
#######################################################
#                                                     #
#                        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   20 (  100),  selected   20 , name T0321TS103_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS103_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    M       1      E      45          1.034
LGA    W       2      T      46          2.957
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      P      49           -
LGA    -       -      M      50           -
LGA    -       -      L      51           -
LGA    -       -      T      52           -
LGA    -       -      Q      53           -
LGA    -       -      N      54           -
LGA    -       -      L      55           -
LGA    -       -      L      56           -
LGA    -       -      G      57           -
LGA    -       -      L      58           -
LGA    -       -      P      59           -
LGA    -       -      L      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    -       -      G      65           -
LGA    -       -      C      66           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    E       3      N      71          3.456
LGA    I       4      Y      72          1.060
LGA    Y       5      V      73          1.149
LGA    D       6      E      74          0.822
LGA    A       7      A      75          0.252
LGA    S      76      S      76          0.417
LGA    L      79      I      77          0.357
LGA    A      80      G      78          0.626
LGA    A      81      L      79          0.532
LGA    I      82      A      80          0.244
LGA    N      83      A      81          0.762
LGA    A      84      I      82          1.061
LGA    Y      85      N      83          1.065
LGA    Y      86      A      84          0.567
LGA    N      87      Y      85          2.355
LGA    N      88      Y      86          2.307
LGA    -       -      N      87           -
LGA    P      89      N      88          0.677
LGA    Q      90      P      89          0.895
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)   20   96    5.0     20    1.44    10.00     19.764     1.302

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.594801 * X  +   0.473542 * Y  +   0.649592 * Z  +   3.191511
  Y_new =  -0.353446 * X  +   0.571724 * Y  +  -0.740410 * Z  +  65.298889
  Z_new =  -0.722003 * X  +  -0.669992 * Y  +  -0.172691 * Z  + 111.217094 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.823056    1.318537  [ DEG:  -104.4534     75.5466 ]
  Theta =   0.806693    2.334899  [ DEG:    46.2201    133.7799 ]
  Phi   =  -2.605430    0.536162  [ DEG:  -149.2802     30.7198 ]
 
# 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: T0321TS103_2-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS103_2-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20   96   5.0   20   1.44   10.00  19.764
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS103_2-D1
PFRMAT TS
TARGET T0321
MODEL 2
PARENT 2b4g_A
ATOM      1  N   MET     1       3.475  57.118  53.592  1.00  1.00
ATOM      2  CA  MET     1       2.952  58.316  52.945  1.00  1.00
ATOM      3  C   MET     1       1.510  58.086  52.539  1.00  1.00
ATOM      4  O   MET     1       0.774  57.392  53.226  1.00  1.00
ATOM      5  CB  MET     1       3.781  58.595  51.678  1.00  1.00
ATOM      6  N   TRP     2       1.105  58.641  51.410  1.00  1.00
ATOM      7  CA  TRP     2      -0.317  58.633  51.029  1.00  1.00
ATOM      8  C   TRP     2      -0.851  57.213  50.825  1.00  1.00
ATOM      9  O   TRP     2      -2.012  56.953  51.091  1.00  1.00
ATOM     10  CB  TRP     2      -0.568  59.493  49.790  1.00  1.00
ATOM     11  N   GLU     3       0.008  56.284  50.407  1.00  1.00
ATOM     12  CA  GLU     3      -0.400  54.880  50.238  1.00  1.00
ATOM     13  C   GLU     3      -1.017  54.251  51.485  1.00  1.00
ATOM     14  O   GLU     3      -1.881  53.390  51.365  1.00  1.00
ATOM     15  CB  GLU     3       0.801  53.995  49.902  1.00  1.00
ATOM     16  N   ILE     4      -0.574  54.680  52.669  1.00  1.00
ATOM     17  CA  ILE     4      -0.907  53.929  53.884  1.00  1.00
ATOM     18  C   ILE     4      -1.975  54.567  54.769  1.00  1.00
ATOM     19  O   ILE     4      -2.318  54.020  55.816  1.00  1.00
ATOM     20  CB  ILE     4       0.371  53.612  54.695  1.00  1.00
ATOM     21  N   TYR     5      -2.563  55.685  54.337  1.00  1.00
ATOM     22  CA  TYR     5      -3.511  56.376  55.237  1.00  1.00
ATOM     23  C   TYR     5      -4.724  55.516  55.659  1.00  1.00
ATOM     24  O   TYR     5      -4.951  55.333  56.859  1.00  1.00
ATOM     25  CB  TYR     5      -3.927  57.743  54.702  1.00  1.00
ATOM     26  N   ASP     6      -5.500  54.981  54.699  1.00  1.00
ATOM     27  CA  ASP     6      -6.580  54.078  55.115  1.00  1.00
