
#######################################################
#                                                     #
#                        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   53 (  212),  selected   53 , name T0348AL243_1
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348AL243_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      L       9          1.748
LGA    V      10      V      10          1.090
LGA    C      11      C      11          0.689
LGA    P      12      P      12          0.502
LGA    L      13      L      13          0.900
LGA    C      14      C      14          1.415
LGA    K      15      K      15          1.205
LGA    G      16      G      16          0.979
LGA    P      17      P      17          0.714
LGA    L      18      L      18          0.543
LGA    V      19      V      19          0.969
LGA    F      20      F      20          0.572
LGA    D      21      D      21          0.660
LGA    K      24      K      22          0.912
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    D      25      D      25          0.872
LGA    E      26      E      26          0.573
LGA    L      27      L      27          0.449
LGA    I      28      I      28          0.530
LGA    C      29      C      29          1.395
LGA    G      31      K      30          1.855
LGA    D      32      G      31          1.803
LGA    -       -      D      32           -
LGA    R      33      R      33          1.253
LGA    L      34      L      34          1.667
LGA    A      35      A      35          0.785
LGA    F      36      F      36          0.395
LGA    P      37      P      37          1.100
LGA    I      38      I      38          0.890
LGA    K      39      K      39          4.098
LGA    D      40      D      40          1.343
LGA    G      41      G      41          1.059
LGA    I      42      I      42          0.647
LGA    P      43      P      43          1.102
LGA    M      44      M      44          1.040
LGA    M      45      M      45          0.946
LGA    L      46      L      46          1.869
LGA    E      47      E      47          2.953
LGA    S      48      S      48          1.659
LGA    E      49      E      49           -
LGA    A      50      A      50           -
LGA    R      51      R      51           -
LGA    E      52      E      52           -
LGA    L      53      L      53           -
LGA    A      54      A      54           -
LGA    P      55      P      55           -
LGA    E      56      E      56           -
LGA    E      57      E      57           -
LGA    E      58      E      58           -
LGA    V      59      V      59           -
LGA    K      60      K      60           -
LGA    L      61      L      61           -
LGA    E      62      E      62           -
LGA    H      63      -       -           -
LGA    H      64      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   53   61    5.0     37    1.37    94.59     57.679     2.522

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.801073 * X  +   0.563585 * Y  +   0.201626 * Z  + -16.859682
  Y_new =   0.597362 * X  +   0.774100 * Y  +   0.209590 * Z  +   8.058526
  Z_new =  -0.037958 * X  +   0.288341 * Y  +  -0.956775 * Z  +  81.656494 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.848882   -0.292710  [ DEG:   163.2289    -16.7711 ]
  Theta =   0.037967    3.103626  [ DEG:     2.1753    177.8247 ]
  Phi   =   2.500848   -0.640744  [ DEG:   143.2881    -36.7120 ]
 
# 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_1                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348AL243_1.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   53   61   5.0   37   1.37   94.59  57.679
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL243_1
REMARK Aligment from pdb entry: 1p91A
ATOM      1  N   LEU     9      11.931  35.104  57.534  1.00  0.00              
ATOM      2  CA  LEU     9      10.590  34.733  57.971  1.00  0.00              
ATOM      3  C   LEU     9      10.580  33.930  59.267  1.00  0.00              
ATOM      4  O   LEU     9      11.618  33.517  59.771  1.00  0.00              
ATOM      5  N   VAL    10       9.390  33.732  59.811  1.00  0.00              
