
#######################################################
#                                                     #
#                        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 T0363AL381_4
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363AL381_4.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           -
LGA    -       -      N      14           -
LGA    -       -      I      15           -
LGA    -       -      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      S      29           -
LGA    Q      31      F      30          3.221
LGA    V      32      Q      31          2.528
LGA    D      33      V      32          3.103
LGA    -       -      D      33           -
LGA    E      34      E      34          2.848
LGA    G      35      G      35          1.571
LGA    I      36      I      36          0.593
LGA    T      37      T      37          0.413
LGA    V      38      V      38          0.649
LGA    Q      39      Q      39          0.493
LGA    T      40      T      40          0.421
LGA    A      41      A      41          0.541
LGA    I      42      I      42          0.631
LGA    T      43      T      43          0.511
LGA    Q      44      Q      44          1.242
LGA    S      45      S      45          2.007
LGA    G      46      G      46          2.556
LGA    I      47      I      47          3.396
LGA    -       -      L      48           -
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    D      55      E      53           #
LGA    L      56      I      54          4.400
LGA    S      57      D      55          1.310
LGA    T      58      L      56           #
LGA    -       -      S      57           -
LGA    -       -      T      58           -
LGA    N      59      N      59          4.341
LGA    K      60      K      60          3.187
LGA    I      61      I      61          2.268
LGA    G      62      G      62          1.936
LGA    I      63      I      63          1.213
LGA    F      64      F      64          2.777
LGA    S      65      -       -           -
LGA    R      66      -       -           -
LGA    P      67      -       -           -
LGA    I      68      -       -           -
LGA    K      69      -       -           -
LGA    L      70      -       -           -
LGA    T      71      -       -           -
LGA    D      72      -       -           -
LGA    V      73      -       -           -
LGA    L      74      -       -           -
LGA    K      75      -       -           -
LGA    E      76      -       -           -
LGA    G      77      -       -           -
LGA    D      78      S      65          3.808
LGA    R      79      R      66          5.492
LGA    I      80      P      67           -
LGA    E      81      I      68           -
LGA    I      82      K      69           -
LGA    Y      83      L      70           -
LGA    -       -      T      71           -
LGA    -       -      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     27    2.55    77.78     25.150     1.018

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.291306 * X  +  -0.015790 * Y  +  -0.956500 * Z  +  45.298225
  Y_new =   0.751361 * X  +   0.615096 * Y  +  -0.238984 * Z  + -12.930996
  Z_new =   0.592113 * X  +  -0.788294 * Y  +  -0.167317 * Z  +  16.704185 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.779945    1.361648  [ DEG:  -101.9833     78.0167 ]
  Theta =  -0.633678   -2.507915  [ DEG:   -36.3071   -143.6929 ]
  Phi   =   1.940658   -1.200935  [ DEG:   111.1915    -68.8085 ]
 
# 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: T0363AL381_4                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL381_4.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   27   2.55   77.78  25.150
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL381_4
