
#######################################################
#                                                     #
#                        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 T0304TS168_5-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS168_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      G      21           -
LGA    L      22      L      22           -
LGA    P      23      P      23           -
LGA    C      24      C      24           -
LGA    T      25      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    V      26      Q      36          4.087
LGA    T      27      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    P      28      L      41           #
LGA    C      29      H      42           #
LGA    F      30      Y      43           -
LGA    G      31      -       -           -
LGA    A      32      -       -           -
LGA    R      33      -       -           -
LGA    L      34      L      44          1.009
LGA    V      35      A      45          0.878
LGA    Q      36      D      46          2.736
LGA    E      37      R      47          3.693
LGA    G      38      A      48          3.835
LGA    N      39      -       -           -
LGA    R      40      G      49          1.439
LGA    L      41      -       -           -
LGA    H      42      -       -           -
LGA    Y      43      I      50          2.012
LGA    L      44      R      51          4.226
LGA    A      45      G      52           #
LGA    D      46      L      53          2.386
LGA    R      47      F      54          4.466
LGA    A      48      -       -           -
LGA    G      49      -       -           -
LGA    I      50      -       -           -
LGA    R      51      -       -           -
LGA    G      52      -       -           -
LGA    L      53      S      55          1.353
LGA    F      54      D      56          2.318
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      -       -           -
LGA    D      58      A      57          3.319
LGA    A      59      D      58           #
LGA    -       -      A      59           -
LGA    Y      60      Y      60          3.391
LGA    H      61      H      61          2.510
LGA    L      62      L      62          2.050
LGA    D      63      D      63          0.307
LGA    Q      64      Q      64          1.169
LGA    A      65      A      65          2.128
LGA    F      66      F      66          2.334
LGA    P      67      P      67          2.309
LGA    L      68      L      68          2.174
LGA    L      69      L      69          1.877
LGA    M      70      M      70          1.723
LGA    K      71      K      71          1.712
LGA    Q      72      Q      72          1.425
LGA    L      73      L      73          1.027
LGA    E      74      E      74          1.128
LGA    L      75      L      75          1.054
LGA    M      76      M      76          0.799
LGA    L      77      L      77          0.844
LGA    T      78      T      78          1.005
LGA    S      79      S      79          0.678
LGA    G      80      G      80          3.493
LGA    E      81      E      81          4.506
LGA    L      82      L      82          5.009
LGA    -       -      N      83           -
LGA    -       -      P      84           -
LGA    N      83      R      85           #
LGA    P      84      -       -           -
LGA    R      85      -       -           -
LGA    H      86      H      86           #
LGA    Q      87      Q      87          3.349
LGA    H      88      H      88          5.189
LGA    -       -      T      89           -
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      89      T     103          1.698
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    V      90      V     110          3.351
LGA    T      91      Y     111           -
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      L     112          3.437
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      A     113          0.861
LGA    V     110      V     114          3.566
LGA    Y     111      Y     115           -
LGA    L     112      P     116           -
LGA    A     113      T     117           -
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     44    2.69    65.91     29.929     1.577

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.464224 * X  +  -0.881594 * Y  +   0.085371 * Z  +  46.262280
