
#######################################################
#                                                     #
#                        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   49 (  196),  selected   49 , name T0307AL044_2-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307AL044_2-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    D      32      I      10           -
LGA    G      33      M      11           -
LGA    K      34      T      12           -
LGA    I      35      F      13           -
LGA    K      36      S      14           -
LGA    P      37      G      15           -
LGA    E      39      Q      16           -
LGA    V      42      E      17           -
LGA    M      43      L      18           -
LGA    T      44      T      19           -
LGA    R      45      A      20           -
LGA    E      46      I      21           -
LGA    F      47      I      22           -
LGA    F      50      K      23           -
LGA    G      51      M      24           -
LGA    I      52      A      25           -
LGA    Q      54      K      26           -
LGA    D      55      S      27           -
LGA    K      62      M      28           -
LGA    A      63      V      29           -
LGA    S      64      M      30           -
LGA    -       -      A      31           -
LGA    -       -      D      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    -       -      I      35           -
LGA    -       -      K      36           -
LGA    -       -      P      37           -
LGA    -       -      A      38           -
LGA    -       -      E      39           -
LGA    -       -      I      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      M      43           -
LGA    -       -      T      44           -
LGA    -       -      R      45           -
LGA    -       -      E      46           -
LGA    -       -      F      47           -
LGA    -       -      M      48           -
LGA    -       -      R      49           -
LGA    -       -      F      50           -
LGA    -       -      G      51           -
LGA    -       -      I      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      V      57           -
LGA    -       -      D      58           -
LGA    -       -      L      59           -
LGA    D      65      L      60           #
LGA    -       -      L      61           -
LGA    -       -      K      62           -
LGA    Q      71      A      63          2.427
LGA    V      73      S      64          2.549
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    A      74      I      67          1.627
LGA    L      75      E      68          1.529
LGA    I      76      A      69          1.051
LGA    -       -      S      70           -
LGA    -       -      Q      71           -
LGA    -       -      A      72           -
LGA    A      77      V      73          4.753
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    R      78      I      76          2.697
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    -       -      M      79           -
LGA    -       -      D      80           -
LGA    -       -      E      81           -
LGA    -       -      E      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      K      85           -
LGA    -       -      Y      86           -
LGA    -       -      V      87           -
LGA    M      79      A      88          2.611
LGA    D      80      S      89          1.466
LGA    E      81      Y      90          1.412
LGA    -       -      L      91           -
LGA    -       -      G      92           -
LGA    R      83      V      93          0.499
LGA    K      85      I      94          1.323
LGA    Y      86      M      95          3.762
LGA    V      87      A      96          3.040
LGA    A      88      S      97           -
LGA    S      89      D      98           -
LGA    -       -      G      99           -
LGA    -       -      D     100           -
LGA    -       -      I     101           -
LGA    -       -      D     102           -
LGA    -       -      D     103           -
LGA    Y      90      N     104          4.204
LGA    L      91      E     105          3.948
LGA    G      92      L     106          3.357
LGA    V      93      A     107          1.910
LGA    M      95      L     108          2.834
LGA    -       -      W     109           -
LGA    -       -      T     110           -
