
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS393_5-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      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      L       9           #
LGA    T      26      R      10          3.807
LGA    L      27      D      11          2.033
LGA    P      28      F      12          0.933
LGA    V      29      L      13          2.275
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    D      30      L      16          0.377
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    P      31      Q      19          4.335
LGA    H      32      G      20          4.084
LGA    L      33      E      21          4.224
LGA    E      34      L      22          1.364
LGA    I      35      K      23          2.644
LGA    T      36      -       -           -
LGA    E      37      -       -           -
LGA    I      38      R      24          2.456
LGA    A      39      -       -           -
LGA    D      40      I      25          1.006
LGA    R      41      -       -           -
LGA    T      42      -       -           -
LGA    L      43      T      26          1.843
LGA    R      44      L      27          4.656
LGA    A      45      P      28           -
LGA    G      46      V      29           -
LGA    G      47      D      30           -
LGA    P      48      P      31           -
LGA    A      49      H      32           -
LGA    L      50      L      33           -
LGA    L      51      E      34           -
LGA    F      52      I      35           -
LGA    E      53      T      36           -
LGA    N      54      E      37           -
LGA    P      55      I      38           -
LGA    K      56      A      39           -
LGA    G      57      D      40           -
LGA    Y      58      R      41           -
LGA    S      59      T      42           -
LGA    M      60      L      43           -
LGA    P      61      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    V      62      G      47          2.468
LGA    L      63      P      48          4.203
LGA    C      64      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    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    N      65      C      64          4.127
LGA    L      66      N      65           #
LGA    F      67      L      66           -
LGA    G      68      F      67           -
LGA    T      69      G      68           -
LGA    P      70      T      69           -
LGA    K      71      P      70           -
LGA    R      72      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           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    V      73      Y     317           #
LGA    A      74      -       -           -
LGA    M      75      H     318           #
LGA    G      76      S     319          4.453
LGA    M      77      T     320           -
LGA    G      78      Y     321           -
LGA    Q      79      T     322           -
LGA    E      80      G     323           -
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      -       -           -
LGA    A     315      -       -           -
LGA    I     316      -       -           -
LGA    Y     317      -       -           -
LGA    H     318      -       -           -
LGA    S     319      -       -           -
LGA    T     320      R     324          2.040
LGA    Y     321      P     325          3.242
LGA    T     322      -       -           -
LGA    G     323      -       -           -
LGA    R     324      -       -           -
LGA    P     325      -       -           -
LGA    P     326      -       -           -
LGA    D     327      -       -           -
LGA    E     328      P     326           #
LGA    P     329      D     327          1.273
LGA    A     330      -       -           -
LGA    V     331      E     328          2.951
