
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0348AL381_2
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348AL381_2.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          0.764
LGA    C      11      C      11          0.807
LGA    P      12      P      12          1.791
LGA    L      13      L      13          2.116
LGA    C      14      C      14          1.075
LGA    K      15      K      15          0.466
LGA    G      16      G      16          2.815
LGA    P      17      -       -           -
LGA    L      18      P      17          0.387
LGA    V      19      L      18          0.932
LGA    F      20      V      19          1.278
LGA    D      21      F      20          2.983
LGA    K      22      D      21          2.754
LGA    S      23      K      22          6.110
LGA    K      24      S      23          1.820
LGA    D      25      K      24          2.012
LGA    -       -      D      25           -
LGA    E      26      E      26          1.054
LGA    L      27      L      27          0.597
LGA    I      28      I      28          0.830
LGA    C      29      C      29          0.901
LGA    K      30      K      30          1.368
LGA    G      31      G      31          1.268
LGA    D      32      D      32          1.671
LGA    R      33      R      33          2.948
LGA    L      34      L      34          2.047
LGA    A      35      A      35          2.002
LGA    -       -      F      36           -
LGA    -       -      P      37           -
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      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)   26   61    5.0     25    2.08    68.00     35.581     1.147

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.572907 * X  +   0.127291 * Y  +   0.809676 * Z  +  10.288702
  Y_new =  -0.757670 * X  +   0.459010 * Y  +   0.463947 * Z  +  32.000145
  Z_new =  -0.312593 * X  +  -0.879265 * Y  +   0.359415 * Z  +  50.795746 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.182755    1.958838  [ DEG:   -67.7669    112.2331 ]
  Theta =   0.317921    2.823671  [ DEG:    18.2156    161.7845 ]
  Phi   =  -0.923375    2.218218  [ DEG:   -52.9055    127.0945 ]
 
# 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_2                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348AL381_2.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26   61   5.0   25   2.08   68.00  35.581
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL381_2
REMARK Aligment from pdb entry: 1rlyA
ATOM      1  N   VAL    10       7.291  33.888  59.863  1.00  0.00              
ATOM      2  CA  VAL    10       8.038  32.846  60.570  1.00  0.00              
ATOM      3  C   VAL    10       7.331  31.503  60.438  1.00  0.00              
ATOM      4  O   VAL    10       6.455  31.336  59.589  1.00  0.00              
ATOM      5  N   CYS    11       7.735  30.540  61.257  1.00  0.00              
ATOM      6  CA  CYS    11       7.153  29.212  61.197  1.00  0.00              
ATOM      7  C   CYS    11       5.767  29.140  61.823  1.00  0.00              
ATOM      8  O   CYS    11       5.552  29.598  62.945  1.00  0.00              
ATOM      9  N   PRO    12       4.804  28.527  61.101  1.00  0.00              
ATOM     10  CA  PRO    12       3.439  28.360  61.593  1.00  0.00              
ATOM     11  C   PRO    12       3.435  27.534  62.864  1.00  0.00              
ATOM     12  O   PRO    12       2.639  27.771  63.773  1.00  0.00              
ATOM     13  N   LEU    13       4.363  26.580  62.940  1.00  0.00              
ATOM     14  CA  LEU    13       4.500  25.741  64.116  1.00  0.00              
ATOM     15  C   LEU    13       5.378  26.453  65.131  1.00  0.00              
ATOM     16  O   LEU    13       5.170  26.354  66.341  1.00  0.00              
ATOM     17  N   CYS    14       6.319  27.229  64.633  1.00  0.00              
ATOM     18  CA  CYS    14       7.179  27.999  65.502  1.00  0.00              
ATOM     19  C   CYS    14       7.403  29.399  64.956  1.00  0.00              
ATOM     20  O   CYS    14       8.382  29.665  64.241  1.00  0.00              
ATOM     21  N   LYS    15       6.510  30.329  65.318  1.00  0.00              
ATOM     22  CA  LYS    15       6.619  31.722  64.901  1.00  0.00              
ATOM     23  C   LYS    15       7.960  32.308  65.318  1.00  0.00              
ATOM     24  O   LYS    15       8.383  33.349  64.815  1.00  0.00              
ATOM     25  N   GLY    16       8.640  31.609  66.227  1.00  0.00              
ATOM     26  CA  GLY    16       9.945  32.028  66.692  1.00  0.00              
ATOM     27  C   GLY    16      11.011  31.582  65.697  1.00  0.00              
ATOM     28  O   GLY    16      11.773  32.398  65.181  1.00  0.00              
ATOM     29  N   PRO    17      11.060  30.273  65.429  1.00  0.00              
ATOM     30  CA  PRO    17      12.041  29.733  64.490  1.00  0.00              
ATOM     31  C   PRO    17      11.796  30.267  63.092  1.00  0.00              
ATOM     32  O   PRO    17      10.700  30.152  62.539  1.00  0.00              
ATOM     33  N   LEU    18      12.841  30.880  62.563  1.00  0.00              
ATOM     34  CA  LEU    18      12.792  31.490  61.245  1.00  0.00              
ATOM     35  C   LEU    18      13.097  30.495  60.127  1.00  0.00              
ATOM     36  O   LEU    18      14.200  29.953  60.046  1.00  0.00              
