
#######################################################
#                                                     #
#                        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   48 (  192),  selected   48 , name T0348AL243_2
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348AL243_2.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       2           -
LGA    D       2      A       3          3.150
LGA    A       3      K       4          3.051
LGA    K       4      F       5          2.430
LGA    F       5      L       6          0.431
LGA    L       6      E       7          4.447
LGA    E       7      -       -           -
LGA    I       8      I       8          2.782
LGA    L       9      L       9          2.770
LGA    V      10      V      10          1.494
LGA    C      11      C      11          1.415
LGA    P      12      P      12          2.821
LGA    L      13      L      13          1.748
LGA    C      14      C      14          1.380
LGA    K      15      K      15          2.780
LGA    G      16      G      16          3.013
LGA    P      17      P      17          1.453
LGA    L      18      L      18          1.497
LGA    V      19      V      19          0.834
LGA    F      20      F      20          0.460
LGA    D      21      D      21          1.205
LGA    K      22      K      22          2.306
LGA    S      23      S      23          3.900
LGA    K      24      K      24          3.588
LGA    D      25      D      25          2.846
LGA    E      26      E      26          1.281
LGA    L      27      L      27          0.870
LGA    I      28      I      28          1.679
LGA    C      29      C      29          1.300
LGA    K      30      K      30          1.449
LGA    G      31      G      31          2.950
LGA    D      32      D      32          3.198
LGA    -       -      R      33           -
LGA    R      33      L      34          0.951
LGA    L      34      A      35          3.265
LGA    A      35      F      36          1.341
LGA    I      38      P      37          3.022
LGA    K      39      I      38          0.896
LGA    D      40      K      39          4.119
LGA    G      41      D      40           -
LGA    S      48      G      41           -
LGA    E      49      I      42           -
LGA    A      50      P      43           -
LGA    R      51      M      44           -
LGA    E      52      M      45           -
LGA    L      53      L      46           -
LGA    A      54      E      47           -
LGA    P      55      S      48           -
LGA    E      56      E      49           -
LGA    E      57      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)   48   61    5.0     36    2.42    69.44     45.589     1.428

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.502250 * X  +  -0.025588 * Y  +   0.864344 * Z  +  11.209875
  Y_new =  -0.750228 * X  +   0.509950 * Y  +  -0.420843 * Z  +  34.355965
  Z_new =  -0.430004 * X  +  -0.859823 * Y  +  -0.275320 * Z  +  48.206795 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.880685    1.260908  [ DEG:  -107.7553     72.2447 ]
  Theta =   0.444497    2.697096  [ DEG:    25.4678    154.5322 ]
  Phi   =  -2.160733    0.980860  [ DEG:  -123.8009     56.1991 ]
 
# 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: T0348AL243_2                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348AL243_2.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   61   5.0   36   2.42   69.44  45.589
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL243_2
REMARK Aligment from pdb entry: 1dl6A
ATOM      1  N   ASP     2      -2.240  46.101  47.077  1.00  0.00              
ATOM      2  CA  ASP     2      -2.923  44.877  47.480  1.00  0.00              
ATOM      3  C   ASP     2      -2.155  44.166  48.590  1.00  0.00              
