
#######################################################
#                                                     #
#                        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  126 (  126),  selected  126 , name T0372TS599_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS599_4-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    P       3      P       3           -
LGA    F       4      F       4           -
LGA    K       5      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    D       6      F      39           #
LGA    I       7      -       -           -
LGA    T       8      -       -           -
LGA    L       9      -       -           -
LGA    A      10      -       -           -
LGA    D      11      -       -           -
LGA    R      12      -       -           -
LGA    D      13      -       -           -
LGA    T      14      -       -           -
LGA    I      15      -       -           -
LGA    T      16      -       -           -
LGA    A      17      -       -           -
LGA    F      18      -       -           -
LGA    T      19      -       -           -
LGA    M      20      -       -           -
LGA    K      21      -       -           -
LGA    S      22      -       -           -
LGA    D      23      -       -           -
LGA    R      24      -       -           -
LGA    R      25      -       -           -
LGA    N      26      -       -           -
LGA    C      27      -       -           -
LGA    D      28      -       -           -
LGA    L      29      -       -           -
LGA    S      30      -       -           -
LGA    F      31      -       -           -
LGA    S      32      -       -           -
LGA    N      33      -       -           -
LGA    L      34      -       -           -
LGA    C      35      -       -           -
LGA    S      36      -       -           -
LGA    W      37      -       -           -
LGA    R      38      -       -           -
LGA    F      39      -       -           -
LGA    L      40      -       -           -
LGA    Y      41      L      40           #
LGA    D      42      Y      41          2.863
LGA    T      43      D      42          2.139
LGA    Q      44      T      43          1.103
LGA    F      45      Q      44          0.792
LGA    A      46      F      45          1.772
LGA    V      47      A      46          1.780
LGA    I      48      V      47          4.107
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    D      49      D      50           #
LGA    D      50      F      51          3.560
LGA    F      51      L      52          0.931
LGA    L      52      V      53          1.132
LGA    V      53      F      54          0.751
LGA    F      54      K      55          0.787
LGA    K      55      F      56          1.088
LGA    F      56      W      57          1.682
LGA    W      57      A      58          2.228
LGA    A      58      G      59          2.909
LGA    G      59      E      60          1.931
LGA    E      60      -       -           -
LGA    Q      61      Q      61          0.805
LGA    L      62      L      62          1.440
LGA    A      63      A      63          1.028
LGA    Y      64      Y      64          0.812
LGA    M      65      M      65          1.232
LGA    M      66      M      66          3.193
LGA    P      67      P      67          2.575
LGA    V      68      V      68          3.865
LGA    G      69      G      69          3.961
LGA    N      70      N      70          4.998
LGA    G      71      G      71          2.987
LGA    D      72      D      72          2.362
LGA    L      73      L      73          1.447
LGA    K      74      K      74          1.384
LGA    A      75      A      75          1.498
LGA    V      76      V      76          1.571
LGA    L      77      L      77          1.285
LGA    R      78      R      78          1.314
LGA    K      79      K      79          1.047
LGA    L      80      L      80          0.893
LGA    I      81      I      81          1.024
LGA    E      82      E      82          0.962
LGA    D      83      D      83          0.712
LGA    A      84      A      84          0.761
LGA    D      85      D      85          1.088
LGA    K      86      K      86          1.495
LGA    E      87      E      87          1.351
LGA    K      88      K      88          1.011
