
#######################################################
#                                                     #
#                        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  130 (  130),  selected  130 , name T0354TS599_4
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS599_4.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      E       2           -
LGA    M       1      I       3          2.038
LGA    E       2      Q       4          5.433
LGA    I       3      -       -           -
LGA    Q       4      -       -           -
LGA    E       5      E       5          1.740
LGA    I       6      I       6          2.204
LGA    S       7      S       7          2.332
LGA    K       8      K       8          0.927
LGA    L       9      L       9          1.651
LGA    A      10      A      10          2.729
LGA    I      11      I      11          2.596
LGA    E      12      E      12          2.468
LGA    A      13      A      13          3.373
LGA    L      14      L      14          3.709
LGA    E      15      E      15          3.569
LGA    D      16      D      16           #
LGA    I      17      I      17          4.145
LGA    K      18      K      18          3.205
LGA    G      19      G      19          2.743
LGA    K      20      K      20          2.964
LGA    D      21      D      21          2.684
LGA    I      22      I      22          1.496
LGA    I      23      I      23          2.301
LGA    E      24      E      24          2.071
LGA    L      25      L      25          1.713
LGA    D      26      D      26          2.154
LGA    T      27      T      27          2.160
LGA    S      28      S      28          3.747
LGA    K      29      -       -           -
LGA    L      30      K      29          0.757
LGA    T      31      L      30          5.548
LGA    S      32      T      31          2.073
LGA    L      33      S      32           #
LGA    F      34      L      33           -
LGA    Q      35      F      34          3.058
LGA    R      36      Q      35          3.401
LGA    M      37      R      36          2.054
LGA    I      38      M      37          1.825
LGA    V      39      I      38          1.624
LGA    A      40      V      39          1.229
LGA    T      41      A      40          1.568
LGA    G      42      T      41          1.179
LGA    D      43      G      42          3.164
LGA    S      44      D      43          1.384
LGA    N      45      S      44          3.118
LGA    -       -      N      45           -
LGA    R      46      R      46          3.171
LGA    Q      47      Q      47          3.180
LGA    V      48      V      48          3.784
LGA    K      49      K      49          2.665
LGA    A      50      A      50          1.917
LGA    L      51      L      51          2.928
LGA    A      52      A      52          2.496
LGA    N      53      N      53          1.294
LGA    S      54      S      54          1.976
LGA    V      55      V      55          2.141
LGA    Q      56      Q      56          0.920
LGA    V      57      V      57          1.450
LGA    K      58      K      58          2.314
LGA    L      59      L      59          1.720
LGA    K      60      K      60          1.729
LGA    E      61      E      61          2.443
LGA    A      62      A      62          3.001
LGA    G      63      G      63          2.974
LGA    V      64      V      64          2.163
LGA    D      65      D      65          2.141
LGA    I      66      I      66          1.983
LGA    V      67      V      67          1.719
LGA    G      68      G      68          2.139
LGA    -       -      S      69           -
LGA    S      69      E      70          4.501
LGA    E      70      G      71          5.796
LGA    G      71      H      72           -
LGA    H      72      E      73           -
LGA    E      73      -       -           -
LGA    S      74      -       -           -
LGA    G      75      S      74           #
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    E      76      W      77          2.101
LGA    W      77      V      78          4.448
LGA    V      78      L      79          1.241
LGA    L      79      V      80          3.472
LGA    V      80      D      81          2.045
LGA    D      81      A      82          2.325
LGA    A      82      G      83          4.335
LGA    G      83      -       -           -
LGA    D      84      -       -           -
LGA    V      85      D      84          2.242
LGA    V      86      V      85          2.611
LGA    V      87      V      86          2.335
LGA    H      88      V      87          2.439
LGA    V      89      H      88          2.182