  Y_new =   0.210017 * X  +  -0.015924 * Y  +   0.977568 * Z  +  22.057791
  Z_new =  -0.860459 * X  +   0.471740 * Y  +   0.192542 * Z  +  48.154945 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.183282   -1.958310  [ DEG:    67.7971   -112.2029 ]
  Theta =   1.036169    2.105424  [ DEG:    59.3681    120.6319 ]
  Phi   =   2.716742   -0.424851  [ DEG:   155.6578    -24.3422 ]
 
# 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: T0304TS168_5-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS168_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   44   2.69   65.91  29.929
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS168_5-D1
PFRMAT TS
TARGET T0304
MODEL 5
PARENT N/A
ATOM     17  CA  ARG    17      37.128  26.521  76.162  1.00 25.00           C
ATOM     18  CA  PRO    18      40.670  27.221  74.837  1.00 25.00           C
ATOM     19  CA  TRP    19      42.115  24.460  72.608  1.00 25.00           C
ATOM     20  CA  TRP    20      45.571  23.691  71.104  1.00 25.00           C
ATOM     21  CA  GLY    21      47.894  25.651  68.864  1.00 25.00           C
ATOM     22  CA  LEU    22      48.813  24.390  65.334  1.00 25.00           C
ATOM     23  CA  PRO    23      51.820  25.310  63.137  1.00 25.00           C
ATOM     24  CA  CYS    24      51.478  25.088  59.412  1.00 25.00           C
ATOM     25  CA  THR    25      48.723  27.743  59.807  1.00 25.00           C
ATOM     26  CA  VAL    26      48.434  27.648  56.016  1.00 25.00           C
ATOM     27  CA  THR    27      45.423  25.327  55.873  1.00 25.00           C
ATOM     28  CA  PRO    28      47.871  22.512  56.219  1.00 25.00           C
ATOM     29  CA  CYS    29      45.533  20.770  53.805  1.00 25.00           C
ATOM     30  CA  PHE    30      46.327  17.079  54.450  1.00 25.00           C
ATOM     31  CA  GLY    31      47.088  14.151  52.100  1.00 25.00           C
ATOM     32  CA  ALA    32      43.348  13.695  51.416  1.00 25.00           C
ATOM     33  CA  ARG    33      43.005  17.433  50.657  1.00 25.00           C
ATOM     34  CA  LEU    34      45.985  17.245  48.258  1.00 25.00           C
ATOM     35  CA  VAL    35      44.413  14.225  46.504  1.00 25.00           C
ATOM     36  CA  GLN    36      41.099  16.116  46.165  1.00 25.00           C
ATOM     37  CA  GLU    37      42.943  19.132  44.691  1.00 25.00           C
ATOM     38  CA  GLY    38      44.736  16.847  42.195  1.00 25.00           C
ATOM     39  CA  ASN    39      41.391  15.278  41.190  1.00 25.00           C
ATOM     40  CA  ARG    40      39.879  18.761  40.689  1.00 25.00           C
ATOM     41  CA  LEU    41      42.871  19.774  38.522  1.00 25.00           C
ATOM     42  CA  HIS    42      42.463  16.592  36.430  1.00 25.00           C
ATOM     43  CA  TYR    43      38.734  17.337  35.977  1.00 25.00           C
ATOM     44  CA  LEU    44      39.557  20.914  34.880  1.00 25.00           C
ATOM     45  CA  ALA    45      42.121  19.578  32.368  1.00 25.00           C
ATOM     46  CA  ASP    46      39.528  17.120  30.991  1.00 25.00           C
ATOM     47  CA  ARG    47      36.985  19.961  30.636  1.00 25.00           C
ATOM     48  CA  ALA    48      37.964  23.648  30.871  1.00 25.00           C
ATOM     49  CA  GLY    49      39.870  23.453  27.519  1.00 25.00           C
ATOM     50  CA  ILE    50      43.452  22.967  28.732  1.00 25.00           C
ATOM     51  CA  ARG    51      46.416  20.750  27.846  1.00 25.00           C
ATOM     52  CA  GLY    52      45.368  18.118  25.339  1.00 25.00           C
ATOM     53  CA  LEU    53      42.261  15.898  25.403  1.00 25.00           C
ATOM     54  CA  PHE    54      43.443  13.111  27.682  1.00 25.00           C
ATOM     55  CA  SER    55      44.928   9.791  28.855  1.00 25.00           C
ATOM     56  CA  ASP    56      48.605   9.209  27.867  1.00 25.00           C
ATOM     57  CA  ALA    57      51.140  11.718  26.473  1.00 25.00           C
ATOM     58  CA  ASP    58      48.585  14.547  26.851  1.00 25.00           C
ATOM     59  CA  ALA    59      47.910  13.485  30.469  1.00 25.00           C
ATOM     60  CA  TYR    60      51.671  13.457  31.188  1.00 25.00           C
ATOM     61  CA  HIS    61      52.013  16.958  29.676  1.00 25.00           C
ATOM     62  CA  LEU    62      49.105  18.202  31.836  1.00 25.00           C
