
#######################################################
#                                                     #
#                        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  124 (  124),  selected  124 , name T0356TS393_4-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS393_4-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N       7      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    D       8      G      20          4.508
LGA    L       9      E      21          4.171
LGA    R      10      L      22          2.805
LGA    D      11      K      23          3.180
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    T      14      R      24          1.779
LGA    L      15      I      25          2.133
LGA    L      16      -       -           -
LGA    E      17      T      26           #
LGA    Q      18      L      27          2.597
LGA    Q      19      P      28          3.005
LGA    G      20      V      29          1.735
LGA    E      21      D      30           #
LGA    L      22      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    K      23      I      38          1.027
LGA    R      24      A      39          2.938
LGA    I      25      D      40           #
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    T      26      P      61           #
LGA    L      27      V      62          3.785
LGA    P      28      L      63          4.045
LGA    V      29      C      64           #
LGA    D      30      N      65          4.337
LGA    P      31      L      66          2.727
LGA    H      32      F      67          3.908
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    I      35      -       -           -
LGA    T      36      -       -           -
LGA    E      37      -       -           -
LGA    I      38      -       -           -
LGA    A      39      -       -           -
LGA    D      40      -       -           -
LGA    R      41      -       -           -
LGA    T      42      -       -           -
LGA    L      43      -       -           -
LGA    R      44      -       -           -
LGA    A      45      -       -           -
LGA    G      46      -       -           -
LGA    G      47      -       -           -
LGA    P      48      -       -           -
LGA    A      49      -       -           -
LGA    L      50      -       -           -
LGA    L      51      -       -           -
LGA    F      52      G      68          2.555
LGA    E      53      T      69          2.349
LGA    N      54      -       -           -
LGA    P      55      -       -           -
LGA    K      56      -       -           -
LGA    G      57      -       -           -
LGA    Y      58      -       -           -
LGA    S      59      -       -           -
LGA    M      60      -       -           -
LGA    P      61      -       -           -
LGA    V      62      -       -           -
LGA    L      63      P      70          3.417
LGA    C      64      K      71           -
LGA    N      65      R      72           -
LGA    L      66      -       -           -
LGA    F      67      -       -           -
LGA    G      68      -       -           -
LGA    T      69      -       -           -
LGA    P      70      -       -           -
LGA    K      71      -       -           -
LGA    R      72      -       -           -
LGA    V      73      -       -           -
LGA    A      74      -       -           -
LGA    M      75      -       -           -
LGA    G      76      -       -           -
LGA    M      77      -       -           -
LGA    G      78      -       -           -
LGA    Q      79      -       -           -
LGA    E      80      -       -           -
LGA    D      81      -       -           -
LGA    V      82      -       -           -
LGA    S      83      -       -           -
LGA    A      84      -       -           -
LGA    L      85      -       -           -
LGA    R      86      -       -           -
LGA    E      87      -       -           -
LGA    V      88      -       -           -
LGA    G      89      -       -           -
LGA    K      90      -       -           -
LGA    L      91      -       -           -
LGA    L      92      -       -           -