ATOM     37  N   VAL    19      12.116  30.288  59.245  1.00  0.00              
ATOM     38  CA  VAL    19      12.303  29.389  58.113  1.00  0.00              
ATOM     39  C   VAL    19      13.525  29.842  57.318  1.00  0.00              
ATOM     40  O   VAL    19      13.737  31.030  57.107  1.00  0.00              
ATOM     41  N   PHE    20      14.341  28.914  56.885  1.00  0.00              
ATOM     42  CA  PHE    20      15.523  29.282  56.143  1.00  0.00              
ATOM     43  C   PHE    20      15.268  29.254  54.652  1.00  0.00              
ATOM     44  O   PHE    20      14.412  28.523  54.163  1.00  0.00              
ATOM     45  N   ASP    21      15.654  28.531  50.877  1.00  0.00              
ATOM     46  CA  ASP    21      16.000  27.379  50.089  1.00  0.00              
ATOM     47  C   ASP    21      16.251  26.109  50.905  1.00  0.00              
ATOM     48  O   ASP    21      17.353  25.885  51.406  1.00  0.00              
ATOM     49  N   LYS    22      15.218  25.266  51.004  1.00  0.00              
ATOM     50  CA  LYS    22      15.315  23.998  51.726  1.00  0.00              
ATOM     51  C   LYS    22      16.241  23.044  50.992  1.00  0.00              
ATOM     52  O   LYS    22      15.804  22.316  50.101  1.00  0.00              
ATOM     53  N   SER    23      17.514  23.033  51.367  1.00  0.00              
ATOM     54  CA  SER    23      18.471  22.137  50.730  1.00  0.00              
ATOM     55  C   SER    23      18.302  22.170  49.213  1.00  0.00              
ATOM     56  O   SER    23      18.357  21.135  48.550  1.00  0.00              
ATOM     57  N   LYS    24      18.068  23.374  48.686  1.00  0.00              
ATOM     58  CA  LYS    24      17.854  23.591  47.253  1.00  0.00              
ATOM     59  C   LYS    24      16.361  23.664  46.948  1.00  0.00              
ATOM     60  O   LYS    24      15.908  23.211  45.897  1.00  0.00              
ATOM     61  N   ASP    25      15.602  24.237  47.881  1.00  0.00              
ATOM     62  CA  ASP    25      14.167  24.359  47.700  1.00  0.00              
ATOM     63  C   ASP    25      13.629  25.716  48.121  1.00  0.00              
ATOM     64  O   ASP    25      14.160  26.753  47.724  1.00  0.00              
ATOM     65  N   GLU    26      12.560  25.701  48.913  1.00  0.00              
ATOM     66  CA  GLU    26      11.924  26.932  49.385  1.00  0.00              
ATOM     67  C   GLU    26      12.391  27.290  50.802  1.00  0.00              
ATOM     68  O   GLU    26      13.566  27.150  51.122  1.00  0.00              
ATOM     69  N   LEU    27      11.477  27.772  51.642  1.00  0.00              
ATOM     70  CA  LEU    27      11.818  28.168  53.005  1.00  0.00              
ATOM     71  C   LEU    27      11.666  27.005  53.987  1.00  0.00              
ATOM     72  O   LEU    27      10.575  26.520  54.232  1.00  0.00              
ATOM     73  N   ILE    28      12.786  26.528  54.484  1.00  0.00              
ATOM     74  CA  ILE    28      12.814  25.374  55.369  1.00  0.00              
ATOM     75  C   ILE    28      12.860  25.754  56.843  1.00  0.00              
ATOM     76  O   ILE    28      13.796  26.391  57.311  1.00  0.00              
ATOM     77  N   CYS    29      11.839  25.348  57.576  1.00  0.00              
ATOM     78  CA  CYS    29      11.774  25.636  58.992  1.00  0.00              
ATOM     79  C   CYS    29      12.639  24.647  59.770  1.00  0.00              
ATOM     80  O   CYS    29      12.266  23.498  59.937  1.00  0.00              
ATOM     81  N   LYS    30      13.793  25.082  60.284  1.00  0.00              
ATOM     82  CA  LYS    30      14.712  24.205  61.011  1.00  0.00              
ATOM     83  C   LYS    30      14.060  23.319  62.061  1.00  0.00              
ATOM     84  O   LYS    30      14.670  22.347  62.505  1.00  0.00              
ATOM     85  N   GLY    31      12.845  23.633  62.477  1.00  0.00              
ATOM     86  CA  GLY    31      12.194  22.826  63.501  1.00  0.00              
ATOM     87  C   GLY    31      11.171  21.867  62.930  1.00  0.00              
ATOM     88  O   GLY    31      11.274  20.671  63.167  1.00  0.00              
ATOM     89  N   ASP    32      10.248  22.327  62.095  1.00  0.00              
ATOM     90  CA  ASP    32       9.338  21.372  61.478  1.00  0.00              
ATOM     91  C   ASP    32       9.912  21.047  60.124  1.00  0.00              
ATOM     92  O   ASP    32       9.508  20.097  59.479  1.00  0.00              
ATOM     93  N   ARG    33      10.877  21.870  59.725  1.00  0.00              
ATOM     94  CA  ARG    33      11.571  21.717  58.468  1.00  0.00              
ATOM     95  C   ARG    33      10.679  21.891  57.257  1.00  0.00              
ATOM     96  O   ARG    33      10.970  21.397  56.167  1.00  0.00              
ATOM     97  N   LEU    34       9.581  22.583  57.479  1.00  0.00              
ATOM     98  CA  LEU    34       8.585  22.839  56.452  1.00  0.00              
ATOM     99  C   LEU    34       9.140  23.724  55.341  1.00  0.00              
ATOM    100  O   LEU    34       9.948  24.613  55.598  1.00  0.00              
ATOM    101  N   ALA    35       8.715  23.464  54.110  1.00  0.00              
ATOM    102  CA  ALA    35       9.180  24.224  52.971  1.00  0.00              
ATOM    103  C   ALA    35       8.060  25.067  52.377  1.00  0.00              
ATOM    104  O   ALA    35       7.009  24.546  52.006  1.00  0.00              
END
