
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348AL381_3.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          0.670
LGA    C      11      C      11          0.709
LGA    P      12      P      12          1.513
LGA    L      13      L      13          1.285
LGA    C      14      C      14          1.485
LGA    K      15      K      15          1.684
LGA    G      16      G      16          3.108
LGA    P      17      P      17          3.343
LGA    L      18      L      18          1.928
LGA    V      19      V      19          1.234
LGA    F      20      F      20          1.057
LGA    D      21      D      21          1.282
LGA    K      22      K      22          1.782
LGA    S      23      S      23          2.935
LGA    K      24      K      24          2.288
LGA    D      25      D      25          4.470
LGA    E      26      E      26          1.655
LGA    L      27      L      27          1.589
LGA    I      28      I      28          1.146
LGA    C      29      C      29          0.428
LGA    K      30      K      30          1.230
LGA    G      31      G      31          0.981
LGA    D      32      D      32          0.678
LGA    R      33      R      33          0.880
LGA    L      34      L      34          0.461
LGA    A      35      A      35          1.038
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     26    1.83   100.00     38.985     1.344

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.250275 * X  +  -0.200983 * Y  +   0.947084 * Z  +   8.944037
  Y_new =  -0.941808 * X  +   0.277278 * Y  +  -0.190039 * Z  +  31.487125
  Z_new =  -0.224411 * X  +  -0.939533 * Y  +  -0.258683 * Z  +  47.053963 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.839470    1.302122  [ DEG:  -105.3939     74.6061 ]
  Theta =   0.226338    2.915254  [ DEG:    12.9682    167.0318 ]
  Phi   =  -1.830532    1.311060  [ DEG:  -104.8818     75.1182 ]
 
# 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_3                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348AL381_3.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   26   1.83  100.00  38.985
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL381_3
REMARK Aligment from pdb entry: 1dl6A
ATOM      1  N   VAL    10       7.906  33.967  58.531  1.00  0.00              
ATOM      2  CA  VAL    10       8.224  33.008  59.585  1.00  0.00              
ATOM      3  C   VAL    10       7.205  31.874  59.626  1.00  0.00              
ATOM      4  O   VAL    10       6.239  31.862  58.863  1.00  0.00              
ATOM      5  N   CYS    11       7.431  30.923  60.526  1.00  0.00              
ATOM      6  CA  CYS    11       6.541  29.778  60.681  1.00  0.00              
ATOM      7  C   CYS    11       5.360  30.131  61.588  1.00  0.00              
ATOM      8  O   CYS    11       5.544  30.703  62.661  1.00  0.00              
ATOM      9  N   PRO    12       4.126  29.795  61.167  1.00  0.00              
ATOM     10  CA  PRO    12       2.920  30.086  61.952  1.00  0.00              
ATOM     11  C   PRO    12       2.984  29.504  63.359  1.00  0.00              
ATOM     12  O   PRO    12       2.511  30.117  64.317  1.00  0.00              
ATOM     13  N   LEU    13       3.566  28.318  63.475  1.00  0.00              
ATOM     14  CA  LEU    13       3.685  27.647  64.766  1.00  0.00              
ATOM     15  C   LEU    13       5.094  27.780  65.344  1.00  0.00              
ATOM     16  O   LEU    13       5.437  27.110  66.317  1.00  0.00              
ATOM     17  N   CYS    14       5.909  28.646  64.746  1.00  0.00              
ATOM     18  CA  CYS    14       7.274  28.855  65.217  1.00  0.00              
ATOM     19  C   CYS    14       7.764  30.258  64.868  1.00  0.00              
ATOM     20  O   CYS    14       8.356  30.472  63.810  1.00  0.00              
ATOM     21  N   LYS    15       7.526  31.237  65.759  1.00  0.00              
ATOM     22  CA  LYS    15       7.948  32.623  65.539  1.00  0.00              
ATOM     23  C   LYS    15       9.463  32.784  65.620  1.00  0.00              
ATOM     24  O   LYS    15      10.075  33.430  64.770  1.00  0.00              
ATOM     25  N   GLY    16      10.061  32.193  66.649  1.00  0.00              
ATOM     26  CA  GLY    16      11.505  32.269  66.841  1.00  0.00              
ATOM     27  C   GLY    16      12.239  31.575  65.700  1.00  0.00              
ATOM     28  O   GLY    16      13.285  32.040  65.246  1.00  0.00              
ATOM     29  N   PRO    17      11.685  30.458  65.240  1.00  0.00              
ATOM     30  CA  PRO    17      12.286  29.698  64.151  1.00  0.00              
ATOM     31  C   PRO    17      11.698  30.114  62.807  1.00  0.00              
ATOM     32  O   PRO    17      10.487  30.049  62.602  1.00  0.00              
ATOM     33  N   LEU    18      11.478  29.645  58.652  1.00  0.00              
ATOM     34  CA  LEU    18      11.660  28.662  57.589  1.00  0.00              
ATOM     35  C   LEU    18      12.824  29.058  56.685  1.00  0.00              
ATOM     36  O   LEU    18      12.753  30.059  55.971  1.00  0.00              
ATOM     37  N   VAL    19      13.895  28.272  56.719  1.00  0.00              
ATOM     38  CA  VAL    19      15.069  28.549  55.901  1.00  0.00              
