
#######################################################
#                                                     #
#                        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 T0356TS168_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS168_2-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           -
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    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    N       7      P      28          2.569
LGA    D       8      V      29          1.383
LGA    L       9      D      30          0.620
LGA    R      10      P      31           #
LGA    D      11      -       -           -
LGA    F      12      H      32          6.268
LGA    L      13      -       -           -
LGA    T      14      -       -           -
LGA    L      15      -       -           -
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      L      33          3.274
LGA    I      25      E      34          3.570
LGA    T      26      -       -           -
LGA    L      27      -       -           -
LGA    P      28      -       -           -
LGA    V      29      I      35          3.718
LGA    D      30      T      36          4.616
LGA    P      31      E      37          4.781
LGA    H      32      I      38          3.963
LGA    L      33      A      39          3.225
LGA    E      34      D      40          3.767
LGA    I      35      R      41          2.897
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      -       -           -
LGA    E      53      -       -           -
LGA    N      54      -       -           -
LGA    P      55      -       -           -
LGA    K      56      -       -           -
LGA    G      57      -       -           -
LGA    Y      58      T      42          4.064
LGA    S      59      L      43           #
LGA    M      60      R      44          4.155
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    P      61      P      48          3.593
LGA    V      62      A      49          4.512
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    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    L      63      G      68          1.082
LGA    -       -      T      69           -
LGA    C      64      P      70           #
LGA    N      65      K      71           -
LGA    L      66      R      72           -
LGA    F      67      V      73           -
LGA    G      68      A      74           -
LGA    T      69      M      75           -
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      G      76           #
LGA    A     315      -       -           -
LGA    I     316      -       -           -
LGA    Y     317      -       -           -
LGA    H     318      -       -           -
LGA    S     319      -       -           -
LGA    T     320      M      77          4.826
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    Y     321      L      85          1.486
LGA    T     322      R      86          3.040
LGA    G     323      E      87           -
LGA    R     324      V      88           -
LGA    P     325      G      89           -
LGA    P     326      K      90           -
LGA    D     327      L      91           -
LGA    E     328      L      92           -
LGA    P     329      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    A     330      E     328           #
LGA    V     331      P     329           -
LGA    L     332      A     330           -
LGA    -       -      V     331           -
LGA    G     333      L     332          2.560
LGA    -       -      G     333           -
LGA    V     334      V     334          3.418
LGA    A     335      A     335          3.276
LGA    L     336      L     336          2.016
LGA    N     337      N     337          1.208
