
#######################################################
#                                                     #
#                        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  132 (  132),  selected  132 , name T0312TS599_2-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected  132 , name T0312_D1.pdb
# PARAMETERS: T0312TS599_2-D1.T0312_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G       9      -       -           -
LGA    K      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      G       9           #
LGA    -       -      K      10           -
LGA    L      13      G      11           #
LGA    L      14      F      12          4.669
LGA    R      15      L      13          4.233
LGA    L      16      L      14          3.110
LGA    D      17      R      15          2.730
LGA    Y      18      L      16          2.351
LGA    G      19      D      17          2.288
LGA    K      20      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    -       -      R      24           -
LGA    D      21      Q      25           #
LGA    L      22      I      26          5.519
LGA    V      23      E      27          5.254
LGA    -       -      E      28           -
LGA    R      24      F      29          2.123
LGA    Q      25      L      30          4.854
LGA    I      26      E      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    E      27      G      34          4.227
LGA    E      28      I      35          3.461
LGA    F      29      -       -           -
LGA    L      30      H      36           #
LGA    E      31      -       -           -
LGA    E      32      -       -           -
LGA    K      33      -       -           -
LGA    G      34      -       -           -
LGA    I      35      -       -           -
LGA    H      36      -       -           -
LGA    A      37      A      37          3.041
LGA    A      38      A      38          0.507
LGA    H      39      H      39          1.676
LGA    I      40      I      40          2.406
LGA    S      41      S      41          2.476
LGA    A      42      A      42          3.439
LGA    I      43      I      43          3.043
LGA    G      44      G      44          3.090
LGA    A      45      A      45          3.011
LGA    V      46      -       -           -
LGA    R      47      V      46           #
LGA    -       -      R      47           -
LGA    -       -      S      48           -
LGA    -       -      A      49           -
LGA    -       -      V      50           -
LGA    -       -      I      51           -
LGA    -       -      G      52           -
LGA    -       -      Y      53           -
LGA    -       -      Y      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    -       -      K      59           -
LGA    -       -      E      60           -
LGA    -       -      Y      61           -
LGA    -       -      V      62           -
LGA    -       -      K      63           -
LGA    -       -      K      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      M      67           -
LGA    -       -      E      68           -
LGA    -       -      P      69           -
LGA    -       -      L      70           -
LGA    S      48      E      71          1.220
LGA    A      49      I      72          2.237
LGA    -       -      L      73           -
LGA    V      50      S      74          4.568
LGA    I      51      L      75          3.543
LGA    G      52      S      76          2.880
LGA    Y      53      G      77          3.516
LGA    Y      54      N      78          1.309
LGA    D      55      V      79          0.765
LGA    Q      56      S      80          1.294
LGA    E      57      M      81          2.527
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    K      58      P      86           #
LGA    K      59      F      87          3.157
LGA    E      60      C      88           #
LGA    Y      61      -       -           -
LGA    V      62      -       -           -
LGA    K      63      -       -           -
LGA    K      64      -       -           -
LGA    E      65      -       -           -
LGA    L      66      -       -           -
LGA    M      67      -       -           -
LGA    E      68      -       -           -
LGA    P      69      -       -           -
LGA    L      70      -       -           -
LGA    E      71      -       -           -
LGA    I      72      -       -           -
LGA    L      73      -       -           -
LGA    S      74      H      89           #
LGA    L      75      I      90          2.633
LGA    S      76      H      91          1.357
LGA    G      77      V      92          1.285
LGA    N      78      L      93          2.062
LGA    V      79      L      94          0.624
LGA    S      80      G      95          2.343
LGA    M      81      K      96          1.779
LGA    K      82      D      97          1.473
LGA    D      83      G      98          1.612
LGA    S      84      E      99          4.153
LGA    K      85      V     100          2.568
LGA    P      86      Y     101          2.366
LGA    F      87      G     102          2.750
LGA    C      88      G     103          1.963
LGA    H      89      -       -           -
LGA    I      90      H     104          2.874
LGA    H      91      -       -           -
