    196  CA  THR    63       8.349   5.011   9.105  1.00  0.00              
ATOM    197  C   THR    63       8.285   5.007  10.637  1.00  0.00              
ATOM    198  O   THR    63       8.749   4.063  11.293  1.00  0.00              
ATOM    199  N   ASP    64       7.758   6.099  11.197  1.00  0.00              
ATOM    200  CA  ASP    64       7.552   6.264  12.634  1.00  0.00              
ATOM    201  C   ASP    64       6.604   5.198  13.189  1.00  0.00              
ATOM    202  O   ASP    64       6.754   4.787  14.347  1.00  0.00              
ATOM    203  N   ALA    65       5.584   4.841  12.407  1.00  0.00              
ATOM    204  CA  ALA    65       4.640   3.786  12.756  1.00  0.00              
ATOM    205  C   ALA    65       5.059   2.390  12.281  1.00  0.00              
ATOM    206  O   ALA    65       4.242   1.461  12.300  1.00  0.00              
ATOM    207  N   GLY    66       6.320   2.273  11.832  1.00  0.00              
ATOM    208  CA  GLY    66       7.004   0.999  11.555  1.00  0.00              
ATOM    209  C   GLY    66       6.511   0.342  10.279  1.00  0.00              
ATOM    210  O   GLY    66       6.654  -0.889  10.128  1.00  0.00              
END
