
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0348AL381_1
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348AL381_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          0.615
LGA    C      11      C      11          1.035
LGA    P      12      P      12          1.253
LGA    L      13      L      13          1.393
LGA    C      14      C      14          2.605
LGA    K      15      K      15          3.313
LGA    G      16      G      16          1.616
LGA    P      17      P      17          1.933
LGA    L      18      L      18          0.830
LGA    V      19      V      19          0.423
LGA    F      20      F      20          0.478
LGA    D      21      D      21          0.875
LGA    K      22      K      22          0.631
LGA    S      23      S      23          0.631
LGA    K      24      K      24          1.341
LGA    D      25      D      25          0.978
LGA    E      26      E      26          0.852
LGA    L      27      L      27          0.797
LGA    I      28      I      28          1.225
LGA    C      29      C      29          0.688
LGA    K      30      K      30          2.140
LGA    G      31      G      31          1.157
LGA    D      32      D      32          0.520
LGA    R      33      R      33          1.457
LGA    L      34      L      34          1.590
LGA    P      37      A      35          1.912
LGA    I      38      F      36          2.416
LGA    K      39      P      37          2.381
LGA    D      40      I      38          3.138
LGA    G      41      K      39          2.641
LGA    I      42      D      40          4.502
LGA    P      43      G      41          3.393
LGA    M      44      I      42           -
LGA    M      45      P      43           -
LGA    -       -      M      44           -
LGA    -       -      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)   34   61    5.0     32    1.87    78.12     47.915     1.621

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.019635 * X  +  -0.402085 * Y  +   0.915392 * Z  +   9.785436
  Y_new =  -0.893826 * X  +  -0.417298 * Y  +  -0.164126 * Z  +  29.738909
  Z_new =   0.447984 * X  +  -0.814979 * Y  +  -0.367588 * Z  +  50.792953 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.994515    1.147078  [ DEG:  -114.2773     65.7227 ]
  Theta =  -0.464509   -2.677084  [ DEG:   -26.6144   -153.3856 ]
  Phi   =  -1.548833    1.592760  [ DEG:   -88.7416     91.2584 ]
 
# 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: T0348AL381_1                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348AL381_1.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34   61   5.0   32   1.87   78.12  47.915
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL381_1
REMARK Aligment from pdb entry: 1pft
ATOM      1  N   VAL    10       8.291  34.013  59.595  1.00  0.00              
ATOM      2  CA  VAL    10       8.488  33.093  60.699  1.00  0.00              
ATOM      3  C   VAL    10       7.858  31.736  60.403  1.00  0.00              
ATOM      4  O   VAL    10       7.455  31.448  59.278  1.00  0.00              
ATOM      5  N   CYS    11       7.683  30.954  61.465  1.00  0.00              
ATOM      6  CA  CYS    11       6.882  29.747  61.416  1.00  0.00              
ATOM      7  C   CYS    11       5.520  30.004  62.116  1.00  0.00              
ATOM      8  O   CYS    11       5.394  29.812  63.338  1.00  0.00              
ATOM      9  N   PRO    12       4.464  29.988  61.268  1.00  0.00              
ATOM     10  CA  PRO    12       3.059  29.953  61.739  1.00  0.00              
ATOM     11  C   PRO    12       2.673  28.650  62.437  1.00  0.00              
ATOM     12  O   PRO    12       1.532  28.491  62.873  1.00  0.00              
ATOM     13  N   LEU    13       3.527  27.644  62.250  1.00  0.00              
ATOM     14  CA  LEU    13       3.250  26.303  62.745  1.00  0.00              
ATOM     15  C   LEU    13       3.625  26.189  64.217  1.00  0.00              
ATOM     16  O   LEU    13       2.763  26.216  65.094  1.00  0.00              
ATOM     17  N   CYS    14       4.932  26.122  64.482  1.00  0.00              
ATOM     18  CA  CYS    14       5.405  25.669  65.787  1.00  0.00              
ATOM     19  C   CYS    14       5.726  26.831  66.708  1.00  0.00              
ATOM     20  O   CYS    14       6.178  26.626  67.842  1.00  0.00              
ATOM     21  N   LYS    15       5.666  28.046  66.171  1.00  0.00              
ATOM     22  CA  LYS    15       6.320  29.202  66.785  1.00  0.00              
ATOM     23  C   LYS    15       7.823  28.966  66.882  1.00  0.00              
