
#######################################################
#                                                     #
#                        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 (  208),  selected   52 , name T0349AL243_3
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349AL243_3.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       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    A      10      N       8          4.723
LGA    V      11      D       9          1.165
LGA    L      12      -       -           -
LGA    L      13      A      10          2.516
LGA    S      14      V      11          2.231
LGA    A      15      L      12          2.606
LGA    V      16      L      13          2.470
LGA    G      17      S      14          1.225
LGA    A      18      A      15          1.149
LGA    L      19      V      16          1.621
LGA    L      20      G      17          2.866
LGA    D      21      A      18          3.015
LGA    G      22      L      19          2.433
LGA    -       -      L      20           -
LGA    -       -      D      21           -
LGA    A      23      G      22          0.679
LGA    D      24      A      23          0.990
LGA    -       -      D      24           -
LGA    I      25      I      25          3.139
LGA    G      26      G      26          3.382
LGA    H      27      H      27          3.335
LGA    L      28      L      28          2.133
LGA    V      29      V      29          2.300
LGA    L      30      L      30          2.130
LGA    D      31      D      31          4.211
LGA    Q      32      Q      32          3.043
LGA    N      33      N      33          4.817
LGA    S      35      M      34          4.831
LGA    I      36      S      35          1.145
LGA    L      37      I      36          5.219
LGA    -       -      L      37           -
LGA    E      38      E      38           #
LGA    G      39      G      39          4.275
LGA    S      40      S      40          1.631
LGA    L      41      L      41          4.289
LGA    G      42      G      42           -
LGA    V      43      V      43           -
LGA    I      44      I      44           -
LGA    P      45      P      45           -
LGA    R      46      R      46           -
LGA    R      47      R      47           -
LGA    V      48      V      48           -
LGA    L      49      L      49           -
LGA    V      50      V      50           -
LGA    A      56      H      51           -
LGA    G      57      E      52           -
LGA    A      58      D      53           -
LGA    R      59      D      54           -
LGA    R      60      L      55           -
LGA    L      61      A      56           -
LGA    L      62      G      57           -
LGA    T      63      A      58           -
LGA    D      64      R      59           -
LGA    A      65      R      60           -
LGA    G      66      L      61           -
LGA    L      67      L      62           -
LGA    -       -      T      63           -
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    -       -      L      67           -
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     29    3.03    44.83     24.997     0.927

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.135630 * X  +  -0.990644 * Y  +   0.015107 * Z  +   9.595659
  Y_new =  -0.425472 * X  +  -0.044468 * Y  +   0.903879 * Z  + -18.331253
  Z_new =  -0.894750 * X  +  -0.129021 * Y  +  -0.427522 * Z  +  63.724346 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.848497    0.293096  [ DEG:  -163.2068     16.7931 ]
  Theta =   1.107872    2.033721  [ DEG:    63.4764    116.5236 ]
  Phi   =  -1.262204    1.879389  [ DEG:   -72.3190    107.6810 ]
 
# 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_3                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL243_3.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   29   3.03   44.83  24.997
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL243_3
REMARK Aligment from pdb entry: 1rp0A
ATOM      1  N   ALA    10      -5.671  -9.409   3.182  1.00  0.00              
ATOM      2  CA  ALA    10      -5.419  -9.198   4.602  1.00  0.00              
