
#######################################################
#                                                     #
#                        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 T0351TS393_5
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS393_5.T0351.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    L       3      L       3           -
LGA    Y       4      Y       4           -
LGA    D       5      D       5           -
LGA    A       6      -       -           -
LGA    I       7      -       -           -
LGA    M       8      -       -           -
LGA    Y       9      -       -           -
LGA    K      10      -       -           -
LGA    Y      11      -       -           -
LGA    P      12      -       -           -
LGA    N      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      -       -           -
LGA    S      16      -       -           -
LGA    R      17      -       -           -
LGA    K      18      -       -           -
LGA    D      19      -       -           -
LGA    F      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      -       -           -
LGA    R      23      -       -           -
LGA    N      24      -       -           -
LGA    D      25      -       -           -
LGA    G      26      -       -           -
LGA    N      27      -       -           -
LGA    G      28      -       -           -
LGA    S      29      -       -           -
LGA    Y      30      -       -           -
LGA    I      31      A       6           #
LGA    E      32      I       7          2.894
LGA    K      33      M       8          5.412
LGA    W      34      Y       9           -
LGA    -       -      K      10           -
LGA    -       -      Y      11           -
LGA    -       -      P      12           -
LGA    N      35      N      13          2.867
LGA    L      36      A      14          4.468
LGA    R      37      V      15          2.784
LGA    A      38      S      16          3.967
LGA    P      39      R      17          3.506
LGA    L      40      K      18          3.448
LGA    -       -      D      19           -
LGA    -       -      F      20           -
LGA    P      41      E      21          2.769
LGA    T      42      L      22          2.043
LGA    -       -      R      23           -
LGA    -       -      N      24           -
LGA    -       -      D      25           -
LGA    -       -      G      26           -
LGA    -       -      N      27           -
LGA    -       -      G      28           -
LGA    -       -      S      29           -
LGA    Q      43      Y      30          3.725
LGA    A      44      I      31          3.764
LGA    E      45      E      32           #
LGA    L      46      K      33           #
LGA    E      47      W      34          3.548
LGA    T      48      N      35          3.668
LGA    W      49      L      36          3.100
LGA    -       -      R      37           -
LGA    -       -      A      38           -
LGA    W      50      P      39          3.813
LGA    E      51      L      40           #
LGA    E      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    K      55      -       -           -
LGA    N      56      -       -           -
LGA    P      57      -       -           -
LGA    P      58      -       -           -
LGA    Y      59      -       -           -
LGA    E      60      -       -           -
LGA    P      61      -       -           -
LGA    P      62      -       -           -
LGA    D      63      -       -           -
LGA    Q      64      -       -           -
LGA    V      65      -       -           -
LGA    E      66      -       -           -
LGA    L      67      -       -           -
LGA    L      68      -       -           -
LGA    A      69      -       -           -
LGA    Q      70      -       -           -
LGA    E      71      -       -           -
LGA    L      72      -       -           -
LGA    S      73      -       -           -
