
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0349AL243_4-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL243_4-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    D       9      D       9          3.949
LGA    A      10      A      10          5.083
LGA    V      11      V      11          2.144
LGA    L      12      L      12          1.390
LGA    L      13      L      13          0.660
LGA    S      14      S      14          0.689
LGA    A      15      A      15          0.944
LGA    V      16      V      16          1.034
LGA    G      17      G      17          1.176
LGA    A      18      A      18          1.469
LGA    L      19      L      19          1.546
LGA    L      20      L      20          1.779
LGA    D      21      D      21          2.110
LGA    G      22      G      22          2.418
LGA    A      23      A      23          2.816
LGA    D      24      D      24          2.320
LGA    I      25      I      25          2.113
LGA    G      26      G      26          1.922
LGA    H      27      H      27          2.507
LGA    L      28      L      28          3.878
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    V      29      L      49           #
LGA    V      48      V      50          1.516
LGA    L      49      H      51          0.486
LGA    V      50      E      52          5.188
LGA    H      51      D      53          2.615
LGA    E      52      -       -           -
LGA    D      53      -       -           -
LGA    D      54      D      54          3.228
LGA    L      55      L      55          2.786
LGA    A      56      A      56          2.522
LGA    G      57      G      57          2.075
LGA    A      58      A      58          1.083
LGA    R      59      R      59          1.712
LGA    R      60      R      60          0.848
LGA    L      61      L      61          1.885
LGA    L      62      L      62          1.356
LGA    T      63      T      63          2.517
LGA    D      64      D      64          4.098
LGA    -       -      A      65           -
LGA    L      67      G      66          1.985
LGA    A      68      L      67          2.564
LGA    -       -      A      68           -
LGA    H      69      H      69          5.299
LGA    E      70      E      70           -
LGA    L      71      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   57    5.0     38    2.57    86.84     49.663     1.426

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.233012 * X  +  -0.860709 * Y  +   0.452642 * Z  +  -6.163530
  Y_new =   0.864523 * X  +  -0.029801 * Y  +  -0.501709 * Z  + -19.679201
  Z_new =   0.445315 * X  +   0.508224 * Y  +   0.737159 * Z  + -61.730251 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.603601   -2.537992  [ DEG:    34.5838   -145.4162 ]
  Theta =  -0.461526   -2.680066  [ DEG:   -26.4435   -153.5565 ]
  Phi   =   1.307525   -1.834067  [ DEG:    74.9157   -105.0843 ]
 
# 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: T0349AL243_4-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL243_4-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   57   5.0   38   2.57   86.84  49.663
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL243_4-D1
REMARK Aligment from pdb entry: 1u8sA
ATOM      1  N   ASP     9       0.424 -10.734   7.145  1.00  0.00              
ATOM      2  CA  ASP     9      -0.979 -10.374   7.080  1.00  0.00              
ATOM      3  C   ASP     9      -1.714 -10.574   8.401  1.00  0.00              
ATOM      4  O   ASP     9      -1.830 -11.688   8.911  1.00  0.00              
ATOM      5  N   ALA    10      -5.107  -8.504  10.880  1.00  0.00              
ATOM      6  CA  ALA    10      -6.269  -7.633  10.688  1.00  0.00              
ATOM      7  C   ALA    10      -5.994  -6.155  10.963  1.00  0.00              
ATOM      8  O   ALA    10      -5.226  -5.809  11.865  1.00  0.00              
ATOM      9  N   VAL    11      -6.630  -5.293  10.172  1.00  0.00              
ATOM     10  CA  VAL    11      -6.455  -3.863  10.344  1.00  0.00              
ATOM     11  C   VAL    11      -5.096  -3.332   9.925  1.00  0.00              
ATOM     12  O   VAL    11      -4.852  -2.127   9.985  1.00  0.00              
ATOM     13  N   LEU    12      -4.205  -4.219   9.495  1.00  0.00              
