
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0363AL509_1
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363AL509_1.T0363.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L      10           -
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    I      13      I      13          1.643
LGA    N      14      N      14          0.706
LGA    I      15      I      15          0.727
LGA    E      16      E      16          1.729
LGA    I      17      I      17          1.570
LGA    A      18      A      18          1.617
LGA    Y      19      Y      19          1.498
LGA    F      21      A      20          1.140
LGA    P      22      F      21          2.923
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    L      27      L      27          0.679
LGA    K      28      K      28          0.567
LGA    S      29      S      29          0.237
LGA    F      30      F      30          1.439
LGA    Q      31      Q      31          1.436
LGA    V      32      V      32          1.296
LGA    D      33      D      33          0.704
LGA    E      34      E      34          1.642
LGA    G      35      G      35          0.667
LGA    I      36      I      36          1.051
LGA    T      37      T      37          0.966
LGA    V      38      V      38          0.805
LGA    Q      39      Q      39          1.513
LGA    T      40      T      40          1.192
LGA    A      41      A      41          1.001
LGA    I      42      I      42          1.654
LGA    T      43      T      43          1.496
LGA    Q      44      Q      44          1.451
LGA    S      45      S      45          2.432
LGA    -       -      G      46           -
LGA    -       -      I      47           -
LGA    -       -      L      48           -
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -
LGA    -       -      S      57           -
LGA    -       -      T      58           -
LGA    I      63      N      59          3.080
LGA    F      64      K      60          2.566
LGA    S      65      I      61          1.783
LGA    R      66      G      62          1.113
LGA    P      67      I      63          0.870
LGA    I      68      F      64          1.263
LGA    K      69      -       -           -
LGA    L      70      -       -           -
LGA    T      71      -       -           -
LGA    D      72      -       -           -
LGA    R      79      S      65          5.476
LGA    I      80      R      66           -
LGA    E      81      P      67           -
LGA    I      82      I      68           -
LGA    Y      83      K      69           -
LGA    R      84      L      70           -
LGA    P      85      T      71           -
LGA    L      86      D      72           -
LGA    -       -      V      73           -
LGA    -       -      L      74           -
LGA    -       -      K      75           -
LGA    -       -      E      76           -
LGA    -       -      G      77           -
LGA    -       -      D      78           -
LGA    -       -      R      79           -
LGA    -       -      I      80           -
LGA    -       -      E      81           -
LGA    -       -      I      82           -
LGA    -       -      Y      83           -
LGA    -       -      R      84           -
LGA    -       -      P      85           -
LGA    -       -      L      86           -
LGA    -       -      L      87           -
LGA    -       -      A      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   80    5.0     35    1.75    74.29     40.038     1.890

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.563333 * X  +  -0.796616 * Y  +  -0.219224 * Z  +  46.382160
  Y_new =   0.766746 * X  +   0.405186 * Y  +   0.497921 * Z  + -26.741444
  Z_new =  -0.307825 * X  +  -0.448585 * Y  +   0.839056 * Z  +  36.351185 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.490966    2.650626  [ DEG:   -28.1303    151.8697 ]