ATOM      6  CA  VAL    10       9.250  32.945  61.013  1.00  0.00              
ATOM      7  C   VAL    10       8.393  31.766  60.600  1.00  0.00              
ATOM      8  O   VAL    10       7.745  31.812  59.555  1.00  0.00              
ATOM      9  N   CYS    11       8.384  30.699  61.387  1.00  0.00              
ATOM     10  CA  CYS    11       7.582  29.557  60.983  1.00  0.00              
ATOM     11  C   CYS    11       6.124  29.813  61.281  1.00  0.00              
ATOM     12  O   CYS    11       5.770  30.185  62.390  1.00  0.00              
ATOM     13  N   PRO    12       5.256  29.648  60.278  1.00  0.00              
ATOM     14  CA  PRO    12       3.836  29.875  60.522  1.00  0.00              
ATOM     15  C   PRO    12       3.401  28.993  61.669  1.00  0.00              
ATOM     16  O   PRO    12       2.437  29.314  62.369  1.00  0.00              
ATOM     17  N   LEU    13       4.133  27.894  61.870  1.00  0.00              
ATOM     18  CA  LEU    13       3.817  26.937  62.926  1.00  0.00              
ATOM     19  C   LEU    13       4.618  26.964  64.231  1.00  0.00              
ATOM     20  O   LEU    13       4.010  27.021  65.306  1.00  0.00              
ATOM     21  N   CYS    14       5.950  26.898  64.177  1.00  0.00              
ATOM     22  CA  CYS    14       6.716  26.928  65.427  1.00  0.00              
ATOM     23  C   CYS    14       7.267  28.307  65.710  1.00  0.00              
ATOM     24  O   CYS    14       7.883  28.545  66.755  1.00  0.00              
ATOM     25  N   LYS    15       7.047  29.213  64.766  1.00  0.00              
ATOM     26  CA  LYS    15       7.502  30.581  64.919  1.00  0.00              
ATOM     27  C   LYS    15       9.010  30.709  65.119  1.00  0.00              
ATOM     28  O   LYS    15       9.468  31.566  65.886  1.00  0.00              
ATOM     29  N   GLY    16       9.780  29.850  64.456  1.00  0.00              
ATOM     30  CA  GLY    16      11.231  29.914  64.555  1.00  0.00              
ATOM     31  C   GLY    16      11.768  30.308  63.199  1.00  0.00              
ATOM     32  O   GLY    16      11.112  30.119  62.185  1.00  0.00              
ATOM     33  N   PRO    17      12.970  30.866  63.159  1.00  0.00              
ATOM     34  CA  PRO    17      13.578  31.299  61.909  1.00  0.00              
ATOM     35  C   PRO    17      13.438  30.351  60.741  1.00  0.00              
ATOM     36  O   PRO    17      13.718  29.170  60.857  1.00  0.00              
ATOM     37  N   LEU    18      13.003  30.869  59.606  1.00  0.00              
ATOM     38  CA  LEU    18      12.881  30.030  58.437  1.00  0.00              
ATOM     39  C   LEU    18      14.163  30.124  57.621  1.00  0.00              
ATOM     40  O   LEU    18      14.430  31.135  56.974  1.00  0.00              
ATOM     41  N   VAL    19      14.959  29.064  57.679  1.00  0.00              
ATOM     42  CA  VAL    19      16.206  28.976  56.935  1.00  0.00              
ATOM     43  C   VAL    19      15.818  28.534  55.536  1.00  0.00              
ATOM     44  O   VAL    19      14.909  27.720  55.375  1.00  0.00              
ATOM     45  N   PHE    20      16.490  29.063  54.523  1.00  0.00              
ATOM     46  CA  PHE    20      16.152  28.699  53.152  1.00  0.00              
ATOM     47  C   PHE    20      17.128  27.798  52.416  1.00  0.00              
ATOM     48  O   PHE    20      18.325  28.035  52.471  1.00  0.00              
ATOM     49  N   ASP    21      16.609  26.788  51.708  1.00  0.00              
ATOM     50  CA  ASP    21      17.432  25.862  50.911  1.00  0.00              
ATOM     51  C   ASP    21      16.895  25.878  49.486  1.00  0.00              
ATOM     52  O   ASP    21      15.793  25.424  49.205  1.00  0.00              
ATOM     53  N   LYS    24      17.703  26.423  48.592  1.00  0.00              
ATOM     54  CA  LYS    24      17.344  26.610  47.195  1.00  0.00              
ATOM     55  C   LYS    24      16.017  27.354  47.080  1.00  0.00              
ATOM     56  O   LYS    24      15.997  28.588  47.068  1.00  0.00              
ATOM     57  N   ASP    25      14.910  26.622  46.985  1.00  0.00              
