
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0321AL242_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321AL242_2-D1.T0321_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      W       2           -
LGA    -       -      E       3           -
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    -       -      M       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      G      11           -
LGA    -       -      I      12           -
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    -       -      D      19           -
LGA    -       -      E      20           -
LGA    -       -      L      21           -
LGA    -       -      V      22           -
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    -       -      V      29           -
LGA    -       -      I      30           -
LGA    -       -      R      31           -
LGA    -       -      S      32           -
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    -       -      G      37           -
LGA    -       -      L      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      N      41           -
LGA    -       -      R      42           -
LGA    -       -      P      43           -
LGA    -       -      F      44           -
LGA    -       -      E      45           -
LGA    -       -      T      46           -
LGA    -       -      R      47           -
LGA    M       1      M      48          4.090
LGA    W       2      P      49          3.161
LGA    E       3      M      50          1.007
LGA    I       4      L      51          1.278
LGA    Y       5      T      52          2.731
LGA    D       6      Q      53          2.797
LGA    A       7      N      54          1.849
LGA    M       8      L      55          1.947
LGA    I       9      -       -           -
LGA    N      10      L      56          1.428
LGA    G      11      G      57          2.586
LGA    I      12      L      58          5.669
LGA    P      13      -       -           -
LGA    E      14      -       -           -
LGA    D      15      -       -           -
LGA    F      16      P      59          2.318
LGA    L      17      L      60          3.986
LGA    V      18      R      61          2.835
LGA    D      19      V      62          1.661
LGA    E      20      A      63           #
LGA    L      21      A      64           -
LGA    V      22      G      65           -
LGA    C      23      C      66           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    G      24      S      69           #
LGA    W      70      -       -           -
LGA    N      71      -       -           -
LGA    Y      72      -       -           -
LGA    V      73      W      70          3.062
LGA    E      74      N      71          1.987
LGA    A      75      Y      72          2.399
LGA    S      76      V      73          1.477
LGA    I      77      E      74          0.316
LGA    G      78      A      75          1.234
LGA    L      79      S      76          1.578
LGA    A      80      I      77          1.231
LGA    A      81      G      78          0.804
LGA    I      82      L      79          1.030
LGA    N      83      A      80          1.436
LGA    A      84      A      81          1.201
LGA    Y      85      I      82          1.058
LGA    Y      86      N      83          1.099
LGA    N      87      A      84          1.328
LGA    N      88      Y      85          2.068
LGA    P      89      Y      86           -
LGA    -       -      N      87           -
LGA    -       -      N      88           -
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      A      92           -
LGA    -       -      R      93           -
LGA    -       -      E      94           -
LGA    -       -      H      95           -