ATOM     14  CA  LEU    12      -2.885  -3.775   9.076  1.00  0.00              
ATOM     15  C   LEU    12      -3.019  -2.759   7.937  1.00  0.00              
ATOM     16  O   LEU    12      -2.328  -1.744   7.924  1.00  0.00              
ATOM     17  N   LEU    13      -3.929  -3.019   7.000  1.00  0.00              
ATOM     18  CA  LEU    13      -4.153  -2.097   5.888  1.00  0.00              
ATOM     19  C   LEU    13      -4.784  -0.798   6.411  1.00  0.00              
ATOM     20  O   LEU    13      -4.441   0.299   5.955  1.00  0.00              
ATOM     21  N   SER    14      -5.707  -0.937   7.366  1.00  0.00              
ATOM     22  CA  SER    14      -6.377   0.203   7.989  1.00  0.00              
ATOM     23  C   SER    14      -5.347   1.199   8.522  1.00  0.00              
ATOM     24  O   SER    14      -5.483   2.404   8.347  1.00  0.00              
ATOM     25  N   ALA    15      -4.317   0.679   9.178  1.00  0.00              
ATOM     26  CA  ALA    15      -3.256   1.509   9.742  1.00  0.00              
ATOM     27  C   ALA    15      -2.667   2.437   8.696  1.00  0.00              
ATOM     28  O   ALA    15      -2.602   3.651   8.886  1.00  0.00              
ATOM     29  N   VAL    16      -2.224   1.840   7.594  1.00  0.00              
ATOM     30  CA  VAL    16      -1.618   2.578   6.504  1.00  0.00              
ATOM     31  C   VAL    16      -2.511   3.690   5.992  1.00  0.00              
ATOM     32  O   VAL    16      -2.086   4.841   5.881  1.00  0.00              
ATOM     33  N   GLY    17      -3.751   3.332   5.674  1.00  0.00              
ATOM     34  CA  GLY    17      -4.725   4.280   5.164  1.00  0.00              
ATOM     35  C   GLY    17      -5.020   5.367   6.185  1.00  0.00              
ATOM     36  O   GLY    17      -5.306   6.510   5.822  1.00  0.00              
ATOM     37  N   ALA    18      -4.958   5.011   7.465  1.00  0.00              
ATOM     38  CA  ALA    18      -5.230   5.973   8.524  1.00  0.00              
ATOM     39  C   ALA    18      -4.086   6.974   8.621  1.00  0.00              
ATOM     40  O   ALA    18      -4.296   8.197   8.629  1.00  0.00              
ATOM     41  N   LEU    19      -2.870   6.448   8.685  1.00  0.00              
ATOM     42  CA  LEU    19      -1.694   7.290   8.794  1.00  0.00              
ATOM     43  C   LEU    19      -1.593   8.272   7.634  1.00  0.00              
ATOM     44  O   LEU    19      -1.336   9.460   7.841  1.00  0.00              
ATOM     45  N   LEU    20      -1.825   7.790   6.419  1.00  0.00              
ATOM     46  CA  LEU    20      -1.735   8.647   5.242  1.00  0.00              
ATOM     47  C   LEU    20      -2.819   9.722   5.182  1.00  0.00              
ATOM     48  O   LEU    20      -2.524  10.900   4.914  1.00  0.00              
ATOM     49  N   ASP    21      -4.068   9.324   5.427  1.00  0.00              
ATOM     50  CA  ASP    21      -5.189  10.267   5.395  1.00  0.00              
ATOM     51  C   ASP    21      -5.141  11.301   6.528  1.00  0.00              
ATOM     52  O   ASP    21      -5.490  12.459   6.325  1.00  0.00              
ATOM     53  N   GLY    22      -4.712  10.887   7.718  1.00  0.00              
ATOM     54  CA  GLY    22      -4.615  11.818   8.838  1.00  0.00              
ATOM     55  C   GLY    22      -3.484  12.813   8.614  1.00  0.00              
ATOM     56  O   GLY    22      -3.462  13.887   9.226  1.00  0.00              
ATOM     57  N   ALA    23      -2.534  12.456   7.755  1.00  0.00              
ATOM     58  CA  ALA    23      -1.415  13.348   7.459  1.00  0.00              
ATOM     59  C   ALA    23      -1.866  14.358   6.402  1.00  0.00              
ATOM     60  O   ALA    23      -1.075  15.180   5.932  1.00  0.00              
ATOM     61  N   ASP    24      -3.144  14.275   6.034  1.00  0.00              
ATOM     62  CA  ASP    24      -3.713  15.183   5.053  1.00  0.00              
ATOM     63  C   ASP    24      -3.416  14.838   3.608  1.00  0.00              
ATOM     64  O   ASP    24      -3.579  15.677   2.721  1.00  0.00              
ATOM     65  N   ILE    25      -2.989  13.605   3.354  1.00  0.00              
ATOM     66  CA  ILE    25      -2.675  13.208   1.988  1.00  0.00              