LGA    H      89      H      89          1.932
LGA    N      90      N      90          2.729
LGA    F      91      F      91          2.289
LGA    C      92      C      92          0.823
LGA    M      93      M      93          2.379
LGA    L      94      L      94          4.242
LGA    -       -      G      95           -
LGA    G      95      V      96          5.023
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    V      96      N      99           #
LGA    C      97      M     100           #
LGA    S      98      R     101           -
LGA    N      99      A     102           -
LGA    M     100      D     103           -
LGA    R     101      L     104           -
LGA    A     102      E     105           -
LGA    D     103      A     106           -
LGA    L     104      I     107           -
LGA    E     105      L     108           -
LGA    A     106      P     109           -
LGA    I     107      E     110           -
LGA    L     108      R     111           -
LGA    P     109      F     112           -
LGA    E     110      I     113           -
LGA    R     111      F     114           -
LGA    F     112      T     115           -
LGA    I     113      E     116           -
LGA    F     114      D     117           -
LGA    T     115      K     290           -
LGA    E     116      Y     291           -
LGA    D     117      M     292           -
LGA    K     290      A     293           -
LGA    Y     291      C     294           -
LGA    M     292      L     295           -
LGA    A     293      K     296           -
LGA    C     294      D     297           -
LGA    L     295      H     298           -
LGA    K     296      -       -           -
LGA    D     297      -       -           -
LGA    H     298      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  126  126    5.0     52    2.22    65.38     33.817     2.238

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.497846 * X  +   0.862616 * Y  +   0.089682 * Z  +  52.116741
  Y_new =   0.038607 * X  +   0.125349 * Y  +  -0.991361 * Z  +  34.301704
  Z_new =  -0.866406 * X  +  -0.490083 * Y  +  -0.095708 * Z  +   5.767793 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.763658    1.377935  [ DEG:  -101.0502     78.9498 ]
  Theta =   1.047959    2.093634  [ DEG:    60.0436    119.9564 ]
  Phi   =   3.064199   -0.077394  [ DEG:   175.5657     -4.4343 ]
 
# 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: T0372TS599_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS599_4-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  126  126   5.0   52   2.22   65.38  33.817
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS599_4-D1
PFRMAT TS                                                                       
TARGET T0372                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      37.695  23.863  16.121  1.00  0.00              
ATOM      2  CA  ILE     2      39.771  26.377  14.537  1.00  0.00              
ATOM      3  CA  PRO     3      40.937  27.627  10.718  1.00  0.00              
ATOM      4  CA  PHE     4      44.161  29.381   9.850  1.00  0.00              
ATOM      5  CA  LYS     5      43.965  32.811   8.505  1.00  0.00              
ATOM      6  CA  ASP     6      47.398  33.905   7.586  1.00  0.00              
ATOM      7  CA  ILE     7      49.465  32.378  10.345  1.00  0.00              
ATOM      8  CA  THR     8      52.927  31.287   9.496  1.00  0.00              
ATOM      9  CA  LEU     9      54.385  28.139  10.905  1.00  0.00              
ATOM     10  CA  ALA    10      58.116  28.423  10.794  1.00  0.00              
ATOM     11  CA  ASP    11      60.110  25.266  10.230  1.00  0.00              
ATOM     12  CA  ARG    12      58.160  22.764  12.209  1.00  0.00              
ATOM     13  CA  ASP    13      60.884  21.678  14.693  1.00  0.00              
ATOM     14  CA  THR    14      61.671  25.300  15.543  1.00  0.00              
ATOM     15  CA  ILE    15      58.035  26.226  16.099  1.00  0.00              
ATOM     16  CA  THR    16      57.442  23.316  18.391  1.00  0.00              
ATOM     17  CA  ALA    17      60.496  24.023  20.440  1.00  0.00              
ATOM     18  CA  PHE    18      59.530  27.679  20.929  1.00  0.00              
ATOM     19  CA  THR    19      56.030  26.915  21.991  1.00  0.00              