LGA    -       -      G      96           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   96    5.0     31    2.31    12.90     24.566     1.287

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.470441 * X  +   0.359777 * Y  +   0.805758 * Z  + -21.704704
  Y_new =   0.360067 * X  +   0.911901 * Y  +  -0.196946 * Z  +  56.788563
  Z_new =  -0.805628 * X  +   0.197475 * Y  +  -0.558540 * Z  +  64.484428 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.801753   -0.339839  [ DEG:   160.5286    -19.4714 ]
  Theta =   0.936735    2.204858  [ DEG:    53.6709    126.3290 ]
  Phi   =   2.488320   -0.653273  [ DEG:   142.5702    -37.4298 ]
 
# 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: T0321AL242_2-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321AL242_2-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   96   5.0   31   2.31   12.90  24.566
REMARK  ---------------------------------------------------------- 
MOLECULE T0321AL242_2-D1
REMARK Aligment from pdb entry: 1r6v_A
ATOM      1  N   MET     1      -9.070  59.385  49.567  1.00  0.00              
ATOM      2  CA  MET     1      -8.551  58.648  50.719  1.00  0.00              
ATOM      3  C   MET     1      -8.554  59.506  51.986  1.00  0.00              
ATOM      4  O   MET     1      -8.751  58.992  53.101  1.00  0.00              
ATOM      5  N   TRP     2      -8.333  60.810  51.821  1.00  0.00              
ATOM      6  CA  TRP     2      -8.346  61.710  52.960  1.00  0.00              
ATOM      7  C   TRP     2      -9.750  61.845  53.558  1.00  0.00              
ATOM      8  O   TRP     2      -9.899  61.772  54.776  1.00  0.00              
ATOM      9  N   GLU     3     -10.783  62.007  52.733  1.00  0.00              
ATOM     10  CA  GLU     3     -12.117  62.136  53.300  1.00  0.00              
ATOM     11  C   GLU     3     -12.645  60.800  53.838  1.00  0.00              
ATOM     12  O   GLU     3     -13.419  60.787  54.792  1.00  0.00              
ATOM     13  N   ILE     4     -12.223  59.687  53.247  1.00  0.00              
ATOM     14  CA  ILE     4     -12.630  58.381  53.771  1.00  0.00              
ATOM     15  C   ILE     4     -12.014  58.231  55.178  1.00  0.00              
ATOM     16  O   ILE     4     -12.690  57.802  56.117  1.00  0.00              
ATOM     17  N   TYR     5     -10.736  58.581  55.323  1.00  0.00              
ATOM     18  CA  TYR     5     -10.099  58.513  56.636  1.00  0.00              
ATOM     19  C   TYR     5     -10.895  59.367  57.639  1.00  0.00              
ATOM     20  O   TYR     5     -11.135  58.952  58.780  1.00  0.00              
ATOM     21  N   ASP     6     -11.304  60.564  57.221  1.00  0.00              
ATOM     22  CA  ASP     6     -12.099  61.428  58.100  1.00  0.00              
ATOM     23  C   ASP     6     -13.395  60.728  58.495  1.00  0.00              
ATOM     24  O   ASP     6     -13.813  60.804  59.643  1.00  0.00              
ATOM     25  N   ALA     7     -14.044  60.070  57.531  1.00  0.00              
ATOM     26  CA  ALA     7     -15.286  59.362  57.829  1.00  0.00              
ATOM     27  C   ALA     7     -15.087  58.174  58.763  1.00  0.00              
ATOM     28  O   ALA     7     -15.929  57.904  59.628  1.00  0.00              
ATOM     29  N   MET     8     -13.978  57.458  58.591  1.00  0.00              
ATOM     30  CA  MET     8     -13.675  56.298  59.438  1.00  0.00              
ATOM     31  C   MET     8     -13.365  56.771  60.847  1.00  0.00              
ATOM     32  O   MET     8     -13.811  56.177  61.831  1.00  0.00              
ATOM     33  N   ILE     9     -12.617  57.861  60.937  1.00  0.00              
ATOM     34  CA  ILE     9     -12.293  58.416  62.255  1.00  0.00              
ATOM     35  C   ILE     9     -13.581  58.905  62.945  1.00  0.00              