ATOM      3  C   ALA    10      -4.207  -8.306   4.869  1.00  0.00              
ATOM      4  O   ALA    10      -4.207  -7.504   5.806  1.00  0.00              
ATOM      5  N   VAL    11      -3.149  -8.451   4.087  1.00  0.00              
ATOM      6  CA  VAL    11      -1.971  -7.640   4.327  1.00  0.00              
ATOM      7  C   VAL    11      -2.206  -6.159   3.974  1.00  0.00              
ATOM      8  O   VAL    11      -1.873  -5.275   4.744  1.00  0.00              
ATOM      9  N   LEU    12      -2.765  -5.899   2.801  1.00  0.00              
ATOM     10  CA  LEU    12      -3.050  -4.534   2.406  1.00  0.00              
ATOM     11  C   LEU    12      -4.052  -3.828   3.281  1.00  0.00              
ATOM     12  O   LEU    12      -3.889  -2.665   3.571  1.00  0.00              
ATOM     13  N   LEU    13      -5.115  -4.521   3.691  1.00  0.00              
ATOM     14  CA  LEU    13      -6.064  -3.926   4.617  1.00  0.00              
ATOM     15  C   LEU    13      -5.398  -3.580   5.940  1.00  0.00              
ATOM     16  O   LEU    13      -5.655  -2.530   6.509  1.00  0.00              
ATOM     17  N   SER    14      -4.576  -4.490   6.439  1.00  0.00              
ATOM     18  CA  SER    14      -3.863  -4.276   7.694  1.00  0.00              
ATOM     19  C   SER    14      -2.906  -3.081   7.590  1.00  0.00              
ATOM     20  O   SER    14      -2.768  -2.300   8.522  1.00  0.00              
ATOM     21  N   ALA    15      -2.220  -2.938   6.462  1.00  0.00              
ATOM     22  CA  ALA    15      -1.325  -1.807   6.251  1.00  0.00              
ATOM     23  C   ALA    15      -2.101  -0.502   6.178  1.00  0.00              
ATOM     24  O   ALA    15      -1.757   0.487   6.836  1.00  0.00              
ATOM     25  N   VAL    16      -3.178  -0.477   5.401  1.00  0.00              
ATOM     26  CA  VAL    16      -3.993   0.733   5.320  1.00  0.00              
ATOM     27  C   VAL    16      -4.605   1.149   6.658  1.00  0.00              
ATOM     28  O   VAL    16      -4.664   2.343   6.976  1.00  0.00              
ATOM     29  N   GLY    17      -5.077   0.164   7.422  1.00  0.00              
ATOM     30  CA  GLY    17      -5.627   0.356   8.753  1.00  0.00              
ATOM     31  C   GLY    17      -4.575   0.973   9.677  1.00  0.00              
ATOM     32  O   GLY    17      -4.849   1.918  10.406  1.00  0.00              
ATOM     33  N   ALA    18      -3.356   0.443   9.636  1.00  0.00              
ATOM     34  CA  ALA    18      -2.286   0.962  10.480  1.00  0.00              
ATOM     35  C   ALA    18      -1.889   2.393  10.112  1.00  0.00              
ATOM     36  O   ALA    18      -1.769   3.231  11.000  1.00  0.00              
ATOM     37  N   LEU    19      -1.715   2.671   8.820  1.00  0.00              
ATOM     38  CA  LEU    19      -1.281   3.989   8.369  1.00  0.00              
ATOM     39  C   LEU    19      -2.338   5.042   8.723  1.00  0.00              
ATOM     40  O   LEU    19      -2.001   6.134   9.176  1.00  0.00              
ATOM     41  N   LEU    20      -3.601   4.702   8.498  1.00  0.00              
ATOM     42  CA  LEU    20      -4.653   5.714   8.528  1.00  0.00              
ATOM     43  C   LEU    20      -5.068   6.029   9.956  1.00  0.00              
ATOM     44  O   LEU    20      -5.893   6.908  10.172  1.00  0.00              
ATOM     45  N   ASP    21      -4.490   5.331  10.926  1.00  0.00              
ATOM     46  CA  ASP    21      -4.591   5.767  12.312  1.00  0.00              
ATOM     47  C   ASP    21      -4.001   7.161  12.504  1.00  0.00              
ATOM     48  O   ASP    21      -4.351   7.860  13.436  1.00  0.00              
ATOM     49  N   GLY    22      -3.087   7.569  11.625  1.00  0.00              
ATOM     50  CA  GLY    22      -2.654   8.956  11.525  1.00  0.00              
ATOM     51  C   GLY    22      -3.620   9.697  10.604  1.00  0.00              
ATOM     52  O   GLY    22      -3.671   9.409   9.405  1.00  0.00              
ATOM     53  N   ALA    23      -4.432  10.596  11.142  1.00  0.00              