  Theta =   0.312906    2.828686  [ DEG:    17.9282    162.0718 ]
  Phi   =   0.937155   -2.204438  [ DEG:    53.6950   -126.3050 ]
 
# 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: T0363AL509_1                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL509_1.T0363.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   80   5.0   35   1.75   74.29  40.038
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL509_1
REMARK Aligment from pdb entry: 1vjkA_
ATOM      1  N   ILE    13      18.501   5.111   8.843  1.00  0.00              
ATOM      2  CA  ILE    13      18.286   6.538   9.094  1.00  0.00              
ATOM      3  C   ILE    13      18.777   7.271   7.833  1.00  0.00              
ATOM      4  O   ILE    13      19.953   7.148   7.479  1.00  0.00              
ATOM      5  N   ASN    14      17.892   7.999   7.152  1.00  0.00              
ATOM      6  CA  ASN    14      18.283   8.713   5.945  1.00  0.00              
ATOM      7  C   ASN    14      18.394  10.189   6.245  1.00  0.00              
ATOM      8  O   ASN    14      17.401  10.821   6.671  1.00  0.00              
ATOM      9  N   ILE    15      19.582  10.744   6.049  1.00  0.00              
ATOM     10  CA  ILE    15      19.815  12.160   6.313  1.00  0.00              
ATOM     11  C   ILE    15      20.091  12.882   5.010  1.00  0.00              
ATOM     12  O   ILE    15      20.598  12.286   4.030  1.00  0.00              
ATOM     13  N   GLU    16      19.765  14.157   4.963  1.00  0.00              
ATOM     14  CA  GLU    16      20.023  14.995   3.821  1.00  0.00              
ATOM     15  C   GLU    16      21.251  15.803   4.134  1.00  0.00              
ATOM     16  O   GLU    16      21.236  16.615   5.070  1.00  0.00              
ATOM     17  N   ILE    17      22.314  15.609   3.377  1.00  0.00              
ATOM     18  CA  ILE    17      23.553  16.348   3.557  1.00  0.00              
ATOM     19  C   ILE    17      23.621  17.493   2.578  1.00  0.00              
ATOM     20  O   ILE    17      23.441  17.271   1.380  1.00  0.00              
ATOM     21  N   ALA    18      23.846  18.713   3.082  1.00  0.00              
ATOM     22  CA  ALA    18      23.975  19.897   2.227  1.00  0.00              
ATOM     23  C   ALA    18      25.403  20.383   2.326  1.00  0.00              
ATOM     24  O   ALA    18      25.887  20.714   3.423  1.00  0.00              
ATOM     25  N   TYR    19      26.084  20.424   1.192  1.00  0.00              
ATOM     26  CA  TYR    19      27.456  20.931   1.126  1.00  0.00              
ATOM     27  C   TYR    19      27.460  22.383   0.747  1.00  0.00              
ATOM     28  O   TYR    19      26.622  22.836  -0.054  1.00  0.00              
ATOM     29  N   PHE    21      28.441  23.109   1.295  1.00  0.00              
ATOM     30  CA  PHE    21      28.566  24.531   1.043  1.00  0.00              
ATOM     31  C   PHE    21      29.924  24.906   0.516  1.00  0.00              
ATOM     32  O   PHE    21      30.929  24.281   0.846  1.00  0.00              
ATOM     33  N   PRO    22      29.949  25.974  -0.280  1.00  0.00              
ATOM     34  CA  PRO    22      31.194  26.583  -0.742  1.00  0.00              
ATOM     35  C   PRO    22      32.096  25.527  -1.399  1.00  0.00              
ATOM     36  O   PRO    22      31.614  24.766  -2.249  1.00  0.00              
ATOM     37  N   LEU    27      24.064  18.598  -2.668  1.00  0.00              
ATOM     38  CA  LEU    27      23.392  17.887  -1.590  1.00  0.00              
ATOM     39  C   LEU    27      23.289  16.433  -1.951  1.00  0.00              
ATOM     40  O   LEU    27      23.353  16.062  -3.128  1.00  0.00              
ATOM     41  N   LYS    28      23.123  15.594  -0.936  1.00  0.00              