LGA    L     332      P     329          1.937
LGA    G     333      A     330          1.766
LGA    V     334      V     331          1.561
LGA    A     335      L     332          0.966
LGA    L     336      G     333          0.546
LGA    N     337      V     334          0.953
LGA    E     338      A     335          1.118
LGA    V     339      L     336          0.939
LGA    F     340      N     337          1.027
LGA    V     341      E     338          1.127
LGA    P     342      V     339          0.287
LGA    I     343      F     340          1.014
LGA    L     344      V     341          1.178
LGA    Q     345      P     342          1.927
LGA    K     346      I     343          2.806
LGA    Q     347      L     344          3.262
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     38    2.54     2.63     21.119     1.439

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.583824 * X  +   0.761874 * Y  +   0.280530 * Z  +  61.951889
  Y_new =   0.667542 * X  +  -0.647131 * Y  +   0.368251 * Z  +  71.827805
  Z_new =   0.462100 * X  +  -0.027728 * Y  +  -0.886394 * Z  +  76.903778 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.110321    0.031272  [ DEG:  -178.2083      1.7917 ]
  Theta =  -0.480362   -2.661231  [ DEG:   -27.5227   -152.4773 ]
  Phi   =   0.852200   -2.289393  [ DEG:    48.8275   -131.1725 ]
 
# 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_5-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS393_5-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   38   2.54    2.63  21.119
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS393_5-D1
PFRMAT TS
TARGET T0356
MODEL 5
PARENT N/A
ATOM      7  CA  ASN     7      70.285  94.132  81.735  1.00 25.00           C
ATOM      8  CA  ASP     8      67.511  93.362  84.260  1.00 25.00           C
ATOM      9  CA  LEU     9      69.050  89.921  84.939  1.00 25.00           C
ATOM     10  CA  ARG    10      72.482  91.534  85.472  1.00 25.00           C
ATOM     11  CA  ASP    11      70.944  94.063  87.903  1.00 25.00           C
ATOM     12  CA  PHE    12      69.238  91.220  89.819  1.00 25.00           C
ATOM     13  CA  LEU    13      72.561  89.326  90.016  1.00 25.00           C
ATOM     14  CA  THR    14      74.305  92.474  91.326  1.00 25.00           C
ATOM     15  CA  LEU    15      71.569  92.922  93.967  1.00 25.00           C
ATOM     16  CA  LEU    16      71.968  89.266  95.035  1.00 25.00           C
ATOM     17  CA  GLU    17      75.759  89.735  95.316  1.00 25.00           C
ATOM     18  CA  GLN    18      75.236  92.876  97.445  1.00 25.00           C
ATOM     19  CA  GLN    19      77.524  91.768 100.199  1.00 25.00           C
ATOM     20  CA  GLY    20      80.382  89.750  98.599  1.00 25.00           C
ATOM     21  CA  GLU    21      77.777  87.101  99.413  1.00 25.00           C
ATOM     22  CA  LEU    22      74.029  86.453  99.468  1.00 25.00           C
ATOM     23  CA  LYS    23      73.850  84.514  96.268  1.00 25.00           C
ATOM     24  CA  ARG    24      72.814  84.266  92.635  1.00 25.00           C
ATOM     25  CA  ILE    25      71.974  83.491  88.979  1.00 25.00           C
ATOM     26  CA  THR    26      75.139  82.884  86.925  1.00 25.00           C
ATOM     27  CA  LEU    27      73.086  82.617  83.665  1.00 25.00           C
ATOM     28  CA  PRO    28      70.042  80.678  84.892  1.00 25.00           C
ATOM     29  CA  VAL    29      67.480  82.691  86.860  1.00 25.00           C
ATOM     30  CA  ASP    30      64.000  83.108  85.438  1.00 25.00           C
ATOM     31  CA  PRO    31      60.283  82.258  85.643  1.00 25.00           C
ATOM     32  CA  HIS    32      57.416  80.835  87.746  1.00 25.00           C
ATOM     33  CA  LEU    33      59.288  77.511  88.093  1.00 25.00           C