ATOM     54  CA  ALA    23      -5.508  11.240  10.366  1.00  0.00              
ATOM     55  C   ALA    23      -5.010  12.206   9.302  1.00  0.00              
ATOM     56  O   ALA    23      -5.802  12.562   8.430  1.00  0.00              
ATOM     57  N   ASP    24      -3.728  12.547   9.356  1.00  0.00              
ATOM     58  CA  ASP    24      -3.096  13.530   8.492  1.00  0.00              
ATOM     59  C   ASP    24      -2.544  12.877   7.226  1.00  0.00              
ATOM     60  O   ASP    24      -2.042  13.555   6.327  1.00  0.00              
ATOM     61  N   ILE    25      -2.602  11.553   7.175  1.00  0.00              
ATOM     62  CA  ILE    25      -2.022  10.809   6.058  1.00  0.00              
ATOM     63  C   ILE    25      -3.096  10.335   5.100  1.00  0.00              
ATOM     64  O   ILE    25      -4.052   9.664   5.470  1.00  0.00              
ATOM     65  N   GLY    26      -2.953  10.709   3.835  1.00  0.00              
ATOM     66  CA  GLY    26      -3.875  10.265   2.803  1.00  0.00              
ATOM     67  C   GLY    26      -3.529   8.892   2.263  1.00  0.00              
ATOM     68  O   GLY    26      -2.366   8.652   1.889  1.00  0.00              
ATOM     69  N   HIS    27      -4.522   8.012   2.282  1.00  0.00              
ATOM     70  CA  HIS    27      -4.359   6.638   1.862  1.00  0.00              
ATOM     71  C   HIS    27      -5.305   6.233   0.752  1.00  0.00              
ATOM     72  O   HIS    27      -6.515   6.105   0.974  1.00  0.00              
ATOM     73  N   LEU    28      -4.750   5.948  -0.427  1.00  0.00              
ATOM     74  CA  LEU    28      -5.538   5.364  -1.504  1.00  0.00              
ATOM     75  C   LEU    28      -5.315   3.853  -1.520  1.00  0.00              
ATOM     76  O   LEU    28      -4.177   3.433  -1.397  1.00  0.00              
ATOM     77  N   VAL    29      -6.373   3.083  -1.664  1.00  0.00              
ATOM     78  CA  VAL    29      -6.268   1.633  -1.813  1.00  0.00              
ATOM     79  C   VAL    29      -6.741   1.323  -3.219  1.00  0.00              
ATOM     80  O   VAL    29      -7.862   1.635  -3.606  1.00  0.00              
ATOM     81  N   LEU    30      -5.875   0.659  -3.975  1.00  0.00              
ATOM     82  CA  LEU    30      -6.153   0.259  -5.347  1.00  0.00              
ATOM     83  C   LEU    30      -6.387  -1.259  -5.285  1.00  0.00              
ATOM     84  O   LEU    30      -5.528  -2.030  -4.842  1.00  0.00              
ATOM     85  N   ASP    31      -7.574  -1.703  -5.691  1.00  0.00              
ATOM     86  CA  ASP    31      -7.907  -3.125  -5.676  1.00  0.00              
ATOM     87  C   ASP    31      -8.582  -3.500  -6.987  1.00  0.00              
ATOM     88  O   ASP    31      -9.639  -2.955  -7.353  1.00  0.00              
ATOM     89  N   GLN    32      -8.014  -4.485  -7.686  1.00  0.00              
ATOM     90  CA  GLN    32      -8.466  -4.803  -9.024  1.00  0.00              
ATOM     91  C   GLN    32      -9.823  -5.490  -8.989  1.00  0.00              
ATOM     92  O   GLN    32     -10.646  -5.312  -9.885  1.00  0.00              
ATOM     93  N   ASN    33     -10.054  -6.312  -7.976  1.00  0.00              
ATOM     94  CA  ASN    33     -11.354  -6.988  -7.884  1.00  0.00              
ATOM     95  C   ASN    33     -12.441  -6.007  -7.529  1.00  0.00              
ATOM     96  O   ASN    33     -12.203  -5.015  -6.851  1.00  0.00              
ATOM     97  N   SER    35     -13.669  -6.315  -7.937  1.00  0.00              
ATOM     98  CA  SER    35     -14.794  -5.528  -7.430  1.00  0.00              
ATOM     99  C   SER    35     -14.906  -5.681  -5.920  1.00  0.00              
ATOM    100  O   SER    35     -15.138  -4.707  -5.222  1.00  0.00              
ATOM    101  N   ILE    36     -14.758  -6.915  -5.405  1.00  0.00              
ATOM    102  CA  ILE    36     -14.770  -7.129  -3.959  1.00  0.00              
ATOM    103  C   ILE    36     -13.372  -6.955  -3.388  1.00  0.00              
ATOM    104  O   ILE    36     -12.471  -7.611  -3.879  1.00  0.00              
ATOM    105  N   LEU    37     -13.208  -6.174  -2.339  1.00  0.00              