ATOM     42  CA  LYS    28      22.976  14.168  -1.143  1.00  0.00              
ATOM     43  C   LYS    28      22.301  13.529   0.037  1.00  0.00              
ATOM     44  O   LYS    28      22.491  13.966   1.179  1.00  0.00              
ATOM     45  N   SER    29      21.495  12.522  -0.228  1.00  0.00              
ATOM     46  CA  SER    29      20.871  11.730   0.803  1.00  0.00              
ATOM     47  C   SER    29      21.771  10.594   1.179  1.00  0.00              
ATOM     48  O   SER    29      22.233   9.837   0.297  1.00  0.00              
ATOM     49  N   PHE    30      22.001  10.410   2.468  1.00  0.00              
ATOM     50  CA  PHE    30      22.855   9.346   2.937  1.00  0.00              
ATOM     51  C   PHE    30      22.094   8.459   3.908  1.00  0.00              
ATOM     52  O   PHE    30      21.640   8.907   4.980  1.00  0.00              
ATOM     53  N   GLN    31      21.924   7.204   3.526  1.00  0.00              
ATOM     54  CA  GLN    31      21.294   6.199   4.373  1.00  0.00              
ATOM     55  C   GLN    31      22.349   5.607   5.305  1.00  0.00              
ATOM     56  O   GLN    31      23.419   5.183   4.861  1.00  0.00              
ATOM     57  N   VAL    32      22.040   5.603   6.600  1.00  0.00              
ATOM     58  CA  VAL    32      22.950   5.158   7.632  1.00  0.00              
ATOM     59  C   VAL    32      22.275   4.080   8.458  1.00  0.00              
ATOM     60  O   VAL    32      21.056   4.059   8.546  1.00  0.00              
ATOM     61  N   ASP    33      23.044   3.168   9.062  1.00  0.00              
ATOM     62  CA  ASP    33      22.453   2.139   9.915  1.00  0.00              
ATOM     63  C   ASP    33      21.831   2.724  11.174  1.00  0.00              
ATOM     64  O   ASP    33      22.214   3.802  11.641  1.00  0.00              
ATOM     65  N   GLU    34      20.865   1.991  11.711  1.00  0.00              
ATOM     66  CA  GLU    34      20.272   2.288  12.996  1.00  0.00              
ATOM     67  C   GLU    34      21.353   2.655  14.019  1.00  0.00              
ATOM     68  O   GLU    34      22.384   1.994  14.103  1.00  0.00              
ATOM     69  N   GLY    35      21.102   3.725  14.771  1.00  0.00              
ATOM     70  CA  GLY    35      22.003   4.153  15.834  1.00  0.00              
ATOM     71  C   GLY    35      23.113   5.073  15.359  1.00  0.00              
ATOM     72  O   GLY    35      23.981   5.480  16.150  1.00  0.00              
ATOM     73  N   ILE    36      23.106   5.414  14.078  1.00  0.00              
ATOM     74  CA  ILE    36      24.171   6.245  13.545  1.00  0.00              
ATOM     75  C   ILE    36      24.294   7.551  14.269  1.00  0.00              
ATOM     76  O   ILE    36      23.294   8.193  14.629  1.00  0.00              
ATOM     77  N   THR    37      25.551   7.954  14.443  1.00  0.00              
ATOM     78  CA  THR    37      25.907   9.206  15.083  1.00  0.00              
ATOM     79  C   THR    37      26.559  10.154  14.080  1.00  0.00              
ATOM     80  O   THR    37      26.994   9.748  12.990  1.00  0.00              
ATOM     81  N   VAL    38      26.685  11.425  14.443  1.00  0.00              
ATOM     82  CA  VAL    38      27.386  12.391  13.597  1.00  0.00              
ATOM     83  C   VAL    38      28.763  11.869  13.141  1.00  0.00              
ATOM     84  O   VAL    38      29.121  11.969  11.946  1.00  0.00              
ATOM     85  N   GLN    39      29.536  11.275  14.061  1.00  0.00              
ATOM     86  CA  GLN    39      30.852  10.774  13.660  1.00  0.00              
ATOM     87  C   GLN    39      30.765   9.693  12.552  1.00  0.00              
ATOM     88  O   GLN    39      31.662   9.599  11.698  1.00  0.00              
ATOM     89  N   THR    40      29.697   8.887  12.572  1.00  0.00              