ATOM     58  CA  ASP    25      13.612  27.277  46.873  1.00  0.00              
ATOM     59  C   ASP    25      12.597  26.788  47.871  1.00  0.00              
ATOM     60  O   ASP    25      11.409  26.715  47.590  1.00  0.00              
ATOM     61  N   GLU    26      13.082  26.456  49.052  1.00  0.00              
ATOM     62  CA  GLU    26      12.209  26.004  50.115  1.00  0.00              
ATOM     63  C   GLU    26      12.649  26.681  51.406  1.00  0.00              
ATOM     64  O   GLU    26      13.813  27.061  51.565  1.00  0.00              
ATOM     65  N   LEU    27      11.711  26.860  52.320  1.00  0.00              
ATOM     66  CA  LEU    27      12.033  27.450  53.604  1.00  0.00              
ATOM     67  C   LEU    27      11.836  26.332  54.605  1.00  0.00              
ATOM     68  O   LEU    27      10.828  25.619  54.560  1.00  0.00              
ATOM     69  N   ILE    28      12.815  26.148  55.477  1.00  0.00              
ATOM     70  CA  ILE    28      12.735  25.092  56.464  1.00  0.00              
ATOM     71  C   ILE    28      13.031  25.658  57.806  1.00  0.00              
ATOM     72  O   ILE    28      13.931  26.450  57.925  1.00  0.00              
ATOM     73  N   CYS    29      12.299  25.257  58.827  1.00  0.00              
ATOM     74  CA  CYS    29      12.628  25.749  60.152  1.00  0.00              
ATOM     75  C   CYS    29      13.285  24.638  61.003  1.00  0.00              
ATOM     76  O   CYS    29      13.303  23.459  60.630  1.00  0.00              
ATOM     77  N   GLY    31      13.870  25.017  62.142  1.00  0.00              
ATOM     78  CA  GLY    31      14.515  24.052  63.018  1.00  0.00              
ATOM     79  C   GLY    31      13.753  22.764  63.240  1.00  0.00              
ATOM     80  O   GLY    31      14.363  21.699  63.356  1.00  0.00              
ATOM     81  N   ASP    32      12.427  22.841  63.289  1.00  0.00              
ATOM     82  CA  ASP    32      11.650  21.639  63.527  1.00  0.00              
ATOM     83  C   ASP    32      11.050  21.007  62.292  1.00  0.00              
ATOM     84  O   ASP    32       9.948  20.470  62.318  1.00  0.00              
ATOM     85  N   ARG    33      11.817  21.082  61.210  1.00  0.00              
ATOM     86  CA  ARG    33      11.476  20.469  59.935  1.00  0.00              
ATOM     87  C   ARG    33      10.114  20.796  59.384  1.00  0.00              
ATOM     88  O   ARG    33       9.313  19.905  59.144  1.00  0.00              
ATOM     89  N   LEU    34       9.855  22.088  59.218  1.00  0.00              
ATOM     90  CA  LEU    34       8.617  22.589  58.630  1.00  0.00              
ATOM     91  C   LEU    34       9.143  23.190  57.334  1.00  0.00              
ATOM     92  O   LEU    34      10.014  24.059  57.344  1.00  0.00              
ATOM     93  N   ALA    35       8.648  22.692  56.217  1.00  0.00              
ATOM     94  CA  ALA    35       9.129  23.159  54.932  1.00  0.00              
ATOM     95  C   ALA    35       8.039  23.858  54.144  1.00  0.00              
ATOM     96  O   ALA    35       6.903  23.391  54.091  1.00  0.00              
ATOM     97  N   PHE    36       8.376  25.001  53.560  1.00  0.00              
ATOM     98  CA  PHE    36       7.415  25.726  52.754  1.00  0.00              
ATOM     99  C   PHE    36       8.081  25.996  51.420  1.00  0.00              
ATOM    100  O   PHE    36       9.127  26.629  51.351  1.00  0.00              
ATOM    101  N   PRO    37       7.479  25.486  50.358  1.00  0.00              
ATOM    102  CA  PRO    37       8.029  25.661  49.030  1.00  0.00              
ATOM    103  C   PRO    37       7.519  26.912  48.366  1.00  0.00              
ATOM    104  O   PRO    37       6.473  27.460  48.736  1.00  0.00              
ATOM    105  N   ILE    38       8.274  27.352  47.371  1.00  0.00              
ATOM    106  CA  ILE    38       7.945  28.543  46.612  1.00  0.00              
ATOM    107  C   ILE    38       7.184  28.176  45.374  1.00  0.00              
ATOM    108  O   ILE    38       7.644  27.329  44.626  1.00  0.00              