LGA    E     338      E     338          0.735
LGA    V     339      V     339          0.815
LGA    F     340      F     340          0.860
LGA    V     341      V     341          1.558
LGA    P     342      P     342          1.481
LGA    I     343      I     343          0.729
LGA    L     344      L     344          0.979
LGA    Q     345      Q     345          1.170
LGA    K     346      K     346          0.909
LGA    Q     347      Q     347          1.952

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  124  124    5.0     36    3.03    41.67     18.523     1.151

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.516452 * X  +  -0.754456 * Y  +   0.405059 * Z  +  64.897697
  Y_new =  -0.840766 * X  +   0.536494 * Y  +  -0.072715 * Z  +  65.849304
  Z_new =  -0.162452 * X  +  -0.378113 * Y  +  -0.911394 * Z  +  77.921333 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.748330    0.393262  [ DEG:  -157.4677     22.5323 ]
  Theta =   0.163175    2.978418  [ DEG:     9.3492    170.6508 ]
  Phi   =  -2.121638    1.019954  [ DEG:  -121.5609     58.4391 ]
 
# 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: T0356TS168_2-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS168_2-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   36   3.03   41.67  18.523
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS168_2-D1
PFRMAT TS
TARGET T0356
MODEL 2
PARENT N/A
ATOM      7  CA  ASN     7      62.671  68.231 103.209  1.00 25.00           C
ATOM      8  CA  ASP     8      59.492  66.975 101.480  1.00 25.00           C
ATOM      9  CA  LEU     9      61.417  63.983 100.061  1.00 25.00           C
ATOM     10  CA  ARG    10      62.801  63.189 103.542  1.00 25.00           C
ATOM     11  CA  ASP    11      59.269  63.368 105.014  1.00 25.00           C
ATOM     12  CA  PHE    12      57.985  61.012 102.282  1.00 25.00           C
ATOM     13  CA  LEU    13      60.836  58.562 103.019  1.00 25.00           C
ATOM     14  CA  THR    14      60.004  58.681 106.755  1.00 25.00           C
ATOM     15  CA  LEU    15      56.315  57.999 105.981  1.00 25.00           C
ATOM     16  CA  LEU    16      57.302  55.030 103.774  1.00 25.00           C
ATOM     17  CA  GLU    17      59.521  53.653 106.575  1.00 25.00           C
ATOM     18  CA  GLN    18      56.638  54.013 109.070  1.00 25.00           C
ATOM     19  CA  GLN    19      54.919  50.698 108.568  1.00 25.00           C
ATOM     20  CA  GLY    20      51.403  51.937 107.763  1.00 25.00           C
ATOM     21  CA  GLU    21      52.478  54.172 104.888  1.00 25.00           C
ATOM     22  CA  LEU    22      50.899  56.235 102.078  1.00 25.00           C
ATOM     23  CA  LYS    23      54.001  57.500 100.414  1.00 25.00           C
ATOM     24  CA  ARG    24      56.507  58.780  97.928  1.00 25.00           C
ATOM     25  CA  ILE    25      58.153  60.891  95.249  1.00 25.00           C
ATOM     26  CA  THR    26      61.077  58.584  94.490  1.00 25.00           C
ATOM     27  CA  LEU    27      64.376  60.368  93.792  1.00 25.00           C
ATOM     28  CA  PRO    28      62.560  61.062  90.543  1.00 25.00           C
ATOM     29  CA  VAL    29      60.298  63.845  91.807  1.00 25.00           C
ATOM     30  CA  ASP    30      61.623  67.182  92.953  1.00 25.00           C
ATOM     31  CA  PRO    31      57.963  68.116  93.223  1.00 25.00           C
ATOM     32  CA  HIS    32      56.061  69.558  90.229  1.00 25.00           C
ATOM     33  CA  LEU    33      56.448  66.242  88.354  1.00 25.00           C
ATOM     34  CA  GLU    34      55.143  64.335  91.408  1.00 25.00           C
ATOM     35  CA  ILE    35      52.137  66.699  91.631  1.00 25.00           C
