
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS393_3-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N       7      -       -           -
LGA    D       8      -       -           -
LGA    L       9      -       -           -
LGA    R      10      N       7           #
LGA    D      11      D       8           -
LGA    F      12      -       -           -
LGA    L      13      L       9           #
LGA    -       -      R      10           -
LGA    T      14      D      11           #
LGA    L      15      F      12           -
LGA    L      16      -       -           -
LGA    E      17      -       -           -
LGA    Q      18      -       -           -
LGA    Q      19      -       -           -
LGA    G      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      -       -           -
LGA    K      23      -       -           -
LGA    R      24      -       -           -
LGA    I      25      L      13          2.319
LGA    T      26      T      14           #
LGA    L      27      L      15           -
LGA    P      28      -       -           -
LGA    V      29      L      16          5.138
LGA    D      30      E      17          3.798
LGA    -       -      Q      18           -
LGA    P      31      Q      19          4.421
LGA    H      32      G      20          2.106
LGA    L      33      E      21          3.904
LGA    E      34      L      22          1.616
LGA    I      35      K      23          2.010
LGA    T      36      -       -           -
LGA    E      37      -       -           -
LGA    I      38      R      24          1.650
LGA    A      39      I      25          2.564
LGA    D      40      -       -           -
LGA    R      41      -       -           -
LGA    T      42      T      26          1.269
LGA    L      43      L      27          1.283
LGA    R      44      P      28          2.460
LGA    A      45      V      29          3.194
LGA    G      46      D      30           #
LGA    G      47      P      31           -
LGA    P      48      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    A      49      I      35           #
LGA    L      50      T      36           -
LGA    L      51      E      37           -
LGA    F      52      I      38           -
LGA    E      53      A      39           -
LGA    N      54      D      40           -
LGA    P      55      R      41           -
LGA    K      56      -       -           -
LGA    G      57      -       -           -
LGA    Y      58      -       -           -
LGA    S      59      -       -           -
LGA    M      60      -       -           -
LGA    P      61      -       -           -
LGA    V      62      -       -           -
LGA    L      63      T      42          3.009
LGA    C      64      L      43          0.310
LGA    N      65      R      44          4.425
LGA    L      66      A      45           -
LGA    F      67      G      46           -
LGA    G      68      G      47           -
LGA    T      69      P      48           -
LGA    P      70      A      49           -
LGA    K      71      L      50           -
LGA    -       -      L      51           -
LGA    R      72      F      52           #
LGA    V      73      E      53           -
LGA    A      74      N      54           -
LGA    M      75      P      55          5.351
LGA    G      76      K      56           #
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      G      57          3.279
LGA    V      88      Y      58          4.058
LGA    G      89      S      59           -
LGA    K      90      M      60           -
LGA    L      91      P      61           -
LGA    L      92      V      62           -
LGA    A      93      L      63           -
LGA    F      94      C      64           -
LGA    L      95      N      65           -
LGA    K      96      L      66           -
LGA    D     314      F      67           -
LGA    A     315      G      68           -
LGA    I     316      T      69           -
LGA    Y     317      -       -           -
LGA    H     318      -       -           -
