
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0349AL333_3-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL333_3-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    R       2      R       2           -
LGA    E       3      E       3           -
LGA    L       4      L       4           -
LGA    L       5      L       5           -
LGA    R       6      -       -           -
LGA    T       7      -       -           -
LGA    N       8      -       -           -
LGA    D       9      -       -           -
LGA    A      10      R       6          4.945
LGA    V      11      T       7          0.536
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    L      12      L      12          3.616
LGA    L      13      L      13          1.681
LGA    S      14      S      14          1.723
LGA    A      15      A      15          4.460
LGA    V      16      V      16           -
LGA    G      17      G      17           -
LGA    A      18      A      18           -
LGA    -       -      L      19           -
LGA    -       -      L      20           -
LGA    L      19      D      21          4.307
LGA    L      20      G      22           -
LGA    D      21      A      23           -
LGA    G      22      D      24          2.413
LGA    A      23      I      25          1.625
LGA    D      24      G      26          1.155
LGA    I      25      H      27          2.206
LGA    G      26      L      28          2.102
LGA    H      27      V      29          1.697
LGA    L      28      -       -           -
LGA    V      29      -       -           -
LGA    P      45      -       -           -
LGA    R      46      -       -           -
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      -       -           -
LGA    V      50      P      45           #
LGA    H      51      R      46           -
LGA    E      52      R      47           -
LGA    D      53      V      48           -
LGA    -       -      L      49           -
LGA    -       -      V      50           -
LGA    -       -      H      51           -
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    -       -      L      55           -
LGA    -       -      A      56           -
LGA    -       -      G      57           -
LGA    -       -      A      58           -
LGA    -       -      R      59           -
LGA    -       -      R      60           -
LGA    -       -      L      61           -
LGA    -       -      L      62           -
LGA    -       -      T      63           -
LGA    D      54      D      64          2.839
LGA    L      55      A      65          4.473
LGA    A      56      G      66           #
LGA    G      57      -       -           -
LGA    A      58      L      67          2.303
LGA    R      59      A      68          2.265
LGA    R      60      H      69          2.889
LGA    L      61      -       -           -
LGA    L      62      E      70          1.320
LGA    T      63      L      71          4.427
LGA    E      70      R      72           #
LGA    L      71      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50   57    5.0     20    2.93    25.00     22.930     0.659

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.358919 * X  +   0.375402 * Y  +  -0.854547 * Z  +  22.021591
  Y_new =  -0.801918 * X  +  -0.592513 * Y  +   0.076523 * Z  +  12.482807
  Z_new =  -0.477604 * X  +   0.712742 * Y  +   0.513705 * Z  +  -2.591304 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.946283   -2.195310  [ DEG:    54.2180   -125.7820 ]
  Theta =   0.497925    2.643668  [ DEG:    28.5290    151.4710 ]
  Phi   =  -1.991632    1.149961  [ DEG:  -114.1121     65.8879 ]
 
# 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: T0349AL333_3-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL333_3-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50   57   5.0   20   2.93   25.00  22.930
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL333_3-D1
REMARK Aligment from pdb entry: 1lu4_A
ATOM      1  N   MET     1      -4.713 -13.460   7.142  1.00  0.00              
