
#######################################################
#                                                     #
#                        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   37 (  148),  selected   37 , name T0348AL380_1
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348AL380_1.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    V      10      V      10          0.707
LGA    C      11      C      11          1.072
LGA    P      12      P      12          1.238
LGA    L      13      L      13          1.575
LGA    C      14      C      14          2.707
LGA    K      15      K      15          3.825
LGA    G      16      G      16          1.662
LGA    P      17      P      17          1.681
LGA    L      18      L      18          0.803
LGA    V      19      V      19          0.593
LGA    F      20      F      20          0.476
LGA    D      21      D      21          0.784
LGA    K      22      K      22          0.529
LGA    S      23      S      23          0.490
LGA    K      24      K      24          1.080
LGA    D      25      D      25          0.811
LGA    E      26      E      26          0.720
LGA    L      27      L      27          0.713
LGA    I      28      I      28          1.216
LGA    C      29      C      29          0.693
LGA    K      30      K      30          2.261
LGA    G      31      G      31          1.138
LGA    D      32      D      32          0.483
LGA    R      33      R      33          1.365
LGA    F      36      L      34          1.504
LGA    P      37      A      35          1.789
LGA    I      38      F      36          2.226
LGA    K      39      P      37          2.116
LGA    D      40      I      38          3.457
LGA    G      41      K      39          2.941
LGA    I      42      -       -           -
LGA    P      43      D      40          2.809
LGA    M      44      G      41           #
LGA    M      45      I      42           -
LGA    L      46      P      43           -
LGA    E      47      M      44           -
LGA    S      48      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    -       -      A      50           -
LGA    -       -      R      51           -
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    -       -      A      54           -
LGA    -       -      P      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      E      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      E      62           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37   61    5.0     31    1.73    77.42     47.096     1.698

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.042772 * X  +  -0.377920 * Y  +   0.924850 * Z  +   9.658434
  Y_new =  -0.883638 * X  +  -0.446278 * Y  +  -0.141495 * Z  +  29.538860
  Z_new =   0.466214 * X  +  -0.811180 * Y  +  -0.353032 * Z  +  50.779064 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.981282    1.160311  [ DEG:  -113.5191     66.4809 ]
  Theta =  -0.485006   -2.656587  [ DEG:   -27.7888   -152.2112 ]
  Phi   =  -1.522429    1.619164  [ DEG:   -87.2288     92.7712 ]
 
# 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: T0348AL380_1                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348AL380_1.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37   61   5.0   31   1.73   77.42  47.096
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL380_1
REMARK Aligment from pdb entry: 1pft
ATOM      1  N   VAL    10       7.914  33.936  59.473  1.00  0.00              
ATOM      2  CA  VAL    10       8.127  33.045  60.598  1.00  0.00              
ATOM      3  C   VAL    10       7.544  31.663  60.322  1.00  0.00              
ATOM      4  O   VAL    10       7.165  31.339  59.199  1.00  0.00              
ATOM      5  N   CYS    11       7.381  30.897  61.398  1.00  0.00              