LGA    S     319      -       -           -
LGA    T     320      -       -           -
LGA    Y     321      -       -           -
LGA    T     322      -       -           -
LGA    G     323      P      70           #
LGA    R     324      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    P     325      A      74           #
LGA    P     326      M      75          3.101
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    D     327      Q      79          0.871
LGA    E     328      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    P     329      S      83          2.668
LGA    A     330      A      84          3.816
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    V     331      E      87          1.316
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           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    L     332      N     337           #
LGA    G     333      E     338          5.746
LGA    V     334      V     339           #
LGA    A     335      F     340          3.282
LGA    L     336      V     341          0.640
LGA    N     337      P     342          2.613
LGA    E     338      I     343          1.823
LGA    V     339      L     344          2.334
LGA    F     340      -       -           -
LGA    V     341      Q     345          4.029
LGA    P     342      K     346           -
LGA    I     343      Q     347           -
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     32    3.14     9.38     15.942     0.988

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.703253 * X  +   0.700260 * Y  +  -0.122761 * Z  +  59.578598
  Y_new =   0.507214 * X  +   0.373199 * Y  +  -0.776825 * Z  +  70.286629
  Z_new =  -0.498165 * X  +  -0.608571 * Y  +  -0.617635 * Z  +  76.253532 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.363587    0.778006  [ DEG:  -135.4235     44.5765 ]
  Theta =   0.521482    2.620111  [ DEG:    29.8787    150.1213 ]
  Phi   =   2.516754   -0.624839  [ DEG:   144.1994    -35.8006 ]
 
# 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_3-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS393_3-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   32   3.14    9.38  15.942
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS393_3-D1
PFRMAT TS
TARGET T0356
MODEL 3
PARENT N/A
ATOM      7  CA  ASN     7      73.058  89.164  79.414  1.00 25.00           C
ATOM      8  CA  ASP     8      69.866  90.398  81.133  1.00 25.00           C
ATOM      9  CA  LEU     9      69.322  86.931  82.664  1.00 25.00           C
ATOM     10  CA  ARG    10      72.938  86.893  83.926  1.00 25.00           C
ATOM     11  CA  ASP    11      72.460  90.365  85.470  1.00 25.00           C
ATOM     12  CA  PHE    12      69.244  89.188  87.185  1.00 25.00           C
ATOM     13  CA  LEU    13      71.073  86.116  88.559  1.00 25.00           C
ATOM     14  CA  THR    14      73.889  88.351  89.880  1.00 25.00           C
ATOM     15  CA  LEU    15      71.317  90.639  91.560  1.00 25.00           C
ATOM     16  CA  LEU    16      69.629  87.600  93.169  1.00 25.00           C
ATOM     17  CA  GLU    17      73.021  86.359  94.443  1.00 25.00           C
ATOM     18  CA  GLN    18      73.765  89.820  95.904  1.00 25.00           C
ATOM     19  CA  GLN    19      77.092  88.297  96.909  1.00 25.00           C
ATOM     20  CA  GLY    20      76.509  84.768  98.099  1.00 25.00           C
ATOM     21  CA  GLU    21      77.119  83.444  94.598  1.00 25.00           C
ATOM     22  CA  LEU    22      78.302  81.215  91.681  1.00 25.00           C
ATOM     23  CA  LYS    23      74.557  80.911  90.928  1.00 25.00           C
ATOM     24  CA  ARG    24      70.897  80.905  90.031  1.00 25.00           C
ATOM     25  CA  ILE    25      67.103  80.830  89.642  1.00 25.00           C
ATOM     26  CA  THR    26      67.050  82.777  92.901  1.00 25.00           C
ATOM     27  CA  LEU    27      65.502  85.510  95.087  1.00 25.00           C
ATOM     28  CA  PRO    28      62.705  86.976  93.080  1.00 25.00           C