LGA    Q      74      P      41           #
LGA    E      75      T      42          1.833
LGA    K      76      Q      43          1.584
LGA    L      77      A      44          1.018
LGA    A      78      E      45          0.911
LGA    R      79      L      46          0.739
LGA    K      80      E      47          0.576
LGA    Q      81      T      48          0.337
LGA    L      82      W      49          0.405
LGA    E      83      W      50          0.566
LGA    E      84      E      51          0.467
LGA    L      85      E      52          0.787
LGA    N      86      L      53          1.360
LGA    K      87      Q      54          1.404
LGA    T      88      K      55          0.420
LGA    L      89      N      56          1.720
LGA    G      90      -       -           -
LGA    N      91      -       -           -
LGA    E      92      -       -           -
LGA    L      93      -       -           -
LGA    S      94      -       -           -
LGA    D      95      -       -           -
LGA    I      96      -       -           -
LGA    K      97      -       -           -
LGA    L      98      -       -           -
LGA    S      99      -       -           -
LGA    L     100      -       -           -
LGA    L     101      -       -           -
LGA    S     102      -       -           -
LGA    L     103      -       -           -
LGA    K     104      -       -           -
LGA    G     105      -       -           -
LGA    D     106      -       -           -
LGA    Y     107      -       -           -
LGA    A     108      -       -           -
LGA    E     109      -       -           -
LGA    L     110      -       -           -
LGA    E     111      -       -           -
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117   56    5.0     31    2.67     6.45     38.358     1.120

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.859778 * X  +   0.444623 * Y  +   0.251182 * Z  +   3.785402
  Y_new =  -0.260047 * X  +   0.042120 * Y  +  -0.964677 * Z  +  -0.418879
  Z_new =  -0.439498 * X  +  -0.894727 * Y  +   0.079410 * Z  +  -0.381952 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.482275    1.659317  [ DEG:   -84.9281     95.0719 ]
  Theta =   0.455039    2.686553  [ DEG:    26.0718    153.9282 ]
  Phi   =  -2.847882    0.293711  [ DEG:  -163.1716     16.8284 ]
 
# 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: T0351TS393_5                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS393_5.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117   56   5.0   31   2.67    6.45  38.358
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS393_5
PFRMAT TS
TARGET T0351
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1       9.050 -15.148  -3.269  1.00 25.00           C
ATOM      2  CA  ILE     2      10.560 -11.779  -2.553  1.00 25.00           C
ATOM      3  CA  LEU     3      11.299  -9.620   0.470  1.00 25.00           C
ATOM      4  CA  TYR     4      13.598  -9.208   3.469  1.00 25.00           C
ATOM      5  CA  ASP     5      16.614  -6.999   2.706  1.00 25.00           C
ATOM      6  CA  ALA     6      14.104  -4.519   1.333  1.00 25.00           C
ATOM      7  CA  ILE     7      11.820  -1.738   0.098  1.00 25.00           C
ATOM      8  CA  MET     8      12.529   1.788   1.224  1.00 25.00           C
ATOM      9  CA  TYR     9      12.281   3.486  -2.151  1.00 25.00           C
ATOM     10  CA  LYS    10       9.792   4.394  -4.842  1.00 25.00           C
ATOM     11  CA  TYR    11       8.319   7.926  -5.142  1.00 25.00           C
ATOM     12  CA  PRO    12       5.357  10.285  -4.396  1.00 25.00           C
ATOM     13  CA  ASN    13       7.578  13.385  -3.910  1.00 25.00           C
ATOM     14  CA  ALA    14      11.316  12.949  -4.640  1.00 25.00           C
ATOM     15  CA  VAL    15      14.123  15.459  -5.002  1.00 25.00           C
ATOM     16  CA  SER    16      13.836  19.221  -4.485  1.00 25.00           C