ATOM     20  CA  MET    20      57.235  24.324  24.563  1.00  0.00              
ATOM     21  CA  LYS    21      59.647  26.768  26.105  1.00  0.00              
ATOM     22  CA  SER    22      57.068  29.480  26.477  1.00  0.00              
ATOM     23  CA  ASP    23      54.248  27.354  27.949  1.00  0.00              
ATOM     24  CA  ARG    24      51.556  28.128  25.492  1.00  0.00              
ATOM     25  CA  ARG    25      49.168  25.513  24.568  1.00  0.00              
ATOM     26  CA  ASN    26      47.534  25.902  21.427  1.00  0.00              
ATOM     27  CA  CYS    27      44.300  24.287  21.126  1.00  0.00              
ATOM     28  CA  ASP    28      43.065  24.924  17.732  1.00  0.00              
ATOM     29  CA  LEU    29      46.263  24.146  15.916  1.00  0.00              
ATOM     30  CA  SER    30      48.228  21.165  17.049  1.00  0.00              
ATOM     31  CA  PHE    31      51.884  22.017  16.555  1.00  0.00              
ATOM     32  CA  SER    32      52.393  19.674  13.650  1.00  0.00              
ATOM     33  CA  ASN    33      49.510  21.065  11.749  1.00  0.00              
ATOM     34  CA  LEU    34      50.211  24.789  11.858  1.00  0.00              
ATOM     35  CA  CYS    35      49.159  26.769   8.945  1.00  0.00              
ATOM     36  CA  SER    36      48.902  29.367   6.395  1.00  0.00              
ATOM     37  CA  TRP    37      45.847  30.265   4.381  1.00  0.00              
ATOM     38  CA  ARG    38      45.762  31.825   1.009  1.00  0.00              
ATOM     39  CA  PHE    39      42.505  31.020  -0.844  1.00  0.00              
ATOM     40  CA  LEU    40      41.303  34.489  -1.630  1.00  0.00              
ATOM     41  CA  TYR    41      44.490  36.506  -1.435  1.00  0.00              
ATOM     42  CA  ASP    42      43.427  39.421   0.653  1.00  0.00              
ATOM     43  CA  THR    43      44.776  42.748  -0.425  1.00  0.00              
ATOM     44  CA  GLN    44      44.353  45.665   1.808  1.00  0.00              
ATOM     45  CA  PHE    45      45.318  49.136   0.660  1.00  0.00              
ATOM     46  CA  ALA    46      45.027  52.119   3.069  1.00  0.00              
ATOM     47  CA  VAL    47      45.193  55.644   1.661  1.00  0.00              
ATOM     48  CA  ILE    48      45.718  58.471   4.099  1.00  0.00              
ATOM     49  CA  ASP    49      45.145  62.110   3.222  1.00  0.00              
ATOM     50  CA  ASP    50      41.355  62.243   3.417  1.00  0.00              
ATOM     51  CA  PHE    51      40.595  58.730   4.165  1.00  0.00              
ATOM     52  CA  LEU    52      40.214  56.016   1.500  1.00  0.00              
ATOM     53  CA  VAL    53      40.129  52.367   2.394  1.00  0.00              
ATOM     54  CA  PHE    54      40.432  49.760  -0.408  1.00  0.00              
ATOM     55  CA  LYS    55      39.720  46.143   0.248  1.00  0.00              
ATOM     56  CA  PHE    56      40.494  43.580  -2.345  1.00  0.00              
ATOM     57  CA  TRP    57      39.431  40.027  -1.938  1.00  0.00              
ATOM     58  CA  ALA    58      40.417  37.549  -4.594  1.00  0.00              
ATOM     59  CA  GLY    59      37.769  35.623  -6.536  1.00  0.00              
ATOM     60  CA  GLU    60      35.962  38.659  -7.788  1.00  0.00              
ATOM     61  CA  GLN    61      35.458  40.668  -4.736  1.00  0.00              
ATOM     62  CA  LEU    62      36.271  44.342  -4.655  1.00  0.00              
ATOM     63  CA  ALA    63      35.214  46.365  -1.636  1.00  0.00              
ATOM     64  CA  TYR    64      35.684  50.097  -1.501  1.00  0.00              
ATOM     65  CA  MET    65      35.183  51.987   1.704  1.00  0.00              
ATOM     66  CA  MET    66      34.634  55.717   1.507  1.00  0.00              
ATOM     67  CA  PRO    67      34.791  58.064   4.489  1.00  0.00              
ATOM     68  CA  VAL    68      31.568  60.008   4.989  1.00  0.00              
ATOM     69  CA  GLY    69      31.415  63.753   4.647  1.00  0.00              
ATOM     70  CA  ASN    70      28.590  64.758   2.278  1.00  0.00              
ATOM     71  CA  GLY    71      30.433  66.962  -0.146  1.00  0.00              
ATOM     72  CA  ASP    72      33.166  64.564  -0.959  1.00  0.00              
ATOM     73  CA  LEU    73      31.263  61.344  -1.124  1.00  0.00              
