
#######################################################
#                                                     #
#                        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 T0348TS307_5u
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS307_5u.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    F       5      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    L       6      F       5           #
LGA    E       7      L       6          4.386
LGA    I       8      E       7          2.042
LGA    L       9      I       8          2.422
LGA    -       -      L       9           -
LGA    V      10      V      10          0.812
LGA    C      11      C      11          1.086
LGA    P      12      P      12          1.320
LGA    L      13      L      13          1.179
LGA    C      14      C      14          1.711
LGA    K      15      K      15          2.234
LGA    G      16      G      16          1.403
LGA    P      17      P      17          2.712
LGA    L      18      L      18          0.729
LGA    V      19      V      19          0.430
LGA    F      20      F      20          0.845
LGA    D      21      D      21          0.991
LGA    K      22      K      22          1.082
LGA    S      23      S      23          1.086
LGA    K      24      K      24          1.215
LGA    D      25      D      25          1.081
LGA    E      26      E      26          1.081
LGA    L      27      L      27          1.156
LGA    I      28      I      28          1.293
LGA    C      29      C      29          1.085
LGA    K      30      K      30          2.395
LGA    G      31      G      31          1.546
LGA    D      32      D      32          0.696
LGA    R      33      R      33          1.820
LGA    L      34      L      34          2.086
LGA    A      35      A      35          2.127
LGA    I      38      F      36          2.610
LGA    K      39      P      37          2.384
LGA    D      40      I      38          3.183
LGA    G      41      K      39          3.122
LGA    -       -      D      40           -
LGA    I      42      G      41          3.103
LGA    M      44      I      42           #
LGA    M      45      P      43           -
LGA    L      46      M      44           -
LGA    E      47      M      45           -
LGA    S      48      L      46           -
LGA    E      49      E      47           -
LGA    A      50      S      48           -
LGA    R      51      E      49           -
LGA    E      52      A      50           -
LGA    L      53      R      51           -
LGA    A      54      E      52           -
LGA    P      55      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     34    1.93    76.47     50.502     1.672

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.045438 * X  +  -0.416155 * Y  +   0.908158 * Z  +  10.274912
  Y_new =  -0.870339 * X  +  -0.429747 * Y  +  -0.240474 * Z  +  29.764105
  Z_new =   0.490353 * X  +  -0.801332 * Y  +  -0.342668 * Z  +  50.377068 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.974887    1.166705  [ DEG:  -113.1527     66.8473 ]
  Theta =  -0.512495   -2.629098  [ DEG:   -29.3638   -150.6362 ]
  Phi   =  -1.622957    1.518636  [ DEG:   -92.9886     87.0114 ]
 
# 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: T0348TS307_5u                                 
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS307_5u.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   34   1.93   76.47  50.502
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS307_5u
PFRMAT   TS
TARGET   T0348
MODEL    5  UNREFINED
PARENT   1pft
ATOM     1   N   PHE     5      -0.528  37.214  53.119  1.00                    
ATOM     1   CA  PHE     5      -1.411  37.948  54.015  1.00                    
ATOM     1   C   PHE     5      -0.639  38.431  55.240  1.00                    
ATOM     1   O   PHE     5       0.069  37.658  55.884  1.00                    
ATOM     1   N   LEU     6      -0.668  39.743  55.450  1.00                    
ATOM     1   CA  LEU     6       0.210  40.389  56.417  1.00                    
ATOM     1   C   LEU     6       1.652  40.367  55.920  1.00                    
ATOM     1   O   LEU     6       1.905  40.370  54.716  1.00                    
ATOM     1   N   GLU     7       2.584  40.442  56.865  1.00                    
ATOM     1   CA  GLU     7       3.987  40.669  56.544  1.00                    
ATOM     1   C   GLU     7       4.524  39.536  55.674  1.00                    
ATOM     1   O   GLU     7       5.312  39.761  54.760  1.00                    
ATOM     1   N   ILE     8       4.165  38.313  56.050  1.00                    
ATOM     1   CA  ILE     8       4.732  37.121  55.435  1.00                    
ATOM     1   C   ILE     8       6.207  36.985  55.798  1.00                    