ATOM      2  CA  MET     1      -3.674 -14.225   6.468  1.00  0.00              
ATOM      3  C   MET     1      -4.567 -15.100   5.575  1.00  0.00              
ATOM      4  O   MET     1      -5.705 -15.346   6.025  1.00  0.00              
ATOM      5  N   ARG     2      -3.932 -15.331   4.453  1.00  0.00              
ATOM      6  CA  ARG     2      -4.483 -16.141   3.380  1.00  0.00              
ATOM      7  C   ARG     2      -5.989 -15.961   3.314  1.00  0.00              
ATOM      8  O   ARG     2      -6.454 -14.918   2.803  1.00  0.00              
ATOM      9  N   GLU     3     -16.363   2.645  -5.040  1.00  0.00              
ATOM     10  CA  GLU     3     -15.950   1.596  -5.971  1.00  0.00              
ATOM     11  C   GLU     3     -15.929   0.248  -5.266  1.00  0.00              
ATOM     12  O   GLU     3     -15.657   0.159  -4.052  1.00  0.00              
ATOM     13  N   LEU     4     -16.191  -0.838  -5.972  1.00  0.00              
ATOM     14  CA  LEU     4     -15.964  -2.141  -5.343  1.00  0.00              
ATOM     15  C   LEU     4     -14.498  -2.425  -5.160  1.00  0.00              
ATOM     16  O   LEU     4     -13.646  -1.928  -5.899  1.00  0.00              
ATOM     17  N   LEU     5     -14.210  -3.236  -4.139  1.00  0.00              
ATOM     18  CA  LEU     5     -12.829  -3.677  -3.922  1.00  0.00              
ATOM     19  C   LEU     5     -12.879  -5.127  -3.480  1.00  0.00              
ATOM     20  O   LEU     5     -13.708  -5.492  -2.625  1.00  0.00              
ATOM     21  N   ARG     6     -11.997  -5.956  -3.992  1.00  0.00              
ATOM     22  CA  ARG     6     -11.932  -7.377  -3.642  1.00  0.00              
ATOM     23  C   ARG     6     -10.637  -7.643  -2.912  1.00  0.00              
ATOM     24  O   ARG     6      -9.565  -7.500  -3.510  1.00  0.00              
ATOM     25  N   THR     7     -10.729  -7.978  -1.642  1.00  0.00              
ATOM     26  CA  THR     7      -9.599  -8.302  -0.814  1.00  0.00              
ATOM     27  C   THR     7      -8.746  -9.421  -1.344  1.00  0.00              
ATOM     28  O   THR     7      -7.538  -9.502  -1.064  1.00  0.00              
ATOM     29  N   ASN     8      -9.348 -10.297  -2.148  1.00  0.00              
ATOM     30  CA  ASN     8      -8.574 -11.426  -2.662  1.00  0.00              
ATOM     31  C   ASN     8      -7.457 -10.878  -3.554  1.00  0.00              
ATOM     32  O   ASN     8      -6.469 -11.591  -3.733  1.00  0.00              
ATOM     33  N   ASP     9      -7.633  -9.671  -4.094  1.00  0.00              
ATOM     34  CA  ASP     9      -6.563  -9.098  -4.932  1.00  0.00              
ATOM     35  C   ASP     9      -5.289  -8.856  -4.156  1.00  0.00              
ATOM     36  O   ASP     9      -4.269  -8.676  -4.809  1.00  0.00              
ATOM     37  N   ALA    10       3.036  -8.219  -1.012  1.00  0.00              
ATOM     38  CA  ALA    10       3.212  -7.511   0.257  1.00  0.00              
ATOM     39  C   ALA    10       2.104  -6.438   0.386  1.00  0.00              
ATOM     40  O   ALA    10       1.763  -5.746  -0.571  1.00  0.00              
ATOM     41  N   VAL    11       1.540  -6.365   1.590  1.00  0.00              
ATOM     42  CA  VAL    11       0.416  -5.465   1.773  1.00  0.00              
ATOM     43  C   VAL    11       0.362  -5.001   3.224  1.00  0.00              
ATOM     44  O   VAL    11       0.895  -5.693   4.129  1.00  0.00              
ATOM     45  N   LEU    12      -0.319  -3.904   3.435  1.00  0.00              
ATOM     46  CA  LEU    12      -0.541  -3.390   4.792  1.00  0.00              
ATOM     47  C   LEU    12      -2.029  -3.054   4.873  1.00  0.00              
ATOM     48  O   LEU    12      -2.539  -2.268   4.079  1.00  0.00              
ATOM     49  N   LEU    13      -2.697  -3.628   5.909  1.00  0.00              
ATOM     50  CA  LEU    13      -4.026  -3.170   6.273  1.00  0.00              
ATOM     51  C   LEU    13      -3.906  -2.217   7.452  1.00  0.00              
