
#######################################################
#                                                     #
#                        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 (  196),  selected   48 , name T0358AL316_3-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358AL316_3-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10           -
LGA    P      11      P      11           -
LGA    F      12      -       -           -
LGA    T      13      -       -           -
LGA    R      14      -       -           -
LGA    R      15      -       -           -
LGA    Q      16      -       -           -
LGA    A      17      -       -           -
LGA    Q      18      -       -           -
LGA    A      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      -       -           -
LGA    T      22      -       -           -
LGA    T      23      -       -           -
LGA    Y      24      -       -           -
LGA    S      25      F      12          3.284
LGA    N      26      T      13          2.898
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    I      27      A      17          2.651
LGA    T      28      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    -       -      L      29           -
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    L      29      F      37           #
LGA    E      30      R      38          2.833
LGA    D      31      L      39          3.595
LGA    D      32      V      40          1.262
LGA    F      37      V      41          0.975
LGA    R      38      R      42          0.988
LGA    L      39      D      43          1.414
LGA    V      40      T      44          0.922
LGA    D      43      -       -           -
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      -       -           -
LGA    R      47      E      45          2.472
LGA    M      48      G      46          2.284
LGA    R      51      R      47          1.263
LGA    A      52      M      48          1.671
LGA    W      53      V      49          2.956
LGA    N      54      W      50          3.739
LGA    F      55      R      51          1.816
LGA    E      56      A      52          3.367
LGA    -       -      W      53           -
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    P      57      A      59          3.245
LGA    I      67      G      60          2.196
LGA    R      68      E      61          2.992
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    T      69      N      64          4.989
LGA    S      70      R      65           -
LGA    G      71      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    I      72      T      69           #
LGA    R      73      S      70           -
LGA    T      74      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   65    5.0     22    2.66     9.09     24.771     0.797

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.344802 * X  +  -0.627784 * Y  +   0.697853 * Z  +  -0.142354
  Y_new =   0.800456 * X  +   0.584961 * Y  +   0.130730 * Z  + -13.905192
  Z_new =  -0.490287 * X  +   0.513525 * Y  +   0.704210 * Z  +  -7.470187 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.630069   -2.511523  [ DEG:    36.1003   -143.8997 ]
  Theta =   0.512419    2.629174  [ DEG:    29.3594    150.6406 ]
  Phi   =   1.164060   -1.977533  [ DEG:    66.6957   -113.3043 ]
 
# 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: T0358AL316_3-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL316_3-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   65   5.0   22   2.66    9.09  24.771
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL316_3-D1
REMARK Aligment from pdb entry: 2dlb_A
ATOM     37  N   GLY    10      13.115 -14.384 -10.117  1.00  0.00              
ATOM     38  CA  GLY    10      14.236 -15.017 -10.779  1.00  0.00              
ATOM     39  C   GLY    10      15.360 -13.984 -10.829  1.00  0.00              