ATOM     1   O   ILE     8       7.086  37.366  55.027  1.00                    
ATOM     1   N   LEU     9       6.459  36.350  56.937  1.00                    
ATOM     1   CA  LEU     9       7.803  35.922  57.300  1.00                    
ATOM     1   C   LEU     9       7.746  34.948  58.475  1.00                    
ATOM     1   O   LEU     9       6.707  34.321  58.710  1.00                    
ATOM     1   N   VAL    10       8.930  34.550  58.936  1.00                    
ATOM     1   CA  VAL    10       9.051  33.674  60.086  1.00                    
ATOM     1   C   VAL    10       8.337  32.347  59.844  1.00                    
ATOM     1   O   VAL    10       7.933  32.031  58.727  1.00                    
ATOM     1   N   CYS    11       8.096  31.631  60.939  1.00                    
ATOM     1   CA  CYS    11       7.219  30.476  60.933  1.00                    
ATOM     1   C   CYS    11       5.867  30.855  61.596  1.00                    
ATOM     1   O   CYS    11       5.710  30.731  62.823  1.00                    
ATOM     1   N   PRO    12       4.824  30.865  60.730  1.00                    
ATOM     1   CA  PRO    12       3.413  30.945  61.177  1.00                    
ATOM     1   C   PRO    12       2.932  29.704  61.928  1.00                    
ATOM     1   O   PRO    12       1.777  29.641  62.351  1.00                    
ATOM     1   N   LEU    13       3.721  28.638  61.806  1.00                    
ATOM     1   CA  LEU    13       3.350  27.343  62.359  1.00                    
ATOM     1   C   LEU    13       3.695  27.277  63.841  1.00                    
ATOM     1   O   LEU    13       2.823  27.402  64.700  1.00                    
ATOM     1   N   CYS    14       4.991  27.139  64.132  1.00                    
ATOM     1   CA  CYS    14       5.414  26.720  65.466  1.00                    
ATOM     1   C   CYS    14       5.796  27.903  66.336  1.00                    
ATOM     1   O   CYS    14       6.217  27.725  67.486  1.00                    
ATOM     1   N   LYS    15       5.823  29.091  65.741  1.00                    
ATOM     1   CA  LYS    15       6.542  30.232  66.311  1.00                    
ATOM     1   C   LYS    15       8.025  29.904  66.447  1.00                    
ATOM     1   O   LYS    15       8.539  29.688  67.540  1.00                    
ATOM     1   N   GLY    16       8.688  29.785  65.297  1.00                    
ATOM     1   CA  GLY    16      10.142  29.721  65.257  1.00                    
ATOM     1   C   GLY    16      10.675  30.552  64.092  1.00                    
ATOM     1   O   GLY    16      10.458  30.216  62.929  1.00                    
ATOM     1   N   PRO    17      11.233  31.710  64.427  1.00                    
ATOM     1   CA  PRO    17      11.543  32.733  63.433  1.00                    
ATOM     1   C   PRO    17      12.698  32.311  62.529  1.00                    
ATOM     1   O   PRO    17      13.051  33.027  61.590  1.00                    
ATOM     1   N   LEU    18      14.017  30.391  59.857  1.00                    
ATOM     1   CA  LEU    18      13.795  29.599  58.653  1.00                    
ATOM     1   C   LEU    18      15.100  29.423  57.885  1.00                    
ATOM     1   O   LEU    18      16.119  30.021  58.223  1.00                    
ATOM     1   N   VAL    19      15.006  28.719  56.761  1.00                    
ATOM     1   CA  VAL    19      16.183  28.376  55.974  1.00                    
ATOM     1   C   VAL    19      15.786  28.052  54.537  1.00                    
ATOM     1   O   VAL    19      14.629  27.744  54.257  1.00                    
ATOM     1   N   PHE    20      16.727  28.267  53.624  1.00                    
ATOM     1   CA  PHE    20      16.443  28.221  52.197  1.00                    
ATOM     1   C   PHE    20      16.880  26.882  51.611  1.00                    
ATOM     1   O   PHE    20      17.563  26.100  52.271  1.00                    
ATOM     1   N   ASP    21      16.311  26.556  50.454  1.00                    
ATOM     1   CA  ASP    21      16.485  25.249  49.847  1.00                    
ATOM     1   C   ASP    21      16.630  25.398  48.319  1.00                    
ATOM     1   O   ASP    21      15.655  25.285  47.561  1.00                    
ATOM     1   N   LYS    22      17.856  25.764  47.893  1.00                    
ATOM     1   CA  LYS    22      18.135  26.129  46.481  1.00                    
ATOM     1   C   LYS    22      17.843  25.001  45.490  1.00                    
ATOM     1   O   LYS    22      17.922  25.197  44.279  1.00                    
ATOM     1   N   SER    23      17.772  23.789  46.030  1.00                    
ATOM     1   CA  SER    23      17.614  22.591  45.216  1.00                    