ATOM     67  C   ILE    25      -3.814  12.475   1.299  1.00  0.00              
ATOM     68  O   ILE    25      -4.739  11.974   1.938  1.00  0.00              
ATOM     69  N   GLY    26      -3.737  12.434  -0.023  1.00  0.00              
ATOM     70  CA  GLY    26      -4.724  11.760  -0.840  1.00  0.00              
ATOM     71  C   GLY    26      -4.126  10.456  -1.335  1.00  0.00              
ATOM     72  O   GLY    26      -2.924  10.376  -1.595  1.00  0.00              
ATOM     73  N   HIS    27      -4.959   9.429  -1.441  1.00  0.00              
ATOM     74  CA  HIS    27      -4.515   8.143  -1.950  1.00  0.00              
ATOM     75  C   HIS    27      -5.091   8.103  -3.364  1.00  0.00              
ATOM     76  O   HIS    27      -6.294   7.915  -3.550  1.00  0.00              
ATOM     77  N   LEU    28      -4.227   8.301  -4.358  1.00  0.00              
ATOM     78  CA  LEU    28      -4.641   8.320  -5.758  1.00  0.00              
ATOM     79  C   LEU    28      -4.925   6.932  -6.328  1.00  0.00              
ATOM     80  O   LEU    28      -5.829   6.745  -7.150  1.00  0.00              
ATOM     81  N   VAL    29      -4.162   5.950  -5.880  1.00  0.00              
ATOM     82  CA  VAL    29      -4.348   4.596  -6.374  1.00  0.00              
ATOM     83  C   VAL    29      -3.501   3.679  -5.493  1.00  0.00              
ATOM     84  O   VAL    29      -2.705   4.152  -4.677  1.00  0.00              
ATOM    137  N   VAL    48       0.409   8.123  -3.270  1.00  0.00              
ATOM    138  CA  VAL    48      -0.292   9.178  -2.549  1.00  0.00              
ATOM    139  C   VAL    48       0.286  10.503  -3.014  1.00  0.00              
ATOM    140  O   VAL    48       1.299  10.528  -3.711  1.00  0.00              
ATOM    141  N   LEU    49      -0.353  11.596  -2.617  1.00  0.00              
ATOM    142  CA  LEU    49       0.094  12.930  -2.980  1.00  0.00              
ATOM    143  C   LEU    49      -0.407  13.883  -1.914  1.00  0.00              
ATOM    144  O   LEU    49      -1.375  13.590  -1.208  1.00  0.00              
ATOM    145  N   VAL    50       0.249  15.029  -1.802  1.00  0.00              
ATOM    146  CA  VAL    50      -0.154  16.011  -0.818  1.00  0.00              
ATOM    147  C   VAL    50       0.830  17.144  -0.879  1.00  0.00              
ATOM    148  O   VAL    50       1.669  17.180  -1.777  1.00  0.00              
ATOM    149  N   HIS    51       0.733  18.079   0.052  1.00  0.00              
ATOM    150  CA  HIS    51       1.666  19.193   0.059  1.00  0.00              
ATOM    151  C   HIS    51       3.010  18.657   0.551  1.00  0.00              
ATOM    152  O   HIS    51       3.083  17.559   1.114  1.00  0.00              
ATOM    153  N   GLU    52       4.099  19.411   0.331  1.00  0.00              
ATOM    154  CA  GLU    52       5.408  18.931   0.797  1.00  0.00              
ATOM    155  C   GLU    52       5.417  18.658   2.305  1.00  0.00              
ATOM    156  O   GLU    52       6.026  17.695   2.778  1.00  0.00              
ATOM    157  N   ASP    53       4.711  19.487   3.059  1.00  0.00              
ATOM    158  CA  ASP    53       4.656  19.292   4.497  1.00  0.00              
ATOM    159  C   ASP    53       4.016  17.957   4.859  1.00  0.00              
ATOM    160  O   ASP    53       4.528  17.224   5.701  1.00  0.00              
ATOM    161  N   ASP    54       2.896  17.641   4.215  1.00  0.00              
ATOM    162  CA  ASP    54       2.184  16.395   4.493  1.00  0.00              
ATOM    163  C   ASP    54       2.934  15.157   3.996  1.00  0.00              
ATOM    164  O   ASP    54       3.006  14.137   4.690  1.00  0.00              
ATOM    165  N   LEU    55       3.482  15.240   2.790  1.00  0.00              
ATOM    166  CA  LEU    55       4.232  14.127   2.255  1.00  0.00              
ATOM    167  C   LEU    55       5.443  13.893   3.159  1.00  0.00              
ATOM    168  O   LEU    55       5.777  12.749   3.482  1.00  0.00              
ATOM    169  N   ALA    56       6.099  14.972   3.575  1.00  0.00              
ATOM    170  CA  ALA    56       7.260  14.826   4.443  1.00  0.00              
ATOM    171  C   ALA    56       6.817  14.188   5.747  1.00  0.00              