ATOM     29  CA  VAL    29      64.329  85.811  89.902  1.00 25.00           C
ATOM     30  CA  ASP    30      61.684  86.477  87.274  1.00 25.00           C
ATOM     31  CA  PRO    31      61.585  82.678  87.395  1.00 25.00           C
ATOM     32  CA  HIS    32      58.582  83.248  89.703  1.00 25.00           C
ATOM     33  CA  LEU    33      57.541  79.585  89.292  1.00 25.00           C
ATOM     34  CA  GLU    34      61.103  78.453  90.126  1.00 25.00           C
ATOM     35  CA  ILE    35      61.105  80.674  93.245  1.00 25.00           C
ATOM     36  CA  THR    36      57.740  79.200  94.327  1.00 25.00           C
ATOM     37  CA  GLU    37      59.104  75.656  93.830  1.00 25.00           C
ATOM     38  CA  ILE    38      62.194  76.526  95.921  1.00 25.00           C
ATOM     39  CA  ALA    39      59.955  77.933  98.690  1.00 25.00           C
ATOM     40  CA  ASP    40      57.841  74.740  98.637  1.00 25.00           C
ATOM     41  CA  ARG    41      61.013  72.608  98.884  1.00 25.00           C
ATOM     42  CA  THR    42      62.222  74.708 101.850  1.00 25.00           C
ATOM     43  CA  LEU    43      58.828  74.275 103.572  1.00 25.00           C
ATOM     44  CA  ARG    44      58.995  70.492 103.006  1.00 25.00           C
ATOM     45  CA  ALA    45      62.689  69.600 102.669  1.00 25.00           C
ATOM     46  CA  GLY    46      65.564  71.107 100.719  1.00 25.00           C
ATOM     47  CA  GLY    47      66.032  74.026  98.326  1.00 25.00           C
ATOM     48  CA  PRO    48      66.833  73.689  94.659  1.00 25.00           C
ATOM     49  CA  ALA    49      64.375  74.339  91.852  1.00 25.00           C
ATOM     50  CA  LEU    50      64.099  74.894  88.129  1.00 25.00           C
ATOM     51  CA  LEU    51      62.702  77.268  85.454  1.00 25.00           C
ATOM     52  CA  PHE    52      60.160  79.496  83.592  1.00 25.00           C
ATOM     53  CA  GLU    53      57.223  81.770  84.576  1.00 25.00           C
ATOM     54  CA  ASN    54      55.354  84.492  86.524  1.00 25.00           C
ATOM     55  CA  PRO    55      55.112  86.988  89.355  1.00 25.00           C
ATOM     56  CA  LYS    56      55.005  87.623  93.111  1.00 25.00           C
ATOM     57  CA  GLY    57      51.747  86.475  94.763  1.00 25.00           C
ATOM     58  CA  TYR    58      50.611  83.709  92.419  1.00 25.00           C
ATOM     59  CA  SER    59      48.884  80.862  94.333  1.00 25.00           C
ATOM     60  CA  MET    60      52.169  78.916  94.378  1.00 25.00           C
ATOM     61  CA  PRO    61      51.190  76.430  91.674  1.00 25.00           C
ATOM     62  CA  VAL    62      52.245  77.318  88.179  1.00 25.00           C
ATOM     63  CA  LEU    63      52.545  73.755  86.996  1.00 25.00           C
ATOM     64  CA  CYS    64      54.230  70.699  85.480  1.00 25.00           C
ATOM     65  CA  ASN    65      53.055  68.941  88.643  1.00 25.00           C
ATOM     66  CA  LEU    66      51.582  68.546  92.075  1.00 25.00           C
ATOM     67  CA  PHE    67      54.613  70.570  93.301  1.00 25.00           C
ATOM     68  CA  GLY    68      54.567  69.822  97.057  1.00 25.00           C
ATOM     69  CA  THR    69      54.037  66.195  95.886  1.00 25.00           C
ATOM     70  CA  PRO    70      57.376  64.932  94.658  1.00 25.00           C
ATOM     71  CA  LYS    71      59.277  68.250  94.457  1.00 25.00           C
ATOM     72  CA  ARG    72      60.904  67.553  97.853  1.00 25.00           C
ATOM     73  CA  VAL    73      61.928  64.057  96.672  1.00 25.00           C
ATOM     74  CA  ALA    74      63.436  65.549  93.484  1.00 25.00           C
ATOM     75  CA  MET    75      65.378  68.107  95.571  1.00 25.00           C
ATOM     76  CA  GLY    76      66.685  65.307  97.832  1.00 25.00           C
ATOM     77  CA  MET    77      67.780  63.302  94.758  1.00 25.00           C
ATOM     78  CA  GLY    78      71.110  62.333  96.452  1.00 25.00           C
ATOM     79  CA  GLN    79      73.406  59.950  98.392  1.00 25.00           C