ATOM     1   C   SER    23      16.175  22.489  44.706  1.00                    
ATOM     1   O   SER    23      15.949  22.313  43.510  1.00                    
ATOM     1   N   LYS    24      15.247  22.891  45.571  1.00                    
ATOM     1   CA  LYS    24      13.834  22.891  45.229  1.00                    
ATOM     1   C   LYS    24      13.362  24.307  44.909  1.00                    
ATOM     1   O   LYS    24      12.304  24.498  44.313  1.00                    
ATOM     1   N   ASP    25      14.079  25.282  45.456  1.00                    
ATOM     1   CA  ASP    25      13.628  26.667  45.456  1.00                    
ATOM     1   C   ASP    25      12.707  26.926  46.645  1.00                    
ATOM     1   O   ASP    25      11.681  27.590  46.515  1.00                    
ATOM     1   N   GLU    26      13.026  26.280  47.762  1.00                    
ATOM     1   CA  GLU    26      12.120  26.226  48.905  1.00                    
ATOM     1   C   GLU    26      12.662  27.089  50.043  1.00                    
ATOM     1   O   GLU    26      13.861  27.356  50.111  1.00                    
ATOM     1   N   LEU    27      11.798  27.354  51.016  1.00                    
ATOM     1   CA  LEU    27      12.217  27.939  52.283  1.00                    
ATOM     1   C   LEU    27      11.447  27.305  53.438  1.00                    
ATOM     1   O   LEU    27      10.224  27.393  53.505  1.00                    
ATOM     1   N   ILE    28      12.182  26.620  54.306  1.00                    
ATOM     1   CA  ILE    28      11.579  25.775  55.326  1.00                    
ATOM     1   C   ILE    28      11.765  26.411  56.706  1.00                    
ATOM     1   O   ILE    28      12.656  27.239  56.893  1.00                    
ATOM     1   N   CYS    29      11.092  25.828  57.690  1.00                    
ATOM     1   CA  CYS    29      11.400  26.081  59.095  1.00                    
ATOM     1   C   CYS    29      12.716  25.406  59.473  1.00                    
ATOM     1   O   CYS    29      13.013  24.306  59.012  1.00                    
ATOM     1   N   LYS    30      13.399  26.002  60.445  1.00                    
ATOM     1   CA  LYS    30      14.581  25.397  61.039  1.00                    
ATOM     1   C   LYS    30      14.224  24.727  62.366  1.00                    
ATOM     1   O   LYS    30      15.072  24.592  63.246  1.00                    
ATOM     1   N   GLY    31      12.921  24.558  62.575  1.00                    
ATOM     1   CA  GLY    31      12.404  24.055  63.837  1.00                    
ATOM     1   C   GLY    31      11.469  22.876  63.609  1.00                    
ATOM     1   O   GLY    31      11.882  21.718  63.715  1.00                    
ATOM     1   N   ASP    32      10.304  23.169  63.022  1.00                    
ATOM     1   CA  ASP    32       9.251  22.165  62.918  1.00                    
ATOM     1   C   ASP    32       9.385  21.342  61.644  1.00                    
ATOM     1   O   ASP    32       8.592  20.427  61.406  1.00                    
ATOM     1   N   ARG    33      10.185  21.868  60.711  1.00                    
ATOM     1   CA  ARG    33      10.417  21.186  59.446  1.00                    
ATOM     1   C   ARG    33       9.572  21.789  58.324  1.00                    
ATOM     1   O   ARG    33       9.535  21.242  57.216  1.00                    
ATOM     1   N   LEU    34       8.633  22.641  58.738  1.00                    
ATOM     1   CA  LEU    34       7.581  23.121  57.856  1.00                    
ATOM     1   C   LEU    34       8.176  24.001  56.756  1.00                    
ATOM     1   O   LEU    34       8.688  25.086  57.040  1.00                    
ATOM     1   N   ALA    35       7.851  23.652  55.514  1.00                    
ATOM     1   CA  ALA    35       8.106  24.521  54.376  1.00                    
ATOM     1   C   ALA    35       7.344  25.839  54.536  1.00                    
ATOM     1   O   ALA    35       6.296  25.879  55.179  1.00                    
ATOM     1   N   ILE    38       7.702  26.786  53.677  1.00                    
ATOM     1   CA  ILE    38       6.990  28.054  53.579  1.00                    
ATOM     1   C   ILE    38       6.394  28.204  52.179  1.00                    
ATOM     1   O   ILE    38       5.245  27.829  51.947  1.00                    
ATOM     1   N   LYS    39       7.264  28.521  51.226  1.00                    
ATOM     1   CA  LYS    39       6.948  28.371  49.808  1.00                    
ATOM     1   C   LYS    39       8.008  27.506  49.128  1.00                    
ATOM     1   O   LYS    39       9.010  27.146  49.744  1.00                    
ATOM     1   N   ASP    40       7.626  26.956  47.979  1.00                    
