
#######################################################
#                                                     #
#                        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  104 (  104),  selected  104 , name T0343TS168_4
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343TS168_4.T0343.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      -       -           -
LGA    W       3      T       2          3.524
LGA    R       4      W       3          4.487
LGA    E       5      R       4           -
LGA    I       6      E       5           -
LGA    L       7      I       6          4.301
LGA    R       8      -       -           -
LGA    K       9      -       -           -
LGA    E      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    D      14      -       -           -
LGA    L      15      -       -           -
LGA    G      16      -       -           -
LGA    E      17      -       -           -
LGA    F      18      -       -           -
LGA    I      19      -       -           -
LGA    V      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      -       -           -
LGA    V      23      -       -           -
LGA    Y      24      -       -           -
LGA    I      25      L       7          2.090
LGA    D      26      R       8          3.146
LGA    C      27      -       -           -
LGA    P      28      -       -           -
LGA    C      29      -       -           -
LGA    E      30      -       -           -
LGA    P      31      -       -           -
LGA    I      32      -       -           -
LGA    P      33      K       9          3.571
LGA    P      34      E      10          2.039
LGA    T      35      G      11          1.315
LGA    L      36      F      12          1.625
LGA    A      37      L      13          4.342
LGA    -       -      D      14           -
LGA    I      38      L      15           #
LGA    Y      39      G      16           -
LGA    D      40      E      17           -
LGA    K      41      F      18           -
LGA    K      42      I      19           -
LGA    G      43      V      20           -
LGA    D      44      E      21           -
LGA    E      45      -       -           -
LGA    W      46      -       -           -
LGA    Y      47      -       -           -
LGA    K      48      L      22          5.580
LGA    V      49      V      23          1.706
LGA    E      50      Y      24          2.146
LGA    E      51      I      25          4.207
LGA    A      52      D      26          1.837
LGA    P      53      C      27          3.437
LGA    N      54      P      28           #
LGA    -       -      C      29           -
LGA    -       -      E      30           -
LGA    -       -      P      31           -
LGA    V      55      I      32           #
LGA    Q      56      P      33           -
LGA    N      57      -       -           -
LGA    Y      58      P      34          5.456
LGA    R      59      -       -           -
LGA    E      60      -       -           -
LGA    A      61      T      35           #
LGA    V      62      L      36           #
LGA    E      63      -       -           -
LGA    W      64      -       -           -
LGA    A      65      A      37          5.684
LGA    I      66      -       -           -
LGA    E      67      -       -           -
LGA    V      68      I      38           #
LGA    L      69      Y      39           -
LGA    E      70      D      40           -
LGA    R      71      -       -           -
LGA    I      72      -       -           -
LGA    R      73      -       -           -
LGA    D      74      -       -           -
LGA    G      75      -       -           -
LGA    E      76      -       -           -
LGA    N      77      -       -           -
LGA    V      78      K      41           #