LGA    M      90      V      89          3.050
LGA    L      91      M      90          3.076
LGA    P      92      L      91          3.666
LGA    -       -      P      92           -
LGA    A      93      A      93          2.021
LGA    V      94      V      94          2.463
LGA    R      95      R      95          4.293
LGA    D      96      D      96          3.785
LGA    Y      97      Y      97           #
LGA    Y      98      -       -           -
LGA    D      99      -       -           -
LGA    I     100      -       -           -
LGA    E     101      -       -           -
LGA    A     102      -       -           -
LGA    L     103      -       -           -
LGA    W     104      Y      98          5.598
LGA    G     105      D      99           -
LGA    G     106      -       -           -
LGA    Q     107      -       -           -
LGA    K     108      -       -           -
LGA    P     109      -       -           -
LGA    S     110      -       -           -
LGA    F     111      -       -           -
LGA    A     112      -       -           -
LGA    V     113      -       -           -
LGA    G     114      -       -           -
LGA    A     115      -       -           -
LGA    A     116      -       -           -
LGA    K     117      -       -           -
LGA    P     118      -       -           -
LGA    W     119      -       -           -
LGA    S     120      I     100           #
LGA    -       -      E     101           -
LGA    -       -      A     102           -
LGA    A     121      L     103          1.719
LGA    V     122      W     104           #
LGA    L     123      G     105           -
LGA    E     124      G     106           -
LGA    H     125      Q     107          2.918
LGA    H     126      K     108          1.540
LGA    H     127      P     109          5.503
LGA    H     128      S     110           -
LGA    H     129      F     111           -
LGA    H     130      A     112           -
LGA    -       -      V     113           -
LGA    -       -      G     114           -
LGA    -       -      A     115           -
LGA    -       -      A     116           -
LGA    -       -      K     117           -
LGA    -       -      P     118           -
LGA    -       -      W     119           -
LGA    -       -      S     120           -
LGA    -       -      A     121           -
LGA    -       -      V     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  130  122    5.0     88    2.86    59.09     44.510     2.974

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.213412 * X  +   0.924274 * Y  +   0.316502 * Z  +  38.433678
  Y_new =   0.904310 * X  +  -0.309482 * Y  +   0.294014 * Z  +  26.565523
  Z_new =   0.369701 * X  +   0.223470 * Y  +  -0.901877 * Z  +  22.802198 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.898702   -0.242891  [ DEG:   166.0834    -13.9166 ]
  Theta =  -0.378688   -2.762905  [ DEG:   -21.6972   -158.3028 ]
  Phi   =   1.339043   -1.802550  [ DEG:    76.7215   -103.2785 ]
 
# 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: T0354TS599_4                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS599_4.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  130  122   5.0   88   2.86   59.09  44.510
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS599_4
PFRMAT TS                                                                       
TARGET T0354                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      49.796  19.200  17.162  1.00  0.00              
ATOM      2  CA  GLU     2      50.842  23.270  17.281  1.00  0.00              
ATOM      3  CA  ILE     3      47.619  23.175  18.822  1.00  0.00              
ATOM      4  CA  GLN     4      48.332  20.178  20.673  1.00  0.00              
ATOM      5  CA  GLU     5      51.477  21.561  22.426  1.00  0.00              
ATOM      6  CA  ILE     6      49.522  24.590  23.394  1.00  0.00              
ATOM      7  CA  SER     7      46.705  22.428  24.846  1.00  0.00              
ATOM      8  CA  LYS     8      49.244  20.567  26.972  1.00  0.00              
ATOM      9  CA  LEU     9      50.754  23.846  28.232  1.00  0.00              
ATOM     10  CA  ALA    10      47.320  25.209  29.135  1.00  0.00              
ATOM     11  CA  ILE    11      46.396  22.025  30.940  1.00  0.00              
ATOM     12  CA  GLU    12      49.569  21.945  32.964  1.00  0.00              
ATOM     13  CA  ALA    13      49.162  25.602  33.979  1.00  0.00              
ATOM     14  CA  LEU    14      45.574  24.991  34.972  1.00  0.00              
ATOM     15  CA  GLU    15      46.464  21.999  37.058  1.00  0.00              