ATOM     63  CA  ASP    63      50.746  16.699  34.953  1.00 25.00           C
ATOM     64  CA  GLN    64      54.056  18.407  34.065  1.00 25.00           C
ATOM     65  CA  ALA    65      52.238  21.748  33.611  1.00 25.00           C
ATOM     66  CA  PHE    66      50.531  21.309  37.011  1.00 25.00           C
ATOM     67  CA  PRO    67      53.914  20.552  38.639  1.00 25.00           C
ATOM     68  CA  LEU    68      55.418  23.684  37.027  1.00 25.00           C
ATOM     69  CA  LEU    69      52.485  25.784  38.315  1.00 25.00           C
ATOM     70  CA  MET    70      52.972  24.354  41.833  1.00 25.00           C
ATOM     71  CA  LYS    71      56.708  25.181  41.679  1.00 25.00           C
ATOM     72  CA  GLN    72      55.896  28.755  40.569  1.00 25.00           C
ATOM     73  CA  LEU    73      53.414  29.117  43.463  1.00 25.00           C
ATOM     74  CA  GLU    74      56.060  27.848  45.923  1.00 25.00           C
ATOM     75  CA  LEU    75      58.596  30.357  44.528  1.00 25.00           C
ATOM     76  CA  MET    76      56.041  33.185  44.907  1.00 25.00           C
ATOM     77  CA  LEU    77      55.365  32.124  48.525  1.00 25.00           C
ATOM     78  CA  THR    78      59.127  32.095  49.245  1.00 25.00           C
ATOM     79  CA  SER    79      59.321  35.663  47.840  1.00 25.00           C
ATOM     80  CA  GLY    80      58.641  39.391  47.413  1.00 25.00           C
ATOM     81  CA  GLU    81      56.104  38.947  50.266  1.00 25.00           C
ATOM     82  CA  LEU    82      52.348  39.509  50.042  1.00 25.00           C
ATOM     83  CA  ASN    83      52.750  42.561  52.290  1.00 25.00           C
ATOM     84  CA  PRO    84      49.788  44.166  50.585  1.00 25.00           C
ATOM     85  CA  ARG    85      49.150  43.271  46.986  1.00 25.00           C
ATOM     86  CA  HIS    86      48.104  40.132  45.137  1.00 25.00           C
ATOM     87  CA  GLN    87      47.297  38.065  48.185  1.00 25.00           C
ATOM     88  CA  HIS    88      46.056  34.593  49.272  1.00 25.00           C
ATOM     89  CA  THR    89      47.143  30.983  49.991  1.00 25.00           C
ATOM     90  CA  VAL    90      49.279  27.987  50.955  1.00 25.00           C
ATOM     91  CA  THR    91      52.090  25.383  51.025  1.00 25.00           C
ATOM     92  CA  LEU    92      52.745  23.677  47.682  1.00 25.00           C
ATOM     93  CA  TYR    93      53.694  20.177  46.629  1.00 25.00           C
ATOM     94  CA  ALA    94      52.480  16.545  47.053  1.00 25.00           C
ATOM     95  CA  LYS    95      50.869  13.198  47.839  1.00 25.00           C
ATOM     96  CA  GLY    96      49.952  12.375  44.235  1.00 25.00           C
ATOM     97  CA  LEU    97      49.714  15.964  42.846  1.00 25.00           C
ATOM     98  CA  THR    98      49.301  19.661  43.668  1.00 25.00           C
ATOM     99  CA  CYS    99      46.573  21.911  42.312  1.00 25.00           C
ATOM    100  CA  LYS   100      43.599  23.962  43.461  1.00 25.00           C
ATOM    101  CA  ALA   101      41.467  24.185  46.587  1.00 25.00           C
ATOM    102  CA  ASP   102      38.338  24.814  48.616  1.00 25.00           C
ATOM    103  CA  THR   103      37.070  21.797  46.659  1.00 25.00           C
ATOM    104  CA  LEU   104      34.165  23.917  45.508  1.00 25.00           C
ATOM    105  CA  SER   105      34.370  27.689  44.750  1.00 25.00           C
ATOM    106  CA  SER   106      38.138  28.033  44.506  1.00 25.00           C
ATOM    107  CA  CYS   107      38.550  24.848  42.397  1.00 25.00           C
ATOM    108  CA  ASP   108      39.402  27.139  39.429  1.00 25.00           C
ATOM    109  CA  TYR   109      43.149  27.526  39.600  1.00 25.00           C
ATOM    110  CA  VAL   110      46.667  26.156  38.944  1.00 25.00           C
ATOM    111  CA  TYR   111      48.511  26.713  42.186  1.00 25.00           C
ATOM    112  CA  LEU   112      48.223  25.387  45.721  1.00 25.00           C
ATOM    113  CA  ALA   113      47.644  22.218  47.775  1.00 25.00           C
ATOM    114  CA  VAL   114      49.911  20.510  50.355  1.00 25.00           C
ATOM    115  CA  TYR   115      51.681  17.646  52.181  1.00 25.00           C
ATOM    116  CA  PRO   116      55.096  16.876  53.676  1.00 25.00           C
ATOM    117  CA  THR   117      56.366  15.107  56.815  1.00 25.00           C
TER
END