ATOM     24  O   LYS    15       8.370  28.732  67.956  1.00  0.00              
ATOM     25  N   GLY    16      10.872  31.072  64.905  1.00  0.00              
ATOM     26  CA  GLY    16      11.097  32.158  63.958  1.00  0.00              
ATOM     27  C   GLY    16      12.259  31.856  63.016  1.00  0.00              
ATOM     28  O   GLY    16      12.549  32.638  62.109  1.00  0.00              
ATOM     29  N   PRO    17      13.055  30.864  63.403  1.00  0.00              
ATOM     30  CA  PRO    17      14.173  30.421  62.578  1.00  0.00              
ATOM     31  C   PRO    17      13.661  29.560  61.422  1.00  0.00              
ATOM     32  O   PRO    17      13.479  28.353  61.575  1.00  0.00              
ATOM     33  N   LEU    18      13.651  30.156  60.235  1.00  0.00              
ATOM     34  CA  LEU    18      13.458  29.410  58.998  1.00  0.00              
ATOM     35  C   LEU    18      14.758  29.356  58.202  1.00  0.00              
ATOM     36  O   LEU    18      15.742  30.003  58.554  1.00  0.00              
ATOM     37  N   VAL    19      14.689  28.701  57.046  1.00  0.00              
ATOM     38  CA  VAL    19      15.871  28.474  56.226  1.00  0.00              
ATOM     39  C   VAL    19      15.470  28.193  54.781  1.00  0.00              
ATOM     40  O   VAL    19      14.330  27.824  54.504  1.00  0.00              
ATOM     41  N   PHE    20      16.379  28.513  53.866  1.00  0.00              
ATOM     42  CA  PHE    20      16.072  28.517  52.442  1.00  0.00              
ATOM     43  C   PHE    20      16.584  27.238  51.785  1.00  0.00              
ATOM     44  O   PHE    20      17.328  26.472  52.396  1.00  0.00              
ATOM     45  N   ASP    21      16.016  26.931  50.623  1.00  0.00              
ATOM     46  CA  ASP    21      16.263  25.668  49.950  1.00  0.00              
ATOM     47  C   ASP    21      16.370  25.900  48.429  1.00  0.00              
ATOM     48  O   ASP    21      15.391  25.760  47.682  1.00  0.00              
ATOM     49  N   LYS    22      17.562  26.364  48.003  1.00  0.00              
ATOM     50  CA  LYS    22      17.791  26.814  46.607  1.00  0.00              
ATOM     51  C   LYS    22      17.555  25.718  45.567  1.00  0.00              
ATOM     52  O   LYS    22      17.599  25.976  44.365  1.00  0.00              
ATOM     53  N   SER    23      17.572  24.480  46.048  1.00  0.00              
ATOM     54  CA  SER    23      17.476  23.314  45.179  1.00  0.00              
ATOM     55  C   SER    23      16.038  23.143  44.687  1.00  0.00              
ATOM     56  O   SER    23      15.802  23.010  43.487  1.00  0.00              
ATOM     57  N   LYS    24      15.102  23.442  45.583  1.00  0.00              
ATOM     58  CA  LYS    24      13.686  23.366  45.263  1.00  0.00              
ATOM     59  C   LYS    24      13.118  24.762  45.020  1.00  0.00              
ATOM     60  O   LYS    24      12.039  24.911  44.450  1.00  0.00              
ATOM     61  N   ASP    25      13.781  25.754  45.603  1.00  0.00              
ATOM     62  CA  ASP    25      13.241  27.105  45.677  1.00  0.00              
ATOM     63  C   ASP    25      12.327  27.246  46.891  1.00  0.00              
ATOM     64  O   ASP    25      11.258  27.847  46.809  1.00  0.00              
ATOM     65  N   GLU    26      12.707  26.570  47.970  1.00  0.00              
ATOM     66  CA  GLU    26      11.828  26.403  49.123  1.00  0.00              
ATOM     67  C   GLU    26      12.334  27.244  50.293  1.00  0.00              
ATOM     68  O   GLU    26      13.514  27.586  50.356  1.00  0.00              
ATOM     69  N   LEU    27      11.472  27.405  51.291  1.00  0.00              
ATOM     70  CA  LEU    27      11.876  27.955  52.578  1.00  0.00              
ATOM     71  C   LEU    27      11.169  27.218  53.713  1.00  0.00              
ATOM     72  O   LEU    27       9.944  27.223  53.802  1.00  0.00              
ATOM     73  N   ILE    28      11.962  26.543  54.535  1.00  0.00              
ATOM     74  CA  ILE    28      11.434  25.612  55.521  1.00  0.00              
ATOM     75  C   ILE    28      11.603  26.192  56.928  1.00  0.00              
ATOM     76  O   ILE    28      12.442  27.066  57.142  1.00  0.00              
ATOM     77  N   CYS    29      10.988  25.520  57.893  1.00  0.00              
ATOM     78  CA  CYS    29      11.303  25.726  59.303  1.00  0.00              
ATOM     79  C   CYS    29      12.667  25.121  59.628  1.00  0.00              