REMARK Aligment from pdb entry: 2cu3A
ATOM      1  N   GLN    31      18.107   9.854   3.556  1.00  0.00              
ATOM      2  CA  GLN    31      19.075   8.766   3.640  1.00  0.00              
ATOM      3  C   GLN    31      18.904   7.953   4.925  1.00  0.00              
ATOM      4  O   GLN    31      18.665   8.478   6.005  1.00  0.00              
ATOM      5  N   VAL    32      18.998   6.618   4.772  1.00  0.00              
ATOM      6  CA  VAL    32      18.863   5.706   5.900  1.00  0.00              
ATOM      7  C   VAL    32      20.081   5.782   6.820  1.00  0.00              
ATOM      8  O   VAL    32      20.981   4.953   6.783  1.00  0.00              
ATOM      9  N   ASP    33      20.105   6.844   7.647  1.00  0.00              
ATOM     10  CA  ASP    33      21.290   7.100   8.456  1.00  0.00              
ATOM     11  C   ASP    33      21.030   6.900   9.952  1.00  0.00              
ATOM     12  O   ASP    33      21.915   7.027  10.787  1.00  0.00              
ATOM     13  N   GLU    34      19.757   6.614  10.286  1.00  0.00              
ATOM     14  CA  GLU    34      19.414   6.431  11.692  1.00  0.00              
ATOM     15  C   GLU    34      20.363   5.448  12.380  1.00  0.00              
ATOM     16  O   GLU    34      20.690   4.390  11.859  1.00  0.00              
ATOM     17  N   GLY    35      20.816   5.810  13.577  1.00  0.00              
ATOM     18  CA  GLY    35      21.710   4.947  14.324  1.00  0.00              
ATOM     19  C   GLY    35      23.182   5.263  14.149  1.00  0.00              
ATOM     20  O   GLY    35      23.998   4.922  15.008  1.00  0.00              
ATOM     21  N   ILE    36      23.523   5.905  13.034  1.00  0.00              
ATOM     22  CA  ILE    36      24.906   6.275  12.748  1.00  0.00              
ATOM     23  C   ILE    36      25.225   7.626  13.377  1.00  0.00              
ATOM     24  O   ILE    36      24.329   8.438  13.601  1.00  0.00              
ATOM     25  N   THR    37      26.498   7.858  13.673  1.00  0.00              
ATOM     26  CA  THR    37      26.923   9.132  14.245  1.00  0.00              
ATOM     27  C   THR    37      27.373  10.033  13.103  1.00  0.00              
ATOM     28  O   THR    37      27.692   9.555  12.013  1.00  0.00              
ATOM     29  N   VAL    38      27.408  11.338  13.354  1.00  0.00              
ATOM     30  CA  VAL    38      27.836  12.283  12.332  1.00  0.00              
ATOM     31  C   VAL    38      29.255  11.985  11.848  1.00  0.00              
ATOM     32  O   VAL    38      29.534  12.064  10.654  1.00  0.00              
ATOM     33  N   GLN    39      30.150  11.637  12.767  1.00  0.00              
ATOM     34  CA  GLN    39      31.522  11.321  12.378  1.00  0.00              
ATOM     35  C   GLN    39      31.540  10.168  11.385  1.00  0.00              
ATOM     36  O   GLN    39      32.261  10.203  10.393  1.00  0.00              
ATOM     37  N   THR    40      30.752   9.138  11.669  1.00  0.00              
ATOM     38  CA  THR    40      30.683   7.979  10.794  1.00  0.00              
ATOM     39  C   THR    40      30.173   8.416   9.429  1.00  0.00              
ATOM     40  O   THR    40      30.727   8.038   8.402  1.00  0.00              
ATOM     41  N   ALA    41      29.119   9.227   9.424  1.00  0.00              
ATOM     42  CA  ALA    41      28.546   9.713   8.177  1.00  0.00              
ATOM     43  C   ALA    41      29.539  10.556   7.382  1.00  0.00              
ATOM     44  O   ALA    41      29.668  10.393   6.165  1.00  0.00              
ATOM     45  N   ILE    42      30.244  11.453   8.067  1.00  0.00              