ATOM      6  CA  CYS    11       6.620  29.663  61.363  1.00  0.00              
ATOM      7  C   CYS    11       5.242  29.890  62.042  1.00  0.00              
ATOM      8  O   CYS    11       5.107  29.718  63.266  1.00  0.00              
ATOM      9  N   PRO    12       4.198  29.822  61.182  1.00  0.00              
ATOM     10  CA  PRO    12       2.789  29.752  61.636  1.00  0.00              
ATOM     11  C   PRO    12       2.436  28.450  62.355  1.00  0.00              
ATOM     12  O   PRO    12       1.296  28.263  62.781  1.00  0.00              
ATOM     13  N   LEU    13       3.324  27.470  62.200  1.00  0.00              
ATOM     14  CA  LEU    13       3.085  26.130  62.718  1.00  0.00              
ATOM     15  C   LEU    13       3.445  26.057  64.197  1.00  0.00              
ATOM     16  O   LEU    13       2.571  26.073  65.062  1.00  0.00              
ATOM     17  N   CYS    14       4.749  26.038  64.478  1.00  0.00              
ATOM     18  CA  CYS    14       5.221  25.627  65.798  1.00  0.00              
ATOM     19  C   CYS    14       5.492  26.817  66.699  1.00  0.00              
ATOM     20  O   CYS    14       5.936  26.650  67.842  1.00  0.00              
ATOM     21  N   LYS    15       8.180  28.999  65.700  1.00  0.00              
ATOM     22  CA  LYS    15       9.633  29.078  65.653  1.00  0.00              
ATOM     23  C   LYS    15      10.074  29.989  64.508  1.00  0.00              
ATOM     24  O   LYS    15       9.883  29.665  63.338  1.00  0.00              
ATOM     25  N   GLY    16      10.520  31.186  64.873  1.00  0.00              
ATOM     26  CA  GLY    16      10.722  32.261  63.907  1.00  0.00              
ATOM     27  C   GLY    16      11.906  31.978  62.986  1.00  0.00              
ATOM     28  O   GLY    16      12.181  32.751  62.066  1.00  0.00              
ATOM     29  N   PRO    17      12.728  31.020  63.403  1.00  0.00              
ATOM     30  CA  PRO    17      13.870  30.597  62.600  1.00  0.00              
ATOM     31  C   PRO    17      13.401  29.697  61.456  1.00  0.00              
ATOM     32  O   PRO    17      13.256  28.488  61.631  1.00  0.00              
ATOM     33  N   LEU    18      13.387  30.269  60.257  1.00  0.00              
ATOM     34  CA  LEU    18      13.234  29.492  59.033  1.00  0.00              
ATOM     35  C   LEU    18      14.545  29.465  58.254  1.00  0.00              
ATOM     36  O   LEU    18      15.504  30.150  58.605  1.00  0.00              
ATOM     37  N   VAL    19      14.512  28.786  57.111  1.00  0.00              
ATOM     38  CA  VAL    19      15.712  28.581  56.310  1.00  0.00              
ATOM     39  C   VAL    19      15.338  28.259  54.867  1.00  0.00              
ATOM     40  O   VAL    19      14.215  27.848  54.583  1.00  0.00              
ATOM     41  N   PHE    20      16.248  28.590  53.956  1.00  0.00              
ATOM     42  CA  PHE    20      15.960  28.555  52.529  1.00  0.00              
ATOM     43  C   PHE    20      16.521  27.281  51.905  1.00  0.00              
ATOM     44  O   PHE    20      17.281  26.552  52.540  1.00  0.00              
ATOM     45  N   ASP    21      15.978  26.932  50.742  1.00  0.00              
ATOM     46  CA  ASP    21      16.274  25.666  50.098  1.00  0.00              
ATOM     47  C   ASP    21      16.394  25.870  48.574  1.00  0.00              
ATOM     48  O   ASP    21      15.429  25.683  47.818  1.00  0.00              
ATOM     49  N   LYS    22      17.575  26.365  48.153  1.00  0.00              
ATOM     50  CA  LYS    22      17.807  26.794  46.751  1.00  0.00              
ATOM     51  C   LYS    22      17.620  25.670  45.730  1.00  0.00              
ATOM     52  O   LYS    22      17.671  25.906  44.524  1.00  0.00              
ATOM     53  N   SER    23      17.671  24.443  46.237  1.00  0.00              
