
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0363AL242_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL242_2-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    Q      12      N      14          1.460
LGA    I      13      I      15          0.720
LGA    N      14      E      16          2.036
LGA    I      15      I      17          1.848
LGA    E      16      A      18          1.861
LGA    I      17      Y      19          1.614
LGA    A      18      A      20          2.668
LGA    Y      19      -       -           -
LGA    A      20      -       -           -
LGA    F      21      -       -           -
LGA    P      22      F      21          2.304
LGA    E      23      P      22          3.474
LGA    R      24      E      23           -
LGA    Y      25      -       -           -
LGA    Y      26      R      24          3.771
LGA    L      27      Y      25          3.121
LGA    K      28      Y      26          3.661
LGA    S      29      L      27          1.313
LGA    F      30      K      28          1.114
LGA    Q      31      S      29          0.905
LGA    V      32      F      30          0.968
LGA    D      33      Q      31          0.951
LGA    E      34      V      32          2.342
LGA    G      35      D      33          3.132
LGA    I      36      E      34           #
LGA    -       -      G      35           -
LGA    T      37      I      36          0.599
LGA    V      38      T      37          0.606
LGA    Q      39      V      38          0.775
LGA    T      40      Q      39          0.539
LGA    A      41      T      40          0.467
LGA    I      42      A      41          1.240
LGA    T      43      I      42          1.505
LGA    Q      44      T      43          1.082
LGA    S      45      Q      44          1.401
LGA    G      46      S      45          2.748
LGA    -       -      G      46           -
LGA    I      47      I      47          4.087
LGA    L      48      L      48           #
LGA    S      49      S      49          4.907
LGA    Q      50      Q      50          2.162
LGA    F      51      F      51          4.744
LGA    P      52      P      52          1.153
LGA    E      53      E      53          3.819
LGA    I      54      I      54          2.811
LGA    D      55      D      55          2.509
LGA    L      56      L      56          2.344

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   46    5.0     38    2.40    31.58     58.614     1.520

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.029621 * X  +  -0.831104 * Y  +  -0.555327 * Z  +  71.457855
  Y_new =   0.813906 * X  +  -0.342561 * Y  +   0.469264 * Z  +  10.885897
  Z_new =  -0.580241 * X  +  -0.438084 * Y  +   0.686588 * Z  +  27.553873 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.567935    2.573657  [ DEG:   -32.5403    147.4597 ]
  Theta =   0.619024    2.522568  [ DEG:    35.4675    144.5325 ]
  Phi   =   1.607174   -1.534419  [ DEG:    92.0843    -87.9157 ]
 
# 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: T0363AL242_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL242_2-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   46   5.0   38   2.40   31.58  58.614
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL242_2-D1
REMARK Aligment from pdb entry: 1jw9_D
ATOM      1  N   GLN    12      15.759   8.477   5.084  1.00  0.00              
ATOM      2  CA  GLN    12      17.050   8.990   4.526  1.00  0.00              
ATOM      3  C   GLN    12      17.534  10.114   5.435  1.00  0.00              
ATOM      4  O   GLN    12      16.759  10.655   6.203  1.00  0.00              
ATOM      5  N   ILE    13      18.835  10.345   5.427  1.00  0.00              
ATOM      6  CA  ILE    13      19.425  11.551   6.017  1.00  0.00              
ATOM      7  C   ILE    13      19.735  12.581   4.944  1.00  0.00              
ATOM      8  O   ILE    13      20.389  12.263   3.937  1.00  0.00              
ATOM      9  N   ASN    14      19.266  13.808   5.142  1.00  0.00              
ATOM     10  CA  ASN    14      19.548  14.877   4.192  1.00  0.00              
ATOM     11  C   ASN    14      20.863  15.519   4.634  1.00  0.00              
ATOM     12  O   ASN    14      21.044  15.808   5.821  1.00  0.00              
ATOM     13  N   ILE    15      21.812  15.638   3.715  1.00  0.00              
ATOM     14  CA  ILE    15      23.095  16.229   4.068  1.00  0.00              