ATOM     80  CA  GLU    80      76.160  58.276 100.303  1.00 25.00           C
ATOM     81  CA  ASP    81      78.722  59.562 102.868  1.00 25.00           C
ATOM     82  CA  VAL    82      78.824  61.887 105.876  1.00 25.00           C
ATOM     83  CA  SER    83      76.575  64.091 108.054  1.00 25.00           C
ATOM     84  CA  ALA    84      74.691  65.287 104.941  1.00 25.00           C
ATOM     85  CA  LEU    85      74.221  61.660 103.803  1.00 25.00           C
ATOM     86  CA  ARG    86      72.895  60.719 107.270  1.00 25.00           C
ATOM     87  CA  GLU    87      70.451  63.666 107.163  1.00 25.00           C
ATOM     88  CA  VAL    88      69.252  62.578 103.692  1.00 25.00           C
ATOM     89  CA  GLY    89      68.738  59.003 104.963  1.00 25.00           C
ATOM     90  CA  LYS    90      66.741  60.327 107.952  1.00 25.00           C
ATOM     91  CA  LEU    91      64.575  62.436 105.601  1.00 25.00           C
ATOM     92  CA  LEU    92      63.951  59.373 103.388  1.00 25.00           C
ATOM     93  CA  ALA    93      62.959  57.321 106.467  1.00 25.00           C
ATOM     94  CA  PHE    94      60.555  60.090 107.569  1.00 25.00           C
ATOM     95  CA  LEU    95      59.007  60.174 104.067  1.00 25.00           C
ATOM     96  CA  LYS    96      55.423  60.590 105.274  1.00 25.00           C
ATOM    314  CA  ASP   314      50.356  64.382  75.357  1.00 25.00           C
ATOM    315  CA  ALA   315      52.573  63.042  72.565  1.00 25.00           C
ATOM    316  CA  ILE   316      54.863  61.667  69.907  1.00 25.00           C
ATOM    317  CA  TYR   317      54.936  65.407  70.080  1.00 25.00           C
ATOM    318  CA  HIS   318      54.989  68.719  68.273  1.00 25.00           C
ATOM    319  CA  SER   319      55.922  72.229  67.093  1.00 25.00           C
ATOM    320  CA  THR   320      58.513  74.677  68.261  1.00 25.00           C
ATOM    321  CA  TYR   321      58.567  78.478  68.535  1.00 25.00           C
ATOM    322  CA  THR   322      61.953  77.318  69.720  1.00 25.00           C
ATOM    323  CA  GLY   323      64.355  78.171  72.483  1.00 25.00           C
ATOM    324  CA  ARG   324      67.247  75.849  73.264  1.00 25.00           C
ATOM    325  CA  PRO   325      68.555  78.691  75.459  1.00 25.00           C
ATOM    326  CA  PRO   326      66.705  82.024  74.935  1.00 25.00           C
ATOM    327  CA  ASP   327      64.631  82.925  71.912  1.00 25.00           C
ATOM    328  CA  GLU   328      64.557  81.292  68.509  1.00 25.00           C
ATOM    329  CA  PRO   329      60.853  81.116  67.550  1.00 25.00           C
ATOM    330  CA  ALA   330      61.757  81.634  63.864  1.00 25.00           C
ATOM    331  CA  VAL   331      64.375  78.846  64.090  1.00 25.00           C
ATOM    332  CA  LEU   332      61.788  76.514  65.683  1.00 25.00           C
ATOM    333  CA  GLY   333      59.297  77.327  62.891  1.00 25.00           C
ATOM    334  CA  VAL   334      61.975  76.594  60.254  1.00 25.00           C
ATOM    335  CA  ALA   335      62.763  73.251  61.949  1.00 25.00           C
ATOM    336  CA  LEU   336      59.039  72.363  61.984  1.00 25.00           C
ATOM    337  CA  ASN   337      58.771  73.231  58.264  1.00 25.00           C
ATOM    338  CA  GLU   338      61.816  71.034  57.508  1.00 25.00           C
ATOM    339  CA  VAL   339      60.253  68.146  59.478  1.00 25.00           C
ATOM    340  CA  PHE   340      56.978  68.562  57.537  1.00 25.00           C
ATOM    341  CA  VAL   341      58.906  68.523  54.227  1.00 25.00           C
ATOM    342  CA  PRO   342      60.738  65.337  55.305  1.00 25.00           C
ATOM    343  CA  ILE   343      57.401  63.699  56.226  1.00 25.00           C
ATOM    344  CA  LEU   344      55.955  64.670  52.815  1.00 25.00           C
ATOM    345  CA  GLN   345      59.021  63.188  51.066  1.00 25.00           C
ATOM    346  CA  LYS   346      58.630  59.948  53.071  1.00 25.00           C
ATOM    347  CA  GLN   347      54.927  59.773  52.112  1.00 25.00           C
TER
END