ATOM      4  O   ASP     2      -2.670  43.977  49.692  1.00  0.00              
ATOM      5  N   ALA     3      -0.920  43.775  48.292  1.00  0.00              
ATOM      6  CA  ALA     3      -0.081  43.085  49.265  1.00  0.00              
ATOM      7  C   ALA     3       1.396  43.379  49.016  1.00  0.00              
ATOM      8  O   ALA     3       1.903  43.168  47.915  1.00  0.00              
ATOM      9  N   LYS     4       2.080  43.868  50.045  1.00  0.00              
ATOM     10  CA  LYS     4       3.497  44.191  49.937  1.00  0.00              
ATOM     11  C   LYS     4       4.343  43.227  50.764  1.00  0.00              
ATOM     12  O   LYS     4       5.493  42.949  50.425  1.00  0.00              
ATOM     13  N   PHE     5       3.767  42.722  51.850  1.00  0.00              
ATOM     14  CA  PHE     5       4.469  41.790  52.724  1.00  0.00              
ATOM     15  C   PHE     5       4.795  40.491  51.996  1.00  0.00              
ATOM     16  O   PHE     5       4.089  39.492  52.139  1.00  0.00              
ATOM     17  N   LEU     6       5.868  40.511  51.212  1.00  0.00              
ATOM     18  CA  LEU     6       6.288  39.336  50.459  1.00  0.00              
ATOM     19  C   LEU     6       6.998  38.329  51.364  1.00  0.00              
ATOM     20  O   LEU     6       6.547  37.194  51.517  1.00  0.00              
ATOM     21  N   GLU     7       8.125  38.733  51.976  1.00  0.00              
ATOM     22  CA  GLU     7       8.896  37.860  52.865  1.00  0.00              
ATOM     23  C   GLU     7       8.215  37.655  54.214  1.00  0.00              
ATOM     24  O   GLU     7       7.798  38.614  54.862  1.00  0.00              
ATOM     25  N   ILE     8       8.108  36.397  54.632  1.00  0.00              
ATOM     26  CA  ILE     8       7.479  36.064  55.905  1.00  0.00              
ATOM     27  C   ILE     8       8.521  35.975  57.015  1.00  0.00              
ATOM     28  O   ILE     8       9.432  35.150  56.961  1.00  0.00              
ATOM     29  N   LEU     9       8.381  36.836  58.019  1.00  0.00              
ATOM     30  CA  LEU     9       9.307  36.860  59.139  1.00  0.00              
ATOM     31  C   LEU     9       9.104  35.660  60.058  1.00  0.00              
ATOM     32  O   LEU     9       8.182  35.639  60.873  1.00  0.00              
ATOM     33  N   VAL    10       9.976  34.665  59.926  1.00  0.00              
ATOM     34  CA  VAL    10       9.897  33.462  60.750  1.00  0.00              
ATOM     35  C   VAL    10       8.583  32.721  60.522  1.00  0.00              
ATOM     36  O   VAL    10       7.729  33.167  59.756  1.00  0.00              
ATOM     37  N   CYS    11       8.433  31.586  61.196  1.00  0.00              
ATOM     38  CA  CYS    11       7.230  30.772  61.079  1.00  0.00              
ATOM     39  C   CYS    11       6.136  31.286  62.018  1.00  0.00              
ATOM     40  O   CYS    11       6.390  31.542  63.194  1.00  0.00              
ATOM     41  N   PRO    12       4.900  31.446  61.510  1.00  0.00              
ATOM     42  CA  PRO    12       3.774  31.935  62.315  1.00  0.00              
ATOM     43  C   PRO    12       3.537  31.092  63.562  1.00  0.00              
ATOM     44  O   PRO    12       3.189  31.614  64.621  1.00  0.00              
ATOM     45  N   LEU    13       3.722  29.785  63.427  1.00  0.00              
ATOM     46  CA  LEU    13       3.520  28.864  64.542  1.00  0.00              
ATOM     47  C   LEU    13       4.848  28.430  65.162  1.00  0.00              
ATOM     48  O   LEU    13       4.887  27.504  65.972  1.00  0.00              
ATOM     49  N   CYS    14       5.935  29.099  64.785  1.00  0.00              
ATOM     50  CA  CYS    14       7.253  28.770  65.317  1.00  0.00              