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      D      44           -
LGA    K      79      E      45          0.465
LGA    L      80      W      46          3.889
LGA    V      81      Y      47           #
LGA    S      82      K      48          3.457
LGA    L      83      V      49          3.062
LGA    D      84      E      50          2.531
LGA    -       -      E      51           -
LGA    G      85      A      52          1.141
LGA    P      86      P      53          2.398
LGA    A      87      N      54          2.381
LGA    P      88      V      55          4.583
LGA    -       -      Q      56           -
LGA    P      89      E      63           #
LGA    -       -      W      64           -
LGA    -       -      A      65           -
LGA    -       -      I      66           -
LGA    K      90      E      67          3.966
LGA    V      91      V      68          3.669
LGA    M      92      L      69          3.472
LGA    K      93      E      70          2.861
LGA    R      94      R      71          1.747
LGA    L      95      I      72          1.787
LGA    S      96      R      73          2.099
LGA    L      97      D      74          2.050
LGA    A      98      G      75          0.960
LGA    L      99      E      76          0.844
LGA    Q     100      N      77          0.399
LGA    K     101      V      78          2.097
LGA    L     102      K      79           -
LGA    -       -      L      80           -
LGA    -       -      V      81           -
LGA    -       -      S      82           -
LGA    -       -      L      83           -
LGA    -       -      D      84           -
LGA    -       -      G      85           -
LGA    -       -      P      86           -
LGA    -       -      A      87           -
LGA    -       -      P      88           -
LGA    -       -      P      89           -
LGA    -       -      K      90           -
LGA    -       -      V      91           -
LGA    T     103      M      92          4.195
LGA    E     104      K      93          1.424
LGA    -       -      R      94           -
LGA    -       -      L      95           -
LGA    -       -      S      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      L      99           -
LGA    -       -      Q     100           -
LGA    -       -      K     101           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104   94    5.0     41    3.15    12.20     26.679     1.263

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.560683 * X  +  -0.702990 * Y  +  -0.437538 * Z  +  24.188833
  Y_new =  -0.827961 * X  +   0.469117 * Y  +   0.307262 * Z  +  19.585289
  Z_new =  -0.010746 * X  +   0.534541 * Y  +  -0.845074 * Z  +  13.254573 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.577591   -0.564001  [ DEG:   147.6851    -32.3149 ]
  Theta =   0.010746    3.130847  [ DEG:     0.6157    179.3843 ]
  Phi   =  -2.166045    0.975547  [ DEG:  -124.1053     55.8947 ]
 
# 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: T0343TS168_4                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343TS168_4.T0343.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  104   94   5.0   41   3.15   12.20  26.679
REMARK  ---------------------------------------------------------- 
MOLECULE T0343TS168_4
PFRMAT TS
TARGET T0343
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      23.119  13.759  35.409  1.00 25.00           C
ATOM      2  CA  THR     2      25.906  12.493  33.063  1.00 25.00           C
ATOM      3  CA  TRP     3      25.705  13.416  29.388  1.00 25.00           C
ATOM      4  CA  ARG     4      28.153  15.903  27.962  1.00 25.00           C
ATOM      5  CA  GLU     5      30.029  13.385  25.770  1.00 25.00           C
ATOM      6  CA  ILE     6      29.743  15.745  22.769  1.00 25.00           C
ATOM      7  CA  LEU     7      31.084  18.641  24.887  1.00 25.00           C