LGA    A      96      L     111          0.677
LGA    -       -      I     112           -
LGA    -       -      S     113           -
LGA    S      97      T     114          2.318
LGA    -       -      L     115           -
LGA    -       -      C     116           -
LGA    D      98      G     117           #
LGA    G      99      L     118           -
LGA    I     101      P     119           -
LGA    D     102      T     120           -
LGA    -       -      M     121           -
LGA    -       -      T     122           -
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      N     128           -
LGA    -       -      N     129           -
LGA    -       -      M     130           -
LGA    -       -      K     131           -
LGA    -       -      N     132           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   49  123    5.0     21    2.64     0.00     11.780     0.765

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.165963 * X  +   0.048307 * Y  +   0.984948 * Z  +  -4.400217
  Y_new =  -0.115580 * X  +  -0.992868 * Y  +   0.029220 * Z  +  33.601070
  Z_new =   0.979335 * X  +  -0.108991 * Y  +   0.170363 * Z  +   7.308167 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.569140    2.572453  [ DEG:   -32.6093    147.3907 ]
  Theta =  -1.367148   -1.774445  [ DEG:   -78.3318   -101.6682 ]
  Phi   =  -2.533275    0.608318  [ DEG:  -145.1460     34.8541 ]
 
# 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: T0307AL044_2-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307AL044_2-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   49  123   5.0   21   2.64    0.00  11.780
REMARK  ---------------------------------------------------------- 
MOLECULE T0307AL044_2-D1
REMARK Aligment from pdb entry: 1pmi
ATOM      1  N   ASP    32      52.411   2.879  22.634  1.00  0.00              
ATOM      2  CA  ASP    32      51.803   2.380  21.383  1.00  0.00              
ATOM      3  C   ASP    32      51.346   3.546  20.498  1.00  0.00              
ATOM      4  O   ASP    32      51.736   3.627  19.311  1.00  0.00              
ATOM      5  N   GLY    33      50.561   4.441  21.081  1.00  0.00              
ATOM      6  CA  GLY    33      50.030   5.599  20.365  1.00  0.00              
ATOM      7  C   GLY    33      51.165   6.465  19.823  1.00  0.00              
ATOM      8  O   GLY    33      51.024   7.009  18.711  1.00  0.00              
ATOM      9  N   LYS    34      52.158   6.671  20.685  1.00  0.00              
ATOM     10  CA  LYS    34      53.278   7.546  20.365  1.00  0.00              
ATOM     11  C   LYS    34      54.066   7.034  19.165  1.00  0.00              
ATOM     12  O   LYS    34      54.492   7.822  18.295  1.00  0.00              
ATOM     13  N   ILE    35      54.294   5.729  19.171  1.00  0.00              
ATOM     14  CA  ILE    35      54.982   5.054  18.062  1.00  0.00              
ATOM     15  C   ILE    35      54.152   5.148  16.786  1.00  0.00              
ATOM     16  O   ILE    35      54.678   5.543  15.706  1.00  0.00              
ATOM     17  N   LYS    36      52.848   4.910  16.866  1.00  0.00              
ATOM     18  CA  LYS    36      51.982   4.987  15.675  1.00  0.00              
ATOM     19  C   LYS    36      51.571   6.366  15.208  1.00  0.00              
ATOM     20  O   LYS    36      51.473   6.604  13.946  1.00  0.00              
ATOM     21  N   PRO    37      51.314   7.305  16.077  1.00  0.00              
ATOM     22  CA  PRO    37      50.834   8.642  15.742  1.00  0.00              
ATOM     23  C   PRO    37      51.393   9.750  16.604  1.00  0.00              
ATOM     24  O   PRO    37      50.677  10.539  17.247  1.00  0.00              
ATOM     25  N   GLU    39      52.689  10.014  16.357  1.00  0.00              
ATOM     26  CA  GLU    39      53.468  11.046  17.009  1.00  0.00              
ATOM     27  C   GLU    39      52.976  12.460  16.888  1.00  0.00              
ATOM     28  O   GLU    39      53.269  13.349  17.738  1.00  0.00              
ATOM     29  N   VAL    42      52.237  12.776  15.873  1.00  0.00              
ATOM     30  CA  VAL    42      51.610  14.047  15.551  1.00  0.00              
ATOM     31  C   VAL    42      50.460  14.308  16.521  1.00  0.00              
ATOM     32  O   VAL    42      50.254  15.454  16.910  1.00  0.00              
ATOM     33  N   MET    43      49.773  13.232  16.887  1.00  0.00              