ATOM     15  C   ILE    15      23.262  17.437   3.156  1.00  0.00              
ATOM     16  O   ILE    15      23.177  17.302   1.961  1.00  0.00              
ATOM     17  N   GLU    16      23.460  18.623   3.745  1.00  0.00              
ATOM     18  CA  GLU    16      23.609  19.876   3.015  1.00  0.00              
ATOM     19  C   GLU    16      25.045  20.332   3.126  1.00  0.00              
ATOM     20  O   GLU    16      25.697  20.074   4.135  1.00  0.00              
ATOM     21  N   ILE    17      25.555  20.981   2.096  1.00  0.00              
ATOM     22  CA  ILE    17      26.903  21.482   2.088  1.00  0.00              
ATOM     23  C   ILE    17      26.796  22.961   1.809  1.00  0.00              
ATOM     24  O   ILE    17      26.020  23.363   0.946  1.00  0.00              
ATOM     25  N   ALA    18      27.562  23.792   2.508  1.00  0.00              
ATOM     26  CA  ALA    18      27.566  25.213   2.247  1.00  0.00              
ATOM     27  C   ALA    18      28.996  25.743   2.081  1.00  0.00              
ATOM     28  O   ALA    18      29.999  25.112   2.530  1.00  0.00              
ATOM     29  N   TYR    19      29.037  26.921   1.484  1.00  0.00              
ATOM     30  CA  TYR    19      30.252  27.699   1.323  1.00  0.00              
ATOM     31  C   TYR    19      31.383  26.940   0.631  1.00  0.00              
ATOM     32  O   TYR    19      31.151  26.312  -0.398  1.00  0.00              
ATOM     33  N   ALA    20      32.594  26.997   1.147  1.00  0.00              
ATOM     34  CA  ALA    20      33.696  26.302   0.506  1.00  0.00              
ATOM     35  C   ALA    20      33.472  24.783   0.460  1.00  0.00              
ATOM     36  O   ALA    20      33.976  24.138  -0.489  1.00  0.00              
ATOM     37  N   PHE    21      32.817  24.200   1.454  1.00  0.00              
ATOM     38  CA  PHE    21      32.539  22.740   1.425  1.00  0.00              
ATOM     39  C   PHE    21      31.832  22.434   0.098  1.00  0.00              
ATOM     40  O   PHE    21      32.239  21.569  -0.660  1.00  0.00              
ATOM     41  N   PRO    22      30.754  23.138  -0.171  1.00  0.00              
ATOM     42  CA  PRO    22      29.944  22.969  -1.383  1.00  0.00              
ATOM     43  C   PRO    22      30.772  23.227  -2.614  1.00  0.00              
ATOM     44  O   PRO    22      30.691  22.479  -3.586  1.00  0.00              
ATOM     45  N   GLU    23      31.563  24.276  -2.598  1.00  0.00              
ATOM     46  CA  GLU    23      32.304  24.610  -3.775  1.00  0.00              
ATOM     47  C   GLU    23      33.387  23.530  -4.061  1.00  0.00              
ATOM     48  O   GLU    23      33.680  23.269  -5.202  1.00  0.00              
ATOM     49  N   ARG    24      33.959  22.924  -3.032  1.00  0.00              
ATOM     50  CA  ARG    24      34.952  21.882  -3.233  1.00  0.00              
ATOM     51  C   ARG    24      34.376  20.554  -3.650  1.00  0.00              
ATOM     52  O   ARG    24      35.010  19.833  -4.420  1.00  0.00              
ATOM     53  N   TYR    25      33.205  20.193  -3.140  1.00  0.00              
ATOM     54  CA  TYR    25      32.654  18.854  -3.452  1.00  0.00              
ATOM     55  C   TYR    25      31.691  18.773  -4.618  1.00  0.00              
ATOM     56  O   TYR    25      31.337  17.645  -5.061  1.00  0.00              
ATOM     57  N   TYR    26      31.189  19.905  -5.070  1.00  0.00              
ATOM     58  CA  TYR    26      30.368  19.974  -6.272  1.00  0.00              
ATOM     59  C   TYR    26      28.885  19.721  -6.153  1.00  0.00              
ATOM     60  O   TYR    26      28.186  19.608  -7.166  1.00  0.00              
ATOM     61  N   LEU    27      28.392  19.623  -4.934  1.00  0.00              
ATOM     62  CA  LEU    27      26.977  19.441  -4.730  1.00  0.00              
ATOM     63  C   LEU    27      26.503  20.194  -3.494  1.00  0.00              
ATOM     64  O   LEU    27      27.226  20.340  -2.516  1.00  0.00              
ATOM     65  N   LYS    28      25.285  20.668  -3.598  1.00  0.00              
ATOM     66  CA  LYS    28      24.692  21.478  -2.534  1.00  0.00              
ATOM     67  C   LYS    28      23.958  20.616  -1.520  1.00  0.00              
ATOM     68  O   LYS    28      23.712  21.038  -0.388  1.00  0.00              
ATOM     69  N   SER    29      23.634  19.398  -1.943  1.00  0.00              
ATOM     70  CA  SER    29      22.799  18.480  -1.171  1.00  0.00              
