
#######################################################
#                                                     #
#                        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  101 (  101),  selected  101 , name T0304TS599_5-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS599_5-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R      17      R      17           -
LGA    P      18      P      18           -
LGA    W      19      W      19           -
LGA    W      20      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    G      21      C      24          4.850
LGA    L      22      T      25          2.234
LGA    P      23      V      26          1.521
LGA    C      24      T      27          1.648
LGA    T      25      P      28          1.848
LGA    V      26      C      29          3.511
LGA    T      27      F      30          3.733
LGA    P      28      -       -           -
LGA    C      29      -       -           -
LGA    F      30      -       -           -
LGA    G      31      -       -           -
LGA    A      32      G      31          4.267
LGA    R      33      A      32          1.628
LGA    L      34      R      33           #
LGA    V      35      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    Q      36      R      47          5.006
LGA    E      37      A      48           -
LGA    G      38      G      49           -
LGA    N      39      I      50           -
LGA    R      40      -       -           -
LGA    L      41      -       -           -
LGA    H      42      -       -           -
LGA    Y      43      -       -           -
LGA    L      44      -       -           -
LGA    A      45      -       -           -
LGA    D      46      -       -           -
LGA    R      47      -       -           -
LGA    A      48      -       -           -
LGA    G      49      R      51           #
LGA    I      50      G      52          2.495
LGA    R      51      -       -           -
LGA    G      52      -       -           -
LGA    L      53      L      53          1.217
LGA    F      54      F      54          1.401
LGA    S      55      S      55          1.821
LGA    D      56      D      56          1.852
LGA    A      57      A      57          2.029
LGA    D      58      D      58          1.225
LGA    A      59      A      59          0.220
LGA    Y      60      Y      60          0.721
LGA    H      61      H      61          0.462
LGA    L      62      L      62          1.181
LGA    D      63      D      63          1.497
LGA    Q      64      Q      64          1.624
LGA    A      65      A      65          1.860
LGA    F      66      F      66          2.437
LGA    P      67      P      67          1.981
LGA    L      68      L      68          0.545
LGA    L      69      L      69          1.290
LGA    M      70      M      70          1.149
LGA    K      71      K      71          0.831
LGA    Q      72      Q      72          1.495
LGA    L      73      L      73          1.586
LGA    E      74      E      74          1.143
LGA    L      75      L      75          2.684
LGA    M      76      M      76          3.237
LGA    L      77      L      77          2.102
LGA    T      78      T      78          2.890
LGA    S      79      -       -           -
LGA    G      80      -       -           -
LGA    E      81      S      79          1.991
LGA    L      82      G      80          2.022
LGA    N      83      E      81           #
LGA    P      84      -       -           -
LGA    R      85      -       -           -
LGA    H      86      -       -           -
LGA    Q      87      L      82           #
LGA    H      88      N      83          2.617
LGA    T      89      P      84          5.123
LGA    V      90      -       -           -
LGA    T      91      -       -           -
LGA    L      92      -       -           -
LGA    Y      93      -       -           -
LGA    A      94      -       -           -
LGA    K      95      -       -           -
LGA    G      96      -       -           -
LGA    L      97      -       -           -
LGA    T      98      -       -           -
LGA    C      99      -       -           -
LGA    K     100      -       -           -
LGA    A     101      -       -           -
LGA    D     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      R      85          6.737
LGA    D     108      H      86          2.232
LGA    Y     109      Q      87          2.898
LGA    V     110      H      88          3.194
LGA    Y     111      T      89          2.635
LGA    L     112      V      90          1.710
LGA    A     113      T      91          1.446
LGA    V     114      L      92          1.373
LGA    Y     115      Y      93          2.181