ATOM     40  O   GLY    10      15.124 -12.793 -11.105  1.00  0.00              
ATOM     41  N   PRO    11      16.572 -14.442 -10.545  1.00  0.00              
ATOM     42  CA  PRO    11      17.708 -13.563 -10.538  1.00  0.00              
ATOM     43  C   PRO    11      19.000 -14.379 -10.535  1.00  0.00              
ATOM     44  O   PRO    11      19.004 -15.579 -10.207  1.00  0.00              
ATOM     45  N   PHE    12      20.108 -13.766 -10.860  1.00  0.00              
ATOM     46  CA  PHE    12      21.393 -14.482 -10.873  1.00  0.00              
ATOM     47  C   PHE    12      22.093 -14.514  -9.530  1.00  0.00              
ATOM     48  O   PHE    12      23.143 -15.139  -9.392  1.00  0.00              
ATOM     49  N   THR    13      21.568 -13.861  -8.503  1.00  0.00              
ATOM     50  CA  THR    13      22.107 -13.844  -7.146  1.00  0.00              
ATOM     51  C   THR    13      21.017 -13.406  -6.192  1.00  0.00              
ATOM     52  O   THR    13      20.052 -12.772  -6.591  1.00  0.00              
ATOM     53  N   ARG    14      21.188 -13.698  -4.907  1.00  0.00              
ATOM     54  CA  ARG    14      20.222 -13.156  -3.929  1.00  0.00              
ATOM     55  C   ARG    14      20.280 -11.650  -3.832  1.00  0.00              
ATOM     56  O   ARG    14      19.280 -11.005  -3.518  1.00  0.00              
ATOM     57  N   ARG    15      21.452 -11.058  -4.090  1.00  0.00              
ATOM     58  CA  ARG    15      21.562  -9.606  -4.086  1.00  0.00              
ATOM     59  C   ARG    15      20.624  -8.981  -5.128  1.00  0.00              
ATOM     60  O   ARG    15      19.909  -8.015  -4.847  1.00  0.00              
ATOM     61  N   GLN    16      20.588  -9.534  -6.351  1.00  0.00              
ATOM     62  CA  GLN    16      19.744  -8.972  -7.391  1.00  0.00              
ATOM     63  C   GLN    16      18.308  -9.260  -7.024  1.00  0.00              
ATOM     64  O   GLN    16      17.438  -8.407  -7.168  1.00  0.00              
ATOM     65  N   ALA    17      18.004 -10.439  -6.474  1.00  0.00              
ATOM     66  CA  ALA    17      16.646 -10.744  -6.012  1.00  0.00              
ATOM     67  C   ALA    17      16.142  -9.708  -5.030  1.00  0.00              
ATOM     68  O   ALA    17      15.001  -9.218  -5.120  1.00  0.00              
ATOM     69  N   GLN    18      17.012  -9.347  -4.074  1.00  0.00              
ATOM     70  CA  GLN    18      16.663  -8.315  -3.104  1.00  0.00              
ATOM     71  C   GLN    18      16.471  -6.934  -3.712  1.00  0.00              
ATOM     72  O   GLN    18      15.555  -6.189  -3.325  1.00  0.00              
ATOM     73  N   ALA    19      17.335  -6.547  -4.663  1.00  0.00              
ATOM     74  CA  ALA    19      17.152  -5.257  -5.341  1.00  0.00              
ATOM     75  C   ALA    19      15.810  -5.201  -6.035  1.00  0.00              
ATOM     76  O   ALA    19      15.130  -4.152  -5.999  1.00  0.00              
ATOM     77  N   VAL    20      15.380  -6.289  -6.675  1.00  0.00              
ATOM     78  CA  VAL    20      14.094  -6.335  -7.372  1.00  0.00              
ATOM     79  C   VAL    20      12.937  -6.144  -6.380  1.00  0.00              
ATOM     80  O   VAL    20      12.039  -5.348  -6.626  1.00  0.00              
ATOM     81  N   THR    21      12.930  -6.894  -5.265  1.00  0.00              
ATOM     82  CA  THR    21      11.891  -6.786  -4.265  1.00  0.00              
ATOM     83  C   THR    21      11.914  -5.412  -3.643  1.00  0.00              
ATOM     84  O   THR    21      10.855  -4.809  -3.370  1.00  0.00              
ATOM     85  N   THR    22      13.093  -4.835  -3.392  1.00  0.00              
ATOM     86  CA  THR    22      13.196  -3.505  -2.793  1.00  0.00              
ATOM     87  C   THR    22      12.538  -2.466  -3.678  1.00  0.00              