ATOM     51  C   CYS    14       8.172  29.989  65.293  1.00  0.00              
ATOM     52  O   CYS    14       8.891  30.215  64.319  1.00  0.00              
ATOM     53  N   LYS    15       8.164  30.792  66.371  1.00  0.00              
ATOM     54  CA  LYS    15       9.002  31.990  66.469  1.00  0.00              
ATOM     55  C   LYS    15      10.481  31.649  66.613  1.00  0.00              
ATOM     56  O   LYS    15      11.331  32.228  65.937  1.00  0.00              
ATOM     57  N   GLY    16      11.923  28.871  65.777  1.00  0.00              
ATOM     58  CA  GLY    16      12.358  28.197  64.560  1.00  0.00              
ATOM     59  C   GLY    16      12.042  29.038  63.328  1.00  0.00              
ATOM     60  O   GLY    16      10.890  29.399  63.091  1.00  0.00              
ATOM     61  N   PRO    17      13.073  29.349  62.550  1.00  0.00              
ATOM     62  CA  PRO    17      12.903  30.150  61.345  1.00  0.00              
ATOM     63  C   PRO    17      12.982  29.287  60.092  1.00  0.00              
ATOM     64  O   PRO    17      13.867  28.441  59.963  1.00  0.00              
ATOM     65  N   LEU    18      12.053  29.511  59.168  1.00  0.00              
ATOM     66  CA  LEU    18      12.021  28.756  57.919  1.00  0.00              
ATOM     67  C   LEU    18      13.325  28.942  57.147  1.00  0.00              
ATOM     68  O   LEU    18      13.621  30.037  56.668  1.00  0.00              
ATOM     69  N   VAL    19      14.102  27.870  57.029  1.00  0.00              
ATOM     70  CA  VAL    19      15.371  27.924  56.315  1.00  0.00              
ATOM     71  C   VAL    19      15.142  27.945  54.810  1.00  0.00              
ATOM     72  O   VAL    19      14.094  27.520  54.329  1.00  0.00              
ATOM     73  N   PHE    20      16.127  28.442  54.069  1.00  0.00              
ATOM     74  CA  PHE    20      16.026  28.517  52.616  1.00  0.00              
ATOM     75  C   PHE    20      17.178  27.776  51.948  1.00  0.00              
ATOM     76  O   PHE    20      18.301  27.766  52.454  1.00  0.00              
ATOM     77  N   ASP    21      16.894  27.157  50.807  1.00  0.00              
ATOM     78  CA  ASP    21      17.907  26.413  50.067  1.00  0.00              
ATOM     79  C   ASP    21      18.766  27.354  49.226  1.00  0.00              
ATOM     80  O   ASP    21      18.766  28.566  49.440  1.00  0.00              
ATOM     81  N   LYS    22      19.499  26.789  48.271  1.00  0.00              
ATOM     82  CA  LYS    22      20.363  27.579  47.402  1.00  0.00              
ATOM     83  C   LYS    22      19.641  27.966  46.115  1.00  0.00              
ATOM     84  O   LYS    22      19.927  29.006  45.522  1.00  0.00              
ATOM     85  N   SER    23      18.700  27.124  45.690  1.00  0.00              
ATOM     86  CA  SER    23      17.930  27.369  44.480  1.00  0.00              
ATOM     87  C   SER    23      17.077  26.157  44.138  1.00  0.00              
ATOM     88  O   SER    23      17.586  25.051  43.952  1.00  0.00              
ATOM     89  N   LYS    24      15.777  26.380  44.059  1.00  0.00              
ATOM     90  CA  LYS    24      14.821  25.321  43.741  1.00  0.00              
ATOM     91  C   LYS    24      14.596  24.403  44.937  1.00  0.00              
ATOM     92  O   LYS    24      14.267  23.228  44.777  1.00  0.00              
ATOM     93  N   ASP    25      14.775  24.947  46.137  1.00  0.00              
ATOM     94  CA  ASP    25      14.585  24.162  47.344  1.00  0.00              
ATOM     95  C   ASP    25      13.480  24.706  48.231  1.00  0.00              
ATOM     96  O   ASP    25      12.996  24.011  49.124  1.00  0.00              
ATOM     97  N   GLU    26      13.078  25.952  47.988  1.00  0.00              
ATOM     98  CA  GLU    26      12.024  26.585  48.772  1.00  0.00              