LGA    A      93      -       -           -
LGA    F      94      -       -           -
LGA    L      95      -       -           -
LGA    K      96      -       -           -
LGA    D     314      V      73          3.265
LGA    A     315      A      74          1.237
LGA    I     316      M      75          3.042
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    Y     317      G      78          3.496
LGA    H     318      Q      79           #
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    S     319      V      88          2.473
LGA    T     320      G      89          2.141
LGA    Y     321      K      90          2.519
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    T     322      A      93          3.903
LGA    G     323      F      94          2.025
LGA    R     324      L      95          4.399
LGA    P     325      K      96          1.991
LGA    P     326      D     314           -
LGA    D     327      A     315           -
LGA    E     328      I     316           -
LGA    P     329      Y     317           -
LGA    A     330      H     318           -
LGA    V     331      S     319           -
LGA    L     332      T     320           -
LGA    G     333      Y     321           -
LGA    V     334      T     322           -
LGA    A     335      G     323           -
LGA    L     336      R     324           -
LGA    N     337      P     325           -
LGA    E     338      P     326           -
LGA    V     339      D     327           -
LGA    F     340      E     328           -
LGA    V     341      P     329           -
LGA    P     342      A     330           -
LGA    I     343      V     331           -
LGA    L     344      L     332           -
LGA    Q     345      G     333           -
LGA    K     346      V     334           -
LGA    Q     347      A     335           -
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  124  124    5.0     30    3.06     3.33     13.696     0.949

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.042464 * X  +   0.989460 * Y  +   0.138442 * Z  +  68.627060
  Y_new =  -0.151432 * X  +  -0.143341 * Y  +   0.978019 * Z  +  76.845863
  Z_new =   0.987555 * X  +   0.020566 * Y  +   0.155923 * Z  +  72.959862 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.131141   -3.010451  [ DEG:     7.5139   -172.4861 ]
  Theta =  -1.412868   -1.728725  [ DEG:   -80.9513    -99.0487 ]
  Phi   =  -1.844191    1.297402  [ DEG:  -105.6643     74.3357 ]
 
# 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: T0356TS393_4-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS393_4-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  124  124   5.0   30   3.06    3.33  13.696
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS393_4-D1
PFRMAT TS
TARGET T0356
MODEL 4
PARENT N/A
ATOM      7  CA  ASN     7      60.273  85.496  91.523  1.00 25.00           C
ATOM      8  CA  ASP     8      56.906  83.817  92.242  1.00 25.00           C
ATOM      9  CA  LEU     9      58.007  80.717  90.281  1.00 25.00           C
ATOM     10  CA  ARG    10      61.284  80.599  92.258  1.00 25.00           C
ATOM     11  CA  ASP    11      59.339  80.867  95.546  1.00 25.00           C
ATOM     12  CA  PHE    12      57.030  78.019  94.441  1.00 25.00           C
ATOM     13  CA  LEU    13      60.071  75.867  93.551  1.00 25.00           C
ATOM     14  CA  THR    14      61.618  76.591  96.978  1.00 25.00           C
ATOM     15  CA  LEU    15      58.333  75.618  98.693  1.00 25.00           C
ATOM     16  CA  LEU    16      58.221  72.360  96.684  1.00 25.00           C
ATOM     17  CA  GLU    17      61.838  71.591  97.681  1.00 25.00           C
ATOM     18  CA  GLN    18      60.988  72.243 101.358  1.00 25.00           C
ATOM     19  CA  GLN    19      62.432  68.690 101.791  1.00 25.00           C
ATOM     20  CA  GLY    20      59.452  66.494 100.783  1.00 25.00           C
ATOM     21  CA  GLU    21      56.457  68.719 100.434  1.00 25.00           C
ATOM     22  CA  LEU    22      53.378  69.086  98.157  1.00 25.00           C
ATOM     23  CA  LYS    23      54.818  68.009  94.806  1.00 25.00           C
ATOM     24  CA  ARG    24      58.123  68.619  93.025  1.00 25.00           C