ATOM     90  CA  THR    40      29.528   7.837  11.542  1.00  0.00              
ATOM     91  C   THR    40      29.213   8.470  10.220  1.00  0.00              
ATOM     92  O   THR    40      29.700   8.004   9.182  1.00  0.00              
ATOM     93  N   ALA    41      28.426   9.532  10.237  1.00  0.00              
ATOM     94  CA  ALA    41      28.135  10.258   9.001  1.00  0.00              
ATOM     95  C   ALA    41      29.401  10.885   8.406  1.00  0.00              
ATOM     96  O   ALA    41      29.624  10.784   7.186  1.00  0.00              
ATOM     97  N   ILE    42      30.248  11.473   9.251  1.00  0.00              
ATOM     98  CA  ILE    42      31.502  12.039   8.771  1.00  0.00              
ATOM     99  C   ILE    42      32.349  10.953   8.112  1.00  0.00              
ATOM    100  O   ILE    42      32.923  11.167   7.014  1.00  0.00              
ATOM    101  N   THR    43      32.439   9.769   8.743  1.00  0.00              
ATOM    102  CA  THR    43      33.185   8.680   8.099  1.00  0.00              
ATOM    103  C   THR    43      32.608   8.249   6.771  1.00  0.00              
ATOM    104  O   THR    43      33.374   7.909   5.843  1.00  0.00              
ATOM    105  N   GLN    44      31.289   8.259   6.652  1.00  0.00              
ATOM    106  CA  GLN    44      30.660   7.885   5.399  1.00  0.00              
ATOM    107  C   GLN    44      30.906   8.941   4.320  1.00  0.00              
ATOM    108  O   GLN    44      31.116   8.573   3.158  1.00  0.00              
ATOM    109  N   SER    45      30.903  10.239   4.678  1.00  0.00              
ATOM    110  CA  SER    45      31.224  11.284   3.697  1.00  0.00              
ATOM    111  C   SER    45      32.632  11.060   3.142  1.00  0.00              
ATOM    112  O   SER    45      32.838  11.117   1.910  1.00  0.00              
ATOM    113  N   ILE    63      36.314  22.005   8.266  1.00  0.00              
ATOM    114  CA  ILE    63      34.898  21.754   8.077  1.00  0.00              
ATOM    115  C   ILE    63      34.220  21.843   9.428  1.00  0.00              
ATOM    116  O   ILE    63      34.728  21.308  10.409  1.00  0.00              
ATOM    117  N   PHE    64      33.042  22.462   9.450  1.00  0.00              
ATOM    118  CA  PHE    64      32.125  22.332  10.572  1.00  0.00              
ATOM    119  C   PHE    64      30.823  21.783  10.046  1.00  0.00              
ATOM    120  O   PHE    64      30.519  21.887   8.841  1.00  0.00              
ATOM    121  N   SER    65      30.050  21.180  10.946  1.00  0.00              
ATOM    122  CA  SER    65      28.739  20.629  10.551  1.00  0.00              
ATOM    123  C   SER    65      27.656  21.143  11.466  1.00  0.00              
ATOM    124  O   SER    65      27.938  21.624  12.580  1.00  0.00              
ATOM    125  N   ARG    66      26.424  21.111  10.994  1.00  0.00              
ATOM    126  CA  ARG    66      25.280  21.448  11.822  1.00  0.00              
ATOM    127  C   ARG    66      24.173  20.494  11.491  1.00  0.00              
ATOM    128  O   ARG    66      23.992  20.084  10.328  1.00  0.00              
ATOM    129  N   PRO    67      23.427  20.095  12.507  1.00  0.00              
ATOM    130  CA  PRO    67      22.277  19.221  12.331  1.00  0.00              
ATOM    131  C   PRO    67      21.008  20.003  12.585  1.00  0.00              
ATOM    132  O   PRO    67      20.813  20.511  13.709  1.00  0.00              
ATOM    133  N   ILE    68      20.152  20.112  11.570  1.00  0.00              
ATOM    134  CA  ILE    68      18.952  20.956  11.632  1.00  0.00              
ATOM    135  C   ILE    68      19.271  22.347  12.198  1.00  0.00              
ATOM    136  O   ILE    68      18.530  22.893  13.039  1.00  0.00              