ATOM     16  CA  ASP    16      49.174  24.025  38.791  1.00  0.00              
ATOM     17  CA  ILE    17      46.670  26.736  39.688  1.00  0.00              
ATOM     18  CA  LYS    18      43.782  24.499  40.697  1.00  0.00              
ATOM     19  CA  GLY    19      41.444  25.291  37.727  1.00  0.00              
ATOM     20  CA  LYS    20      38.819  22.644  37.978  1.00  0.00              
ATOM     21  CA  ASP    21      37.070  22.738  34.674  1.00  0.00              
ATOM     22  CA  ILE    22      38.947  22.658  31.427  1.00  0.00              
ATOM     23  CA  ILE    23      37.523  20.839  28.370  1.00  0.00              
ATOM     24  CA  GLU    24      39.806  20.116  25.490  1.00  0.00              
ATOM     25  CA  LEU    25      38.425  19.096  22.125  1.00  0.00              
ATOM     26  CA  ASP    26      40.825  17.608  19.659  1.00  0.00              
ATOM     27  CA  THR    27      40.035  17.686  16.142  1.00  0.00              
ATOM     28  CA  SER    28      42.594  15.286  14.658  1.00  0.00              
ATOM     29  CA  LYS    29      40.325  13.136  12.566  1.00  0.00              
ATOM     30  CA  LEU    30      38.322  15.696  10.691  1.00  0.00              
ATOM     31  CA  THR    31      40.971  17.663   8.813  1.00  0.00              
ATOM     32  CA  SER    32      39.351  21.067   9.374  1.00  0.00              
ATOM     33  CA  LEU    33      39.027  20.288  13.081  1.00  0.00              
ATOM     34  CA  PHE    34      42.666  19.250  13.296  1.00  0.00              
ATOM     35  CA  GLN    35      43.949  22.623  12.075  1.00  0.00              
ATOM     36  CA  ARG    36      41.694  24.191  14.711  1.00  0.00              
ATOM     37  CA  MET    37      41.732  23.081  18.395  1.00  0.00              
ATOM     38  CA  ILE    38      38.825  24.107  20.684  1.00  0.00              
ATOM     39  CA  VAL    39      39.362  24.713  24.323  1.00  0.00              
ATOM     40  CA  ALA    40      36.450  24.965  26.535  1.00  0.00              
ATOM     41  CA  THR    41      36.938  26.472  29.931  1.00  0.00              
ATOM     42  CA  GLY    42      34.282  26.393  32.548  1.00  0.00              
ATOM     43  CA  ASP    43      36.060  26.693  35.812  1.00  0.00              
ATOM     44  CA  SER    44      34.942  29.897  37.453  1.00  0.00              
ATOM     45  CA  ASN    45      35.459  32.809  35.131  1.00  0.00              
ATOM     46  CA  ARG    46      38.318  34.273  37.033  1.00  0.00              
ATOM     47  CA  GLN    47      40.438  31.124  37.006  1.00  0.00              
ATOM     48  CA  VAL    48      40.023  30.566  33.290  1.00  0.00              
ATOM     49  CA  LYS    49      40.880  34.227  32.536  1.00  0.00              
ATOM     50  CA  ALA    50      44.004  34.093  34.641  1.00  0.00              
ATOM     51  CA  LEU    51      45.047  30.834  32.863  1.00  0.00              
ATOM     52  CA  ALA    52      44.407  32.369  29.421  1.00  0.00              
ATOM     53  CA  ASN    53      46.472  35.398  30.290  1.00  0.00              
ATOM     54  CA  SER    54      49.327  33.068  31.316  1.00  0.00              
ATOM     55  CA  VAL    55      49.018  31.134  28.112  1.00  0.00              
ATOM     56  CA  GLN    56      48.951  34.331  26.019  1.00  0.00              
ATOM     57  CA  VAL    57      52.218  35.449  27.622  1.00  0.00              
ATOM     58  CA  LYS    58      53.805  32.030  26.972  1.00  0.00              
ATOM     59  CA  LEU    59      52.653  32.124  23.379  1.00  0.00              
ATOM     60  CA  LYS    60      54.034  35.667  22.896  1.00  0.00              
ATOM     61  CA  GLU    61      57.367  34.508  24.182  1.00  0.00              
ATOM     62  CA  ALA    62      57.263  31.634  21.678  1.00  0.00              
ATOM     63  CA  GLY    63      56.389  33.923  18.824  1.00  0.00              
ATOM     64  CA  VAL    64      52.720  32.963  18.395  1.00  0.00              
ATOM     65  CA  ASP    65      50.607  35.838  17.211  1.00  0.00              
ATOM     66  CA  ILE    66      47.424  36.558  19.089  1.00  0.00              
ATOM     67  CA  VAL    67      44.735  36.670  16.618  1.00  0.00              
ATOM     68  CA  GLY    68      41.596  37.672  18.407  1.00  0.00              
ATOM     69  CA  SER    69      38.262  36.191  17.523  1.00  0.00              
ATOM     70  CA  GLU    70      34.966  37.548  18.707  1.00  0.00              
ATOM     71  CA  GLY    71      32.051  35.235  18.272  1.00  0.00              
ATOM     72  CA  HIS    72      29.158  37.256  16.990  1.00  0.00              
ATOM     73  CA  GLU    73      26.396  36.344  19.485  1.00  0.00              