ATOM     88  O   THR    22      11.792  -1.613  -3.216  1.00  0.00              
ATOM     89  N   THR    23      12.741  -2.525  -4.987  1.00  0.00              
ATOM     90  CA  THR    23      12.128  -1.536  -5.882  1.00  0.00              
ATOM     91  C   THR    23      10.611  -1.608  -5.761  1.00  0.00              
ATOM     92  O   THR    23       9.899  -0.600  -5.713  1.00  0.00              
ATOM     93  N   TYR    24      10.091  -2.824  -5.727  1.00  0.00              
ATOM     94  CA  TYR    24       8.632  -3.000  -5.623  1.00  0.00              
ATOM     95  C   TYR    24       8.144  -2.365  -4.326  1.00  0.00              
ATOM     96  O   TYR    24       7.173  -1.610  -4.292  1.00  0.00              
ATOM     97  N   SER    25       9.607  -0.136  -2.289  1.00  0.00              
ATOM     98  CA  SER    25       9.793   1.295  -2.227  1.00  0.00              
ATOM     99  C   SER    25       8.686   2.045  -2.942  1.00  0.00              
ATOM    100  O   SER    25       8.268   3.133  -2.531  1.00  0.00              
ATOM    101  N   ASN    26       8.187   1.456  -4.034  1.00  0.00              
ATOM    102  CA  ASN    26       7.067   2.064  -4.784  1.00  0.00              
ATOM    103  C   ASN    26       5.735   1.865  -4.065  1.00  0.00              
ATOM    104  O   ASN    26       4.745   2.377  -4.634  1.00  0.00              
ATOM    105  N   ILE    27       5.649   1.237  -2.921  1.00  0.00              
ATOM    106  CA  ILE    27       4.409   1.118  -2.182  1.00  0.00              
ATOM    107  C   ILE    27       4.312   2.114  -1.025  1.00  0.00              
ATOM    108  O   ILE    27       3.238   2.242  -0.457  1.00  0.00              
ATOM    109  N   THR    28       5.420   2.767  -0.657  1.00  0.00              
ATOM    110  CA  THR    28       5.514   3.493   0.585  1.00  0.00              
ATOM    111  C   THR    28       4.403   4.526   0.775  1.00  0.00              
ATOM    112  O   THR    28       3.998   4.727   1.912  1.00  0.00              
ATOM    113  N   LEU    29       3.985   5.168  -0.318  1.00  0.00              
ATOM    114  CA  LEU    29       3.023   6.255  -0.193  1.00  0.00              
ATOM    115  C   LEU    29       1.602   5.817  -0.516  1.00  0.00              
ATOM    116  O   LEU    29       0.718   6.638  -0.623  1.00  0.00              
ATOM    117  N   GLU    30       1.364   4.513  -0.647  1.00  0.00              
ATOM    118  CA  GLU    30       0.021   4.023  -0.911  1.00  0.00              
ATOM    119  C   GLU    30      -0.950   4.528   0.152  1.00  0.00              
ATOM    120  O   GLU    30      -0.670   4.509   1.346  1.00  0.00              
ATOM    121  N   ASP    31      -2.141   4.953  -0.297  1.00  0.00              
ATOM    122  CA  ASP    31      -3.144   5.520   0.583  1.00  0.00              
ATOM    123  C   ASP    31      -4.152   4.504   1.103  1.00  0.00              
ATOM    124  O   ASP    31      -4.940   4.838   2.000  1.00  0.00              
ATOM    125  N   ASP    32      -4.179   3.321   0.520  1.00  0.00              
ATOM    126  CA  ASP    32      -5.233   2.331   0.838  1.00  0.00              
ATOM    127  C   ASP    32      -4.688   0.942   0.691  1.00  0.00              
ATOM    128  O   ASP    32      -4.024   0.614  -0.308  1.00  0.00              
ATOM    129  N   PHE    37      -4.959   0.103   1.674  1.00  0.00              
ATOM    130  CA  PHE    37      -4.596  -1.303   1.699  1.00  0.00              
ATOM    131  C   PHE    37      -5.875  -2.127   1.802  1.00  0.00              
ATOM    132  O   PHE    37      -6.837  -1.746   2.445  1.00  0.00              
ATOM    133  N   ARG    38      -5.868  -3.272   1.129  1.00  0.00              
ATOM    134  CA  ARG    38      -7.008  -4.170   1.187  1.00  0.00              
ATOM    135  C   ARG    38      -6.570  -5.562   1.560  1.00  0.00              