ATOM     34  CA  GLU    34      62.448  79.378  89.186  1.00 25.00           C
ATOM     35  CA  ILE    35      60.424  81.341  91.776  1.00 25.00           C
ATOM     36  CA  THR    36      58.910  78.082  93.100  1.00 25.00           C
ATOM     37  CA  GLU    37      62.405  76.539  93.367  1.00 25.00           C
ATOM     38  CA  ILE    38      63.649  79.623  95.267  1.00 25.00           C
ATOM     39  CA  ALA    39      60.666  79.384  97.657  1.00 25.00           C
ATOM     40  CA  ASP    40      61.402  75.672  98.243  1.00 25.00           C
ATOM     41  CA  ARG    41      65.073  76.489  98.966  1.00 25.00           C
ATOM     42  CA  THR    42      64.006  79.206 101.445  1.00 25.00           C
ATOM     43  CA  LEU    43      61.650  76.733 103.179  1.00 25.00           C
ATOM     44  CA  ARG    44      64.479  74.164 103.414  1.00 25.00           C
ATOM     45  CA  ALA    45      68.048  75.366 103.830  1.00 25.00           C
ATOM     46  CA  GLY    46      69.995  78.654 103.816  1.00 25.00           C
ATOM     47  CA  GLY    47      69.662  79.836 100.165  1.00 25.00           C
ATOM     48  CA  PRO    48      70.327  76.235  99.013  1.00 25.00           C
ATOM     49  CA  ALA    49      69.018  77.276  95.585  1.00 25.00           C
ATOM     50  CA  LEU    50      68.249  79.128  92.308  1.00 25.00           C
ATOM     51  CA  LEU    51      66.791  82.611  92.769  1.00 25.00           C
ATOM     52  CA  PHE    52      64.279  84.435  90.557  1.00 25.00           C
ATOM     53  CA  GLU    53      61.041  86.268  91.197  1.00 25.00           C
ATOM     54  CA  ASN    54      60.310  89.955  91.376  1.00 25.00           C
ATOM     55  CA  PRO    55      57.271  91.547  92.988  1.00 25.00           C
ATOM     56  CA  LYS    56      58.194  89.372  95.928  1.00 25.00           C
ATOM     57  CA  GLY    57      55.540  86.617  95.557  1.00 25.00           C
ATOM     58  CA  TYR    58      54.462  86.910  91.886  1.00 25.00           C
ATOM     59  CA  SER    59      51.951  84.158  91.117  1.00 25.00           C
ATOM     60  CA  MET    60      53.786  81.570  93.266  1.00 25.00           C
ATOM     61  CA  PRO    61      52.783  78.778  90.875  1.00 25.00           C
ATOM     62  CA  VAL    62      51.927  76.639  87.884  1.00 25.00           C
ATOM     63  CA  LEU    63      54.925  74.264  87.415  1.00 25.00           C
ATOM     64  CA  CYS    64      56.200  70.687  87.422  1.00 25.00           C
ATOM     65  CA  ASN    65      59.707  71.321  88.763  1.00 25.00           C
ATOM     66  CA  LEU    66      61.324  70.079  92.033  1.00 25.00           C
ATOM     67  CA  PHE    67      60.584  70.823  95.696  1.00 25.00           C
ATOM     68  CA  GLY    68      56.897  70.617  96.531  1.00 25.00           C
ATOM     69  CA  THR    69      57.228  66.847  96.734  1.00 25.00           C
ATOM     70  CA  PRO    70      60.530  65.343  97.836  1.00 25.00           C
ATOM     71  CA  LYS    71      59.687  62.807  95.092  1.00 25.00           C
ATOM     72  CA  ARG    72      61.697  64.851  92.552  1.00 25.00           C
ATOM     73  CA  VAL    73      64.671  64.969  94.962  1.00 25.00           C
ATOM     74  CA  ALA    74      64.457  61.177  95.450  1.00 25.00           C
ATOM     75  CA  MET    75      64.386  60.667  91.656  1.00 25.00           C
ATOM     76  CA  GLY    76      67.453  62.929  91.270  1.00 25.00           C
ATOM     77  CA  MET    77      69.288  60.944  93.984  1.00 25.00           C
ATOM     78  CA  GLY    78      72.584  59.186  93.399  1.00 25.00           C
ATOM     79  CA  GLN    79      71.222  55.929  91.958  1.00 25.00           C
ATOM     80  CA  GLU    80      74.360  53.827  92.011  1.00 25.00           C
ATOM     81  CA  ASP    81      72.729  50.339  91.899  1.00 25.00           C
ATOM     82  CA  VAL    82      73.765  48.347  94.953  1.00 25.00           C