ATOM     25  CA  ILE    25      60.223  69.509  90.052  1.00 25.00           C
ATOM     26  CA  THR    26      62.763  71.929  91.475  1.00 25.00           C
ATOM     27  CA  LEU    27      66.036  73.075  93.103  1.00 25.00           C
ATOM     28  CA  PRO    28      66.664  75.535  90.248  1.00 25.00           C
ATOM     29  CA  VAL    29      63.474  76.814  88.489  1.00 25.00           C
ATOM     30  CA  ASP    30      61.415  75.322  85.649  1.00 25.00           C
ATOM     31  CA  PRO    31      61.988  73.235  82.518  1.00 25.00           C
ATOM     32  CA  HIS    32      64.743  70.615  82.979  1.00 25.00           C
ATOM     33  CA  LEU    33      63.264  69.622  86.369  1.00 25.00           C
ATOM     34  CA  GLU    34      59.793  69.288  84.785  1.00 25.00           C
ATOM     35  CA  ILE    35      61.247  67.099  82.000  1.00 25.00           C
ATOM     36  CA  THR    36      62.984  64.894  84.605  1.00 25.00           C
ATOM     37  CA  GLU    37      59.697  64.550  86.541  1.00 25.00           C
ATOM     38  CA  ILE    38      57.873  63.576  83.318  1.00 25.00           C
ATOM     39  CA  ALA    39      60.563  60.959  82.556  1.00 25.00           C
ATOM     40  CA  ASP    40      60.224  59.543  86.098  1.00 25.00           C
ATOM     41  CA  ARG    41      56.422  59.353  85.685  1.00 25.00           C
ATOM     42  CA  THR    42      56.852  57.536  82.340  1.00 25.00           C
ATOM     43  CA  LEU    43      59.276  55.059  83.972  1.00 25.00           C
ATOM     44  CA  ARG    44      56.774  54.437  86.803  1.00 25.00           C
ATOM     45  CA  ALA    45      53.535  53.789  84.960  1.00 25.00           C
ATOM     46  CA  GLY    46      50.808  56.032  83.507  1.00 25.00           C
ATOM     47  CA  GLY    47      51.229  59.760  84.038  1.00 25.00           C
ATOM     48  CA  PRO    48      52.092  61.070  80.554  1.00 25.00           C
ATOM     49  CA  ALA    49      54.446  62.658  77.951  1.00 25.00           C
ATOM     50  CA  LEU    50      56.495  65.662  76.722  1.00 25.00           C
ATOM     51  CA  LEU    51      56.661  68.932  78.679  1.00 25.00           C
ATOM     52  CA  PHE    52      57.028  72.373  80.348  1.00 25.00           C
ATOM     53  CA  GLU    53      57.047  75.613  82.340  1.00 25.00           C
ATOM     54  CA  ASN    54      57.206  73.413  85.447  1.00 25.00           C
ATOM     55  CA  PRO    55      53.690  72.275  86.220  1.00 25.00           C
ATOM     56  CA  LYS    56      50.194  71.140  87.028  1.00 25.00           C
ATOM     57  CA  GLY    57      48.182  68.899  84.727  1.00 25.00           C
ATOM     58  CA  TYR    58      49.817  69.976  81.504  1.00 25.00           C
ATOM     59  CA  SER    59      49.065  71.851  78.233  1.00 25.00           C
ATOM     60  CA  MET    60      52.320  71.262  76.286  1.00 25.00           C
ATOM     61  CA  PRO    61      54.397  74.381  75.627  1.00 25.00           C
ATOM     62  CA  VAL    62      57.320  76.576  74.478  1.00 25.00           C
ATOM     63  CA  LEU    63      59.276  73.311  74.300  1.00 25.00           C
ATOM     64  CA  CYS    64      61.708  70.422  74.289  1.00 25.00           C
ATOM     65  CA  ASN    65      58.888  68.692  72.313  1.00 25.00           C
ATOM     66  CA  LEU    66      59.085  65.162  70.926  1.00 25.00           C
ATOM     67  CA  PHE    67      59.358  62.431  73.566  1.00 25.00           C
ATOM     68  CA  GLY    68      56.614  59.857  74.403  1.00 25.00           C
ATOM     69  CA  THR    69      59.532  57.405  74.418  1.00 25.00           C
ATOM     70  CA  PRO    70      61.729  58.147  71.425  1.00 25.00           C
ATOM     71  CA  LYS    71      63.711  61.375  70.862  1.00 25.00           C
ATOM     72  CA  ARG    72      64.233  61.742  74.639  1.00 25.00           C
ATOM     73  CA  VAL    73      65.446  58.116  74.848  1.00 25.00           C
ATOM     74  CA  ALA    74      67.880  58.738  71.957  1.00 25.00           C
ATOM     75  CA  MET    75      69.199  61.878  73.711  1.00 25.00           C
ATOM     76  CA  GLY    76      69.684  59.895  76.950  1.00 25.00           C
ATOM     77  CA  MET    77      71.575  57.172  75.031  1.00 25.00           C