ATOM     52  O   LEU    13      -3.172  -2.514   8.418  1.00  0.00              
ATOM     53  N   SER    14      -4.621  -1.101   7.401  1.00  0.00              
ATOM     54  CA  SER    14      -4.604  -0.137   8.478  1.00  0.00              
ATOM     55  C   SER    14      -6.040   0.170   8.847  1.00  0.00              
ATOM     56  O   SER    14      -6.798   0.733   8.054  1.00  0.00              
ATOM     57  N   ALA    15      -6.411  -0.230  10.073  1.00  0.00              
ATOM     58  CA  ALA    15      -7.786  -0.022  10.587  1.00  0.00              
ATOM     59  C   ALA    15      -7.829   1.256  11.347  1.00  0.00              
ATOM     60  O   ALA    15      -7.098   1.445  12.348  1.00  0.00              
ATOM     61  N   VAL    16     -14.974  10.242   6.915  1.00  0.00              
ATOM     62  CA  VAL    16     -13.873   9.380   6.414  1.00  0.00              
ATOM     63  C   VAL    16     -13.149  10.052   5.293  1.00  0.00              
ATOM     64  O   VAL    16     -11.917  10.093   5.238  1.00  0.00              
ATOM     65  N   GLY    17     -13.915  10.604   4.344  1.00  0.00              
ATOM     66  CA  GLY    17     -13.295  11.269   3.182  1.00  0.00              
ATOM     67  C   GLY    17     -12.499  12.497   3.603  1.00  0.00              
ATOM     68  O   GLY    17     -11.434  12.768   3.081  1.00  0.00              
ATOM     69  N   ALA    18     -13.022  13.290   4.568  1.00  0.00              
ATOM     70  CA  ALA    18     -12.240  14.455   5.001  1.00  0.00              
ATOM     71  C   ALA    18     -10.903  14.053   5.541  1.00  0.00              
ATOM     72  O   ALA    18      -9.920  14.796   5.369  1.00  0.00              
ATOM     73  N   LEU    19     -10.851  12.935   6.287  1.00  0.00              
ATOM     74  CA  LEU    19      -9.599  12.467   6.865  1.00  0.00              
ATOM     75  C   LEU    19      -8.594  12.044   5.783  1.00  0.00              
ATOM     76  O   LEU    19      -7.445  12.449   5.801  1.00  0.00              
ATOM     77  N   LEU    20      -9.081  11.270   4.793  1.00  0.00              
ATOM     78  CA  LEU    20      -8.226  10.871   3.696  1.00  0.00              
ATOM     79  C   LEU    20      -7.699  12.089   2.963  1.00  0.00              
ATOM     80  O   LEU    20      -6.503  12.117   2.577  1.00  0.00              
ATOM     81  N   ASP    21      -8.562  13.081   2.754  1.00  0.00              
ATOM     82  CA  ASP    21      -8.138  14.297   2.020  1.00  0.00              
ATOM     83  C   ASP    21      -7.127  15.086   2.818  1.00  0.00              
ATOM     84  O   ASP    21      -6.126  15.543   2.286  1.00  0.00              
ATOM     85  N   GLY    22      -7.390  15.329   4.108  1.00  0.00              
ATOM     86  CA  GLY    22      -6.519  16.117   4.962  1.00  0.00              
ATOM     87  C   GLY    22      -5.106  15.561   5.034  1.00  0.00              
ATOM     88  O   GLY    22      -4.167  16.332   5.042  1.00  0.00              
ATOM     89  N   ALA    23      -5.001  14.218   5.088  1.00  0.00              
ATOM     90  CA  ALA    23      -3.725  13.587   5.263  1.00  0.00              
ATOM     91  C   ALA    23      -3.172  13.000   3.984  1.00  0.00              
ATOM     92  O   ALA    23      -2.092  12.387   4.010  1.00  0.00              
ATOM     93  N   ASP    24      -3.842  13.228   2.870  1.00  0.00              
ATOM     94  CA  ASP    24      -3.308  12.774   1.565  1.00  0.00              
ATOM     95  C   ASP    24      -3.018  11.287   1.580  1.00  0.00              
ATOM     96  O   ASP    24      -1.941  10.806   1.225  1.00  0.00              
ATOM     97  N   ILE    25      -4.023  10.491   1.971  1.00  0.00              
ATOM     98  CA  ILE    25      -3.868   9.018   2.001  1.00  0.00              
ATOM     99  C   ILE    25      -4.161   8.467   0.627  1.00  0.00              
ATOM    100  O   ILE    25      -5.285   8.126   0.287  1.00  0.00              
