
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0352TS393_4
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS393_4.T0352.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    T       2      T       2           -
LGA    T       3      T       3           -
LGA    H       4      H       4           -
LGA    D       5      -       -           -
LGA    R       6      -       -           -
LGA    V       7      -       -           -
LGA    R       8      -       -           -
LGA    L       9      -       -           -
LGA    Q      10      -       -           -
LGA    L      11      -       -           -
LGA    Q      12      -       -           -
LGA    A      13      -       -           -
LGA    L      14      -       -           -
LGA    E      15      -       -           -
LGA    A      16      -       -           -
LGA    L      17      -       -           -
LGA    L      18      -       -           -
LGA    R      19      -       -           -
LGA    E      20      -       -           -
LGA    H      21      -       -           -
LGA    Q      22      -       -           -
LGA    H      23      -       -           -
LGA    W      24      -       -           -
LGA    R      25      -       -           -
LGA    N      26      -       -           -
LGA    D      27      -       -           -
LGA    E      28      -       -           -
LGA    P      29      -       -           -
LGA    Q      30      -       -           -
LGA    P      31      -       -           -
LGA    H      32      -       -           -
LGA    Q      33      -       -           -
LGA    F      34      -       -           -
LGA    N      35      -       -           -
LGA    S      36      -       -           -
LGA    T      37      -       -           -
LGA    Q      38      -       -           -
LGA    P      39      -       -           -
LGA    F      40      -       -           -
LGA    F      41      D       5           #
LGA    M      42      -       -           -
LGA    D      43      -       -           -
LGA    T      44      -       -           -
LGA    M      45      -       -           -
LGA    E      46      R       6           #
LGA    P      47      V       7           #
LGA    L      48      R       8           #
LGA    E      49      L       9          2.195
LGA    W      50      Q      10          3.904
LGA    L      51      L      11          1.641
LGA    Q      52      Q      12          4.938
LGA    W      53      A      13           -
LGA    -       -      L      14           -
LGA    V      54      E      15          3.748
LGA    L      55      A      16           -
LGA    I      56      L      17           -
LGA    -       -      L      18           -
LGA    -       -      R      19           -
LGA    -       -      E      20           -
LGA    -       -      H      21           -
LGA    -       -      Q      22           -
LGA    -       -      H      23           -
LGA    -       -      W      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      E      28           -
LGA    -       -      P      29           -
LGA    -       -      Q      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      Q      33           -
LGA    -       -      F      34           -
LGA    -       -      N      35           -
LGA    -       -      S      36           -
LGA    P      57      T      37          2.851
LGA    R      58      Q      38          3.015
LGA    M      59      P      39           #
LGA    H      60      F      40           -
LGA    -       -      F      41           -
LGA    -       -      M      42           -
LGA    D      61      D      43          4.469
LGA    L      62      T      44          1.822
LGA    L      63      M      45          3.621
LGA    D      64      -       -           -
LGA    N      65      -       -           -
LGA    K      66      -       -           -
LGA    Q      67      -       -           -
LGA    P      68      -       -           -
LGA    L      69      E      46          2.948
LGA    P      70      P      47          2.153
LGA    G      71      L      48          3.495
LGA    A      72      E      49           #
LGA    -       -      W      50           -
LGA    F      73      L      51          3.885
LGA    A      74      Q      52          4.253