ATOM    106  CA  LEU    37     -11.957  -6.175  -1.572  1.00  0.00              
ATOM    107  C   LEU    37     -11.920  -7.449  -0.719  1.00  0.00              
ATOM    108  O   LEU    37     -12.899  -8.204  -0.694  1.00  0.00              
ATOM    109  N   GLU    38     -10.804  -7.681  -0.037  1.00  0.00              
ATOM    110  CA  GLU    38     -10.686  -8.779   0.899  1.00  0.00              
ATOM    111  C   GLU    38      -9.675  -9.831   0.497  1.00  0.00              
ATOM    112  O   GLU    38      -9.214 -10.617   1.330  1.00  0.00              
ATOM    113  N   GLY    39      -9.347  -9.907  -0.784  1.00  0.00              
ATOM    114  CA  GLY    39      -8.390 -10.889  -1.258  1.00  0.00              
ATOM    115  C   GLY    39      -8.728 -12.300  -0.810  1.00  0.00              
ATOM    116  O   GLY    39      -9.853 -12.768  -0.991  1.00  0.00              
ATOM    117  N   SER    40      -7.725 -13.008  -0.298  1.00  0.00              
ATOM    118  CA  SER    40      -7.868 -14.386   0.119  1.00  0.00              
ATOM    119  C   SER    40      -8.399 -14.531   1.536  1.00  0.00              
ATOM    120  O   SER    40      -8.371 -15.641   2.086  1.00  0.00              
ATOM    121  N   LEU    41      -8.853 -13.452   2.154  1.00  0.00              
ATOM    122  CA  LEU    41      -9.296 -13.529   3.537  1.00  0.00              
ATOM    123  C   LEU    41     -10.816 -13.628   3.748  1.00  0.00              
ATOM    124  O   LEU    41     -11.323 -13.193   4.802  1.00  0.00              
ATOM    125  N   GLY    42     -10.965 -19.689   5.189  1.00  0.00              
ATOM    126  CA  GLY    42      -9.800 -20.447   5.586  1.00  0.00              
ATOM    127  C   GLY    42      -9.313 -21.284   4.419  1.00  0.00              
ATOM    128  O   GLY    42      -9.324 -20.821   3.296  1.00  0.00              
ATOM    129  N   VAL    43      -8.907 -22.516   4.707  1.00  0.00              
ATOM    130  CA  VAL    43      -8.360 -23.451   3.740  1.00  0.00              
ATOM    131  C   VAL    43      -9.419 -24.398   3.232  1.00  0.00              
ATOM    132  O   VAL    43     -10.370 -24.770   3.948  1.00  0.00              
ATOM    133  N   ILE    44     -13.183 -23.939   3.663  1.00  0.00              
ATOM    134  CA  ILE    44     -13.692 -23.919   5.048  1.00  0.00              
ATOM    135  C   ILE    44     -13.580 -22.506   5.595  1.00  0.00              
ATOM    136  O   ILE    44     -13.059 -21.610   4.933  1.00  0.00              
ATOM    137  N   PRO    45     -14.109 -22.270   6.798  1.00  0.00              
ATOM    138  CA  PRO    45     -14.374 -20.888   7.239  1.00  0.00              
ATOM    139  C   PRO    45     -13.357 -20.344   8.246  1.00  0.00              
ATOM    140  O   PRO    45     -13.061 -19.146   8.271  1.00  0.00              
ATOM    141  N   ARG    46     -12.813 -21.199   9.109  1.00  0.00              
ATOM    142  CA  ARG    46     -12.126 -20.721  10.309  1.00  0.00              
ATOM    143  C   ARG    46     -10.761 -20.161   9.955  1.00  0.00              
ATOM    144  O   ARG    46     -10.053 -20.669   9.082  1.00  0.00              
ATOM    145  N   ARG    47     -10.443 -19.081  10.641  1.00  0.00              
ATOM    146  CA  ARG    47      -9.244 -18.300  10.434  1.00  0.00              
ATOM    147  C   ARG    47      -8.353 -18.470  11.641  1.00  0.00              
ATOM    148  O   ARG    47      -8.640 -18.002  12.777  1.00  0.00              
ATOM    149  N   VAL    48      -7.228 -19.142  11.428  1.00  0.00              
ATOM    150  CA  VAL    48      -6.257 -19.357  12.496  1.00  0.00              
ATOM    151  C   VAL    48      -5.236 -18.223  12.479  1.00  0.00              
ATOM    152  O   VAL    48      -4.646 -17.914  11.442  1.00  0.00              
ATOM    153  N   LEU    49      -5.067 -17.598  13.635  1.00  0.00              
ATOM    154  CA  LEU    49      -4.105 -16.525  13.844  1.00  0.00              
ATOM    155  C   LEU    49      -3.195 -16.890  15.018  1.00  0.00              
ATOM    156  O   LEU    49      -3.644 -17.081  16.172  1.00  0.00              
ATOM    157  N   VAL    50      -1.896 -17.036  14.754  1.00  0.00              