ATOM    101  N   GLY    26      -3.100   8.434  -0.210  1.00  0.00              
ATOM    102  CA  GLY    26      -3.282   8.053  -1.603  1.00  0.00              
ATOM    103  C   GLY    26      -3.176   6.554  -1.803  1.00  0.00              
ATOM    104  O   GLY    26      -2.229   6.014  -2.438  1.00  0.00              
ATOM    105  N   HIS    27      -4.154   5.853  -1.285  1.00  0.00              
ATOM    106  CA  HIS    27      -4.275   4.426  -1.393  1.00  0.00              
ATOM    107  C   HIS    27      -5.735   4.076  -1.132  1.00  0.00              
ATOM    108  O   HIS    27      -6.512   4.924  -0.675  1.00  0.00              
ATOM    109  N   LEU    28      -9.062   3.155   0.497  1.00  0.00              
ATOM    110  CA  LEU    28      -9.676   3.157   1.839  1.00  0.00              
ATOM    111  C   LEU    28     -11.083   2.657   1.717  1.00  0.00              
ATOM    112  O   LEU    28     -11.861   3.051   0.849  1.00  0.00              
ATOM    113  N   VAL    29     -11.432   1.733   2.613  1.00  0.00              
ATOM    114  CA  VAL    29     -12.690   1.009   2.577  1.00  0.00              
ATOM    115  C   VAL    29     -13.658   1.582   3.615  1.00  0.00              
ATOM    116  O   VAL    29     -13.270   1.856   4.744  1.00  0.00              
ATOM    189  N   PRO    45      -5.919   2.642  16.322  1.00  0.00              
ATOM    190  CA  PRO    45      -5.485   2.110  15.024  1.00  0.00              
ATOM    191  C   PRO    45      -4.882   0.716  15.173  1.00  0.00              
ATOM    192  O   PRO    45      -4.335   0.304  16.191  1.00  0.00              
ATOM    193  N   ARG    46      -4.973  -0.050  14.074  1.00  0.00              
ATOM    194  CA  ARG    46      -4.352  -1.376  14.058  1.00  0.00              
ATOM    195  C   ARG    46      -3.756  -1.578  12.678  1.00  0.00              
ATOM    196  O   ARG    46      -4.316  -1.130  11.699  1.00  0.00              
ATOM    197  N   ARG    47      -2.621  -2.267  12.624  1.00  0.00              
ATOM    198  CA  ARG    47      -1.942  -2.629  11.394  1.00  0.00              
ATOM    199  C   ARG    47      -1.856  -4.143  11.242  1.00  0.00              
ATOM    200  O   ARG    47      -1.561  -4.817  12.235  1.00  0.00              
ATOM    201  N   VAL    48      -2.019  -4.606  10.014  1.00  0.00              
ATOM    202  CA  VAL    48      -1.648  -5.959   9.639  1.00  0.00              
ATOM    203  C   VAL    48      -0.650  -5.838   8.517  1.00  0.00              
ATOM    204  O   VAL    48      -0.955  -5.319   7.464  1.00  0.00              
ATOM    205  N   LEU    49       0.555  -6.405   8.747  1.00  0.00              
ATOM    206  CA  LEU    49       1.658  -6.346   7.797  1.00  0.00              
ATOM    207  C   LEU    49       1.769  -7.698   7.116  1.00  0.00              
ATOM    208  O   LEU    49       2.177  -8.685   7.788  1.00  0.00              
ATOM    209  N   VAL    50       1.416  -7.805   5.845  1.00  0.00              
ATOM    210  CA  VAL    50       1.438  -9.074   5.112  1.00  0.00              
ATOM    211  C   VAL    50       2.639  -9.166   4.189  1.00  0.00              
ATOM    212  O   VAL    50       2.951  -8.266   3.418  1.00  0.00              
ATOM    213  N   HIS    51       3.310 -10.307   4.303  1.00  0.00              
ATOM    214  CA  HIS    51       4.268 -10.718   3.300  1.00  0.00              
ATOM    215  C   HIS    51       3.532 -11.374   2.129  1.00  0.00              
ATOM    216  O   HIS    51       2.391 -11.817   2.260  1.00  0.00              
ATOM    217  N   GLU    52       4.227 -11.458   0.969  1.00  0.00              
ATOM    218  CA  GLU    52       3.640 -12.095  -0.211  1.00  0.00              
ATOM    219  C   GLU    52       3.303 -13.550   0.051  1.00  0.00              
ATOM    220  O   GLU    52       2.396 -14.091  -0.560  1.00  0.00              
ATOM    221  N   ASP    53       4.012 -14.189   0.995  1.00  0.00              
ATOM    222  CA  ASP    53       3.718 -15.607   1.270  1.00  0.00              