ATOM     99  C   GLU    26      12.481  26.824  50.208  1.00  0.00              
ATOM    100  O   GLU    26      13.648  26.612  50.541  1.00  0.00              
ATOM    101  N   LEU    27      11.555  27.265  51.053  1.00  0.00              
ATOM    102  CA  LEU    27      11.861  27.530  52.454  1.00  0.00              
ATOM    103  C   LEU    27      11.050  26.614  53.365  1.00  0.00              
ATOM    104  O   LEU    27       9.820  26.651  53.359  1.00  0.00              
ATOM    105  N   ILE    28      11.744  25.784  54.139  1.00  0.00              
ATOM    106  CA  ILE    28      11.091  24.855  55.036  1.00  0.00              
ATOM    107  C   ILE    28      11.315  25.229  56.498  1.00  0.00              
ATOM    108  O   ILE    28      12.290  25.897  56.835  1.00  0.00              
ATOM    109  N   CYS    29      10.406  24.788  57.365  1.00  0.00              
ATOM    110  CA  CYS    29      10.510  25.074  58.792  1.00  0.00              
ATOM    111  C   CYS    29      11.075  23.867  59.543  1.00  0.00              
ATOM    112  O   CYS    29      10.684  22.731  59.282  1.00  0.00              
ATOM    113  N   LYS    30      12.014  24.094  60.481  1.00  0.00              
ATOM    114  CA  LYS    30      12.631  23.011  61.254  1.00  0.00              
ATOM    115  C   LYS    30      11.716  22.454  62.344  1.00  0.00              
ATOM    116  O   LYS    30      12.110  21.563  63.097  1.00  0.00              
ATOM    117  N   GLY    31      10.495  22.979  62.429  1.00  0.00              
ATOM    118  CA  GLY    31       9.539  22.525  63.430  1.00  0.00              
ATOM    119  C   GLY    31       8.331  21.858  62.773  1.00  0.00              
ATOM    120  O   GLY    31       8.233  20.631  62.748  1.00  0.00              
ATOM    121  N   ASP    32       7.413  22.663  62.234  1.00  0.00              
ATOM    122  CA  ASP    32       6.227  22.115  61.577  1.00  0.00              
ATOM    123  C   ASP    32       6.605  21.396  60.285  1.00  0.00              
ATOM    124  O   ASP    32       5.794  20.666  59.714  1.00  0.00              
ATOM    125  N   ARG    33       7.835  21.607  59.824  1.00  0.00              
ATOM    126  CA  ARG    33       8.282  20.970  58.602  1.00  0.00              
ATOM    127  C   ARG    33       7.443  21.374  57.409  1.00  0.00              
ATOM    128  O   ARG    33       6.912  20.521  56.697  1.00  0.00              
ATOM    129  N   LEU    34       7.321  22.680  57.188  1.00  0.00              
ATOM    130  CA  LEU    34       6.538  23.188  56.070  1.00  0.00              
ATOM    131  C   LEU    34       7.443  23.521  54.891  1.00  0.00              
ATOM    132  O   LEU    34       8.661  23.369  54.976  1.00  0.00              
ATOM    133  N   ALA    35       6.840  23.971  53.797  1.00  0.00              
ATOM    134  CA  ALA    35       7.589  24.324  52.597  1.00  0.00              
ATOM    135  C   ALA    35       6.934  25.493  51.866  1.00  0.00              
ATOM    136  O   ALA    35       6.049  25.299  51.035  1.00  0.00              
ATOM    137  N   ILE    38       7.377  26.706  52.181  1.00  0.00              
ATOM    138  CA  ILE    38       6.832  27.903  51.551  1.00  0.00              
ATOM    139  C   ILE    38       7.728  28.385  50.413  1.00  0.00              
ATOM    140  O   ILE    38       8.940  28.517  50.578  1.00  0.00              
ATOM    141  N   LYS    39       7.121  28.644  49.259  1.00  0.00              
ATOM    142  CA  LYS    39       7.878  29.106  48.111  1.00  0.00              
ATOM    143  C   LYS    39       8.293  27.973  47.194  1.00  0.00              
ATOM    144  O   LYS    39       9.482  27.687  47.048  1.00  0.00              
ATOM    145  N   ASP    40       7.312  27.323  46.577  1.00  0.00              