ATOM     36  O   ILE     9     -13.801  58.673  64.139  1.00  0.00              
ATOM     37  N   ASN    10     -14.432  59.596  62.193  1.00  0.00              
ATOM     38  CA  ASN    10     -15.689  60.096  62.731  1.00  0.00              
ATOM     39  C   ASN    10     -16.532  58.927  63.256  1.00  0.00              
ATOM     40  O   ASN    10     -17.056  58.967  64.372  1.00  0.00              
ATOM     41  N   GLY    11     -16.658  57.878  62.449  1.00  0.00              
ATOM     42  CA  GLY    11     -17.461  56.720  62.847  1.00  0.00              
ATOM     43  C   GLY    11     -16.925  56.062  64.114  1.00  0.00              
ATOM     44  O   GLY    11     -17.692  55.645  64.992  1.00  0.00              
ATOM     45  N   ILE    12     -15.608  55.938  64.187  1.00  0.00              
ATOM     46  CA  ILE    12     -14.965  55.344  65.358  1.00  0.00              
ATOM     47  C   ILE    12     -15.222  56.206  66.592  1.00  0.00              
ATOM     48  O   ILE    12     -15.596  55.706  67.660  1.00  0.00              
ATOM     49  N   PRO    13     -15.006  57.503  66.432  1.00  0.00              
ATOM     50  CA  PRO    13     -15.190  58.450  67.526  1.00  0.00              
ATOM     51  C   PRO    13     -16.633  58.531  67.989  1.00  0.00              
ATOM     52  O   PRO    13     -16.893  58.877  69.142  1.00  0.00              
ATOM     53  N   GLU    14     -17.570  58.229  67.093  1.00  0.00              
ATOM     54  CA  GLU    14     -18.978  58.292  67.422  1.00  0.00              
ATOM     55  C   GLU    14     -19.604  56.952  67.765  1.00  0.00              
ATOM     56  O   GLU    14     -20.823  56.801  67.705  1.00  0.00              
ATOM     57  N   ASP    15     -18.767  55.975  68.099  1.00  0.00              
ATOM     58  CA  ASP    15     -19.301  54.706  68.547  1.00  0.00              
ATOM     59  C   ASP    15     -19.512  53.497  67.662  1.00  0.00              
ATOM     60  O   ASP    15     -19.991  52.483  68.181  1.00  0.00              
ATOM     61  N   PHE    16     -19.199  53.564  66.369  1.00  0.00              
ATOM     62  CA  PHE    16     -19.375  52.374  65.528  1.00  0.00              
ATOM     63  C   PHE    16     -18.467  51.256  66.052  1.00  0.00              
ATOM     64  O   PHE    16     -17.312  51.509  66.389  1.00  0.00              
ATOM     65  N   LEU    17     -18.985  50.027  66.150  1.00  0.00              
ATOM     66  CA  LEU    17     -18.170  48.907  66.614  1.00  0.00              
ATOM     67  C   LEU    17     -17.789  47.955  65.484  1.00  0.00              
ATOM     68  O   LEU    17     -16.938  47.084  65.650  1.00  0.00              
ATOM     69  N   VAL    18     -18.439  48.107  64.335  1.00  0.00              
ATOM     70  CA  VAL    18     -18.081  47.306  63.167  1.00  0.00              
ATOM     71  C   VAL    18     -18.430  48.165  61.946  1.00  0.00              
ATOM     72  O   VAL    18     -19.366  48.968  61.993  1.00  0.00              
ATOM     73  N   ASP    19     -17.626  48.056  60.888  1.00  0.00              
ATOM     74  CA  ASP    19     -17.865  48.812  59.644  1.00  0.00              
ATOM     75  C   ASP    19     -17.889  47.858  58.470  1.00  0.00              
ATOM     76  O   ASP    19     -17.147  46.882  58.452  1.00  0.00              
ATOM     77  N   GLU    20     -18.722  48.170  57.480  1.00  0.00              
ATOM     78  CA  GLU    20     -18.839  47.346  56.280  1.00  0.00              
ATOM     79  C   GLU    20     -18.236  48.138  55.112  1.00  0.00              
ATOM     80  O   GLU    20     -18.610  49.285  54.896  1.00  0.00              
ATOM     81  N   LEU    21     -17.282  47.535  54.407  1.00  0.00              
ATOM     82  CA  LEU    21     -16.602  48.172  53.263  1.00  0.00              