ATOM     74  CA  LYS    74      30.189  61.281  -4.667  1.00  0.00              
ATOM     75  CA  ALA    75      33.638  61.992  -6.057  1.00  0.00              
ATOM     76  CA  VAL    76      35.230  59.329  -3.894  1.00  0.00              
ATOM     77  CA  LEU    77      32.749  56.774  -4.969  1.00  0.00              
ATOM     78  CA  ARG    78      33.189  57.597  -8.666  1.00  0.00              
ATOM     79  CA  LYS    79      36.973  57.295  -8.328  1.00  0.00              
ATOM     80  CA  LEU    80      36.717  54.015  -6.594  1.00  0.00              
ATOM     81  CA  ILE    81      34.461  52.643  -9.304  1.00  0.00              
ATOM     82  CA  GLU    82      36.754  53.800 -12.045  1.00  0.00              
ATOM     83  CA  ASP    83      39.876  52.224 -10.469  1.00  0.00              
ATOM     84  CA  ALA    84      38.093  48.925  -9.948  1.00  0.00              
ATOM     85  CA  ASP    85      36.900  48.935 -13.525  1.00  0.00              
ATOM     86  CA  LYS    86      40.337  49.571 -14.985  1.00  0.00              
ATOM     87  CA  GLU    87      41.634  46.602 -12.984  1.00  0.00              
ATOM     88  CA  LYS    88      38.807  44.268 -13.691  1.00  0.00              
ATOM     89  CA  HIS    89      37.502  44.184 -10.136  1.00  0.00              
ATOM     90  CA  ASN    90      33.916  44.246  -9.011  1.00  0.00              
ATOM     91  CA  PHE    91      33.557  47.063  -6.667  1.00  0.00              
ATOM     92  CA  CYS    92      30.999  47.740  -4.029  1.00  0.00              
ATOM     93  CA  MET    93      31.096  51.169  -2.461  1.00  0.00              
ATOM     94  CA  LEU    94      30.350  51.616   1.271  1.00  0.00              
ATOM     95  CA  GLY    95      30.109  55.012   2.848  1.00  0.00              
ATOM     96  CA  VAL    96      31.361  55.047   6.306  1.00  0.00              
ATOM     97  CA  CYS    97      29.457  56.468   9.255  1.00  0.00              
ATOM     98  CA  SER    98      31.119  59.009  11.478  1.00  0.00              
ATOM     99  CA  ASN    99      31.880  56.614  14.322  1.00  0.00              
ATOM    100  CA  MET   100      33.543  54.151  12.016  1.00  0.00              
ATOM    101  CA  ARG   101      35.671  56.816  10.392  1.00  0.00              
ATOM    102  CA  ALA   102      36.954  58.067  13.716  1.00  0.00              
ATOM    103  CA  ASP   103      37.884  54.538  14.788  1.00  0.00              
ATOM    104  CA  LEU   104      39.691  53.817  11.521  1.00  0.00              
ATOM    105  CA  GLU   105      41.621  57.070  11.720  1.00  0.00              
ATOM    106  CA  ALA   106      42.784  56.151  15.183  1.00  0.00              
ATOM    107  CA  ILE   107      43.926  52.705  14.312  1.00  0.00              
ATOM    108  CA  LEU   108      45.794  53.813  11.228  1.00  0.00              
ATOM    109  CA  PRO   109      47.528  56.804  12.893  1.00  0.00              
ATOM    110  CA  GLU   110      49.353  54.953  15.603  1.00  0.00              
ATOM    111  CA  ARG   111      50.977  52.328  13.504  1.00  0.00              
ATOM    112  CA  PHE   112      50.613  53.378  10.058  1.00  0.00              
ATOM    113  CA  ILE   113      49.655  54.955   6.852  1.00  0.00              
ATOM    114  CA  PHE   114      49.716  52.780   3.761  1.00  0.00              
ATOM    115  CA  THR   115      49.501  54.224   0.299  1.00  0.00              
ATOM    116  CA  GLU   116      48.177  51.966  -2.456  1.00  0.00              
ATOM    117  CA  ASP   117      48.851  52.830  -6.064  1.00  0.00              
ATOM    290  CA  LYS   290      46.761  30.158  -4.148  1.00  0.00              
ATOM    291  CA  TYR   291      48.804  32.449  -2.023  1.00  0.00              
ATOM    292  CA  MET   292      52.468  32.791  -2.658  1.00  0.00              
ATOM    293  CA  ALA   293      54.685  34.516  -0.110  1.00  0.00              
ATOM    294  CA  CYS   294      57.917  36.074  -1.336  1.00  0.00              
ATOM    295  CA  LEU   295      60.517  36.897   1.224  1.00  0.00              
ATOM    296  CA  LYS   296      62.779  39.669   0.137  1.00  0.00              
ATOM    297  CA  ASP   297      65.305  39.580   2.870  1.00  0.00              
ATOM    298  CA  HIS   298      65.267  35.799   3.215  1.00  0.00              
TER                                                                             
END