ATOM    109  N   LYS    39       5.794  28.405  41.573  1.00  0.00              
ATOM    110  CA  LYS    39       6.556  28.692  40.367  1.00  0.00              
ATOM    111  C   LYS    39       6.779  30.164  40.110  1.00  0.00              
ATOM    112  O   LYS    39       7.834  30.548  39.608  1.00  0.00              
ATOM    113  N   ASP    40       5.795  30.984  40.470  1.00  0.00              
ATOM    114  CA  ASP    40       5.877  32.433  40.275  1.00  0.00              
ATOM    115  C   ASP    40       6.872  33.156  41.202  1.00  0.00              
ATOM    116  O   ASP    40       7.473  34.160  40.819  1.00  0.00              
ATOM    117  N   GLY    41       7.028  32.665  42.426  1.00  0.00              
ATOM    118  CA  GLY    41       7.971  33.283  43.339  1.00  0.00              
ATOM    119  C   GLY    41       7.499  33.608  44.742  1.00  0.00              
ATOM    120  O   GLY    41       8.299  34.025  45.573  1.00  0.00              
ATOM    121  N   ILE    42       6.221  33.431  45.041  1.00  0.00              
ATOM    122  CA  ILE    42       5.789  33.761  46.392  1.00  0.00              
ATOM    123  C   ILE    42       6.022  32.635  47.355  1.00  0.00              
ATOM    124  O   ILE    42       6.517  31.594  46.986  1.00  0.00              
ATOM    125  N   PRO    43       5.650  32.847  48.599  1.00  0.00              
ATOM    126  CA  PRO    43       5.850  31.843  49.614  1.00  0.00              
ATOM    127  C   PRO    43       4.544  31.661  50.321  1.00  0.00              
ATOM    128  O   PRO    43       4.151  32.529  51.093  1.00  0.00              
ATOM    129  N   MET    44       3.841  30.564  50.082  1.00  0.00              
ATOM    130  CA  MET    44       2.587  30.425  50.798  1.00  0.00              
ATOM    131  C   MET    44       2.998  30.135  52.216  1.00  0.00              
ATOM    132  O   MET    44       3.993  29.458  52.431  1.00  0.00              
ATOM    133  N   MET    45       2.259  30.647  53.184  1.00  0.00              
ATOM    134  CA  MET    45       2.613  30.424  54.577  1.00  0.00              
ATOM    135  C   MET    45       1.381  30.180  55.428  1.00  0.00              
ATOM    136  O   MET    45       1.433  30.272  56.654  1.00  0.00              
ATOM    137  N   LEU    46       0.273  29.852  54.780  1.00  0.00              
ATOM    138  CA  LEU    46      -0.977  29.624  55.495  1.00  0.00              
ATOM    139  C   LEU    46      -1.093  28.154  55.900  1.00  0.00              
ATOM    140  O   LEU    46      -0.194  27.356  55.604  1.00  0.00              
ATOM    141  N   GLU    47      -2.178  27.788  56.628  1.00  0.00              
ATOM    142  CA  GLU    47      -2.358  26.389  57.020  1.00  0.00              
ATOM    143  C   GLU    47      -2.595  25.602  55.731  1.00  0.00              
ATOM    144  O   GLU    47      -2.321  26.081  54.630  1.00  0.00              
ATOM    145  N   SER    48      -3.141  24.405  55.864  1.00  0.00              
ATOM    146  CA  SER    48      -3.380  23.573  54.693  1.00  0.00              
ATOM    147  C   SER    48      -4.815  23.597  54.133  1.00  0.00              
ATOM    148  O   SER    48      -5.001  23.563  52.912  1.00  0.00              
ATOM    149  N   GLU    49      -5.825  23.685  54.998  1.00  0.00              
ATOM    150  CA  GLU    49      -7.205  23.648  54.511  1.00  0.00              
ATOM    151  C   GLU    49      -8.276  24.313  55.374  1.00  0.00              
ATOM    152  O   GLU    49      -9.294  23.679  55.705  1.00  0.00              
ATOM    153  N   ALA    50      -8.073  25.576  55.741  1.00  0.00              
ATOM    154  CA  ALA    50      -9.101  26.232  56.541  1.00  0.00              
ATOM    155  C   ALA    50      -9.521  27.638  56.095  1.00  0.00              
ATOM    156  O   ALA    50      -8.686  28.547  55.949  1.00  0.00              
ATOM    157  N   ARG    51     -10.834  27.794  55.897  1.00  0.00              
ATOM    158  CA  ARG    51     -11.419  29.056  55.468  1.00  0.00              
ATOM    159  C   ARG    51     -10.866  29.512  54.123  1.00  0.00              
ATOM    160  O   ARG    51     -11.270  30.556  53.603  1.00  0.00              