ATOM     80  O   CYS    29      13.025  24.066  59.109  1.00  0.00              
ATOM     81  N   LYS    30      13.328  25.713  60.617  1.00  0.00              
ATOM     82  CA  LYS    30      14.557  25.159  61.163  1.00  0.00              
ATOM     83  C   LYS    30      14.267  24.405  62.462  1.00  0.00              
ATOM     84  O   LYS    30      15.138  24.283  63.321  1.00  0.00              
ATOM     85  N   GLY    31      12.982  24.141  62.681  1.00  0.00              
ATOM     86  CA  GLY    31      12.522  23.546  63.925  1.00  0.00              
ATOM     87  C   GLY    31      11.661  22.321  63.654  1.00  0.00              
ATOM     88  O   GLY    31      12.149  21.188  63.697  1.00  0.00              
ATOM     89  N   ASP    32      10.469  22.565  63.100  1.00  0.00              
ATOM     90  CA  ASP    32       9.481  21.500  62.963  1.00  0.00              
ATOM     91  C   ASP    32       9.644  20.750  61.648  1.00  0.00              
ATOM     92  O   ASP    32       8.908  19.797  61.378  1.00  0.00              
ATOM     93  N   ARG    33      10.392  21.370  60.730  1.00  0.00              
ATOM     94  CA  ARG    33      10.644  20.765  59.430  1.00  0.00              
ATOM     95  C   ARG    33       9.742  21.365  58.351  1.00  0.00              
ATOM     96  O   ARG    33       9.720  20.871  57.219  1.00  0.00              
ATOM     97  N   LEU    34       8.758  22.134  58.821  1.00  0.00              
ATOM     98  CA  LEU    34       7.661  22.586  57.979  1.00  0.00              
ATOM     99  C   LEU    34       8.179  23.554  56.915  1.00  0.00              
ATOM    100  O   LEU    34       8.625  24.655  57.243  1.00  0.00              
ATOM    101  N   PRO    37       7.854  23.244  55.662  1.00  0.00              
ATOM    102  CA  PRO    37       8.032  24.181  54.564  1.00  0.00              
ATOM    103  C   PRO    37       7.189  25.437  54.799  1.00  0.00              
ATOM    104  O   PRO    37       6.152  25.378  55.459  1.00  0.00              
ATOM    105  N   ILE    38       7.470  26.446  53.982  1.00  0.00              
ATOM    106  CA  ILE    38       6.676  27.667  53.957  1.00  0.00              
ATOM    107  C   ILE    38       6.046  27.845  52.575  1.00  0.00              
ATOM    108  O   ILE    38       4.920  27.407  52.342  1.00  0.00              
ATOM    109  N   LYS    39       6.877  28.263  51.625  1.00  0.00              
ATOM    110  CA  LYS    39       6.546  28.160  50.207  1.00  0.00              
ATOM    111  C   LYS    39       7.647  27.399  49.469  1.00  0.00              
ATOM    112  O   LYS    39       8.681  27.077  50.052  1.00  0.00              
ATOM    113  N   ASP    40       7.279  26.882  48.301  1.00  0.00              
ATOM    114  CA  ASP    40       8.189  26.073  47.500  1.00  0.00              
ATOM    115  C   ASP    40       7.838  26.204  46.017  1.00  0.00              
ATOM    116  O   ASP    40       7.980  25.243  45.257  1.00  0.00              
ATOM    117  N   GLY    41       7.678  27.453  45.587  1.00  0.00              
ATOM    118  CA  GLY    41       7.563  27.773  44.171  1.00  0.00              
ATOM    119  C   GLY    41       7.909  29.239  43.928  1.00  0.00              
ATOM    120  O   GLY    41       7.066  30.023  43.497  1.00  0.00              
ATOM    121  N   ILE    42       9.114  29.614  44.343  1.00  0.00              
ATOM    122  CA  ILE    42       9.516  31.013  44.379  1.00  0.00              
ATOM    123  C   ILE    42       9.831  31.513  42.973  1.00  0.00              
ATOM    124  O   ILE    42      10.993  31.679  42.606  1.00  0.00              
ATOM    125  N   PRO    43       8.793  31.545  42.139  1.00  0.00              
ATOM    126  CA  PRO    43       8.919  32.068  40.785  1.00  0.00              
ATOM    127  C   PRO    43       7.547  32.172  40.126  1.00  0.00              
ATOM    128  O   PRO    43       6.665  31.354  40.377  1.00  0.00              
ATOM    129  N   MET    44       7.438  33.101  39.183  1.00  0.00              
ATOM    130  CA  MET    44       6.267  33.192  38.322  1.00  0.00              
ATOM    131  C   MET    44       6.583  34.024  37.082  1.00  0.00              
ATOM    132  O   MET    44       6.045  35.114  36.902  1.00  0.00              
ATOM    133  N   MET    45       7.336  33.419  36.169  1.00  0.00              
ATOM    134  CA  MET    45       7.548  33.987  34.845  1.00  0.00              
ATOM    135  C   MET    45       7.284  32.936  33.770  1.00  0.00              
ATOM    136  O   MET    45       6.352  33.069  32.978  1.00  0.00              
END