ATOM     28  C   ASP     6      -6.163  52.861  55.954  1.00  1.00
ATOM     29  O   ASP     6      -6.899  52.445  56.870  1.00  1.00
ATOM     30  CB  ASP     6      -7.206  53.636  53.767  1.00  1.00
ATOM     31  N   ALA     7      -5.015  52.272  55.633  1.00  1.00
ATOM     32  CA  ALA     7      -4.477  51.177  56.431  1.00  1.00
ATOM     33  C   ALA     7      -4.164  51.647  57.867  1.00  1.00
ATOM     34  O   ALA     7      -4.511  50.965  58.820  1.00  1.00
ATOM     35  CB  ALA     7      -3.217  50.562  55.752  1.00  1.00
ATOM     36  N   SER    76      -3.520  52.816  58.004  1.00  1.00
ATOM     37  CA  SER    76      -3.184  53.372  59.329  1.00  1.00
ATOM     38  C   SER    76      -4.444  53.668  60.116  1.00  1.00
ATOM     39  O   SER    76      -4.548  53.275  61.263  1.00  1.00
ATOM     40  CB  SER    76      -2.345  54.631  59.214  1.00  1.00
ATOM     41  N   LEU    79      -5.397  54.354  59.479  1.00  1.00
ATOM     42  CA  LEU    79      -6.617  54.738  60.154  1.00  1.00
ATOM     43  C   LEU    79      -7.410  53.538  60.638  1.00  1.00
ATOM     44  O   LEU    79      -7.956  53.582  61.716  1.00  1.00
ATOM     45  CB  LEU    79      -7.507  55.613  59.277  1.00  1.00
ATOM     46  N   ALA    80      -7.445  52.483  59.823  1.00  1.00
ATOM     47  CA  ALA    80      -8.147  51.252  60.141  1.00  1.00
ATOM     48  C   ALA    80      -7.500  50.566  61.332  1.00  1.00
ATOM     49  O   ALA    80      -8.191  50.108  62.254  1.00  1.00
ATOM     50  CB  ALA    80      -8.140  50.315  58.917  1.00  1.00
ATOM     51  N   ALA    81      -6.166  50.502  61.314  1.00  1.00
ATOM     52  CA  ALA    81      -5.424  49.883  62.421  1.00  1.00
ATOM     53  C   ALA    81      -5.585  50.671  63.726  1.00  1.00
ATOM     54  O   ALA    81      -5.882  50.105  64.792  1.00  1.00
ATOM     55  CB  ALA    81      -3.947  49.695  62.040  1.00  1.00
ATOM     56  N   ILE    82      -5.429  51.984  63.649  1.00  1.00
ATOM     57  CA  ILE    82      -5.678  52.828  64.830  1.00  1.00
ATOM     58  C   ILE    82      -7.041  52.520  65.454  1.00  1.00
ATOM     59  O   ILE    82      -7.155  52.253  66.665  1.00  1.00
ATOM     60  CB  ILE    82      -5.608  54.331  64.467  1.00  1.00
ATOM     61  N   ASN    83      -8.074  52.567  64.627  1.00  1.00
ATOM     62  CA  ASN    83      -9.427  52.383  65.130  1.00  1.00
ATOM     63  C   ASN    83      -9.685  50.951  65.614  1.00  1.00
ATOM     64  O   ASN    83     -10.355  50.731  66.626  1.00  1.00
ATOM     65  CB  ASN    83     -10.441  52.796  64.069  1.00  1.00
ATOM     66  N   ALA    84      -9.136  49.974  64.906  1.00  1.00
ATOM     67  CA  ALA    84      -9.250  48.569  65.348  1.00  1.00
ATOM     68  C   ALA    84      -8.713  48.360  66.781  1.00  1.00
ATOM     69  O   ALA    84      -9.362  47.748  67.655  1.00  1.00
ATOM     70  CB  ALA    84      -8.537  47.672  64.376  1.00  1.00
ATOM     71  N   TYR    85      -7.531  48.891  67.039  1.00  1.00
ATOM     72  CA  TYR    85      -6.913  48.731  68.342  1.00  1.00
ATOM     73  C   TYR    85      -7.528  49.650  69.376  1.00  1.00
ATOM     74  O   TYR    85      -7.605  49.280  70.536  1.00  1.00
ATOM     75  CB  TYR    85      -5.387  48.895  68.245  1.00  1.00
ATOM     76  N   TYR    86      -7.997  50.821  68.952  1.00  1.00
ATOM     77  CA  TYR    86      -8.709  51.734  69.845  1.00  1.00
ATOM     78  C   TYR    86      -9.929  51.020  70.440  1.00  1.00
ATOM     79  O   TYR    86     -10.189  51.084  71.646  1.00  1.00
ATOM     80  CB  TYR    86      -9.123  53.012  69.103  1.00  1.00
ATOM     81  N   ASN    87     -10.406  47.691  70.499  1.00  1.00
ATOM     82  CA  ASN    87     -10.089  46.395  71.119  1.00  1.00
ATOM     83  C   ASN    87      -9.240  46.520  72.379  1.00  1.00
ATOM     84  O   ASN    87      -9.205  45.601  73.179  1.00  1.00
ATOM     85  CB  ASN    87      -9.392  45.460  70.130  1.00  1.00
ATOM     86  N   ASN    88      -8.558  47.651  72.543  1.00  1.00
ATOM     87  CA  ASN    88      -7.717  47.870  73.708  1.00  1.00
ATOM     88  C   ASN    88      -8.131  49.142  74.436  1.00  1.00
ATOM     89  O   ASN    88      -7.384  50.130  74.433  1.00  1.00
ATOM     90  CB  ASN    88      -6.254  47.968  73.268  1.00  1.00
ATOM     91  N   PRO    89      -9.322  49.129  75.075  1.00  1.00
ATOM     92  CA  PRO    89      -9.824  50.340  75.761  1.00  1.00
ATOM     93  C   PRO    89      -9.026  50.753  77.003  1.00  1.00
ATOM     94  O   PRO    89      -9.149  51.897  77.427  1.00  1.00
ATOM     95  CB  PRO    89     -11.272  49.979  76.120  1.00  1.00
ATOM     96  N   GLN    90      -8.226  49.849  77.574  1.00  1.00
ATOM     97  CA  GLN    90      -7.418  50.246  78.728  1.00  1.00
ATOM     98  C   GLN    90      -5.999  50.675  78.291  1.00  1.00
ATOM     99  O   GLN    90      -5.135  50.960  79.135  1.00  1.00
ATOM    100  CB  GLN    90      -7.422  49.163  79.830  1.00  1.00
TER
END