ATOM     17  CA  ARG    17      10.313  19.327  -5.982  1.00 25.00           C
ATOM     18  CA  LYS    18       9.284  18.966  -9.621  1.00 25.00           C
ATOM     19  CA  ASP    19      10.262  15.287  -9.118  1.00 25.00           C
ATOM     20  CA  PHE    20       6.532  14.489  -9.288  1.00 25.00           C
ATOM     21  CA  GLU    21       6.924  10.947 -10.608  1.00 25.00           C
ATOM     22  CA  LEU    22       7.638   7.258 -10.579  1.00 25.00           C
ATOM     23  CA  ARG    23       7.327   3.505 -10.554  1.00 25.00           C
ATOM     24  CA  ASN    24       5.975   3.488 -14.111  1.00 25.00           C
ATOM     25  CA  ASP    25       3.518   0.592 -14.335  1.00 25.00           C
ATOM     26  CA  GLY    26       5.349  -2.613 -13.639  1.00 25.00           C
ATOM     27  CA  ASN    27       4.567  -4.195 -10.222  1.00 25.00           C
ATOM     28  CA  GLY    28       4.055  -2.559  -6.797  1.00 25.00           C
ATOM     29  CA  SER    29       7.307  -0.546  -7.214  1.00 25.00           C
ATOM     30  CA  TYR    30       6.060   1.640  -4.400  1.00 25.00           C
ATOM     31  CA  ILE    31       2.920   3.183  -2.842  1.00 25.00           C
ATOM     32  CA  GLU    32       3.902   1.782   0.584  1.00 25.00           C
ATOM     33  CA  LYS    33       7.423   3.237   0.197  1.00 25.00           C
ATOM     34  CA  TRP    34       5.940   6.643  -0.735  1.00 25.00           C
ATOM     35  CA  ASN    35       6.489   7.844   2.892  1.00 25.00           C
ATOM     36  CA  LEU    36       3.777   5.554   4.347  1.00 25.00           C
ATOM     37  CA  ARG    37       2.058   8.645   5.588  1.00 25.00           C
ATOM     38  CA  ALA    38       2.759  11.259   2.854  1.00 25.00           C
ATOM     39  CA  PRO    39       0.548  13.868   4.518  1.00 25.00           C
ATOM     40  CA  LEU    40      -2.333  11.524   3.690  1.00 25.00           C
ATOM     41  CA  PRO    41      -5.657  10.705   5.212  1.00 25.00           C
ATOM     42  CA  THR    42      -4.977   7.187   3.989  1.00 25.00           C
ATOM     43  CA  GLN    43      -6.891   5.741   1.002  1.00 25.00           C
ATOM     44  CA  ALA    44      -7.446   9.292  -0.319  1.00 25.00           C
ATOM     45  CA  GLU    45      -3.680   9.699  -0.879  1.00 25.00           C
ATOM     46  CA  LEU    46      -3.574   6.364  -2.759  1.00 25.00           C
ATOM     47  CA  GLU    47      -6.519   7.474  -4.942  1.00 25.00           C
ATOM     48  CA  THR    48      -4.743  10.781  -5.699  1.00 25.00           C
ATOM     49  CA  TRP    49      -1.557   8.881  -6.649  1.00 25.00           C
ATOM     50  CA  TRP    50      -3.580   6.591  -8.957  1.00 25.00           C
ATOM     51  CA  GLU    51      -5.206   9.644 -10.602  1.00 25.00           C
ATOM     52  CA  GLU    52      -1.759  11.231 -11.119  1.00 25.00           C
ATOM     53  CA  LEU    53      -0.471   7.985 -12.690  1.00 25.00           C
ATOM     54  CA  GLN    54      -3.507   7.883 -15.024  1.00 25.00           C
ATOM     55  CA  LYS    55      -3.671  11.519 -16.188  1.00 25.00           C
ATOM     56  CA  ASN    56      -2.318  13.078 -19.452  1.00 25.00           C
ATOM     57  CA  PRO    57      -4.756  15.183 -21.492  1.00 25.00           C
ATOM     58  CA  PRO    58      -7.740  12.930 -22.205  1.00 25.00           C
ATOM     59  CA  TYR    59     -11.370  12.321 -23.078  1.00 25.00           C
ATOM     60  CA  GLU    60     -12.601   9.065 -24.648  1.00 25.00           C
ATOM     61  CA  PRO    61     -14.980   6.413 -23.357  1.00 25.00           C
ATOM     62  CA  PRO    62     -15.523   2.664 -23.853  1.00 25.00           C
ATOM     63  CA  ASP    63     -11.905   1.612 -24.537  1.00 25.00           C
ATOM     64  CA  GLN    64     -10.647   4.224 -22.034  1.00 25.00           C
ATOM     65  CA  VAL    65     -13.127   2.942 -19.413  1.00 25.00           C
ATOM     66  CA  GLU    66     -11.949  -0.651 -20.018  1.00 25.00           C
ATOM     67  CA  LEU    67      -8.302   0.452 -19.621  1.00 25.00           C