ATOM     83  C   LEU    21     -16.628  47.296  52.014  1.00  0.00              
ATOM     84  O   LEU    21     -16.231  46.131  52.078  1.00  0.00              
ATOM     85  N   VAL    22     -17.060  47.842  50.884  1.00  0.00              
ATOM     86  CA  VAL    22     -17.013  47.068  49.644  1.00  0.00              
ATOM     87  C   VAL    22     -16.529  47.997  48.545  1.00  0.00              
ATOM     88  O   VAL    22     -17.263  48.330  47.607  1.00  0.00              
ATOM     89  N   CYS    23     -15.283  48.426  48.693  1.00  0.00              
ATOM     90  CA  CYS    23     -14.624  49.320  47.752  1.00  0.00              
ATOM     91  C   CYS    23     -13.127  49.075  47.813  1.00  0.00              
ATOM     92  O   CYS    23     -12.628  48.400  48.717  1.00  0.00              
ATOM     93  N   GLY    24     -12.397  49.620  46.850  1.00  0.00              
ATOM     94  CA  GLY    24     -10.967  49.447  46.885  1.00  0.00              
ATOM     95  C   GLY    24     -10.226  49.952  45.677  1.00  0.00              
ATOM     96  O   GLY    24     -10.827  50.444  44.722  1.00  0.00              
ATOM     97  N   TRP    70      -8.909  49.810  45.738  1.00  0.00              
ATOM     98  CA  TRP    70      -8.043  50.251  44.660  1.00  0.00              
ATOM     99  C   TRP    70      -6.635  49.721  44.843  1.00  0.00              
ATOM    100  O   TRP    70      -6.276  49.226  45.910  1.00  0.00              
ATOM    101  N   ASN    71      -5.827  49.839  43.794  1.00  0.00              
ATOM    102  CA  ASN    71      -4.449  49.360  43.805  1.00  0.00              
ATOM    103  C   ASN    71      -3.513  50.045  44.819  1.00  0.00              
ATOM    104  O   ASN    71      -2.659  49.401  45.441  1.00  0.00              
ATOM    105  N   TYR    72      -3.689  51.346  44.993  1.00  0.00              
ATOM    106  CA  TYR    72      -2.796  52.102  45.856  1.00  0.00              
ATOM    107  C   TYR    72      -2.650  51.771  47.324  1.00  0.00              
ATOM    108  O   TYR    72      -3.641  51.719  48.040  1.00  0.00              
ATOM    109  N   VAL    73      -1.411  51.539  47.768  1.00  0.00              
ATOM    110  CA  VAL    73      -1.147  51.275  49.186  1.00  0.00              
ATOM    111  C   VAL    73      -1.088  52.667  49.781  1.00  0.00              
ATOM    112  O   VAL    73      -0.194  53.448  49.455  1.00  0.00              
ATOM    113  N   GLU    74      -2.027  52.975  50.661  1.00  0.00              
ATOM    114  CA  GLU    74      -2.078  54.303  51.270  1.00  0.00              
ATOM    115  C   GLU    74      -1.664  54.250  52.722  1.00  0.00              
ATOM    116  O   GLU    74      -2.215  53.465  53.498  1.00  0.00              
ATOM    117  N   ALA    75      -0.687  55.068  53.101  1.00  0.00              
ATOM    118  CA  ALA    75      -0.283  55.085  54.502  1.00  0.00              
ATOM    119  C   ALA    75      -1.367  55.722  55.339  1.00  0.00              
ATOM    120  O   ALA    75      -1.556  55.386  56.519  1.00  0.00              
ATOM    121  N   SER    76      -2.075  56.671  54.738  1.00  0.00              
ATOM    122  CA  SER    76      -3.166  57.336  55.425  1.00  0.00              
ATOM    123  C   SER    76      -4.302  56.366  55.711  1.00  0.00              
ATOM    124  O   SER    76      -4.828  56.321  56.828  1.00  0.00              
ATOM    125  N   ILE    77      -4.685  55.579  54.708  1.00  0.00              
ATOM    126  CA  ILE    77      -5.772  54.628  54.921  1.00  0.00              
ATOM    127  C   ILE    77      -5.375  53.541  55.928  1.00  0.00              
ATOM    128  O   ILE    77      -6.217  53.063  56.697  1.00  0.00              
ATOM    129  N   GLY    78      -4.097  53.165  55.917  1.00  0.00              