ATOM     71  C   SER    29      22.820  17.041  -1.709  1.00  0.00              
ATOM     72  O   SER    29      22.854  16.825  -2.920  1.00  0.00              
ATOM     73  N   PHE    30      22.760  16.092  -0.795  1.00  0.00              
ATOM     74  CA  PHE    30      22.586  14.717  -1.214  1.00  0.00              
ATOM     75  C   PHE    30      21.906  13.943  -0.119  1.00  0.00              
ATOM     76  O   PHE    30      22.264  14.079   1.059  1.00  0.00              
ATOM     77  N   GLN    31      20.963  13.080  -0.509  1.00  0.00              
ATOM     78  CA  GLN    31      20.286  12.216   0.450  1.00  0.00              
ATOM     79  C   GLN    31      21.079  10.926   0.615  1.00  0.00              
ATOM     80  O   GLN    31      21.477  10.321  -0.388  1.00  0.00              
ATOM     81  N   VAL    32      21.394  10.544   1.841  1.00  0.00              
ATOM     82  CA  VAL    32      22.140   9.329   2.074  1.00  0.00              
ATOM     83  C   VAL    32      21.290   8.323   2.885  1.00  0.00              
ATOM     84  O   VAL    32      20.312   8.706   3.527  1.00  0.00              
ATOM     85  N   ASP    33      21.620   7.039   2.769  1.00  0.00              
ATOM     86  CA  ASP    33      20.938   6.050   3.575  1.00  0.00              
ATOM     87  C   ASP    33      21.229   6.373   5.027  1.00  0.00              
ATOM     88  O   ASP    33      22.213   7.034   5.337  1.00  0.00              
ATOM     89  N   GLU    34      20.364   5.904   5.914  1.00  0.00              
ATOM     90  CA  GLU    34      20.514   6.203   7.327  1.00  0.00              
ATOM     91  C   GLU    34      21.383   5.162   8.046  1.00  0.00              
ATOM     92  O   GLU    34      20.961   4.554   9.016  1.00  0.00              
ATOM     93  N   GLY    35      22.598   4.956   7.555  1.00  0.00              
ATOM     94  CA  GLY    35      23.480   3.936   8.111  1.00  0.00              
ATOM     95  C   GLY    35      24.641   4.518   8.834  1.00  0.00              
ATOM     96  O   GLY    35      25.693   3.867   8.999  1.00  0.00              
ATOM     97  N   ILE    36      24.494   5.767   9.252  1.00  0.00              
ATOM     98  CA  ILE    36      25.546   6.465   9.940  1.00  0.00              
ATOM     99  C   ILE    36      25.104   6.747  11.354  1.00  0.00              
ATOM    100  O   ILE    36      24.132   7.460  11.606  1.00  0.00              
ATOM    101  N   THR    37      25.810   6.115  12.270  1.00  0.00              
ATOM    102  CA  THR    37      25.498   6.200  13.688  1.00  0.00              
ATOM    103  C   THR    37      25.670   7.624  14.234  1.00  0.00              
ATOM    104  O   THR    37      24.824   8.078  14.995  1.00  0.00              
ATOM    105  N   VAL    38      26.757   8.276  13.827  1.00  0.00              
ATOM    106  CA  VAL    38      27.069   9.638  14.272  1.00  0.00              
ATOM    107  C   VAL    38      27.512  10.511  13.123  1.00  0.00              
ATOM    108  O   VAL    38      27.798  10.049  12.026  1.00  0.00              
ATOM    109  N   GLN    39      27.622  11.798  13.408  1.00  0.00              
ATOM    110  CA  GLN    39      28.129  12.727  12.423  1.00  0.00              
ATOM    111  C   GLN    39      29.529  12.315  12.049  1.00  0.00              
ATOM    112  O   GLN    39      29.883  12.349  10.881  1.00  0.00              
ATOM    113  N   THR    40      30.344  11.900  13.007  1.00  0.00              
ATOM    114  CA  THR    40      31.672  11.429  12.641  1.00  0.00              
ATOM    115  C   THR    40      31.674  10.281  11.572  1.00  0.00              
ATOM    116  O   THR    40      32.529  10.330  10.658  1.00  0.00              
ATOM    117  N   ALA    41      30.742   9.311  11.634  1.00  0.00              
ATOM    118  CA  ALA    41      30.785   8.181  10.706  1.00  0.00              
ATOM    119  C   ALA    41      30.450   8.682   9.303  1.00  0.00              
ATOM    120  O   ALA    41      31.053   8.287   8.296  1.00  0.00              
ATOM    121  N   ILE    42      29.480   9.581   9.259  1.00  0.00              
ATOM    122  CA  ILE    42      29.052  10.185   8.015  1.00  0.00              
ATOM    123  C   ILE    42      30.212  10.955   7.412  1.00  0.00              
ATOM    124  O   ILE    42      30.509  10.829   6.242  1.00  0.00              
ATOM    125  N   THR    43      30.857  11.799   8.208  1.00  0.00              