LGA    P     116      A      94          2.125
LGA    T     117      K      95          4.338
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      Y     115           -
LGA    -       -      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  101    5.0     52    2.57    51.92     36.423     1.946

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.798578 * X  +  -0.469186 * Y  +   0.377010 * Z  +  43.772915
  Y_new =  -0.068240 * X  +  -0.692915 * Y  +  -0.717782 * Z  +  28.590361
  Z_new =   0.598010 * X  +   0.547478 * Y  +  -0.585365 * Z  +  39.196865 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.389626   -0.751967  [ DEG:   136.9155    -43.0845 ]
  Theta =  -0.641016   -2.500577  [ DEG:   -36.7275   -143.2725 ]
  Phi   =  -0.085245    3.056347  [ DEG:    -4.8842    175.1158 ]
 
# 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: T0304TS599_5-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS599_5-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  101  101   5.0   52   2.57   51.92  36.423
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS599_5-D1
PFRMAT TS                                                                       
TARGET T0304                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM     17  CA  ARG    17      23.335  28.078  35.761  1.00  0.00              
ATOM     18  CA  PRO    18      24.132  31.601  34.626  1.00  0.00              
ATOM     19  CA  TRP    19      26.994  32.622  36.977  1.00  0.00              
ATOM     20  CA  TRP    20      29.005  29.480  37.364  1.00  0.00              
ATOM     21  CA  GLY    21      32.527  30.256  36.289  1.00  0.00              
ATOM     22  CA  LEU    22      34.442  27.045  35.839  1.00  0.00              
ATOM     23  CA  PRO    23      36.396  26.505  32.685  1.00  0.00              
ATOM     24  CA  CYS    24      34.961  23.644  30.621  1.00  0.00              
ATOM     25  CA  THR    25      38.046  21.433  30.305  1.00  0.00              
ATOM     26  CA  VAL    26      38.730  19.927  33.746  1.00  0.00              
ATOM     27  CA  THR    27      42.279  19.147  34.765  1.00  0.00              
ATOM     28  CA  PRO    28      42.790  17.313  37.997  1.00  0.00              
ATOM     29  CA  CYS    29      45.172  19.661  39.807  1.00  0.00              
ATOM     30  CA  PHE    30      42.822  22.608  39.222  1.00  0.00              
ATOM     31  CA  GLY    31      39.531  20.830  39.911  1.00  0.00              
ATOM     32  CA  ALA    32      40.503  19.257  43.271  1.00  0.00              
ATOM     33  CA  ARG    33      41.748  22.585  44.504  1.00  0.00              
ATOM     34  CA  LEU    34      38.476  24.308  43.544  1.00  0.00              
ATOM     35  CA  VAL    35      36.328  21.681  45.290  1.00  0.00              
ATOM     36  CA  GLN    36      38.495  21.851  48.414  1.00  0.00              
ATOM     37  CA  GLU    37      38.284  25.684  48.634  1.00  0.00              
ATOM     38  CA  GLY    38      34.495  25.704  48.294  1.00  0.00              
ATOM     39  CA  ASN    39      34.263  27.041  44.810  1.00  0.00              
ATOM     40  CA  ARG    40      31.391  25.453  42.946  1.00  0.00              
ATOM     41  CA  LEU    41      32.339  25.141  39.334  1.00  0.00              
ATOM     42  CA  HIS    42      29.288  24.915  37.259  1.00  0.00              
ATOM     43  CA  TYR    43      27.047  23.786  34.574  1.00  0.00              
ATOM     44  CA  LEU    44      29.481  22.972  31.729  1.00  0.00              
ATOM     45  CA  ALA    45      31.868  21.450  34.267  1.00  0.00              
ATOM     46  CA  ASP    46      29.154  18.987  35.375  1.00  0.00              
ATOM     47  CA  ARG    47      27.884  17.676  32.070  1.00  0.00              
ATOM     48  CA  ALA    48      31.251  16.766  30.637  1.00  0.00              
ATOM     49  CA  GLY    49      32.541  15.266  33.913  1.00  0.00              
ATOM     50  CA  ILE    50      35.225  17.715  34.966  1.00  0.00              
ATOM     51  CA  ARG    51      38.107  15.170  35.152  1.00  0.00              
ATOM     52  CA  GLY    52      37.122  13.828  31.787  1.00  0.00              
ATOM     53  CA  LEU    53      36.617  16.655  29.381  1.00  0.00              
ATOM     54  CA  PHE    54      40.161  17.422  28.357  1.00  0.00              
ATOM     55  CA  SER    55      42.018  15.233  25.979  1.00  0.00              
ATOM     56  CA  ASP    56      44.783  13.044  27.402  1.00  0.00              
ATOM     57  CA  ALA    57      47.523  15.123  25.764  1.00  0.00              
ATOM     58  CA  ASP    58      46.185  18.288  27.392  1.00  0.00              
ATOM     59  CA  ALA    59      46.127  16.563  30.769  1.00  0.00              