ATOM    158  CA  VAL    50      -0.964 -17.381  15.807  1.00  0.00              
ATOM    159  C   VAL    50      -0.692 -16.204  16.743  1.00  0.00              
ATOM    160  O   VAL    50      -0.603 -15.040  16.322  1.00  0.00              
ATOM    161  N   ALA    56      -0.545 -16.510  18.023  1.00  0.00              
ATOM    162  CA  ALA    56      -0.098 -15.511  18.969  1.00  0.00              
ATOM    163  C   ALA    56       1.313 -15.032  18.638  1.00  0.00              
ATOM    164  O   ALA    56       2.133 -15.821  18.162  1.00  0.00              
ATOM    165  N   GLY    57       1.648 -13.782  18.918  1.00  0.00              
ATOM    166  CA  GLY    57       0.777 -12.797  19.565  1.00  0.00              
ATOM    167  C   GLY    57      -0.065 -11.871  18.684  1.00  0.00              
ATOM    168  O   GLY    57      -0.448 -10.794  19.131  1.00  0.00              
ATOM    169  N   ALA    58      -0.391 -12.281  17.465  1.00  0.00              
ATOM    170  CA  ALA    58      -1.158 -11.416  16.575  1.00  0.00              
ATOM    171  C   ALA    58      -2.606 -11.290  17.008  1.00  0.00              
ATOM    172  O   ALA    58      -3.349 -10.487  16.471  1.00  0.00              
ATOM    173  N   ARG    59      -3.010 -12.078  17.996  1.00  0.00              
ATOM    174  CA  ARG    59      -4.367 -11.957  18.497  1.00  0.00              
ATOM    175  C   ARG    59      -4.537 -10.581  19.173  1.00  0.00              
ATOM    176  O   ARG    59      -5.666 -10.085  19.257  1.00  0.00              
ATOM    177  N   ARG    60      -3.436  -9.967  19.589  1.00  0.00              
ATOM    178  CA  ARG    60      -3.512  -8.594  20.127  1.00  0.00              
ATOM    179  C   ARG    60      -3.995  -7.625  19.053  1.00  0.00              
ATOM    180  O   ARG    60      -4.632  -6.622  19.365  1.00  0.00              
ATOM    181  N   LEU    61      -3.694  -7.902  17.785  1.00  0.00              
ATOM    182  CA  LEU    61      -4.124  -7.048  16.693  1.00  0.00              
ATOM    183  C   LEU    61      -5.622  -7.206  16.531  1.00  0.00              
ATOM    184  O   LEU    61      -6.349  -6.215  16.345  1.00  0.00              
ATOM    185  N   LEU    62      -6.091  -8.452  16.605  1.00  0.00              
ATOM    186  CA  LEU    62      -7.538  -8.699  16.584  1.00  0.00              
ATOM    187  C   LEU    62      -8.285  -7.971  17.701  1.00  0.00              
ATOM    188  O   LEU    62      -9.402  -7.455  17.481  1.00  0.00              
ATOM    189  N   THR    63      -7.686  -7.958  18.889  1.00  0.00              
ATOM    190  CA  THR    63      -8.240  -7.251  20.036  1.00  0.00              
ATOM    191  C   THR    63      -8.448  -5.777  19.681  1.00  0.00              
ATOM    192  O   THR    63      -9.509  -5.199  19.959  1.00  0.00              
ATOM    193  N   ASP    64      -7.416  -5.175  19.097  1.00  0.00              
ATOM    194  CA  ASP    64      -7.510  -3.760  18.765  1.00  0.00              
ATOM    195  C   ASP    64      -8.620  -3.425  17.769  1.00  0.00              
ATOM    196  O   ASP    64      -9.280  -2.385  17.907  1.00  0.00              
ATOM    197  N   ALA    65      -8.792  -4.268  16.748  1.00  0.00              
ATOM    198  CA  ALA    65      -9.786  -4.057  15.721  1.00  0.00              
ATOM    199  C   ALA    65     -11.182  -4.454  16.177  1.00  0.00              
ATOM    200  O   ALA    65     -12.178  -4.041  15.595  1.00  0.00              
ATOM    201  N   GLY    66     -11.256  -5.263  17.227  1.00  0.00              
ATOM    202  CA  GLY    66     -12.522  -5.702  17.798  1.00  0.00              
ATOM    203  C   GLY    66     -13.111  -6.951  17.157  1.00  0.00              
ATOM    204  O   GLY    66     -14.316  -7.047  16.903  1.00  0.00              
ATOM    205  N   LEU    67     -12.248  -7.924  16.919  1.00  0.00              
ATOM    206  CA  LEU    67     -12.660  -9.180  16.330  1.00  0.00              
ATOM    207  C   LEU    67     -12.523 -10.256  17.394  1.00  0.00              
ATOM    208  O   LEU    67     -11.411 -10.478  17.873  1.00  0.00              
END