LGA    V      75      W      53          4.428
LGA    A      76      V      54          2.299
LGA    P      77      L      55          2.584
LGA    Y      78      I      56          2.173
LGA    Y      79      P      57          2.271
LGA    E      80      R      58          1.798
LGA    M      81      M      59          2.698
LGA    A      82      H      60          2.756
LGA    L      83      D      61          1.555
LGA    A      84      L      62          1.702
LGA    -       -      L      63           -
LGA    -       -      D      64           -
LGA    -       -      N      65           -
LGA    T      85      K      66          4.744
LGA    D      86      Q      67          3.671
LGA    H      87      P      68          4.934
LGA    P      88      L      69          3.384
LGA    Q      89      P      70          3.492
LGA    R      90      -       -           -
LGA    A      91      -       -           -
LGA    L      92      G      71          0.971
LGA    I      93      A      72           #
LGA    L      94      -       -           -
LGA    A      95      -       -           -
LGA    E      96      F      73          1.496
LGA    L      97      -       -           -
LGA    E      98      -       -           -
LGA    K      99      A      74          2.696
LGA    L     100      V      75          2.297
LGA    D     101      A      76          2.337
LGA    A     102      -       -           -
LGA    L     103      P      77          3.085
LGA    F     104      Y      78          2.911
LGA    A     105      Y      79          2.560
LGA    D     106      E      80          2.753
LGA    D     107      M      81          2.279
LGA    A     108      A      82          2.042
LGA    S     109      L      83          4.167
LGA    L     110      A      84          1.587
LGA    E     111      -       -           -
LGA    H     112      T      85           #
LGA    H     113      D      86           -
LGA    H     114      H      87           -
LGA    H     115      P      88           -
LGA    H     116      Q      89           -
LGA    H     117      R      90           -
LGA    -       -      A      91           -
LGA    -       -      L      92           -
LGA    -       -      I      93           -
LGA    -       -      L      94           -
LGA    -       -      A      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      E      98           -
LGA    -       -      K      99           -
LGA    -       -      L     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      A     105           -
LGA    -       -      D     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      S     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117  109    5.0     43    3.07    13.95     23.117     1.357

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.068576 * X  +  -0.456504 * Y  +   0.887075 * Z  + -11.693712
  Y_new =   0.687595 * X  +  -0.665878 * Y  +  -0.289517 * Z  +   9.358588
  Z_new =   0.722849 * X  +   0.590094 * Y  +   0.359553 * Z  +  -3.535575 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.023556   -2.118037  [ DEG:    58.6454   -121.3546 ]
  Theta =  -0.807916   -2.333676  [ DEG:   -46.2902   -133.7098 ]
  Phi   =   1.670201   -1.471392  [ DEG:    95.6954    -84.3046 ]
 
# 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: T0352TS393_4                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS393_4.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117  109   5.0   43   3.07   13.95  23.117
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS393_4
PFRMAT TS
TARGET T0352
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1     -21.490  19.404  16.146  1.00 25.00           C
ATOM      2  CA  THR     2     -18.561  21.134  14.309  1.00 25.00           C
ATOM      3  CA  THR     3     -16.198  19.944  11.532  1.00 25.00           C
ATOM      4  CA  HIS     4     -19.403  18.935   9.695  1.00 25.00           C
ATOM      5  CA  ASP     5     -18.917  21.812   7.215  1.00 25.00           C
ATOM      6  CA  ARG     6     -15.294  20.721   6.622  1.00 25.00           C
ATOM      7  CA  VAL     7     -16.452  17.121   6.015  1.00 25.00           C
ATOM      8  CA  ARG     8     -19.085  18.361   3.527  1.00 25.00           C
ATOM      9  CA  LEU     9     -16.426  20.429   1.705  1.00 25.00           C