ATOM     60  CA  TYR    60      49.789  15.572  30.385  1.00  0.00              
ATOM     61  CA  HIS    61      50.714  19.139  29.455  1.00  0.00              
ATOM     62  CA  LEU    62      48.813  20.635  32.408  1.00  0.00              
ATOM     63  CA  ASP    63      50.280  18.133  34.866  1.00  0.00              
ATOM     64  CA  GLN    64      53.767  18.975  33.767  1.00  0.00              
ATOM     65  CA  ALA    65      53.193  22.666  34.116  1.00  0.00              
ATOM     66  CA  PHE    66      51.391  22.637  37.496  1.00  0.00              
ATOM     67  CA  PRO    67      54.070  20.798  39.363  1.00  0.00              
ATOM     68  CA  LEU    68      56.687  23.224  37.996  1.00  0.00              
ATOM     69  CA  LEU    69      54.556  26.227  38.944  1.00  0.00              
ATOM     70  CA  MET    70      53.962  24.960  42.508  1.00  0.00              
ATOM     71  CA  LYS    71      57.659  24.354  42.901  1.00  0.00              
ATOM     72  CA  GLN    72      58.399  27.898  41.725  1.00  0.00              
ATOM     73  CA  LEU    73      55.865  29.342  44.199  1.00  0.00              
ATOM     74  CA  GLU    74      57.383  27.303  47.038  1.00  0.00              
ATOM     75  CA  LEU    75      60.836  28.556  46.112  1.00  0.00              
ATOM     76  CA  MET    76      59.623  32.175  46.047  1.00  0.00              
ATOM     77  CA  LEU    77      57.994  32.005  49.405  1.00  0.00              
ATOM     78  CA  THR    78      61.042  30.441  51.111  1.00  0.00              
ATOM     79  CA  SER    79      63.470  32.843  49.565  1.00  0.00              
ATOM     80  CA  GLY    80      61.938  36.167  50.334  1.00  0.00              
ATOM     81  CA  GLU    81      61.113  36.999  46.708  1.00  0.00              
ATOM     82  CA  LEU    82      57.610  37.879  47.682  1.00  0.00              
ATOM     83  CA  ASN    83      57.772  40.475  50.392  1.00  0.00              
ATOM     84  CA  PRO    84      56.747  40.592  53.998  1.00  0.00              
ATOM     85  CA  ARG    85      53.218  41.828  53.414  1.00  0.00              
ATOM     86  CA  HIS    86      52.683  38.936  50.960  1.00  0.00              
ATOM     87  CA  GLN    87      53.971  36.070  53.171  1.00  0.00              
ATOM     88  CA  HIS    88      50.719  34.113  52.586  1.00  0.00              
ATOM     89  CA  THR    89      51.157  34.425  48.765  1.00  0.00              
ATOM     90  CA  VAL    90      49.028  32.488  46.523  1.00  0.00              
ATOM     91  CA  THR    91      50.247  31.395  43.131  1.00  0.00              
ATOM     92  CA  LEU    92      47.783  30.718  40.368  1.00  0.00              
ATOM     93  CA  TYR    93      48.973  28.847  37.353  1.00  0.00              
ATOM     94  CA  ALA    94      46.930  27.439  34.639  1.00  0.00              
ATOM     95  CA  LYS    95      44.499  30.261  34.079  1.00  0.00              
ATOM     96  CA  GLY    96      46.815  33.178  34.558  1.00  0.00              
ATOM     97  CA  LEU    97      45.281  34.864  37.542  1.00  0.00              
ATOM     98  CA  THR    98      46.769  38.201  38.629  1.00  0.00              
ATOM     99  CA  CYS    99      45.911  39.755  41.875  1.00  0.00              
ATOM    100  CA  LYS   100      45.814  43.385  42.362  1.00  0.00              
ATOM    101  CA  ALA   101      47.572  44.993  45.249  1.00  0.00              
ATOM    102  CA  ASP   102      44.622  46.651  46.961  1.00  0.00              
ATOM    103  CA  THR   103      42.284  43.601  47.050  1.00  0.00              
ATOM    104  CA  LEU   104      44.952  41.102  48.022  1.00  0.00              
ATOM    105  CA  SER   105      46.104  43.414  50.825  1.00  0.00              
ATOM    106  CA  SER   106      42.808  44.237  52.535  1.00  0.00              
ATOM    107  CA  CYS   107      41.993  40.593  53.227  1.00  0.00              
ATOM    108  CA  ASP   108      45.640  39.517  53.742  1.00  0.00              
ATOM    109  CA  TYR   109      46.321  37.480  50.665  1.00  0.00              
ATOM    110  CA  VAL   110      48.583  38.191  47.688  1.00  0.00              
ATOM    111  CA  TYR   111      47.724  36.532  44.442  1.00  0.00              
ATOM    112  CA  LEU   112      50.337  35.990  41.798  1.00  0.00              
ATOM    113  CA  ALA   113      49.339  34.922  38.448  1.00  0.00              
ATOM    114  CA  VAL   114      51.689  32.709  36.355  1.00  0.00              
ATOM    115  CA  TYR   115      50.260  31.157  33.221  1.00  0.00              
ATOM    116  CA  PRO   116      51.620  28.201  31.356  1.00  0.00              
ATOM    117  CA  THR   117      52.549  29.051  27.783  1.00  0.00              
TER                                                                             
END