ATOM      8  CA  ARG     8      34.023  16.470  26.036  1.00 25.00           C
ATOM      9  CA  LYS     9      36.599  13.722  26.472  1.00 25.00           C
ATOM     10  CA  GLU    10      36.621  12.328  22.877  1.00 25.00           C
ATOM     11  CA  GLY    11      35.820   8.681  23.749  1.00 25.00           C
ATOM     12  CA  PHE    12      33.544   8.974  20.759  1.00 25.00           C
ATOM     13  CA  LEU    13      33.764  12.004  18.428  1.00 25.00           C
ATOM     14  CA  ASP    14      32.862   9.796  15.432  1.00 25.00           C
ATOM     15  CA  LEU    15      29.864   8.379  17.347  1.00 25.00           C
ATOM     16  CA  GLY    16      28.715  11.926  18.221  1.00 25.00           C
ATOM     17  CA  GLU    17      29.021  12.958  14.546  1.00 25.00           C
ATOM     18  CA  PHE    18      26.971   9.899  13.492  1.00 25.00           C
ATOM     19  CA  ILE    19      23.263   9.407  12.753  1.00 25.00           C
ATOM     20  CA  VAL    20      22.371  11.146  16.009  1.00 25.00           C
ATOM     21  CA  GLU    21      24.022  14.131  14.277  1.00 25.00           C
ATOM     22  CA  LEU    22      25.227  17.498  13.177  1.00 25.00           C
ATOM     23  CA  VAL    23      25.813  18.098  16.836  1.00 25.00           C
ATOM     24  CA  TYR    24      27.365  19.873  19.800  1.00 25.00           C
ATOM     25  CA  ILE    25      27.285  23.026  21.923  1.00 25.00           C
ATOM     26  CA  ASP    26      28.222  26.309  23.623  1.00 25.00           C
ATOM     27  CA  CYS    27      28.841  29.419  25.695  1.00 25.00           C
ATOM     28  CA  PRO    28      32.141  29.203  27.574  1.00 25.00           C
ATOM     29  CA  CYS    29      35.715  28.163  26.986  1.00 25.00           C
ATOM     30  CA  GLU    30      37.530  31.365  26.095  1.00 25.00           C
ATOM     31  CA  PRO    31      37.813  29.989  22.592  1.00 25.00           C
ATOM     32  CA  ILE    32      34.049  29.458  22.054  1.00 25.00           C
ATOM     33  CA  PRO    33      32.803  26.104  20.609  1.00 25.00           C
ATOM     34  CA  PRO    34      30.758  23.796  18.315  1.00 25.00           C
ATOM     35  CA  THR    35      27.237  23.886  16.802  1.00 25.00           C
ATOM     36  CA  LEU    36      28.711  21.427  14.335  1.00 25.00           C
ATOM     37  CA  ALA    37      30.101  17.880  14.264  1.00 25.00           C
ATOM     38  CA  ILE    38      30.097  16.160  10.844  1.00 25.00           C
ATOM     39  CA  TYR    39      32.574  14.455   8.523  1.00 25.00           C
ATOM     40  CA  ASP    40      34.282  12.682   5.575  1.00 25.00           C
ATOM     41  CA  LYS    41      37.627  14.496   5.258  1.00 25.00           C
ATOM     42  CA  LYS    42      39.940  17.242   6.504  1.00 25.00           C
ATOM     43  CA  GLY    43      38.229  20.586   6.448  1.00 25.00           C
ATOM     44  CA  ASP    44      34.539  20.514   5.699  1.00 25.00           C
ATOM     45  CA  GLU    45      31.186  19.109   6.828  1.00 25.00           C
ATOM     46  CA  TRP    46      28.092  20.283   8.706  1.00 25.00           C
ATOM     47  CA  TYR    47      26.188  23.305   9.865  1.00 25.00           C
ATOM     48  CA  LYS    48      27.121  27.013  10.276  1.00 25.00           C
ATOM     49  CA  VAL    49      23.476  27.267  11.423  1.00 25.00           C
ATOM     50  CA  GLU    50      22.051  30.772  12.127  1.00 25.00           C
ATOM     51  CA  GLU    51      20.750  34.316  12.080  1.00 25.00           C
ATOM     52  CA  ALA    52      23.304  36.884  10.745  1.00 25.00           C
ATOM     53  CA  PRO    53      27.109  37.154  11.141  1.00 25.00           C
ATOM     54  CA  ASN    54      28.499  37.343   7.666  1.00 25.00           C
ATOM     55  CA  VAL    55      25.345  35.766   6.127  1.00 25.00           C