ATOM    146  CA  ASP    40       7.580  26.213  45.670  1.00  0.00              
ATOM    147  C   ASP    40       7.808  26.714  44.247  1.00  0.00              
ATOM    148  O   ASP    40       8.571  26.120  43.484  1.00  0.00              
ATOM    149  N   GLY    41      13.130  36.198  32.592  1.00  0.00              
ATOM    150  CA  GLY    41      14.319  36.493  31.814  1.00  0.00              
ATOM    151  C   GLY    41      14.073  37.554  30.761  1.00  0.00              
ATOM    152  O   GLY    41      13.650  37.247  29.647  1.00  0.00              
ATOM    153  N   SER    48      14.338  38.808  31.114  1.00  0.00              
ATOM    154  CA  SER    48      14.142  39.919  30.190  1.00  0.00              
ATOM    155  C   SER    48      14.900  41.157  30.658  1.00  0.00              
ATOM    156  O   SER    48      14.455  42.285  30.449  1.00  0.00              
ATOM    157  N   GLU    49      16.048  40.939  31.291  1.00  0.00              
ATOM    158  CA  GLU    49      16.868  42.039  31.788  1.00  0.00              
ATOM    159  C   GLU    49      18.302  41.944  31.265  1.00  0.00              
ATOM    160  O   GLU    49      19.186  42.660  31.735  1.00  0.00              
ATOM    161  N   ALA    50      18.526  41.060  30.292  1.00  0.00              
ATOM    162  CA  ALA    50      19.851  40.875  29.708  1.00  0.00              
ATOM    163  C   ALA    50      20.823  40.277  30.722  1.00  0.00              
ATOM    164  O   ALA    50      21.283  39.147  30.563  1.00  0.00              
ATOM    165  N   ARG    51      21.131  41.044  31.764  1.00  0.00              
ATOM    166  CA  ARG    51      22.049  40.591  32.805  1.00  0.00              
ATOM    167  C   ARG    51      23.470  40.473  32.263  1.00  0.00              
ATOM    168  O   ARG    51      23.890  39.404  31.822  1.00  0.00              
ATOM    169  N   GLU    52      24.204  41.580  32.298  1.00  0.00              
ATOM    170  CA  GLU    52      25.578  41.602  31.810  1.00  0.00              
ATOM    171  C   GLU    52      26.358  42.755  32.434  1.00  0.00              
ATOM    172  O   GLU    52      25.777  43.657  33.037  1.00  0.00              
ATOM    173  N   LEU    53      27.678  42.718  32.285  1.00  0.00              
ATOM    174  CA  LEU    53      28.537  43.762  32.834  1.00  0.00              
ATOM    175  C   LEU    53      28.742  44.884  31.821  1.00  0.00              
ATOM    176  O   LEU    53      29.867  45.180  31.421  1.00  0.00              
ATOM    177  N   ALA    54      27.641  45.508  31.411  1.00  0.00              
ATOM    178  CA  ALA    54      27.694  46.599  30.446  1.00  0.00              
ATOM    179  C   ALA    54      28.247  46.117  29.108  1.00  0.00              
ATOM    180  O   ALA    54      29.076  45.209  29.059  1.00  0.00              
ATOM    181  N   PRO    55      27.781  46.731  28.026  1.00  0.00              
ATOM    182  CA  PRO    55      28.229  46.365  26.688  1.00  0.00              
ATOM    183  C   PRO    55      29.648  46.864  26.434  1.00  0.00              
ATOM    184  O   PRO    55      30.105  47.816  27.067  1.00  0.00              
ATOM    185  N   GLU    56      30.340  46.216  25.503  1.00  0.00              
ATOM    186  CA  GLU    56      31.707  46.595  25.164  1.00  0.00              
ATOM    187  C   GLU    56      31.723  47.677  24.090  1.00  0.00              
ATOM    188  O   GLU    56      32.611  48.529  24.066  1.00  0.00              
ATOM    189  N   GLU    57      30.733  47.638  23.204  1.00  0.00              
ATOM    190  CA  GLU    57      30.633  48.616  22.127  1.00  0.00              
ATOM    191  C   GLU    57      29.762  49.796  22.545  1.00  0.00              
ATOM    192  O   GLU    57      28.887  49.663  23.400  1.00  0.00              
END