ATOM    136  O   ARG    38      -5.465  -6.004   1.222  1.00  0.00              
ATOM    137  N   LEU    39      -7.427  -6.263   2.276  1.00  0.00              
ATOM    138  CA  LEU    39      -7.193  -7.642   2.696  1.00  0.00              
ATOM    139  C   LEU    39      -8.239  -8.557   2.064  1.00  0.00              
ATOM    140  O   LEU    39      -9.427  -8.270   2.146  1.00  0.00              
ATOM    141  N   VAL    40      -7.807  -9.663   1.461  1.00  0.00              
ATOM    142  CA  VAL    40      -8.638 -10.763   1.007  1.00  0.00              
ATOM    143  C   VAL    40      -8.769 -11.708   2.204  1.00  0.00              
ATOM    144  O   VAL    40      -7.853 -12.474   2.533  1.00  0.00              
ATOM    145  N   ASP    43      -9.901 -11.611   2.919  1.00  0.00              
ATOM    146  CA  ASP    43     -10.106 -12.317   4.173  1.00  0.00              
ATOM    147  C   ASP    43     -10.372 -13.782   3.897  1.00  0.00              
ATOM    148  O   ASP    43     -10.601 -14.217   2.764  1.00  0.00              
ATOM    149  N   THR    44     -10.311 -14.566   4.963  1.00  0.00              
ATOM    150  CA  THR    44     -10.457 -16.016   4.859  1.00  0.00              
ATOM    151  C   THR    44     -11.773 -16.379   4.188  1.00  0.00              
ATOM    152  O   THR    44     -11.797 -17.381   3.458  1.00  0.00              
ATOM    153  N   GLU    45     -12.850 -15.658   4.409  1.00  0.00              
ATOM    154  CA  GLU    45     -14.129 -15.967   3.815  1.00  0.00              
ATOM    155  C   GLU    45     -14.261 -15.459   2.373  1.00  0.00              
ATOM    156  O   GLU    45     -15.313 -15.667   1.749  1.00  0.00              
ATOM    157  N   GLY    46     -13.213 -14.860   1.818  1.00  0.00              
ATOM    158  CA  GLY    46     -13.235 -14.393   0.448  1.00  0.00              
ATOM    159  C   GLY    46     -13.678 -12.975   0.248  1.00  0.00              
ATOM    160  O   GLY    46     -13.584 -12.472  -0.883  1.00  0.00              
ATOM    161  N   ARG    47     -14.156 -12.318   1.311  1.00  0.00              
ATOM    162  CA  ARG    47     -14.506 -10.920   1.186  1.00  0.00              
ATOM    163  C   ARG    47     -13.258 -10.049   1.251  1.00  0.00              
ATOM    164  O   ARG    47     -12.274 -10.464   1.825  1.00  0.00              
ATOM    165  N   MET    48     -13.347  -8.882   0.657  1.00  0.00              
ATOM    166  CA  MET    48     -12.229  -7.932   0.616  1.00  0.00              
ATOM    167  C   MET    48     -12.595  -6.725   1.436  1.00  0.00              
ATOM    168  O   MET    48     -13.691  -6.159   1.262  1.00  0.00              
ATOM    169  N   ARG    51     -11.709  -6.315   2.312  1.00  0.00              
ATOM    170  CA  ARG    51     -11.925  -5.124   3.124  1.00  0.00              
ATOM    171  C   ARG    51     -10.796  -4.115   2.860  1.00  0.00              
ATOM    172  O   ARG    51      -9.616  -4.480   2.923  1.00  0.00              
ATOM    173  N   ALA    52     -11.182  -2.853   2.630  1.00  0.00              
ATOM    174  CA  ALA    52     -10.257  -1.764   2.388  1.00  0.00              
ATOM    175  C   ALA    52     -10.108  -0.862   3.596  1.00  0.00              
ATOM    176  O   ALA    52     -11.078  -0.607   4.338  1.00  0.00              
ATOM    177  N   TRP    53      -8.907  -0.389   3.821  1.00  0.00              
ATOM    178  CA  TRP    53      -8.568   0.491   4.919  1.00  0.00              
ATOM    179  C   TRP    53      -7.702   1.669   4.469  1.00  0.00              
ATOM    180  O   TRP    53      -6.848   1.511   3.585  1.00  0.00              
ATOM    181  N   ASN    54      -7.910   2.817   5.107  1.00  0.00              
ATOM    182  CA  ASN    54      -7.005   3.928   4.965  1.00  0.00              
ATOM    183  C   ASN    54      -5.634   3.537   5.545  1.00  0.00              
ATOM    184  O   ASN    54      -5.554   3.139   6.699  1.00  0.00              