ATOM    126  CA  THR    43      32.007  12.573   7.722  1.00  0.00              
ATOM    127  C   THR    43      33.184  11.731   7.222  1.00  0.00              
ATOM    128  O   THR    43      33.738  11.991   6.160  1.00  0.00              
ATOM    129  N   GLN    44      33.599  10.758   8.011  1.00  0.00              
ATOM    130  CA  GLN    44      34.709   9.899   7.614  1.00  0.00              
ATOM    131  C   GLN    44      34.370   9.169   6.339  1.00  0.00              
ATOM    132  O   GLN    44      35.209   9.073   5.467  1.00  0.00              
ATOM    133  N   SER    45      33.151   8.639   6.236  1.00  0.00              
ATOM    134  CA  SER    45      32.742   7.971   4.993  1.00  0.00              
ATOM    135  C   SER    45      32.847   8.917   3.791  1.00  0.00              
ATOM    136  O   SER    45      33.404   8.580   2.751  1.00  0.00              
ATOM    137  N   GLY    46      32.318  10.117   3.920  1.00  0.00              
ATOM    138  CA  GLY    46      32.342  11.008   2.784  1.00  0.00              
ATOM    139  C   GLY    46      33.761  11.500   2.462  1.00  0.00              
ATOM    140  O   GLY    46      34.147  11.578   1.284  1.00  0.00              
ATOM    141  N   ILE    47      34.575  11.735   3.506  1.00  0.00              
ATOM    142  CA  ILE    47      35.926  12.250   3.369  1.00  0.00              
ATOM    143  C   ILE    47      36.894  11.344   2.628  1.00  0.00              
ATOM    144  O   ILE    47      37.881  11.814   2.066  1.00  0.00              
ATOM    145  N   LEU    48      40.705  12.798  -2.421  1.00  0.00              
ATOM    146  CA  LEU    48      41.533  13.785  -1.731  1.00  0.00              
ATOM    147  C   LEU    48      40.743  15.068  -1.626  1.00  0.00              
ATOM    148  O   LEU    48      40.809  15.802  -0.632  1.00  0.00              
ATOM    149  N   SER    49      40.012  15.365  -2.691  1.00  0.00              
ATOM    150  CA  SER    49      39.283  16.606  -2.726  1.00  0.00              
ATOM    151  C   SER    49      38.218  16.579  -1.633  1.00  0.00              
ATOM    152  O   SER    49      38.076  17.544  -0.879  1.00  0.00              
ATOM    153  N   GLN    50      37.502  15.465  -1.520  1.00  0.00              
ATOM    154  CA  GLN    50      36.518  15.305  -0.439  1.00  0.00              
ATOM    155  C   GLN    50      37.164  15.368   0.963  1.00  0.00              
ATOM    156  O   GLN    50      36.573  15.903   1.940  1.00  0.00              
ATOM    157  N   PHE    51      38.356  14.804   1.077  1.00  0.00              
ATOM    158  CA  PHE    51      39.050  14.804   2.376  1.00  0.00              
ATOM    159  C   PHE    51      39.464  16.220   2.739  1.00  0.00              
ATOM    160  O   PHE    51      39.507  16.565   3.908  1.00  0.00              
ATOM    161  N   PRO    52      39.780  17.040   1.743  1.00  0.00              
ATOM    162  CA  PRO    52      40.120  18.430   2.035  1.00  0.00              
ATOM    163  C   PRO    52      38.900  19.232   2.523  1.00  0.00              
ATOM    164  O   PRO    52      38.961  19.977   3.525  1.00  0.00              
ATOM    165  N   GLU    53      37.768  19.045   1.844  1.00  0.00              
ATOM    166  CA  GLU    53      36.547  19.737   2.165  1.00  0.00              
ATOM    167  C   GLU    53      36.035  19.415   3.561  1.00  0.00              
ATOM    168  O   GLU    53      35.553  20.299   4.259  1.00  0.00              
ATOM    169  N   ILE    54      36.198  18.160   3.996  1.00  0.00              
ATOM    170  CA  ILE    54      35.634  17.685   5.228  1.00  0.00              
ATOM    171  C   ILE    54      36.679  17.377   6.277  1.00  0.00              
ATOM    172  O   ILE    54      36.413  16.635   7.227  1.00  0.00              
ATOM    173  N   ASP    55      37.842  17.990   6.124  1.00  0.00              
ATOM    174  CA  ASP    55      38.985  17.805   7.011  1.00  0.00              
ATOM    175  C   ASP    55      38.656  18.123   8.461  1.00  0.00              
ATOM    176  O   ASP    55      38.171  19.216   8.819  1.00  0.00              
ATOM    177  N   LEU    56      38.928  17.146   9.313  1.00  0.00              
ATOM    178  CA  LEU    56      38.671  17.320  10.720  1.00  0.00              
ATOM    179  C   LEU    56      39.477  18.515  11.151  1.00  0.00              
ATOM    180  O   LEU    56      40.661  18.654  10.816  1.00  0.00              
END