ATOM     10  CA  GLN    10     -14.129  17.370   1.534  1.00 25.00           C
ATOM     11  CA  LEU    11     -16.999  15.263   0.123  1.00 25.00           C
ATOM     12  CA  GLN    12     -17.713  17.953  -2.508  1.00 25.00           C
ATOM     13  CA  ALA    13     -14.007  18.024  -3.476  1.00 25.00           C
ATOM     14  CA  LEU    14     -13.994  14.208  -3.801  1.00 25.00           C
ATOM     15  CA  GLU    15     -17.117  14.362  -6.013  1.00 25.00           C
ATOM     16  CA  ALA    16     -15.460  17.023  -8.212  1.00 25.00           C
ATOM     17  CA  LEU    17     -12.325  14.845  -8.529  1.00 25.00           C
ATOM     18  CA  LEU    18     -14.484  11.838  -9.512  1.00 25.00           C
ATOM     19  CA  ARG    19     -16.281  13.960 -12.147  1.00 25.00           C
ATOM     20  CA  GLU    20     -12.911  15.128 -13.541  1.00 25.00           C
ATOM     21  CA  HIS    21     -11.697  11.500 -13.715  1.00 25.00           C
ATOM     22  CA  GLN    22     -14.903  10.490 -15.553  1.00 25.00           C
ATOM     23  CA  HIS    23     -14.416  13.368 -18.033  1.00 25.00           C
ATOM     24  CA  TRP    24     -10.793  12.277 -18.626  1.00 25.00           C
ATOM     25  CA  ARG    25     -11.951   8.676 -19.233  1.00 25.00           C
ATOM     26  CA  ASN    26     -15.333   7.884 -20.640  1.00 25.00           C
ATOM     27  CA  ASP    27     -15.470  10.957 -22.949  1.00 25.00           C
ATOM     28  CA  GLU    28     -15.724  11.291 -26.729  1.00 25.00           C
ATOM     29  CA  PRO    29     -12.219  10.167 -27.692  1.00 25.00           C
ATOM     30  CA  GLN    30     -11.079   6.607 -27.936  1.00 25.00           C
ATOM     31  CA  PRO    31      -7.531   7.729 -27.240  1.00 25.00           C
ATOM     32  CA  HIS    32      -5.197  10.311 -25.642  1.00 25.00           C
ATOM     33  CA  GLN    33      -5.747   8.716 -22.204  1.00 25.00           C
ATOM     34  CA  PHE    34      -4.965   5.259 -23.654  1.00 25.00           C
ATOM     35  CA  ASN    35      -1.762   6.625 -25.248  1.00 25.00           C
ATOM     36  CA  SER    36       1.612   7.645 -23.745  1.00 25.00           C
ATOM     37  CA  THR    37       3.449   4.314 -23.387  1.00 25.00           C
ATOM     38  CA  GLN    38       3.278   2.066 -20.252  1.00 25.00           C
ATOM     39  CA  PRO    39       2.031  -0.561 -22.717  1.00 25.00           C
ATOM     40  CA  PHE    40      -1.517  -1.292 -21.552  1.00 25.00           C
ATOM     41  CA  PHE    41      -1.818  -3.870 -18.800  1.00 25.00           C
ATOM     42  CA  MET    42      -5.362  -4.129 -17.402  1.00 25.00           C
ATOM     43  CA  ASP    43      -7.419  -7.310 -17.463  1.00 25.00           C
ATOM     44  CA  THR    44     -11.070  -6.386 -16.814  1.00 25.00           C
ATOM     45  CA  MET    45     -11.815  -2.614 -16.595  1.00 25.00           C
ATOM     46  CA  GLU    46     -12.997  -2.881 -12.951  1.00 25.00           C
ATOM     47  CA  PRO    47     -11.796  -0.392 -10.323  1.00 25.00           C
ATOM     48  CA  LEU    48      -9.830  -0.335  -7.037  1.00 25.00           C
ATOM     49  CA  GLU    49      -6.899   1.398  -8.791  1.00 25.00           C
ATOM     50  CA  TRP    50      -9.291   3.997 -10.272  1.00 25.00           C
ATOM     51  CA  LEU    51     -10.798   4.620  -6.807  1.00 25.00           C
ATOM     52  CA  GLN    52      -7.291   5.062  -5.334  1.00 25.00           C
ATOM     53  CA  TRP    53      -6.409   7.544  -8.114  1.00 25.00           C
ATOM     54  CA  VAL    54      -9.631   9.498  -7.426  1.00 25.00           C
ATOM     55  CA  LEU    55      -8.801   9.595  -3.688  1.00 25.00           C
ATOM     56  CA  ILE    56      -5.275  10.865  -4.479  1.00 25.00           C
ATOM     57  CA  PRO    57      -6.736  13.584  -6.746  1.00 25.00           C
ATOM     58  CA  ARG    58      -9.162  14.628  -3.972  1.00 25.00           C
ATOM     59  CA  MET    59      -6.266  14.804  -1.472  1.00 25.00           C
ATOM     60  CA  HIS    60      -4.254  16.958  -3.918  1.00 25.00           C
ATOM     61  CA  ASP    61      -7.256  19.291  -4.372  1.00 25.00           C
ATOM     62  CA  LEU    62      -7.634  19.586  -0.572  1.00 25.00           C
ATOM     63  CA  LEU    63      -3.908  20.408  -0.241  1.00 25.00           C