ATOM    130  CA  GLY    78      -3.563  52.152  56.836  1.00  0.00              
ATOM    131  C   GLY    78      -3.763  52.707  58.239  1.00  0.00              
ATOM    132  O   GLY    78      -4.267  52.034  59.143  1.00  0.00              
ATOM    133  N   LEU    79      -3.371  53.966  58.404  1.00  0.00              
ATOM    134  CA  LEU    79      -3.503  54.617  59.709  1.00  0.00              
ATOM    135  C   LEU    79      -4.947  54.687  60.181  1.00  0.00              
ATOM    136  O   LEU    79      -5.243  54.500  61.360  1.00  0.00              
ATOM    137  N   ALA    80      -5.864  54.970  59.261  1.00  0.00              
ATOM    138  CA  ALA    80      -7.268  55.061  59.620  1.00  0.00              
ATOM    139  C   ALA    80      -7.831  53.691  60.025  1.00  0.00              
ATOM    140  O   ALA    80      -8.585  53.576  60.995  1.00  0.00              
ATOM    141  N   ALA    81      -7.495  52.664  59.255  1.00  0.00              
ATOM    142  CA  ALA    81      -7.961  51.330  59.586  1.00  0.00              
ATOM    143  C   ALA    81      -7.385  50.866  60.907  1.00  0.00              
ATOM    144  O   ALA    81      -8.096  50.257  61.713  1.00  0.00              
ATOM    145  N   ILE    82      -6.112  51.170  61.141  1.00  0.00              
ATOM    146  CA  ILE    82      -5.459  50.766  62.385  1.00  0.00              
ATOM    147  C   ILE    82      -6.024  51.552  63.573  1.00  0.00              
ATOM    148  O   ILE    82      -6.106  51.036  64.686  1.00  0.00              
ATOM    149  N   ASN    83      -6.408  52.808  63.331  1.00  0.00              
ATOM    150  CA  ASN    83      -7.016  53.650  64.365  1.00  0.00              
ATOM    151  C   ASN    83      -8.332  53.008  64.804  1.00  0.00              
ATOM    152  O   ASN    83      -8.628  52.865  65.991  1.00  0.00              
ATOM    153  N   ALA    84      -9.146  52.634  63.825  1.00  0.00              
ATOM    154  CA  ALA    84     -10.409  52.026  64.160  1.00  0.00              
ATOM    155  C   ALA    84     -10.198  50.713  64.938  1.00  0.00              
ATOM    156  O   ALA    84     -10.847  50.481  65.960  1.00  0.00              
ATOM    157  N   TYR    85      -9.300  49.856  64.466  1.00  0.00              
ATOM    158  CA  TYR    85      -9.081  48.572  65.146  1.00  0.00              
ATOM    159  C   TYR    85      -8.497  48.756  66.556  1.00  0.00              
ATOM    160  O   TYR    85      -8.817  47.985  67.477  1.00  0.00              
ATOM    161  N   TYR    86      -7.671  49.782  66.724  1.00  0.00              
ATOM    162  CA  TYR    86      -7.077  50.062  68.034  1.00  0.00              
ATOM    163  C   TYR    86      -8.163  50.503  69.007  1.00  0.00              
ATOM    164  O   TYR    86      -8.020  50.359  70.221  1.00  0.00              
ATOM    165  N   ASN    87      -9.254  51.039  68.471  1.00  0.00              
ATOM    166  CA  ASN    87     -10.385  51.455  69.282  1.00  0.00              
ATOM    167  C   ASN    87     -11.378  50.294  69.406  1.00  0.00              
ATOM    168  O   ASN    87     -12.492  50.463  69.900  1.00  0.00              
ATOM    169  N   ASN    88     -10.955  49.117  68.943  1.00  0.00              
ATOM    170  CA  ASN    88     -11.778  47.923  69.033  1.00  0.00              
ATOM    171  C   ASN    88     -12.838  47.730  67.969  1.00  0.00              
ATOM    172  O   ASN    88     -13.723  46.898  68.150  1.00  0.00              
ATOM    173  N   PRO    89     -12.761  48.474  66.869  1.00  0.00              
ATOM    174  CA  PRO    89     -13.766  48.333  65.818  1.00  0.00              
ATOM    175  C   PRO    89     -13.346  47.271  64.818  1.00  0.00              
ATOM    176  O   PRO    89     -12.184  47.223  64.392  1.00  0.00              
END