ATOM    185  N   PHE    55      -4.592   3.729   4.741  1.00  0.00              
ATOM    186  CA  PHE    55      -3.215   3.473   5.132  1.00  0.00              
ATOM    187  C   PHE    55      -2.505   4.787   5.375  1.00  0.00              
ATOM    188  O   PHE    55      -2.448   5.609   4.435  1.00  0.00              
ATOM    189  N  AGLU    56      -2.028   4.980   6.596  1.00  0.00              
ATOM    190  N  BGLU    56      -2.021   5.005   6.593  1.00  0.00              
ATOM    191  CA AGLU    56      -1.368   6.157   7.119  1.00  0.00              
ATOM    192  CA BGLU    56      -1.311   6.250   6.861  1.00  0.00              
ATOM    193  C  AGLU    56       0.149   6.156   6.979  1.00  0.00              
ATOM    194  C  BGLU    56       0.190   6.124   6.647  1.00  0.00              
ATOM    195  O  AGLU    56       0.778   7.224   6.877  1.00  0.00              
ATOM    196  O  BGLU    56       0.817   7.090   6.193  1.00  0.00              
ATOM    197  N   PRO    57       0.747   4.986   7.028  1.00  0.00              
ATOM    198  CA  PRO    57       2.191   4.819   7.049  1.00  0.00              
ATOM    199  C   PRO    57       2.569   3.451   6.641  1.00  0.00              
ATOM    200  O   PRO    57       1.801   2.546   6.920  1.00  0.00              
ATOM    201  N   ILE    67       3.731   3.306   6.030  1.00  0.00              
ATOM    202  CA  ILE    67       4.296   2.012   5.731  1.00  0.00              
ATOM    203  C   ILE    67       5.811   2.013   5.870  1.00  0.00              
ATOM    204  O   ILE    67       6.404   2.985   5.419  1.00  0.00              
ATOM    205  N   ARG    68       6.319   0.935   6.421  1.00  0.00              
ATOM    206  CA  ARG    68       7.752   0.676   6.410  1.00  0.00              
ATOM    207  C   ARG    68       7.910  -0.782   6.011  1.00  0.00              
ATOM    208  O   ARG    68       6.969  -1.548   6.182  1.00  0.00              
ATOM    209  N   THR    69       9.058  -1.180   5.532  1.00  0.00              
ATOM    210  CA  THR    69       9.306  -2.576   5.204  1.00  0.00              
ATOM    211  C   THR    69      10.764  -2.921   5.426  1.00  0.00              
ATOM    212  O   THR    69      11.638  -2.048   5.408  1.00  0.00              
ATOM    213  N   SER    70      10.957  -4.241   5.518  1.00  0.00              
ATOM    214  CA  SER    70      12.342  -4.760   5.507  1.00  0.00              
ATOM    215  C   SER    70      12.291  -6.195   5.008  1.00  0.00              
ATOM    216  O   SER    70      11.381  -6.939   5.382  1.00  0.00              
ATOM    217  N   GLY    71      13.267  -6.604   4.198  1.00  0.00              
ATOM    218  CA  GLY    71      13.369  -7.984   3.819  1.00  0.00              
ATOM    219  C   GLY    71      13.848  -8.788   5.040  1.00  0.00              
ATOM    220  O   GLY    71      14.787  -8.353   5.703  1.00  0.00              
ATOM    221  N   ILE    72      13.199  -9.907   5.315  1.00  0.00              
ATOM    222  CA  ILE    72      13.523 -10.809   6.406  1.00  0.00              
ATOM    223  C   ILE    72      14.437 -11.948   5.989  1.00  0.00              
ATOM    224  O   ILE    72      15.460 -12.222   6.612  1.00  0.00              
ATOM    225  N   ARG    73      14.124 -12.629   4.877  1.00  0.00              
ATOM    226  CA  ARG    73      14.805 -13.761   4.368  1.00  0.00              
ATOM    227  C   ARG    73      14.858 -13.678   2.820  1.00  0.00              
ATOM    228  O   ARG    73      13.871 -13.261   2.188  1.00  0.00              
ATOM    229  N   THR    74      15.962 -14.170   2.269  1.00  0.00              
ATOM    230  CA  THR    74      16.089 -14.431   0.842  1.00  0.00              
ATOM    231  C   THR    74      16.694 -15.804   0.666  1.00  0.00              
ATOM    232  O   THR    74      17.771 -16.094   1.228  1.00  0.00              
END