ATOM     64  CA  ASP    64      -4.231  23.086  -2.960  1.00 25.00           C
ATOM     65  CA  ASN    65      -6.808  24.443  -5.468  1.00 25.00           C
ATOM     66  CA  LYS    66      -7.124  27.228  -2.896  1.00 25.00           C
ATOM     67  CA  GLN    67      -6.611  28.995   0.441  1.00 25.00           C
ATOM     68  CA  PRO    68      -4.866  27.480   3.426  1.00 25.00           C
ATOM     69  CA  LEU    69      -4.063  23.833   3.890  1.00 25.00           C
ATOM     70  CA  PRO    70      -3.319  22.918   7.491  1.00 25.00           C
ATOM     71  CA  GLY    71      -3.782  19.807   9.573  1.00 25.00           C
ATOM     72  CA  ALA    72      -5.813  17.725   7.059  1.00 25.00           C
ATOM     73  CA  PHE    73      -5.010  14.567   9.072  1.00 25.00           C
ATOM     74  CA  ALA    74      -7.576  12.586   7.033  1.00 25.00           C
ATOM     75  CA  VAL    75      -6.034  13.888   3.778  1.00 25.00           C
ATOM     76  CA  ALA    76      -2.547  12.872   4.997  1.00 25.00           C
ATOM     77  CA  PRO    77      -3.846   9.378   5.877  1.00 25.00           C
ATOM     78  CA  TYR    78      -5.427   9.063   2.402  1.00 25.00           C
ATOM     79  CA  TYR    79      -2.124  10.121   0.778  1.00 25.00           C
ATOM     80  CA  GLU    80      -0.235   7.524   2.866  1.00 25.00           C
ATOM     81  CA  MET    81      -2.739   4.824   1.815  1.00 25.00           C
ATOM     82  CA  ALA    82      -2.303   5.814  -1.858  1.00 25.00           C
ATOM     83  CA  LEU    83       1.504   5.626  -1.482  1.00 25.00           C
ATOM     84  CA  ALA    84       1.200   2.156   0.110  1.00 25.00           C
ATOM     85  CA  THR    85       1.958   2.768   3.822  1.00 25.00           C
ATOM     86  CA  ASP    86       3.146  -0.839   3.611  1.00 25.00           C
ATOM     87  CA  HIS    87       2.191  -3.071   0.646  1.00 25.00           C
ATOM     88  CA  PRO    88      -1.505  -3.920   1.020  1.00 25.00           C
ATOM     89  CA  GLN    89      -1.731  -0.311   2.281  1.00 25.00           C
ATOM     90  CA  ARG    90      -3.957   0.616  -0.694  1.00 25.00           C
ATOM     91  CA  ALA    91      -6.219  -2.388   0.030  1.00 25.00           C
ATOM     92  CA  LEU    92      -6.468  -1.346   3.707  1.00 25.00           C
ATOM     93  CA  ILE    93      -7.380   2.222   2.659  1.00 25.00           C
ATOM     94  CA  LEU    94     -10.074   0.867   0.299  1.00 25.00           C
ATOM     95  CA  ALA    95     -11.487  -1.305   3.121  1.00 25.00           C
ATOM     96  CA  GLU    96     -11.562   1.731   5.453  1.00 25.00           C
ATOM     97  CA  LEU    97     -13.384   3.774   2.775  1.00 25.00           C
ATOM     98  CA  GLU    98     -15.937   0.955   2.325  1.00 25.00           C
ATOM     99  CA  LYS    99     -16.489   0.818   6.112  1.00 25.00           C
ATOM    100  CA  LEU   100     -17.005   4.611   6.200  1.00 25.00           C
ATOM    101  CA  ASP   101     -19.534   4.357   3.335  1.00 25.00           C
ATOM    102  CA  ALA   102     -21.400   1.578   5.196  1.00 25.00           C
ATOM    103  CA  LEU   103     -21.483   3.723   8.367  1.00 25.00           C
ATOM    104  CA  PHE   104     -22.849   6.683   6.358  1.00 25.00           C
ATOM    105  CA  ALA   105     -25.552   4.436   4.837  1.00 25.00           C
ATOM    106  CA  ASP   106     -26.508   3.183   8.327  1.00 25.00           C
ATOM    107  CA  ASP   107     -26.734   6.791   9.589  1.00 25.00           C
ATOM    108  CA  ALA   108     -28.960   7.718   6.613  1.00 25.00           C
ATOM    109  CA  SER   109     -31.221   4.713   7.338  1.00 25.00           C
ATOM    110  CA  LEU   110     -32.275   3.725   3.850  1.00 25.00           C
ATOM    111  CA  GLU   111     -34.907   6.528   4.107  1.00 25.00           C
ATOM    112  CA  HIS   112     -37.725   5.965   6.590  1.00 25.00           C
ATOM    113  CA  HIS   113     -37.634   6.691  10.326  1.00 25.00           C
ATOM    114  CA  HIS   114     -36.791  10.435  10.682  1.00 25.00           C
ATOM    115  CA  HIS   115     -38.908  13.316   9.362  1.00 25.00           C
ATOM    116  CA  HIS   116     -36.269  15.205   7.411  1.00 25.00           C
ATOM    117  CA  HIS   117     -33.356  14.092   5.278  1.00 25.00           C
TER
END