ATOM    161  N   GLU    52      -9.927  28.741  53.570  1.00  0.00              
ATOM    162  CA  GLU    52      -9.376  29.060  52.254  1.00  0.00              
ATOM    163  C   GLU    52     -10.640  29.072  51.395  1.00  0.00              
ATOM    164  O   GLU    52     -10.836  29.954  50.546  1.00  0.00              
ATOM    165  N   LEU    53     -11.500  28.082  51.672  1.00  0.00              
ATOM    166  CA  LEU    53     -12.822  27.950  51.043  1.00  0.00              
ATOM    167  C   LEU    53     -13.544  29.207  51.545  1.00  0.00              
ATOM    168  O   LEU    53     -13.577  29.488  52.758  1.00  0.00              
ATOM    169  N   ALA    54     -14.126  29.975  50.633  1.00  0.00              
ATOM    170  CA  ALA    54     -14.722  31.201  51.102  1.00  0.00              
ATOM    171  C   ALA    54     -16.015  31.771  50.629  1.00  0.00              
ATOM    172  O   ALA    54     -16.871  31.149  49.965  1.00  0.00              
ATOM    173  N   PRO    55     -12.328  37.936  44.794  1.00  0.00              
ATOM    174  CA  PRO    55     -11.809  36.827  44.015  1.00  0.00              
ATOM    175  C   PRO    55     -11.334  37.391  42.682  1.00  0.00              
ATOM    176  O   PRO    55     -11.717  38.493  42.311  1.00  0.00              
ATOM    177  N   GLU    56     -10.508  36.626  41.978  1.00  0.00              
ATOM    178  CA  GLU    56      -9.942  37.039  40.693  1.00  0.00              
ATOM    179  C   GLU    56     -10.653  38.169  39.964  1.00  0.00              
ATOM    180  O   GLU    56     -10.028  39.149  39.577  1.00  0.00              
ATOM    181  N   GLU    57     -11.956  38.032  39.769  1.00  0.00              
ATOM    182  CA  GLU    57     -12.722  39.054  39.063  1.00  0.00              
ATOM    183  C   GLU    57     -12.475  40.463  39.591  1.00  0.00              
ATOM    184  O   GLU    57     -12.040  41.352  38.853  1.00  0.00              
ATOM    185  N   GLU    58     -12.750  40.657  40.874  1.00  0.00              
ATOM    186  CA  GLU    58     -12.587  41.965  41.485  1.00  0.00              
ATOM    187  C   GLU    58     -11.138  42.391  41.689  1.00  0.00              
ATOM    188  O   GLU    58     -10.822  43.568  41.607  1.00  0.00              
ATOM    189  N   VAL    59     -10.257  41.437  41.955  1.00  0.00              
ATOM    190  CA  VAL    59      -8.847  41.755  42.111  1.00  0.00              
ATOM    191  C   VAL    59      -8.431  42.432  40.802  1.00  0.00              
ATOM    192  O   VAL    59      -7.806  43.486  40.809  1.00  0.00              
ATOM    193  N   LYS    60      -8.816  41.843  39.679  1.00  0.00              
ATOM    194  CA  LYS    60      -8.475  42.399  38.379  1.00  0.00              
ATOM    195  C   LYS    60      -9.066  43.789  38.258  1.00  0.00              
ATOM    196  O   LYS    60      -8.595  44.593  37.458  1.00  0.00              
ATOM    197  N   LEU    61     -10.113  44.065  39.038  1.00  0.00              
ATOM    198  CA  LEU    61     -10.755  45.386  39.022  1.00  0.00              
ATOM    199  C   LEU    61      -9.900  46.362  39.818  1.00  0.00              
ATOM    200  O   LEU    61      -9.294  47.276  39.234  1.00  0.00              
ATOM    201  N   GLU    62      -9.851  46.183  41.146  1.00  0.00              
ATOM    202  CA  GLU    62      -9.026  47.049  41.986  1.00  0.00              
ATOM    203  C   GLU    62      -7.782  47.320  41.152  1.00  0.00              
ATOM    204  O   GLU    62      -7.366  48.462  40.964  1.00  0.00              
ATOM    205  N   HIS    63      -7.220  46.249  40.613  1.00  0.00              
ATOM    206  CA  HIS    63      -6.039  46.378  39.798  1.00  0.00              
ATOM    207  C   HIS    63      -6.269  47.290  38.614  1.00  0.00              
ATOM    208  O   HIS    63      -5.704  48.372  38.540  1.00  0.00              
ATOM    209  N   HIS    64      -7.098  46.861  37.679  1.00  0.00              
ATOM    210  CA  HIS    64      -7.345  47.669  36.502  1.00  0.00              
ATOM    211  C   HIS    64      -7.663  49.124  36.859  1.00  0.00              
ATOM    212  O   HIS    64      -7.296  50.035  36.109  1.00  0.00              
END