ATOM    137  N   LYS    69      20.372  22.919  11.728  1.00  0.00              
ATOM    138  CA  LYS    69      20.734  24.276  12.080  1.00  0.00              
ATOM    139  C   LYS    69      21.451  24.424  13.398  1.00  0.00              
ATOM    140  O   LYS    69      21.641  25.561  13.829  1.00  0.00              
ATOM    141  N   LEU    70      30.019  15.035  18.234  1.00  0.00              
ATOM    142  CA  LEU    70      30.216  13.927  17.294  1.00  0.00              
ATOM    143  C   LEU    70      29.428  12.691  17.675  1.00  0.00              
ATOM    144  O   LEU    70      29.186  11.835  16.845  1.00  0.00              
ATOM    145  N   THR    71      29.015  12.583  18.929  1.00  0.00              
ATOM    146  CA  THR    71      28.261  11.418  19.354  1.00  0.00              
ATOM    147  C   THR    71      26.765  11.629  19.356  1.00  0.00              
ATOM    148  O   THR    71      26.007  10.743  19.740  1.00  0.00              
ATOM    149  N   ASP    72      16.914  14.067   9.321  1.00  0.00              
ATOM    150  CA  ASP    72      17.771  15.182   9.744  1.00  0.00              
ATOM    151  C   ASP    72      18.476  15.796   8.546  1.00  0.00              
ATOM    152  O   ASP    72      18.837  15.078   7.586  1.00  0.00              
ATOM    153  N   ARG    79      18.713  17.096   8.609  1.00  0.00              
ATOM    154  CA  ARG    79      19.439  17.822   7.572  1.00  0.00              
ATOM    155  C   ARG    79      20.784  18.240   8.133  1.00  0.00              
ATOM    156  O   ARG    79      20.856  18.916   9.155  1.00  0.00              
ATOM    157  N   ILE    80      21.868  17.824   7.491  1.00  0.00              
ATOM    158  CA  ILE    80      23.202  18.089   7.998  1.00  0.00              
ATOM    159  C   ILE    80      23.962  18.975   7.043  1.00  0.00              
ATOM    160  O   ILE    80      24.194  18.582   5.890  1.00  0.00              
ATOM    161  N   GLU    81      24.359  20.168   7.484  1.00  0.00              
ATOM    162  CA  GLU    81      25.162  21.054   6.668  1.00  0.00              
ATOM    163  C   GLU    81      26.636  20.744   6.879  1.00  0.00              
ATOM    164  O   GLU    81      27.066  20.389   7.988  1.00  0.00              
ATOM    165  N   ILE    82      27.396  20.877   5.787  1.00  0.00              
ATOM    166  CA  ILE    82      28.835  20.634   5.744  1.00  0.00              
ATOM    167  C   ILE    82      29.460  21.859   5.116  1.00  0.00              
ATOM    168  O   ILE    82      29.277  22.111   3.921  1.00  0.00              
ATOM    169  N   TYR    83      30.183  22.659   5.915  1.00  0.00              
ATOM    170  CA  TYR    83      30.558  24.007   5.481  1.00  0.00              
ATOM    171  C   TYR    83      31.888  24.454   6.066  1.00  0.00              
ATOM    172  O   TYR    83      32.310  23.957   7.121  1.00  0.00              
ATOM    173  N   ARG    84      32.539  25.433   5.438  1.00  0.00              
ATOM    174  CA  ARG    84      33.719  26.029   6.082  1.00  0.00              
ATOM    175  C   ARG    84      33.289  26.750   7.360  1.00  0.00              
ATOM    176  O   ARG    84      32.189  27.288   7.390  1.00  0.00              
ATOM    177  N   PRO    85      34.110  26.750   8.408  1.00  0.00              
ATOM    178  CA  PRO    85      33.695  27.414   9.647  1.00  0.00              
ATOM    179  C   PRO    85      33.268  28.857   9.389  1.00  0.00              
ATOM    180  O   PRO    85      33.941  29.596   8.627  1.00  0.00              
ATOM    181  N   LEU    86      32.146  29.234  10.011  1.00  0.00              
ATOM    182  CA  LEU    86      31.566  30.574   9.886  1.00  0.00              
ATOM    183  C   LEU    86      32.514  31.599  10.505  1.00  0.00              
ATOM    184  O   LEU    86      33.026  31.394  11.610  1.00  0.00              
END