ATOM    172  O   ALA    56       7.547  13.393   6.336  1.00  0.00              
ATOM    173  N   GLY    57       5.617  14.540   6.196  1.00  0.00              
ATOM    174  CA  GLY    57       5.090  13.988   7.434  1.00  0.00              
ATOM    175  C   GLY    57       4.929  12.483   7.294  1.00  0.00              
ATOM    176  O   GLY    57       5.335  11.729   8.174  1.00  0.00              
ATOM    177  N   ALA    58       4.342  12.051   6.182  1.00  0.00              
ATOM    178  CA  ALA    58       4.145  10.633   5.939  1.00  0.00              
ATOM    179  C   ALA    58       5.498   9.948   5.791  1.00  0.00              
ATOM    180  O   ALA    58       5.723   8.884   6.365  1.00  0.00              
ATOM    181  N   ARG    59       6.399  10.548   5.017  1.00  0.00              
ATOM    182  CA  ARG    59       7.724   9.960   4.839  1.00  0.00              
ATOM    183  C   ARG    59       8.359   9.764   6.214  1.00  0.00              
ATOM    184  O   ARG    59       9.053   8.787   6.460  1.00  0.00              
ATOM    185  N   ARG    60       8.080  10.684   7.124  1.00  0.00              
ATOM    186  CA  ARG    60       8.633  10.614   8.469  1.00  0.00              
ATOM    187  C   ARG    60       8.019   9.557   9.381  1.00  0.00              
ATOM    188  O   ARG    60       8.732   8.820  10.061  1.00  0.00              
ATOM    189  N   LEU    61       6.695   9.478   9.387  1.00  0.00              
ATOM    190  CA  LEU    61       6.007   8.562  10.284  1.00  0.00              
ATOM    191  C   LEU    61       5.635   7.171   9.767  1.00  0.00              
ATOM    192  O   LEU    61       5.289   6.288  10.556  1.00  0.00              
ATOM    193  N   LEU    62       5.708   6.965   8.455  1.00  0.00              
ATOM    194  CA  LEU    62       5.373   5.653   7.909  1.00  0.00              
ATOM    195  C   LEU    62       6.344   4.582   8.383  1.00  0.00              
ATOM    196  O   LEU    62       5.922   3.541   8.867  1.00  0.00              
ATOM    197  N   THR    63       7.659   4.819   8.247  1.00  0.00              
ATOM    198  CA  THR    63       8.632   3.812   8.693  1.00  0.00              
ATOM    199  C   THR    63       8.363   3.375  10.136  1.00  0.00              
ATOM    200  O   THR    63       8.412   2.194  10.463  1.00  0.00              
ATOM    201  N   ASP    64       8.065   4.350  10.985  1.00  0.00              
ATOM    202  CA  ASP    64       7.772   4.106  12.393  1.00  0.00              
ATOM    203  C   ASP    64       6.581   3.155  12.549  1.00  0.00              
ATOM    204  O   ASP    64       6.648   2.194  13.320  1.00  0.00              
ATOM    205  N   LEU    67       5.499   3.427  11.815  1.00  0.00              
ATOM    206  CA  LEU    67       4.312   2.582  11.856  1.00  0.00              
ATOM    207  C   LEU    67       4.753   1.171  11.534  1.00  0.00              
ATOM    208  O   LEU    67       4.354   0.219  12.192  1.00  0.00              
ATOM    209  N   ALA    68       5.584   1.050  10.504  1.00  0.00              
ATOM    210  CA  ALA    68       6.080  -0.250  10.097  1.00  0.00              
ATOM    211  C   ALA    68       6.821  -0.939  11.219  1.00  0.00              
ATOM    212  O   ALA    68       6.597  -2.115  11.483  1.00  0.00              
ATOM    213  N   HIS    69       7.701  -0.202  11.882  1.00  0.00              
ATOM    214  CA  HIS    69       8.480  -0.752  12.986  1.00  0.00              
ATOM    215  C   HIS    69       7.524  -1.312  14.037  1.00  0.00              
ATOM    216  O   HIS    69       7.827  -2.294  14.714  1.00  0.00              
ATOM    217  N   GLU    70       6.360  -0.682  14.152  1.00  0.00              
ATOM    218  CA  GLU    70       5.332  -1.100  15.100  1.00  0.00              
ATOM    219  C   GLU    70       4.695  -2.448  14.724  1.00  0.00              
ATOM    220  O   GLU    70       4.655  -3.372  15.546  1.00  0.00              
ATOM    221  N   LEU    71       4.214  -2.556  13.482  1.00  0.00              
ATOM    222  CA  LEU    71       3.552  -3.768  12.989  1.00  0.00              
ATOM    223  C   LEU    71       4.438  -4.758  12.241  1.00  0.00              
ATOM    224  O   LEU    71       3.935  -5.602  11.503  1.00  0.00              
END