ATOM     1   CA  ASP    40       8.493  26.053  47.234  1.00                    
ATOM     1   C   ASP    40       8.173  26.133  45.740  1.00                    
ATOM     1   O   ASP    40       8.263  25.129  45.030  1.00                    
ATOM     1   N   GLY    41       8.102  27.367  45.249  1.00                    
ATOM     1   CA  GLY    41       8.028  27.625  43.817  1.00                    
ATOM     1   C   GLY    41       8.473  29.052  43.511  1.00                    
ATOM     1   O   GLY    41       7.690  29.867  43.028  1.00                    
ATOM     1   N   ILE    42       9.694  29.369  43.930  1.00                    
ATOM     1   CA  ILE    42      10.186  30.739  43.905  1.00                    
ATOM     1   C   ILE    42      10.553  31.148  42.483  1.00                    
ATOM     1   O   ILE    42      11.729  31.221  42.130  1.00                    
ATOM     1   N   MET    44       9.532  31.207  41.630  1.00                    
ATOM     1   CA  MET    44       9.712  31.653  40.255  1.00                    
ATOM     1   C   MET    44       8.361  31.813  39.567  1.00                    
ATOM     1   O   MET    44       7.423  31.067  39.841  1.00                    
ATOM     1   N   MET    45       8.326  32.700  38.579  1.00                    
ATOM     1   CA  MET    45       7.177  32.825  37.694  1.00                    
ATOM     1   C   MET    45       7.565  33.573  36.422  1.00                    
ATOM     1   O   MET    45       7.102  34.686  36.180  1.00                    
ATOM     1   N   LEU    46       8.291  32.878  35.553  1.00                    
ATOM     1   CA  LEU    46       8.559  33.365  34.207  1.00                    
ATOM     1   C   LEU    46       8.243  32.282  33.178  1.00                    
ATOM     1   O   LEU    46       7.334  32.436  32.364  1.00                    
ATOM     1   N   GLU    47       8.872  31.126  33.360  1.00                    
ATOM     1   CA  GLU    47       8.550  29.940  32.587  1.00                    
ATOM     1   C   GLU    47       9.231  30.011  31.207  1.00                    
ATOM     1   O   GLU    47       8.580  30.193  30.168  1.00                    
ATOM     1   N   SER    48      10.577  29.927  31.226  1.00                    
ATOM     1   CA  SER    48      11.384  29.835  29.981  1.00                    
ATOM     1   C   SER    48      11.024  28.637  29.108  1.00                    
ATOM     1   O   SER    48      10.381  28.781  28.071  1.00                    
ATOM     1   N   GLU    49      11.271  27.447  29.653  1.00                    
ATOM     1   CA  GLU    49      11.062  26.212  28.907  1.00                    
ATOM     1   C   GLU    49      10.868  25.044  29.875  1.00                    
ATOM     1   O   GLU    49      11.830  24.373  30.245  1.00                    
ATOM     1   N   ALA    50       9.663  24.960  30.427  1.00                    
ATOM     1   CA  ALA    50       9.386  24.076  31.550  1.00                    
ATOM     1   C   ALA    50       7.926  23.635  31.533  1.00                    
ATOM     1   O   ALA    50       7.623  22.452  31.678  1.00                    
ATOM     1   N   ARG    51       7.051  24.581  31.210  1.00                    
ATOM     1   CA  ARG    51       5.647  24.281  30.964  1.00                    
ATOM     1   C   ARG    51       5.322  24.445  29.482  1.00                    
ATOM     1   O   ARG    51       5.733  25.418  28.851  1.00                    
ATOM     1   N   GLU    52       4.372  23.632  29.023  1.00                    
ATOM     1   CA  GLU    52       3.945  23.665  27.632  1.00                    
ATOM     1   C   GLU    52       5.110  23.315  26.710  1.00                    
ATOM     1   O   GLU    52       6.242  23.739  26.932  1.00                    
ATOM     1   N   LEU    53       4.841  22.409  25.775  1.00                    
ATOM     1   CA  LEU    53       5.818  22.051  24.756  1.00                    
ATOM     1   C   LEU    53       5.180  22.089  23.371  1.00                    
ATOM     1   O   LEU    53       3.962  21.998  23.234  1.00                    
ATOM     1   N   ALA    54       6.000  22.434  22.381  1.00                    
ATOM     1   CA  ALA    54       5.554  22.459  20.995  1.00                    
ATOM     1   C   ALA    54       6.748  22.600  20.056  1.00                    
ATOM     1   O   ALA    54       7.505  23.565  20.142  1.00                    
ATOM     1   N   PRO    55       6.809  21.707  19.074  1.00                    
ATOM     1   CA  PRO    55       7.755  21.834  17.973  1.00                    
ATOM     1   C   PRO    55       9.187  21.793  18.500  1.00                    
ATOM     1   O   PRO    55      10.131  21.751  17.697  1.00                    
TER
END