ATOM     36  CA  THR    36      51.414  66.168  87.907  1.00 25.00           C
ATOM     37  CA  GLU    37      51.598  62.373  88.386  1.00 25.00           C
ATOM     38  CA  ILE    38      49.186  62.605  91.352  1.00 25.00           C
ATOM     39  CA  ALA    39      46.768  64.705  89.252  1.00 25.00           C
ATOM     40  CA  ASP    40      46.948  62.128  86.424  1.00 25.00           C
ATOM     41  CA  ARG    41      46.232  59.308  88.914  1.00 25.00           C
ATOM     42  CA  THR    42      43.229  61.248  90.285  1.00 25.00           C
ATOM     43  CA  LEU    43      41.916  61.779  86.726  1.00 25.00           C
ATOM     44  CA  ARG    44      42.304  58.039  86.000  1.00 25.00           C
ATOM     45  CA  ALA    45      40.887  56.747  89.253  1.00 25.00           C
ATOM     46  CA  GLY    46      42.139  56.951  92.876  1.00 25.00           C
ATOM     47  CA  GLY    47      44.962  54.834  91.310  1.00 25.00           C
ATOM     48  CA  PRO    48      47.471  53.817  94.038  1.00 25.00           C
ATOM     49  CA  ALA    49      49.781  56.522  92.612  1.00 25.00           C
ATOM     50  CA  LEU    50      53.237  57.600  93.711  1.00 25.00           C
ATOM     51  CA  LEU    51      53.051  61.225  94.870  1.00 25.00           C
ATOM     52  CA  PHE    52      54.262  64.706  95.900  1.00 25.00           C
ATOM     53  CA  GLU    53      53.632  68.348  96.779  1.00 25.00           C
ATOM     54  CA  ASN    54      49.920  67.454  97.200  1.00 25.00           C
ATOM     55  CA  PRO    55      48.066  70.491  98.584  1.00 25.00           C
ATOM     56  CA  LYS    56      45.765  73.202  97.241  1.00 25.00           C
ATOM     57  CA  GLY    57      47.174  72.940  93.768  1.00 25.00           C
ATOM     58  CA  TYR    58      50.328  73.074  91.713  1.00 25.00           C
ATOM     59  CA  SER    59      51.249  75.737  89.154  1.00 25.00           C
ATOM     60  CA  MET    60      52.438  73.000  86.793  1.00 25.00           C
ATOM     61  CA  PRO    61      55.570  74.916  85.997  1.00 25.00           C
ATOM     62  CA  VAL    62      58.518  76.410  84.032  1.00 25.00           C
ATOM     63  CA  LEU    63      58.055  73.206  81.985  1.00 25.00           C
ATOM     64  CA  CYS    64      58.356  70.126  79.698  1.00 25.00           C
ATOM     65  CA  ASN    65      55.554  68.199  81.337  1.00 25.00           C
ATOM     66  CA  LEU    66      51.783  67.628  81.930  1.00 25.00           C
ATOM     67  CA  PHE    67      48.922  69.571  83.588  1.00 25.00           C
ATOM     68  CA  GLY    68      46.459  69.318  80.774  1.00 25.00           C
ATOM     69  CA  THR    69      45.170  66.196  82.616  1.00 25.00           C
ATOM     70  CA  PRO    70      47.854  64.135  80.881  1.00 25.00           C
ATOM     71  CA  LYS    71      45.479  64.234  77.877  1.00 25.00           C
ATOM     72  CA  ARG    72      48.384  63.409  75.521  1.00 25.00           C
ATOM     73  CA  VAL    73      49.396  60.471  77.760  1.00 25.00           C
ATOM     74  CA  ALA    74      45.787  59.191  77.756  1.00 25.00           C
ATOM     75  CA  MET    75      45.674  59.448  73.936  1.00 25.00           C
ATOM     76  CA  GLY    76      48.970  57.513  73.684  1.00 25.00           C
ATOM     77  CA  MET    77      47.584  54.803  76.008  1.00 25.00           C
ATOM     78  CA  GLY    78      45.005  52.576  74.314  1.00 25.00           C
ATOM     79  CA  GLN    79      46.930  49.438  73.620  1.00 25.00           C
ATOM     80  CA  GLU    80      46.357  46.924  70.849  1.00 25.00           C
ATOM     81  CA  ASP    81      45.210  46.176  67.271  1.00 25.00           C
ATOM     82  CA  VAL    82      44.550  49.527  65.556  1.00 25.00           C
ATOM     83  CA  SER    83      40.788  49.820  66.209  1.00 25.00           C