ATOM     78  CA  GLY    78      73.526  54.129  76.165  1.00 25.00           C
ATOM     79  CA  GLN    79      75.530  51.141  77.365  1.00 25.00           C
ATOM     80  CA  GLU    80      79.208  52.023  77.375  1.00 25.00           C
ATOM     81  CA  ASP    81      82.401  52.648  75.387  1.00 25.00           C
ATOM     82  CA  VAL    82      82.681  53.493  71.716  1.00 25.00           C
ATOM     83  CA  SER    83      81.458  50.593  69.534  1.00 25.00           C
ATOM     84  CA  ALA    84      79.071  49.476  72.315  1.00 25.00           C
ATOM     85  CA  LEU    85      77.731  53.050  72.632  1.00 25.00           C
ATOM     86  CA  ARG    86      77.191  53.209  68.844  1.00 25.00           C
ATOM     87  CA  GLU    87      75.326  49.867  68.944  1.00 25.00           C
ATOM     88  CA  VAL    88      73.121  51.153  71.800  1.00 25.00           C
ATOM     89  CA  GLY    89      72.359  54.334  69.810  1.00 25.00           C
ATOM     90  CA  LYS    90      71.436  52.228  66.748  1.00 25.00           C
ATOM     91  CA  LEU    91      69.127  50.063  68.903  1.00 25.00           C
ATOM     92  CA  LEU    92      67.460  53.207  70.319  1.00 25.00           C
ATOM     93  CA  ALA    93      66.955  54.565  66.774  1.00 25.00           C
ATOM     94  CA  PHE    94      65.405  51.235  65.691  1.00 25.00           C
ATOM     95  CA  LEU    95      63.055  51.318  68.714  1.00 25.00           C
ATOM     96  CA  LYS    96      60.887  48.161  68.298  1.00 25.00           C
ATOM    314  CA  ASP   314      60.393  77.047  75.106  1.00 25.00           C
ATOM    315  CA  ALA   315      62.894  79.711  74.246  1.00 25.00           C
ATOM    316  CA  ILE   316      66.623  79.930  74.805  1.00 25.00           C
ATOM    317  CA  TYR   317      69.556  79.283  72.431  1.00 25.00           C
ATOM    318  CA  HIS   318      69.473  79.263  68.606  1.00 25.00           C
ATOM    319  CA  SER   319      68.926  78.479  64.936  1.00 25.00           C
ATOM    320  CA  THR   320      66.882  76.222  62.733  1.00 25.00           C
ATOM    321  CA  TYR   321      66.715  74.283  59.420  1.00 25.00           C
ATOM    322  CA  THR   322      69.598  76.510  58.236  1.00 25.00           C
ATOM    323  CA  GLY   323      71.695  73.350  58.205  1.00 25.00           C
ATOM    324  CA  ARG   324      73.210  70.763  55.861  1.00 25.00           C
ATOM    325  CA  PRO   325      74.790  68.237  58.239  1.00 25.00           C
ATOM    326  CA  PRO   326      73.952  65.200  56.081  1.00 25.00           C
ATOM    327  CA  ASP   327      76.869  66.520  53.995  1.00 25.00           C
ATOM    328  CA  GLU   328      79.976  68.089  55.369  1.00 25.00           C
ATOM    329  CA  PRO   329      81.995  71.264  56.080  1.00 25.00           C
ATOM    330  CA  ALA   330      81.008  72.686  52.664  1.00 25.00           C
ATOM    331  CA  VAL   331      77.327  71.902  53.374  1.00 25.00           C
ATOM    332  CA  LEU   332      77.587  73.637  56.777  1.00 25.00           C
ATOM    333  CA  GLY   333      79.173  76.705  55.119  1.00 25.00           C
ATOM    334  CA  VAL   334      76.356  76.788  52.525  1.00 25.00           C
ATOM    335  CA  ALA   335      73.744  76.577  55.318  1.00 25.00           C
ATOM    336  CA  LEU   336      75.463  79.451  57.176  1.00 25.00           C
ATOM    337  CA  ASN   337      75.473  81.549  53.972  1.00 25.00           C
ATOM    338  CA  GLU   338      71.746  80.831  53.461  1.00 25.00           C
ATOM    339  CA  VAL   339      71.025  81.868  57.077  1.00 25.00           C
ATOM    340  CA  PHE   340      72.998  85.110  56.567  1.00 25.00           C
ATOM    341  CA  VAL   341      71.029  85.833  53.362  1.00 25.00           C
ATOM    342  CA  PRO   342      67.735  85.224  55.220  1.00 25.00           C
ATOM    343  CA  ILE   343      68.843  87.598  58.013  1.00 25.00           C
ATOM    344  CA  LEU   344      69.746  90.267  55.419  1.00 25.00           C
ATOM    345  CA  GLN   345      66.320  89.851  53.760  1.00 25.00           C
ATOM    346  CA  LYS   346      64.601  90.211  57.164  1.00 25.00           C
ATOM    347  CA  GLN   347      66.620  93.387  57.875  1.00 25.00           C
TER
END