ATOM     46  CA  ILE    42      31.212  12.318   7.396  1.00  0.00              
ATOM     47  C   ILE    42      32.349  11.520   6.757  1.00  0.00              
ATOM     48  O   ILE    42      32.838  11.874   5.680  1.00  0.00              
ATOM     49  N   THR    43      32.766  10.445   7.418  1.00  0.00              
ATOM     50  CA  THR    43      33.840   9.614   6.886  1.00  0.00              
ATOM     51  C   THR    43      33.352   8.874   5.648  1.00  0.00              
ATOM     52  O   THR    43      34.111   8.668   4.706  1.00  0.00              
ATOM     53  N   GLN    44      32.080   8.486   5.649  1.00  0.00              
ATOM     54  CA  GLN    44      31.505   7.771   4.516  1.00  0.00              
ATOM     55  C   GLN    44      31.298   8.708   3.332  1.00  0.00              
ATOM     56  O   GLN    44      31.107   8.255   2.207  1.00  0.00              
ATOM     57  N   SER    45      31.335  10.012   3.600  1.00  0.00              
ATOM     58  CA  SER    45      31.165  11.035   2.570  1.00  0.00              
ATOM     59  C   SER    45      32.531  11.468   2.030  1.00  0.00              
ATOM     60  O   SER    45      32.611  12.142   1.007  1.00  0.00              
ATOM     61  N   GLY    46      33.597  11.092   2.733  1.00  0.00              
ATOM     62  CA  GLY    46      34.937  11.468   2.310  1.00  0.00              
ATOM     63  C   GLY    46      35.184  12.940   2.591  1.00  0.00              
ATOM     64  O   GLY    46      35.998  13.584   1.939  1.00  0.00              
ATOM     65  N   ILE    47      34.469  13.471   3.576  1.00  0.00              
ATOM     66  CA  ILE    47      34.584  14.874   3.952  1.00  0.00              
ATOM     67  C   ILE    47      35.812  15.219   4.793  1.00  0.00              
ATOM     68  O   ILE    47      36.261  14.426   5.613  1.00  0.00              
ATOM     69  N   ASP    55      36.357  16.407   4.553  1.00  0.00              
ATOM     70  CA  ASP    55      37.506  16.916   5.291  1.00  0.00              
ATOM     71  C   ASP    55      36.887  17.626   6.493  1.00  0.00              
ATOM     72  O   ASP    55      36.317  18.706   6.352  1.00  0.00              
ATOM     73  N   LEU    56      36.991  17.016   7.667  1.00  0.00              
ATOM     74  CA  LEU    56      36.396  17.580   8.876  1.00  0.00              
ATOM     75  C   LEU    56      36.795  19.013   9.190  1.00  0.00              
ATOM     76  O   LEU    56      35.940  19.826   9.530  1.00  0.00              
ATOM     77  N   SER    57      38.080  19.328   9.076  1.00  0.00              
ATOM     78  CA  SER    57      38.543  20.678   9.388  1.00  0.00              
ATOM     79  C   SER    57      38.075  21.716   8.375  1.00  0.00              
ATOM     80  O   SER    57      38.150  22.918   8.633  1.00  0.00              
ATOM     81  N   THR    58      37.584  21.255   7.231  1.00  0.00              
ATOM     82  CA  THR    58      37.141  22.179   6.207  1.00  0.00              
ATOM     83  C   THR    58      35.643  22.385   6.104  1.00  0.00              
ATOM     84  O   THR    58      35.180  23.031   5.169  1.00  0.00              
ATOM     85  N   ASN    59      34.879  21.849   7.050  1.00  0.00              
ATOM     86  CA  ASN    59      33.431  22.003   6.976  1.00  0.00              
ATOM     87  C   ASN    59      32.773  22.320   8.308  1.00  0.00              
ATOM     88  O   ASN    59      33.387  22.219   9.365  1.00  0.00              
ATOM     89  N   LYS    60      31.511  22.721   8.219  1.00  0.00              
ATOM     90  CA  LYS    60      30.682  22.997   9.375  1.00  0.00              
ATOM     91  C   LYS    60      29.511  22.049   9.161  1.00  0.00              