ATOM     56  CA  GLN    56      27.819  33.606   4.157  1.00 25.00           C
ATOM     57  CA  ASN    57      27.717  30.940   6.905  1.00 25.00           C
ATOM     58  CA  TYR    58      23.888  30.979   6.834  1.00 25.00           C
ATOM     59  CA  ARG    59      23.930  30.585   3.025  1.00 25.00           C
ATOM     60  CA  GLU    60      26.354  27.636   3.333  1.00 25.00           C
ATOM     61  CA  ALA    61      24.080  26.008   5.949  1.00 25.00           C
ATOM     62  CA  VAL    62      21.055  26.475   3.647  1.00 25.00           C
ATOM     63  CA  GLU    63      22.989  24.893   0.744  1.00 25.00           C
ATOM     64  CA  TRP    64      23.952  21.928   2.968  1.00 25.00           C
ATOM     65  CA  ALA    65      20.293  21.492   4.012  1.00 25.00           C
ATOM     66  CA  ILE    66      19.211  21.562   0.339  1.00 25.00           C
ATOM     67  CA  GLU    67      21.855  18.926  -0.515  1.00 25.00           C
ATOM     68  CA  VAL    68      20.629  16.725   2.369  1.00 25.00           C
ATOM     69  CA  LEU    69      17.020  17.077   1.136  1.00 25.00           C
ATOM     70  CA  GLU    70      18.109  16.109  -2.406  1.00 25.00           C
ATOM     71  CA  ARG    71      19.950  13.045  -1.029  1.00 25.00           C
ATOM     72  CA  ILE    72      16.831  12.031   0.948  1.00 25.00           C
ATOM     73  CA  ARG    73      14.683  12.400  -2.201  1.00 25.00           C
ATOM     74  CA  ASP    74      17.045  11.537  -5.054  1.00 25.00           C
ATOM     75  CA  GLY    75      18.466   8.481  -3.290  1.00 25.00           C
ATOM     76  CA  GLU    76      21.960   7.511  -2.347  1.00 25.00           C
ATOM     77  CA  ASN    77      20.907   6.878   1.234  1.00 25.00           C
ATOM     78  CA  VAL    78      20.939   8.331   4.778  1.00 25.00           C
ATOM     79  CA  LYS    79      22.233  11.925   4.634  1.00 25.00           C
ATOM     80  CA  LEU    80      23.133  13.132   8.189  1.00 25.00           C
ATOM     81  CA  VAL    81      20.474  14.832  10.327  1.00 25.00           C
ATOM     82  CA  SER    82      18.954  18.319  10.202  1.00 25.00           C
ATOM     83  CA  LEU    83      16.538  21.140  10.918  1.00 25.00           C
ATOM     84  CA  ASP    84      12.774  21.731  11.170  1.00 25.00           C
ATOM     85  CA  GLY    85      12.758  25.461  10.504  1.00 25.00           C
ATOM     86  CA  PRO    86      10.477  28.312  11.631  1.00 25.00           C
ATOM     87  CA  ALA    87      13.746  30.279  12.157  1.00 25.00           C
ATOM     88  CA  PRO    88      15.777  30.056  15.408  1.00 25.00           C
ATOM     89  CA  PRO    89      14.684  28.357  18.642  1.00 25.00           C
ATOM     90  CA  LYS    90      12.839  26.460  15.874  1.00 25.00           C
ATOM     91  CA  VAL    91      15.904  24.229  15.325  1.00 25.00           C
ATOM     92  CA  MET    92      16.094  23.524  19.085  1.00 25.00           C
ATOM     93  CA  LYS    93      12.372  22.621  19.129  1.00 25.00           C
ATOM     94  CA  ARG    94      12.884  20.263  16.154  1.00 25.00           C
ATOM     95  CA  LEU    95      15.838  18.607  17.945  1.00 25.00           C
ATOM     96  CA  SER    96      13.710  18.163  21.098  1.00 25.00           C
ATOM     97  CA  LEU    97      10.905  16.595  19.013  1.00 25.00           C
ATOM     98  CA  ALA    98      13.417  14.206  17.385  1.00 25.00           C
ATOM     99  CA  LEU    99      14.758  13.226  20.836  1.00 25.00           C
ATOM    100  CA  GLN   100      11.190  12.578  22.066  1.00 25.00           C
ATOM    101  CA  LYS   101      10.497  10.406  18.989  1.00 25.00           C
ATOM    102  CA  LEU   102      13.715   8.431  19.628  1.00 25.00           C
ATOM    103  CA  THR   103      14.518   9.491  16.022  1.00 25.00           C
ATOM    104  CA  GLU   104      15.356   5.847  15.601  1.00 25.00           C
TER
END