ATOM     74  CA  SER    74      28.275  37.594  22.561  1.00  0.00              
ATOM     75  CA  GLY    75      29.086  34.471  24.468  1.00  0.00              
ATOM     76  CA  GLU    76      32.810  34.519  24.729  1.00  0.00              
ATOM     77  CA  TRP    77      35.009  33.456  21.771  1.00  0.00              
ATOM     78  CA  VAL    78      38.716  33.907  21.963  1.00  0.00              
ATOM     79  CA  LEU    79      40.974  33.247  18.977  1.00  0.00              
ATOM     80  CA  VAL    80      44.591  32.531  19.630  1.00  0.00              
ATOM     81  CA  ASP    81      46.928  32.139  16.840  1.00  0.00              
ATOM     82  CA  ALA    82      49.860  30.020  17.602  1.00  0.00              
ATOM     83  CA  GLY    83      50.842  27.744  14.778  1.00  0.00              
ATOM     84  CA  ASP    84      47.881  25.355  14.660  1.00  0.00              
ATOM     85  CA  VAL    85      45.002  27.668  15.662  1.00  0.00              
ATOM     86  CA  VAL    86      43.640  27.554  19.165  1.00  0.00              
ATOM     87  CA  VAL    87      40.063  28.563  19.733  1.00  0.00              
ATOM     88  CA  HIS    88      39.113  29.334  23.272  1.00  0.00              
ATOM     89  CA  VAL    89      35.536  29.287  24.047  1.00  0.00              
ATOM     90  CA  MET    90      34.352  30.626  27.358  1.00  0.00              
ATOM     91  CA  LEU    91      30.691  30.198  28.325  1.00  0.00              
ATOM     92  CA  PRO    92      29.182  28.121  31.060  1.00  0.00              
ATOM     93  CA  ALA    93      26.608  30.678  32.082  1.00  0.00              
ATOM     94  CA  VAL    94      25.504  31.454  28.579  1.00  0.00              
ATOM     95  CA  ARG    95      25.126  27.891  27.371  1.00  0.00              
ATOM     96  CA  ASP    96      23.073  26.653  30.255  1.00  0.00              
ATOM     97  CA  TYR    97      20.913  29.793  30.242  1.00  0.00              
ATOM     98  CA  TYR    98      20.128  29.872  26.598  1.00  0.00              
ATOM     99  CA  ASP    99      19.486  26.228  25.602  1.00  0.00              
ATOM    100  CA  ILE   100      21.992  24.862  23.141  1.00  0.00              
ATOM    101  CA  GLU   101      19.985  25.093  19.955  1.00  0.00              
ATOM    102  CA  ALA   102      19.399  28.818  20.584  1.00  0.00              
ATOM    103  CA  LEU   103      23.073  29.525  21.264  1.00  0.00              
ATOM    104  CA  TRP   104      24.286  27.713  18.116  1.00  0.00              
ATOM    105  CA  GLY   105      21.774  29.605  15.977  1.00  0.00              
ATOM    106  CA  GLY   106      22.760  33.010  17.389  1.00  0.00              
ATOM    107  CA  GLN   107      26.525  32.551  16.914  1.00  0.00              
ATOM    108  CA  LYS   108      26.438  31.415  13.330  1.00  0.00              
ATOM    109  CA  PRO   109      27.647  27.814  13.476  1.00  0.00              
ATOM    110  CA  SER   110      29.706  27.451  10.344  1.00  0.00              
ATOM    111  CA  PHE   111      29.703  23.960   8.955  1.00  0.00              
ATOM    112  CA  ALA   112      33.273  23.479   7.929  1.00  0.00              
ATOM    113  CA  VAL   113      33.591  21.653   4.580  1.00  0.00              
ATOM    114  CA  GLY   114      37.221  20.711   4.417  1.00  0.00              
ATOM    115  CA  ALA   115      36.939  16.894   4.515  1.00  0.00              
ATOM    116  CA  ALA   116      33.459  16.148   5.895  1.00  0.00              
ATOM    117  CA  LYS   117      33.168  15.664   9.584  1.00  0.00              
ATOM    118  CA  PRO   118      30.062  17.340  10.836  1.00  0.00              
ATOM    119  CA  TRP   119      30.253  20.417  12.942  1.00  0.00              
ATOM    120  CA  SER   120      30.670  19.106  16.421  1.00  0.00              
ATOM    121  CA  ALA   121      28.215  21.049  18.657  1.00  0.00              
ATOM    122  CA  VAL   122      26.113  18.442  20.372  1.00  0.00              
ATOM    123  CA  LEU   123      24.022  20.227  22.956  1.00  0.00              
ATOM    124  CA  GLU   124      24.849  17.896  25.904  1.00  0.00              
ATOM    125  CA  HIS   125      28.596  17.943  25.304  1.00  0.00              
ATOM    126  CA  HIS   126      30.234  18.177  28.762  1.00  0.00              
ATOM    127  CA  HIS   127      33.532  18.440  26.847  1.00  0.00              
ATOM    128  CA  HIS   128      33.880  16.192  23.297  1.00  0.00              
ATOM    129  CA  HIS   129      37.343  15.375  23.739  1.00  0.00              
ATOM    130  CA  HIS   130      41.510  15.763  24.077  1.00  0.00              
TER                                                                             
END