ATOM     92  O   LYS    60      29.199  21.683   8.028  1.00  0.00              
ATOM     93  N   ILE    61      28.868  21.635  10.242  1.00  0.00              
ATOM     94  CA  ILE    61      27.757  20.703  10.124  1.00  0.00              
ATOM     95  C   ILE    61      26.548  21.212  10.886  1.00  0.00              
ATOM     96  O   ILE    61      26.652  21.534  12.069  1.00  0.00              
ATOM     97  N   GLY    62      25.410  21.297  10.198  1.00  0.00              
ATOM     98  CA  GLY    62      24.119  21.655  10.764  1.00  0.00              
ATOM     99  C   GLY    62      23.291  20.421  11.122  1.00  0.00              
ATOM    100  O   GLY    62      22.939  19.601  10.286  1.00  0.00              
ATOM    101  N   ILE    63      23.031  20.286  12.435  1.00  0.00              
ATOM    102  CA  ILE    63      22.119  19.244  12.893  1.00  0.00              
ATOM    103  C   ILE    63      20.870  19.871  13.512  1.00  0.00              
ATOM    104  O   ILE    63      20.882  20.398  14.616  1.00  0.00              
ATOM    105  N   PHE    64      19.771  19.848  12.738  1.00  0.00              
ATOM    106  CA  PHE    64      18.586  20.566  13.185  1.00  0.00              
ATOM    107  C   PHE    64      18.898  22.040  13.460  1.00  0.00              
ATOM    108  O   PHE    64      19.461  22.750  12.635  1.00  0.00              
ATOM    109  N   SER    65      18.488  22.503  14.653  1.00  0.00              
ATOM    110  CA  SER    65      18.700  23.907  14.990  1.00  0.00              
ATOM    111  C   SER    65      20.082  24.123  15.618  1.00  0.00              
ATOM    112  O   SER    65      20.282  24.995  16.454  1.00  0.00              
ATOM    113  N   ARG    66      21.046  23.272  15.217  1.00  0.00              
ATOM    114  CA  ARG    66      22.387  23.400  15.778  1.00  0.00              
ATOM    115  C   ARG    66      23.472  23.346  14.698  1.00  0.00              
ATOM    116  O   ARG    66      23.337  22.683  13.679  1.00  0.00              
ATOM    117  N   PRO    67      24.582  24.024  14.980  1.00  0.00              
ATOM    118  CA  PRO    67      25.744  23.988  14.098  1.00  0.00              
ATOM    119  C   PRO    67      27.012  23.563  14.842  1.00  0.00              
ATOM    120  O   PRO    67      27.222  23.862  16.012  1.00  0.00              
ATOM    121  N   ILE    68      27.857  22.801  14.124  1.00  0.00              
ATOM    122  CA  ILE    68      29.145  22.389  14.687  1.00  0.00              
ATOM    123  C   ILE    68      30.245  22.468  13.633  1.00  0.00              
ATOM    124  O   ILE    68      30.019  22.276  12.444  1.00  0.00              
ATOM    125  N   LYS    69      31.746  17.826  15.977  1.00  0.00              
ATOM    126  CA  LYS    69      30.386  17.308  15.925  1.00  0.00              
ATOM    127  C   LYS    69      30.097  16.392  17.118  1.00  0.00              
ATOM    128  O   LYS    69      30.981  15.749  17.668  1.00  0.00              
ATOM    129  N   LEU    70      28.828  16.364  17.564  1.00  0.00              
ATOM    130  CA  LEU    70      28.444  15.574  18.723  1.00  0.00              
ATOM    131  C   LEU    70      28.448  14.075  18.409  1.00  0.00              
ATOM    132  O   LEU    70      28.436  13.658  17.258  1.00  0.00              
ATOM    133  N   THR    71      28.439  13.222  19.430  1.00  0.00              
ATOM    134  CA  THR    71      28.430  11.778  19.217  1.00  0.00              
ATOM    135  C   THR    71      27.044  11.141  19.297  1.00  0.00              
ATOM    136  O   THR    71      26.910   9.923  19.168  1.00  0.00              
ATOM    137  N   ASP    72      26.018  11.962  19.496  1.00  0.00              
ATOM    138  CA  ASP    72      24.648  11.467  19.584  1.00  0.00              