ATOM     68  CA  LEU    68      -9.173   2.235 -16.346  1.00 25.00           C
ATOM     69  CA  ALA    69     -10.942  -0.913 -15.072  1.00 25.00           C
ATOM     70  CA  GLN    70      -7.882  -3.030 -15.983  1.00 25.00           C
ATOM     71  CA  GLU    71      -5.600  -0.573 -14.133  1.00 25.00           C
ATOM     72  CA  LEU    72      -7.877  -0.736 -11.058  1.00 25.00           C
ATOM     73  CA  SER    73      -7.793  -4.563 -11.168  1.00 25.00           C
ATOM     74  CA  GLN    74      -3.970  -4.497 -11.398  1.00 25.00           C
ATOM     75  CA  GLU    75      -3.808  -2.119  -8.400  1.00 25.00           C
ATOM     76  CA  LYS    76      -6.112  -4.438  -6.404  1.00 25.00           C
ATOM     77  CA  LEU    77      -3.900  -7.437  -7.288  1.00 25.00           C
ATOM     78  CA  ALA    78      -0.789  -5.503  -6.169  1.00 25.00           C
ATOM     79  CA  ARG    79      -2.506  -4.602  -2.866  1.00 25.00           C
ATOM     80  CA  LYS    80      -3.446  -8.275  -2.325  1.00 25.00           C
ATOM     81  CA  GLN    81       0.173  -9.328  -3.008  1.00 25.00           C
ATOM     82  CA  LEU    82       1.431  -6.716  -0.505  1.00 25.00           C
ATOM     83  CA  GLU    83      -1.050  -7.997   2.117  1.00 25.00           C
ATOM     84  CA  GLU    84       0.129 -11.590   1.511  1.00 25.00           C
ATOM     85  CA  LEU    85       3.775 -10.487   1.907  1.00 25.00           C
ATOM     86  CA  ASN    86       2.905  -8.703   5.182  1.00 25.00           C
ATOM     87  CA  LYS    87       1.136 -11.852   6.456  1.00 25.00           C
ATOM     88  CA  THR    88       4.195 -13.969   5.546  1.00 25.00           C
ATOM     89  CA  LEU    89       6.476 -11.511   7.396  1.00 25.00           C
ATOM     90  CA  GLY    90       4.199 -11.675  10.472  1.00 25.00           C
ATOM     91  CA  ASN    91       4.284 -15.502  10.361  1.00 25.00           C
ATOM     92  CA  GLU    92       8.106 -15.436  10.131  1.00 25.00           C
ATOM     93  CA  LEU    93       8.269 -13.058  13.129  1.00 25.00           C
ATOM     94  CA  SER    94       5.966 -15.376  15.125  1.00 25.00           C
ATOM     95  CA  ASP    95       8.177 -18.376  14.241  1.00 25.00           C
ATOM     96  CA  ILE    96      11.288 -16.442  15.360  1.00 25.00           C
ATOM     97  CA  LYS    97       9.570 -15.541  18.662  1.00 25.00           C
ATOM     98  CA  LEU    98       8.632 -19.214  19.204  1.00 25.00           C
ATOM     99  CA  SER    99      12.249 -20.266  18.521  1.00 25.00           C
ATOM    100  CA  LEU   100      13.508 -17.654  21.024  1.00 25.00           C
ATOM    101  CA  LEU   101      11.027 -18.936  23.645  1.00 25.00           C
ATOM    102  CA  SER   102      12.206 -22.529  23.039  1.00 25.00           C
ATOM    103  CA  LEU   103      15.573 -21.171  24.325  1.00 25.00           C
ATOM    104  CA  LYS   104      16.876 -17.630  25.036  1.00 25.00           C
ATOM    105  CA  GLY   105      17.975 -14.578  27.041  1.00 25.00           C
ATOM    106  CA  ASP   106      18.655 -10.872  27.793  1.00 25.00           C
ATOM    107  CA  TYR   107      19.851  -9.632  24.401  1.00 25.00           C
ATOM    108  CA  ALA   108      22.257  -6.749  25.153  1.00 25.00           C
ATOM    109  CA  GLU   109      22.141  -5.662  21.482  1.00 25.00           C
ATOM    110  CA  LEU   110      18.313  -5.751  21.553  1.00 25.00           C
ATOM    111  CA  GLU   111      18.297  -3.637  24.746  1.00 25.00           C
ATOM    112  CA  HIS   112      20.669  -1.111  23.113  1.00 25.00           C
ATOM    113  CA  HIS   113      18.512   0.605  20.480  1.00 25.00           C
ATOM    114  CA  HIS   114      14.779   0.684  21.040  1.00 25.00           C
ATOM    115  CA  HIS   115      12.933   3.079  18.801  1.00 25.00           C
ATOM    116  CA  HIS   116       9.774   2.737  20.868  1.00 25.00           C
ATOM    117  CA  HIS   117       7.107   0.306  19.825  1.00 25.00           C
TER
END