ATOM     34  CA  MET    43      48.683  13.357  17.861  1.00  0.00              
ATOM     35  C   MET    43      49.116  12.966  19.252  1.00  0.00              
ATOM     36  O   MET    43      48.425  13.371  20.217  1.00  0.00              
ATOM     37  N   THR    44      50.107  12.128  19.340  1.00  0.00              
ATOM     38  CA  THR    44      50.595  11.584  20.660  1.00  0.00              
ATOM     39  C   THR    44      52.034  11.936  20.851  1.00  0.00              
ATOM     40  O   THR    44      52.979  11.260  20.426  1.00  0.00              
ATOM     41  N   ARG    45      52.210  13.080  21.512  1.00  0.00              
ATOM     42  CA  ARG    45      53.490  13.752  21.674  1.00  0.00              
ATOM     43  C   ARG    45      54.496  12.985  22.446  1.00  0.00              
ATOM     44  O   ARG    45      55.729  13.059  22.168  1.00  0.00              
ATOM     45  N   GLU    46      47.960  10.619  34.480  1.00  0.00              
ATOM     46  CA  GLU    46      47.111  10.648  35.664  1.00  0.00              
ATOM     47  C   GLU    46      46.809  12.087  36.008  1.00  0.00              
ATOM     48  O   GLU    46      47.767  12.946  35.873  1.00  0.00              
ATOM     49  N   PHE    47      45.619  12.421  36.420  1.00  0.00              
ATOM     50  CA  PHE    47      45.242  13.783  36.837  1.00  0.00              
ATOM     51  C   PHE    47      44.424  13.715  38.120  1.00  0.00              
ATOM     52  O   PHE    47      43.766  12.670  38.347  1.00  0.00              
ATOM     53  N   PHE    50      44.470  14.715  38.967  1.00  0.00              
ATOM     54  CA  PHE    50      43.610  14.718  40.197  1.00  0.00              
ATOM     55  C   PHE    50      43.044  16.110  40.291  1.00  0.00              
ATOM     56  O   PHE    50      43.880  17.058  40.110  1.00  0.00              
ATOM     57  N   GLY    51      41.788  16.293  40.590  1.00  0.00              
ATOM     58  CA  GLY    51      41.122  17.579  40.725  1.00  0.00              
ATOM     59  C   GLY    51      40.621  17.747  42.170  1.00  0.00              
ATOM     60  O   GLY    51      39.972  16.796  42.672  1.00  0.00              
ATOM     61  N   ILE    52      40.820  18.883  42.777  1.00  0.00              
ATOM     62  CA  ILE    52      40.338  19.216  44.117  1.00  0.00              
ATOM     63  C   ILE    52      39.585  20.554  44.045  1.00  0.00              
ATOM     64  O   ILE    52      40.178  21.526  43.507  1.00  0.00              
ATOM     65  N   GLN    54      38.365  20.566  44.515  1.00  0.00              
ATOM     66  CA  GLN    54      37.536  21.810  44.405  1.00  0.00              
ATOM     67  C   GLN    54      38.040  22.876  45.363  1.00  0.00              
ATOM     68  O   GLN    54      38.151  22.665  46.598  1.00  0.00              
ATOM     69  N   ASP    55      38.326  24.050  44.813  1.00  0.00              
ATOM     70  CA  ASP    55      38.617  25.273  45.545  1.00  0.00              
ATOM     71  C   ASP    55      37.302  26.033  45.837  1.00  0.00              
ATOM     72  O   ASP    55      37.013  26.508  46.918  1.00  0.00              
ATOM     73  N   LYS    62      36.484  26.082  44.747  1.00  0.00              
ATOM     74  CA  LYS    62      35.144  26.563  44.746  1.00  0.00              
ATOM     75  C   LYS    62      34.296  25.407  44.198  1.00  0.00              
ATOM     76  O   LYS    62      34.894  24.471  43.603  1.00  0.00              
ATOM     77  N   ALA    63      33.004  25.463  44.387  1.00  0.00              
ATOM     78  CA  ALA    63      32.113  24.361  43.898  1.00  0.00              
ATOM     79  C   ALA    63      32.409  24.148  42.388  1.00  0.00              
ATOM     80  O   ALA    63      32.521  25.070  41.584  1.00  0.00              
ATOM     81  N   SER    64      32.468  22.849  42.099  1.00  0.00              
ATOM     82  CA  SER    64      32.872  22.381  40.775  1.00  0.00              
ATOM     83  C   SER    64      31.902  21.391  40.216  1.00  0.00              
ATOM     84  O   SER    64      31.311  20.570  40.953  1.00  0.00              
ATOM     85  N   ASP    65      31.856  21.344  38.890  1.00  0.00              
ATOM     86  CA  ASP    65      31.074  20.358  38.147  1.00  0.00              
ATOM     87  C   ASP    65      31.941  19.756  37.040  1.00  0.00              