ATOM    139  C   ASP    72      24.245  10.769  18.286  1.00  0.00              
ATOM    140  O   ASP    72      24.386  11.330  17.199  1.00  0.00              
ATOM    141  N   VAL    73      23.752   9.524  18.381  1.00  0.00              
ATOM    142  CA  VAL    73      23.347   8.809  17.167  1.00  0.00              
ATOM    143  C   VAL    73      22.251   9.583  16.447  1.00  0.00              
ATOM    144  O   VAL    73      21.404  10.205  17.087  1.00  0.00              
ATOM    145  N   LEU    74      22.277   9.554  15.117  1.00  0.00              
ATOM    146  CA  LEU    74      21.264  10.247  14.327  1.00  0.00              
ATOM    147  C   LEU    74      19.916   9.567  14.534  1.00  0.00              
ATOM    148  O   LEU    74      19.850   8.357  14.724  1.00  0.00              
ATOM    149  N   LYS    75      18.847  10.358  14.508  1.00  0.00              
ATOM    150  CA  LYS    75      17.496   9.847  14.711  1.00  0.00              
ATOM    151  C   LYS    75      16.609  10.149  13.501  1.00  0.00              
ATOM    152  O   LYS    75      16.882  11.074  12.737  1.00  0.00              
ATOM    153  N   GLU    76      15.546   9.368  13.336  1.00  0.00              
ATOM    154  CA  GLU    76      14.616   9.593  12.236  1.00  0.00              
ATOM    155  C   GLU    76      14.137  11.036  12.314  1.00  0.00              
ATOM    156  O   GLU    76      13.891  11.549  13.405  1.00  0.00              
ATOM    157  N   GLY    77      14.022  11.691  11.161  1.00  0.00              
ATOM    158  CA  GLY    77      13.562  13.067  11.137  1.00  0.00              
ATOM    159  C   GLY    77      14.660  14.107  11.241  1.00  0.00              
ATOM    160  O   GLY    77      14.419  15.283  10.972  1.00  0.00              
ATOM    161  N   ASP    78      15.860  13.690  11.640  1.00  0.00              
ATOM    162  CA  ASP    78      16.970  14.629  11.756  1.00  0.00              
ATOM    163  C   ASP    78      17.299  15.225  10.398  1.00  0.00              
ATOM    164  O   ASP    78      17.178  14.561   9.367  1.00  0.00              
ATOM    165  N   ARG    79      17.690  16.492  10.410  1.00  0.00              
ATOM    166  CA  ARG    79      18.056  17.194   9.189  1.00  0.00              
ATOM    167  C   ARG    79      19.522  17.575   9.325  1.00  0.00              
ATOM    168  O   ARG    79      19.904  18.310  10.240  1.00  0.00              
ATOM    169  N   ILE    80      20.348  17.059   8.424  1.00  0.00              
ATOM    170  CA  ILE    80      21.772  17.337   8.468  1.00  0.00              
ATOM    171  C   ILE    80      22.247  18.042   7.211  1.00  0.00              
ATOM    172  O   ILE    80      21.913  17.639   6.097  1.00  0.00              
ATOM    173  N   GLU    81      23.014  19.108   7.404  1.00  0.00              
ATOM    174  CA  GLU    81      23.579  19.859   6.297  1.00  0.00              
ATOM    175  C   GLU    81      25.084  19.938   6.521  1.00  0.00              
ATOM    176  O   GLU    81      25.540  20.399   7.570  1.00  0.00              
ATOM    177  N   ILE    82      25.852  19.469   5.544  1.00  0.00              
ATOM    178  CA  ILE    82      27.306  19.526   5.628  1.00  0.00              
ATOM    179  C   ILE    82      27.707  20.632   4.657  1.00  0.00              
ATOM    180  O   ILE    82      27.443  20.529   3.455  1.00  0.00              
ATOM    181  N   TYR    83      28.318  21.695   5.178  1.00  0.00              
ATOM    182  CA  TYR    83      28.714  22.829   4.353  1.00  0.00              
ATOM    183  C   TYR    83      30.208  23.141   4.377  1.00  0.00              
ATOM    184  O   TYR    83      30.820  23.260   5.439  1.00  0.00              
END