ATOM     84  CA  ALA    84      41.437  50.045  69.978  1.00 25.00           C
ATOM     85  CA  LEU    85      44.052  52.780  69.390  1.00 25.00           C
ATOM     86  CA  ARG    86      41.572  54.713  67.201  1.00 25.00           C
ATOM     87  CA  GLU    87      38.896  54.413  69.924  1.00 25.00           C
ATOM     88  CA  VAL    88      41.382  55.692  72.543  1.00 25.00           C
ATOM     89  CA  GLY    89      42.272  58.655  70.286  1.00 25.00           C
ATOM     90  CA  LYS    90      38.555  59.455  69.827  1.00 25.00           C
ATOM     91  CA  LEU    91      38.033  59.321  73.619  1.00 25.00           C
ATOM     92  CA  LEU    92      41.009  61.675  74.136  1.00 25.00           C
ATOM     93  CA  ALA    93      39.575  64.098  71.540  1.00 25.00           C
ATOM     94  CA  PHE    94      36.175  64.010  73.300  1.00 25.00           C
ATOM     95  CA  LEU    95      37.867  64.724  76.661  1.00 25.00           C
ATOM     96  CA  LYS    96      34.710  64.377  78.855  1.00 25.00           C
ATOM    314  CA  ASP   314      67.072  75.161  83.275  1.00 25.00           C
ATOM    315  CA  ALA   315      66.189  71.552  83.793  1.00 25.00           C
ATOM    316  CA  ILE   316      64.919  68.690  81.621  1.00 25.00           C
ATOM    317  CA  TYR   317      67.414  68.851  78.800  1.00 25.00           C
ATOM    318  CA  HIS   318      67.812  70.273  75.344  1.00 25.00           C
ATOM    319  CA  SER   319      66.418  73.137  73.291  1.00 25.00           C
ATOM    320  CA  THR   320      66.178  75.792  70.552  1.00 25.00           C
ATOM    321  CA  TYR   321      63.766  76.865  67.753  1.00 25.00           C
ATOM    322  CA  THR   322      60.423  78.286  66.723  1.00 25.00           C
ATOM    323  CA  GLY   323      58.022  79.593  69.326  1.00 25.00           C
ATOM    324  CA  ARG   324      60.753  80.905  71.638  1.00 25.00           C
ATOM    325  CA  PRO   325      62.268  82.967  74.432  1.00 25.00           C
ATOM    326  CA  PRO   326      61.733  83.137  78.169  1.00 25.00           C
ATOM    327  CA  ASP   327      61.284  80.558  80.969  1.00 25.00           C
ATOM    328  CA  GLU   328      61.014  76.788  81.075  1.00 25.00           C
ATOM    329  CA  PRO   329      62.133  73.248  80.135  1.00 25.00           C
ATOM    330  CA  ALA   330      58.685  72.532  78.629  1.00 25.00           C
ATOM    331  CA  VAL   331      58.863  75.784  76.614  1.00 25.00           C
ATOM    332  CA  LEU   332      62.347  74.834  75.341  1.00 25.00           C
ATOM    333  CA  GLY   333      61.059  71.375  74.319  1.00 25.00           C
ATOM    334  CA  VAL   334      58.120  72.990  72.469  1.00 25.00           C
ATOM    335  CA  ALA   335      60.528  75.351  70.655  1.00 25.00           C
ATOM    336  CA  LEU   336      62.729  72.380  69.657  1.00 25.00           C
ATOM    337  CA  ASN   337      59.655  70.514  68.340  1.00 25.00           C
ATOM    338  CA  GLU   338      58.620  73.597  66.316  1.00 25.00           C
ATOM    339  CA  VAL   339      62.153  73.856  64.858  1.00 25.00           C
ATOM    340  CA  PHE   340      62.059  70.147  63.909  1.00 25.00           C
ATOM    341  CA  VAL   341      58.658  70.640  62.218  1.00 25.00           C
ATOM    342  CA  PRO   342      60.031  73.642  60.276  1.00 25.00           C
ATOM    343  CA  ILE   343      63.054  71.570  59.162  1.00 25.00           C
ATOM    344  CA  LEU   344      60.730  68.751  58.013  1.00 25.00           C
ATOM    345  CA  GLN   345      58.613  71.266  56.048  1.00 25.00           C
ATOM    346  CA  LYS   346      61.771  72.675  54.402  1.00 25.00           C
ATOM    347  CA  GLN   347      62.890  69.134  53.461  1.00 25.00           C
TER
END