ATOM     54  CA  SER    23      17.624  23.257  45.391  1.00  0.00              
ATOM     55  C   SER    23      16.199  23.030  44.884  1.00  0.00              
ATOM     56  O   SER    23      15.983  22.865  43.685  1.00  0.00              
ATOM     57  N   LYS    24      15.242  23.316  45.763  1.00  0.00              
ATOM     58  CA  LYS    24      13.833  23.187  45.427  1.00  0.00              
ATOM     59  C   LYS    24      13.224  24.559  45.149  1.00  0.00              
ATOM     60  O   LYS    24      12.148  24.662  44.563  1.00  0.00              
ATOM     61  N   ASP    25      13.847  25.584  45.720  1.00  0.00              
ATOM     62  CA  ASP    25      13.263  26.918  45.760  1.00  0.00              
ATOM     63  C   ASP    25      12.329  27.053  46.960  1.00  0.00              
ATOM     64  O   ASP    25      11.242  27.617  46.853  1.00  0.00              
ATOM     65  N   GLU    26      12.717  26.412  48.057  1.00  0.00              
ATOM     66  CA  GLU    26      11.829  26.238  49.202  1.00  0.00              
ATOM     67  C   GLU    26      12.292  27.119  50.361  1.00  0.00              
ATOM     68  O   GLU    26      13.460  27.500  50.431  1.00  0.00              
ATOM     69  N   LEU    27      11.413  27.272  51.344  1.00  0.00              
ATOM     70  CA  LEU    27      11.782  27.860  52.625  1.00  0.00              
ATOM     71  C   LEU    27      11.085  27.123  53.766  1.00  0.00              
ATOM     72  O   LEU    27       9.860  27.090  53.840  1.00  0.00              
ATOM     73  N   ILE    28      11.890  26.490  54.611  1.00  0.00              
ATOM     74  CA  ILE    28      11.378  25.563  55.610  1.00  0.00              
ATOM     75  C   ILE    28      11.511  26.176  57.006  1.00  0.00              
ATOM     76  O   ILE    28      12.319  27.081  57.212  1.00  0.00              
ATOM     77  N   CYS    29      10.905  25.503  57.977  1.00  0.00              
ATOM     78  CA  CYS    29      11.196  25.747  59.386  1.00  0.00              
ATOM     79  C   CYS    29      12.574  25.194  59.740  1.00  0.00              
ATOM     80  O   CYS    29      12.973  24.141  59.247  1.00  0.00              
ATOM     81  N   LYS    30      13.203  25.827  60.725  1.00  0.00              
ATOM     82  CA  LYS    30      14.442  25.324  61.297  1.00  0.00              
ATOM     83  C   LYS    30      14.161  24.587  62.607  1.00  0.00              
ATOM     84  O   LYS    30      15.024  24.510  63.480  1.00  0.00              
ATOM     85  N   GLY    31      12.882  24.285  62.816  1.00  0.00              
ATOM     86  CA  GLY    31      12.425  23.700  64.066  1.00  0.00              
ATOM     87  C   GLY    31      11.608  22.443  63.810  1.00  0.00              
ATOM     88  O   GLY    31      12.132  21.328  63.882  1.00  0.00              
ATOM     89  N   ASP    32      10.416  22.637  63.236  1.00  0.00              
ATOM     90  CA  ASP    32       9.465  21.538  63.109  1.00  0.00              
ATOM     91  C   ASP    32       9.669  20.767  61.812  1.00  0.00              
ATOM     92  O   ASP    32       8.968  19.786  61.552  1.00  0.00              
ATOM     93  N   ARG    33      10.408  21.393  60.890  1.00  0.00              
ATOM     94  CA  ARG    33      10.696  20.771  59.606  1.00  0.00              
ATOM     95  C   ARG    33       9.789  21.320  58.505  1.00  0.00              
ATOM     96  O   ARG    33       9.798  20.803  57.382  1.00  0.00              
ATOM     97  N   PHE    36       8.775  22.065  58.946  1.00  0.00              
ATOM     98  CA  PHE    36       7.674  22.464  58.082  1.00  0.00              
ATOM     99  C   PHE    36       8.174  23.428  57.005  1.00  0.00              
ATOM    100  O   PHE    36       8.580  24.549  57.316  1.00  0.00              