ATOM     88  O   ASP    65      32.728  20.492  36.427  1.00  0.00              
ATOM     89  N   GLN    71      31.746  18.480  36.812  1.00  0.00              
ATOM     90  CA  GLN    71      32.484  17.825  35.693  1.00  0.00              
ATOM     91  C   GLN    71      31.662  16.563  35.351  1.00  0.00              
ATOM     92  O   GLN    71      30.712  16.188  36.051  1.00  0.00              
ATOM     93  N   VAL    73      32.126  15.902  34.324  1.00  0.00              
ATOM     94  CA  VAL    73      31.746  14.596  33.877  1.00  0.00              
ATOM     95  C   VAL    73      32.862  13.610  34.329  1.00  0.00              
ATOM     96  O   VAL    73      34.027  13.964  34.175  1.00  0.00              
ATOM     97  N   ALA    74      32.442  12.457  34.774  1.00  0.00              
ATOM     98  CA  ALA    74      33.464  11.442  35.124  1.00  0.00              
ATOM     99  C   ALA    74      32.899  10.069  35.134  1.00  0.00              
ATOM    100  O   ALA    74      32.123   9.696  36.077  1.00  0.00              
ATOM    101  N   LEU    75      33.274   9.273  34.147  1.00  0.00              
ATOM    102  CA  LEU    75      32.892   7.882  33.990  1.00  0.00              
ATOM    103  C   LEU    75      31.469   7.703  33.414  1.00  0.00              
ATOM    104  O   LEU    75      30.581   8.567  33.530  1.00  0.00              
ATOM    105  N   ILE    76      31.284   6.480  32.926  1.00  0.00              
ATOM    106  CA  ILE    76      29.926   6.084  32.432  1.00  0.00              
ATOM    107  C   ILE    76      28.955   6.024  33.593  1.00  0.00              
ATOM    108  O   ILE    76      29.326   5.521  34.679  1.00  0.00              
ATOM    109  N   ALA    77      21.808   0.877  34.774  1.00  0.00              
ATOM    110  CA  ALA    77      20.321   1.049  34.941  1.00  0.00              
ATOM    111  C   ALA    77      19.935   2.449  34.537  1.00  0.00              
ATOM    112  O   ALA    77      18.799   2.675  33.980  1.00  0.00              
ATOM    113  N   ARG    78      20.798   3.417  34.811  1.00  0.00              
ATOM    114  CA  ARG    78      20.526   4.817  34.432  1.00  0.00              
ATOM    115  C   ARG    78      20.605   4.929  32.902  1.00  0.00              
ATOM    116  O   ARG    78      19.800   5.686  32.282  1.00  0.00              
ATOM    117  N   MET    79      15.717   4.145  26.808  1.00  0.00              
ATOM    118  CA  MET    79      14.262   3.844  26.565  1.00  0.00              
ATOM    119  C   MET    79      13.473   5.121  26.436  1.00  0.00              
ATOM    120  O   MET    79      12.520   5.222  25.593  1.00  0.00              
ATOM    121  N   ASP    80      13.797   6.133  27.157  1.00  0.00              
ATOM    122  CA  ASP    80      13.155   7.386  27.368  1.00  0.00              
ATOM    123  C   ASP    80      13.475   8.561  26.576  1.00  0.00              
ATOM    124  O   ASP    80      12.670   9.553  26.539  1.00  0.00              
ATOM    125  N   GLU    81      14.651   8.611  25.924  1.00  0.00              
ATOM    126  CA  GLU    81      15.066   9.807  25.139  1.00  0.00              
ATOM    127  C   GLU    81      15.142   9.410  23.664  1.00  0.00              
ATOM    128  O   GLU    81      16.072   8.730  23.205  1.00  0.00              
ATOM    129  N   ARG    83      14.071   9.797  22.950  1.00  0.00              
ATOM    130  CA  ARG    83      13.876   9.373  21.559  1.00  0.00              
ATOM    131  C   ARG    83      15.063   9.614  20.665  1.00  0.00              
ATOM    132  O   ARG    83      15.503   8.745  19.880  1.00  0.00              
ATOM    133  N   LYS    85      15.651  10.804  20.781  1.00  0.00              
ATOM    134  CA  LYS    85      16.779  11.205  19.916  1.00  0.00              
ATOM    135  C   LYS    85      17.961  10.290  20.103  1.00  0.00              
ATOM    136  O   LYS    85      18.755  10.106  19.137  1.00  0.00              
ATOM    137  N   TYR    86      17.767   7.070  21.386  1.00  0.00              
ATOM    138  CA  TYR    86      17.194   5.771  20.961  1.00  0.00              
ATOM    139  C   TYR    86      17.292   5.601  19.427  1.00  0.00              
ATOM    140  O   TYR    86      17.707   4.588  18.860  1.00  0.00              
ATOM    141  N   VAL    87      16.972   6.696  18.786  1.00  0.00              
ATOM    142  CA  VAL    87      17.034   6.860  17.338  1.00  0.00              