ATOM    223  C   ASP    53       2.518 -15.817   2.181  1.00  0.00              
ATOM    224  O   ASP    53       2.203 -16.954   2.481  1.00  0.00              
ATOM    225  N   ASP    54       5.466   5.481  15.104  1.00  0.00              
ATOM    226  CA  ASP    54       6.266   6.534  14.450  1.00  0.00              
ATOM    227  C   ASP    54       6.448   6.145  12.987  1.00  0.00              
ATOM    228  O   ASP    54       6.380   4.997  12.555  1.00  0.00              
ATOM    229  N   LEU    55       6.823   7.191  12.209  1.00  0.00              
ATOM    230  CA  LEU    55       7.165   6.918  10.807  1.00  0.00              
ATOM    231  C   LEU    55       8.362   6.011  10.652  1.00  0.00              
ATOM    232  O   LEU    55       8.372   5.132   9.791  1.00  0.00              
ATOM    233  N   ALA    56       9.388   6.239  11.473  1.00  0.00              
ATOM    234  CA  ALA    56      10.565   5.388  11.387  1.00  0.00              
ATOM    235  C   ALA    56      10.195   3.935  11.648  1.00  0.00              
ATOM    236  O   ALA    56      10.665   3.031  10.969  1.00  0.00              
ATOM    237  N   GLY    57       9.327   3.738  12.672  1.00  0.00              
ATOM    238  CA  GLY    57       8.971   2.349  12.931  1.00  0.00              
ATOM    239  C   GLY    57       8.184   1.740  11.768  1.00  0.00              
ATOM    240  O   GLY    57       8.413   0.631  11.343  1.00  0.00              
ATOM    241  N   ALA    58       7.205   2.505  11.255  1.00  0.00              
ATOM    242  CA  ALA    58       6.388   2.036  10.132  1.00  0.00              
ATOM    243  C   ALA    58       7.228   1.757   8.890  1.00  0.00              
ATOM    244  O   ALA    58       7.042   0.706   8.259  1.00  0.00              
ATOM    245  N   ARG    59       8.142   2.650   8.576  1.00  0.00              
ATOM    246  CA  ARG    59       9.015   2.447   7.421  1.00  0.00              
ATOM    247  C   ARG    59       9.792   1.144   7.555  1.00  0.00              
ATOM    248  O   ARG    59       9.927   0.374   6.594  1.00  0.00              
ATOM    249  N   ARG    60      10.333   0.862   8.768  1.00  0.00              
ATOM    250  CA  ARG    60      11.088  -0.369   8.938  1.00  0.00              
ATOM    251  C   ARG    60      10.177  -1.601   8.837  1.00  0.00              
ATOM    252  O   ARG    60      10.613  -2.582   8.226  1.00  0.00              
ATOM    253  N   LEU    61       8.975  -1.539   9.392  1.00  0.00              
ATOM    254  CA  LEU    61       8.099  -2.739   9.257  1.00  0.00              
ATOM    255  C   LEU    61       7.746  -2.988   7.792  1.00  0.00              
ATOM    256  O   LEU    61       7.671  -4.128   7.311  1.00  0.00              
ATOM    257  N   LEU    62       7.531  -1.888   7.059  1.00  0.00              
ATOM    258  CA  LEU    62       7.176  -2.058   5.624  1.00  0.00              
ATOM    259  C   LEU    62       8.371  -2.576   4.821  1.00  0.00              
ATOM    260  O   LEU    62       8.194  -3.491   3.988  1.00  0.00              
ATOM    261  N   THR    63       9.575  -2.050   5.090  1.00  0.00              
ATOM    262  CA  THR    63      10.759  -2.585   4.409  1.00  0.00              
ATOM    263  C   THR    63      10.915  -4.066   4.678  1.00  0.00              
ATOM    264  O   THR    63      11.426  -4.813   3.809  1.00  0.00              
ATOM    265  N   GLU    70      10.567  -4.541   5.876  1.00  0.00              
ATOM    266  CA  GLU    70      10.814  -5.949   6.217  1.00  0.00              
ATOM    267  C   GLU    70       9.954  -6.873   5.368  1.00  0.00              
ATOM    268  O   GLU    70      10.282  -8.033   5.218  1.00  0.00              
ATOM    269  N   LEU    71       8.855  -6.371   4.823  1.00  0.00              
ATOM    270  CA  LEU    71       8.033  -7.235   3.941  1.00  0.00              
ATOM    271  C   LEU    71       8.937  -7.564   2.711  1.00  0.00              
ATOM    272  O   LEU    71       8.079  -8.765   2.468  1.00  0.00              
END