ATOM     83  CA  SER    83      71.080  46.635  97.080  1.00 25.00           C
ATOM     84  CA  ALA    84      71.208  49.513  99.603  1.00 25.00           C
ATOM     85  CA  LEU    85      70.844  52.054  96.759  1.00 25.00           C
ATOM     86  CA  ARG    86      67.837  50.120  95.384  1.00 25.00           C
ATOM     87  CA  GLU    87      66.240  50.080  98.865  1.00 25.00           C
ATOM     88  CA  VAL    88      66.797  53.855  99.191  1.00 25.00           C
ATOM     89  CA  GLY    89      65.195  54.412  95.757  1.00 25.00           C
ATOM     90  CA  LYS    90      62.190  52.271  96.784  1.00 25.00           C
ATOM     91  CA  LEU    91      61.829  54.285 100.022  1.00 25.00           C
ATOM     92  CA  LEU    92      61.955  57.555  98.031  1.00 25.00           C
ATOM     93  CA  ALA    93      59.266  56.233  95.645  1.00 25.00           C
ATOM     94  CA  PHE    94      57.070  55.251  98.624  1.00 25.00           C
ATOM     95  CA  LEU    95      57.516  58.741 100.136  1.00 25.00           C
ATOM     96  CA  LYS    96      55.105  60.092 102.805  1.00 25.00           C
ATOM    314  CA  ASP   314      51.056  66.385  61.830  1.00 25.00           C
ATOM    315  CA  ALA   315      51.039  64.009  64.834  1.00 25.00           C
ATOM    316  CA  ILE   316      50.912  63.053  68.536  1.00 25.00           C
ATOM    317  CA  TYR   317      51.606  63.545  72.232  1.00 25.00           C
ATOM    318  CA  HIS   318      54.501  63.121  74.590  1.00 25.00           C
ATOM    319  CA  SER   319      55.467  61.866  78.091  1.00 25.00           C
ATOM    320  CA  THR   320      53.912  60.887  81.451  1.00 25.00           C
ATOM    321  CA  TYR   321      51.026  62.998  82.716  1.00 25.00           C
ATOM    322  CA  THR   322      50.090  66.365  84.225  1.00 25.00           C
ATOM    323  CA  GLY   323      53.014  65.342  86.447  1.00 25.00           C
ATOM    324  CA  ARG   324      53.444  69.099  85.920  1.00 25.00           C
ATOM    325  CA  PRO   325      54.793  69.168  89.494  1.00 25.00           C
ATOM    326  CA  PRO   326      56.066  65.711  90.150  1.00 25.00           C
ATOM    327  CA  ASP   327      58.000  63.659  87.556  1.00 25.00           C
ATOM    328  CA  GLU   328      57.772  66.535  85.116  1.00 25.00           C
ATOM    329  CA  PRO   329      55.938  64.488  82.449  1.00 25.00           C
ATOM    330  CA  ALA   330      54.164  67.648  81.210  1.00 25.00           C
ATOM    331  CA  VAL   331      57.518  69.488  81.023  1.00 25.00           C
ATOM    332  CA  LEU   332      59.031  66.580  79.043  1.00 25.00           C
ATOM    333  CA  GLY   333      56.055  66.640  76.633  1.00 25.00           C
ATOM    334  CA  VAL   334      56.479  70.417  76.165  1.00 25.00           C
ATOM    335  CA  ALA   335      60.211  69.935  75.454  1.00 25.00           C
ATOM    336  CA  LEU   336      59.394  67.215  72.884  1.00 25.00           C
ATOM    337  CA  ASN   337      56.850  69.533  71.204  1.00 25.00           C
ATOM    338  CA  GLU   338      59.453  72.338  71.072  1.00 25.00           C
ATOM    339  CA  VAL   339      61.998  69.936  69.513  1.00 25.00           C
ATOM    340  CA  PHE   340      59.414  68.855  66.902  1.00 25.00           C
ATOM    341  CA  VAL   341      58.671  72.522  66.083  1.00 25.00           C
ATOM    342  CA  PRO   342      62.417  73.220  65.694  1.00 25.00           C
ATOM    343  CA  ILE   343      62.762  70.201  63.364  1.00 25.00           C
ATOM    344  CA  LEU   344      59.800  71.442  61.277  1.00 25.00           C
ATOM    345  CA  GLN   345      61.387  74.920  61.048  1.00 25.00           C
ATOM    346  CA  LYS   346      64.701  73.361  59.929  1.00 25.00           C
ATOM    347  CA  GLN   347      62.867  71.314  57.262  1.00 25.00           C
TER
END