ATOM    143  C   VAL    87      18.430   6.586  16.829  1.00  0.00              
ATOM    144  O   VAL    87      18.559   5.784  15.858  1.00  0.00              
ATOM    145  N   ALA    88      19.427   7.244  17.386  1.00  0.00              
ATOM    146  CA  ALA    88      20.814   7.073  16.953  1.00  0.00              
ATOM    147  C   ALA    88      21.344   5.661  17.146  1.00  0.00              
ATOM    148  O   ALA    88      22.071   5.131  16.279  1.00  0.00              
ATOM    149  N   SER    89      21.085   5.101  18.325  1.00  0.00              
ATOM    150  CA  SER    89      21.532   3.760  18.666  1.00  0.00              
ATOM    151  C   SER    89      20.850   2.666  17.854  1.00  0.00              
ATOM    152  O   SER    89      21.508   1.651  17.493  1.00  0.00              
ATOM    153  N   TYR    90      19.545   2.794  17.657  1.00  0.00              
ATOM    154  CA  TYR    90      18.839   1.716  16.887  1.00  0.00              
ATOM    155  C   TYR    90      18.101   0.816  17.858  1.00  0.00              
ATOM    156  O   TYR    90      18.657   0.372  18.879  1.00  0.00              
ATOM    157  N   LEU    91      16.848   0.485  17.437  1.00  0.00              
ATOM    158  CA  LEU    91      15.972  -0.303  18.358  1.00  0.00              
ATOM    159  C   LEU    91      16.598  -1.651  18.641  1.00  0.00              
ATOM    160  O   LEU    91      16.483  -2.126  19.806  1.00  0.00              
ATOM    161  N   GLY    92      17.208  -2.285  17.649  1.00  0.00              
ATOM    162  CA  GLY    92      17.816  -3.609  17.884  1.00  0.00              
ATOM    163  C   GLY    92      18.872  -3.557  18.991  1.00  0.00              
ATOM    164  O   GLY    92      18.934  -4.448  19.839  1.00  0.00              
ATOM    165  N   VAL    93      19.727  -2.565  18.874  1.00  0.00              
ATOM    166  CA  VAL    93      20.845  -2.352  19.823  1.00  0.00              
ATOM    167  C   VAL    93      20.353  -1.904  21.196  1.00  0.00              
ATOM    168  O   VAL    93      20.871  -2.365  22.229  1.00  0.00              
ATOM    169  N   MET    95      19.355  -1.009  21.171  1.00  0.00              
ATOM    170  CA  MET    95      18.793  -0.544  22.467  1.00  0.00              
ATOM    171  C   MET    95      18.346  -1.765  23.272  1.00  0.00              
ATOM    172  O   MET    95      18.593  -2.063  24.445  1.00  0.00              
ATOM    173  N   ALA    96      20.868  -4.191  24.640  1.00  0.00              
ATOM    174  CA  ALA    96      21.493  -3.561  25.777  1.00  0.00              
ATOM    175  C   ALA    96      20.625  -3.732  27.025  1.00  0.00              
ATOM    176  O   ALA    96      21.042  -4.312  28.043  1.00  0.00              
ATOM    177  N   SER    97      19.375  -3.292  26.861  1.00  0.00              
ATOM    178  CA  SER    97      18.410  -3.312  27.949  1.00  0.00              
ATOM    179  C   SER    97      18.056  -4.726  28.373  1.00  0.00              
ATOM    180  O   SER    97      17.824  -4.925  29.573  1.00  0.00              
ATOM    181  N   ASP    98      22.789  -6.770  36.146  1.00  0.00              
ATOM    182  CA  ASP    98      23.251  -5.679  37.023  1.00  0.00              
ATOM    183  C   ASP    98      23.890  -6.122  38.277  1.00  0.00              
ATOM    184  O   ASP    98      25.179  -5.857  38.370  1.00  0.00              
ATOM    185  N   GLY    99      23.189  -6.590  39.255  1.00  0.00              
ATOM    186  CA  GLY    99      23.961  -7.059  40.495  1.00  0.00              
ATOM    187  C   GLY    99      24.992  -7.995  39.853  1.00  0.00              
ATOM    188  O   GLY    99      24.612  -9.078  39.338  1.00  0.00              
ATOM    189  N   ILE   101      26.148  -7.436  39.622  1.00  0.00              
ATOM    190  CA  ILE   101      27.263  -8.087  38.922  1.00  0.00              
ATOM    191  C   ILE   101      28.552  -7.420  39.368  1.00  0.00              
ATOM    192  O   ILE   101      28.609  -6.168  39.298  1.00  0.00              
ATOM    193  N   ASP   102      31.821 -12.672  34.556  1.00  0.00              
ATOM    194  CA  ASP   102      31.412 -12.807  33.137  1.00  0.00              
ATOM    195  C   ASP   102      30.246 -11.863  32.839  1.00  0.00              
ATOM    196  O   ASP   102      30.171 -11.328  31.708  1.00  0.00              
END