ATOM    101  N   PRO    37       7.875  23.082  55.755  1.00  0.00              
ATOM    102  CA  PRO    37       8.037  24.003  54.640  1.00  0.00              
ATOM    103  C   PRO    37       7.152  25.235  54.840  1.00  0.00              
ATOM    104  O   PRO    37       6.109  25.155  55.488  1.00  0.00              
ATOM    105  N   ILE    38       7.410  26.236  54.006  1.00  0.00              
ATOM    106  CA  ILE    38       6.578  27.430  53.946  1.00  0.00              
ATOM    107  C   ILE    38       5.960  27.559  52.553  1.00  0.00              
ATOM    108  O   ILE    38       4.851  27.081  52.316  1.00  0.00              
ATOM    109  N   LYS    39       6.789  27.986  51.606  1.00  0.00              
ATOM    110  CA  LYS    39       6.479  27.844  50.186  1.00  0.00              
ATOM    111  C   LYS    39       7.614  27.105  49.477  1.00  0.00              
ATOM    112  O   LYS    39       8.650  26.828  50.079  1.00  0.00              
ATOM    113  N   ASP    40       7.278  26.553  48.315  1.00  0.00              
ATOM    114  CA  ASP    40       8.224  25.758  47.542  1.00  0.00              
ATOM    115  C   ASP    40       7.887  25.848  46.052  1.00  0.00              
ATOM    116  O   ASP    40       8.070  24.877  45.314  1.00  0.00              
ATOM    117  N   GLY    41       7.693  27.082  45.595  1.00  0.00              
ATOM    118  CA  GLY    41       7.585  27.370  44.172  1.00  0.00              
ATOM    119  C   GLY    41       7.887  28.841  43.903  1.00  0.00              
ATOM    120  O   GLY    41       7.025  29.589  43.446  1.00  0.00              
ATOM    121  N   ILE    42       9.074  29.264  44.326  1.00  0.00              
ATOM    122  CA  ILE    42       9.430  30.676  44.337  1.00  0.00              
ATOM    123  C   ILE    42       9.747  31.158  42.925  1.00  0.00              
ATOM    124  O   ILE    42      10.907  31.354  42.570  1.00  0.00              
ATOM    125  N   PRO    43       8.719  31.140  42.079  1.00  0.00              
ATOM    126  CA  PRO    43       8.845  31.639  40.716  1.00  0.00              
ATOM    127  C   PRO    43       7.480  31.685  40.039  1.00  0.00              
ATOM    128  O   PRO    43       6.621  30.844  40.295  1.00  0.00              
ATOM    129  N   MET    44       7.352  32.591  39.076  1.00  0.00              
ATOM    130  CA  MET    44       6.191  32.627  38.199  1.00  0.00              
ATOM    131  C   MET    44       6.495  33.444  36.946  1.00  0.00              
ATOM    132  O   MET    44       5.924  34.512  36.737  1.00  0.00              
ATOM    133  N   MET    45       7.279  32.846  36.055  1.00  0.00              
ATOM    134  CA  MET    45       7.489  33.394  34.723  1.00  0.00              
ATOM    135  C   MET    45       7.273  32.314  33.666  1.00  0.00              
ATOM    136  O   MET    45       6.347  32.401  32.860  1.00  0.00              
ATOM    137  N   LEU    46       8.013  31.220  33.812  1.00  0.00              
ATOM    138  CA  LEU    46       7.802  30.030  33.008  1.00  0.00              
ATOM    139  C   LEU    46       8.464  30.204  31.627  1.00  0.00              
ATOM    140  O   LEU    46       7.790  30.350  30.597  1.00  0.00              
ATOM    141  N   GLU    47       9.811  30.251  31.638  1.00  0.00              
ATOM    142  CA  GLU    47      10.614  30.272  30.389  1.00  0.00              
ATOM    143  C   GLU    47      10.367  29.068  29.484  1.00  0.00              
ATOM    144  O   GLU    47       9.705  29.178  28.454  1.00  0.00              
ATOM    145  N   SER    48      10.732  27.894  29.995  1.00  0.00              
ATOM    146  CA  SER    48      10.639  26.665  29.215  1.00  0.00              
ATOM    147  C   SER    48      10.566  25.458  30.151  1.00  0.00              
ATOM    148  O   SER    48      11.591  24.874  30.499  1.00  0.00              
END