ATOM     39  C   VAL    19      14.816  28.170  54.448  1.00  0.00              
ATOM     40  O   VAL    19      13.945  27.354  54.156  1.00  0.00              
ATOM     41  N   PHE    20      15.581  28.766  53.540  1.00  0.00              
ATOM     42  CA  PHE    20      15.433  28.487  52.116  1.00  0.00              
ATOM     43  C   PHE    20      16.746  28.001  51.514  1.00  0.00              
ATOM     44  O   PHE    20      17.825  28.441  51.912  1.00  0.00              
ATOM     45  N   ASP    21      16.648  27.091  50.550  1.00  0.00              
ATOM     46  CA  ASP    21      17.827  26.544  49.890  1.00  0.00              
ATOM     47  C   ASP    21      18.332  27.492  48.805  1.00  0.00              
ATOM     48  O   ASP    21      17.956  28.663  48.769  1.00  0.00              
ATOM     49  N   LYS    22      19.186  26.980  47.925  1.00  0.00              
ATOM     50  CA  LYS    22      19.742  27.784  46.842  1.00  0.00              
ATOM     51  C   LYS    22      18.909  27.643  45.572  1.00  0.00              
ATOM     52  O   LYS    22      18.844  28.565  44.758  1.00  0.00              
ATOM     53  N   SER    23      18.272  26.485  45.409  1.00  0.00              
ATOM     54  CA  SER    23      17.440  26.215  44.245  1.00  0.00              
ATOM     55  C   SER    23      17.003  24.758  44.231  1.00  0.00              
ATOM     56  O   SER    23      17.829  23.845  44.228  1.00  0.00              
ATOM     57  N   LYS    24      15.697  24.555  44.221  1.00  0.00              
ATOM     58  CA  LYS    24      15.115  23.215  44.208  1.00  0.00              
ATOM     59  C   LYS    24      15.213  22.557  45.580  1.00  0.00              
ATOM     60  O   LYS    24      15.266  21.332  45.689  1.00  0.00              
ATOM     61  N   ASP    25      15.236  23.379  46.625  1.00  0.00              
ATOM     62  CA  ASP    25      15.325  22.857  47.977  1.00  0.00              
ATOM     63  C   ASP    25      14.124  23.223  48.829  1.00  0.00              
ATOM     64  O   ASP    25      13.899  22.628  49.883  1.00  0.00              
ATOM     65  N   GLU    26      13.347  24.204  48.375  1.00  0.00              
ATOM     66  CA  GLU    26      12.162  24.645  49.104  1.00  0.00              
ATOM     67  C   GLU    26      12.550  25.319  50.416  1.00  0.00              
ATOM     68  O   GLU    26      13.731  25.548  50.682  1.00  0.00              
ATOM     69  N   LEU    27      11.549  25.634  51.232  1.00  0.00              
ATOM     70  CA  LEU    27      11.784  26.279  52.518  1.00  0.00              
ATOM     71  C   LEU    27      11.320  25.384  53.663  1.00  0.00              
ATOM     72  O   LEU    27      10.140  25.046  53.757  1.00  0.00              
ATOM     73  N   ILE    28      12.254  24.992  54.526  1.00  0.00              
ATOM     74  CA  ILE    28      11.943  24.130  55.645  1.00  0.00              
ATOM     75  C   ILE    28      12.066  24.865  56.976  1.00  0.00              
ATOM     76  O   ILE    28      12.790  25.853  57.085  1.00  0.00              
ATOM     77  N   CYS    29      11.358  24.371  57.990  1.00  0.00              
ATOM     78  CA  CYS    29      11.396  24.980  59.315  1.00  0.00              
ATOM     79  C   CYS    29      12.326  24.195  60.242  1.00  0.00              
ATOM     80  O   CYS    29      12.305  22.966  60.251  1.00  0.00              
ATOM     81  N   LYS    30      13.164  24.894  61.030  1.00  0.00              
ATOM     82  CA  LYS    30      14.105  24.244  61.949  1.00  0.00              
ATOM     83  C   LYS    30      13.432  23.690  63.205  1.00  0.00              
ATOM     84  O   LYS    30      14.099  23.147  64.085  1.00  0.00              
ATOM     85  N   GLY    31      12.110  23.827  63.287  1.00  0.00              
ATOM     86  CA  GLY    31      11.363  23.337  64.439  1.00  0.00              
ATOM     87  C   GLY    31      10.413  22.209  64.037  1.00  0.00              
ATOM     88  O   GLY    31      10.703  21.036  64.270  1.00  0.00              
ATOM     89  N   ASP    32       9.278  22.561  63.429  1.00  0.00              
ATOM     90  CA  ASP    32       8.312  21.551  63.001  1.00  0.00              
ATOM     91  C   ASP    32       8.869  20.716  61.853  1.00  0.00              
ATOM     92  O   ASP    32       8.317  19.668  61.514  1.00  0.00              
ATOM     93  N   ARG    33       9.963  21.182  61.254  1.00  0.00              
ATOM     94  CA  ARG    33      10.563  20.458  60.151  1.00  0.00              
ATOM     95  C   ARG    33       9.616  20.319  58.979  1.00  0.00              
ATOM     96  O   ARG    33       9.365  19.211  58.503  1.00  0.00              
ATOM     97  N   LEU    34       9.087  21.445  58.511  1.00  0.00              
ATOM     98  CA  LEU    34       8.162  21.435  57.386  1.00  0.00              
ATOM     99  C   LEU    34       8.894  21.760  56.089  1.00  0.00              
ATOM    100  O   LEU    34      10.100  22.005  56.097  1.00  0.00              
ATOM    101  N   ALA    35       8.158  21.756  54.983  1.00  0.00              
ATOM    102  CA  ALA    35       8.735  22.047  53.677  1.00  0.00              
ATOM    103  C   ALA    35       7.734  22.774  52.785  1.00  0.00              
ATOM    104  O   ALA    35       6.937  22.145  52.089  1.00  0.00              
END