LGA    V      92      -       -           -
LGA    L      93      -       -           -
LGA    L      94      -       -           -
LGA    G      95      -       -           -
LGA    K      96      -       -           -
LGA    D      97      -       -           -
LGA    G      98      -       -           -
LGA    E      99      -       -           -
LGA    V     100      -       -           -
LGA    Y     101      -       -           -
LGA    G     102      -       -           -
LGA    G     103      -       -           -
LGA    H     104      -       -           -
LGA    L     105      -       -           -
LGA    F     106      -       -           -
LGA    S     107      -       -           -
LGA    A     108      -       -           -
LGA    E     109      L     105          3.037
LGA    V     110      F     106          0.811
LGA    F     111      -       -           -
LGA    A     112      S     107          4.277
LGA    C     113      A     108          2.731
LGA    E     114      -       -           -
LGA    V     115      -       -           -
LGA    F     116      -       -           -
LGA    V     117      E     109          0.943
LGA    L     118      V     110          2.789
LGA    P     119      F     111          1.452
LGA    L     120      A     112          3.046
LGA    S     121      C     113           -
LGA    G     122      E     114           -
LGA    E     123      V     115           -
LGA    A     124      F     116           -
LGA    P     125      V     117           -
LGA    E     126      L     118           -
LGA    R     127      P     119           -
LGA    A     128      L     120           -
LGA    F     129      S     121           -
LGA    D     130      G     122           -
LGA    E     131      E     123           -
LGA    Q     132      A     124           -
LGA    T     133      P     125           -
LGA    G     134      E     126           -
LGA    L     135      R     127           -
LGA    F     136      A     128           -
LGA    L     137      F     129           -
LGA    W     138      D     130           -
LGA    L     139      E     131           -
LGA    E     140      Q     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      L     135           -
LGA    -       -      F     136           -
LGA    -       -      L     137           -
LGA    -       -      W     138           -
LGA    -       -      L     139           -
LGA    -       -      E     140           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  132  132    5.0     55    2.90    18.18     25.595     1.835

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.770812 * X  +   0.566325 * Y  +   0.291763 * Z  +  57.110508
  Y_new =  -0.171656 * X  +   0.625675 * Y  +  -0.760963 * Z  +   4.539309
  Z_new =  -0.613501 * X  +   0.536476 * Y  +   0.579491 * Z  +  16.282764 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.746872   -2.394721  [ DEG:    42.7926   -137.2074 ]
  Theta =   0.660487    2.481106  [ DEG:    37.8431    142.1569 ]
  Phi   =  -0.219120    2.922473  [ DEG:   -12.5546    167.4454 ]
 
# 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: T0312TS599_2-D1                               
REMARK     2: T0312_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS599_2-D1.T0312_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  132  132   5.0   55   2.90   18.18  25.595
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS599_2-D1
PFRMAT TS                                                                       
TARGET T0312                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      9  CA  GLY     9      67.516   9.134  33.158  1.00  0.00              
ATOM     10  CA  LYS    10      64.431  11.358  33.311  1.00  0.00              
ATOM     11  CA  GLY    11      62.174  11.284  30.307  1.00  0.00              
ATOM     12  CA  PHE    12      61.971  14.119  27.837  1.00  0.00              
ATOM     13  CA  LEU    13      59.175  14.405  25.387  1.00  0.00              
ATOM     14  CA  LEU    14      59.788  15.850  21.927  1.00  0.00              
ATOM     15  CA  ARG    15      56.936  16.709  19.638  1.00  0.00              
ATOM     16  CA  LEU    16      57.545  16.700  15.974  1.00  0.00              
ATOM     17  CA  ASP    17      55.149  18.470  13.551  1.00  0.00              
ATOM     18  CA  TYR    18      54.951  17.264  10.013  1.00  0.00              
ATOM     19  CA  GLY    19      58.189  17.661   7.929  1.00  0.00              
ATOM     20  CA  LYS    20      60.274  18.178  11.009  1.00  0.00              
ATOM     21  CA  ASP    21      63.249  16.607  12.691  1.00  0.00              
ATOM     22  CA  LEU    22      62.038  16.212  16.329  1.00  0.00              
ATOM     23  CA  VAL    23      63.488  12.779  16.869  1.00  0.00              
ATOM     24  CA  ARG    24      66.897  13.693  15.579  1.00  0.00              
ATOM     25  CA  GLN    25      67.137  16.775  17.755  1.00  0.00              
ATOM     26  CA  ILE    26      66.048  14.954  20.820  1.00  0.00              
ATOM     27  CA  GLU    27      68.522  12.182  20.329  1.00  0.00              
ATOM     28  CA  GLU    28      71.302  14.619  19.835  1.00  0.00              
ATOM     29  CA  PHE    29      70.442  16.608  22.918  1.00  0.00              
ATOM     30  CA  LEU    30      70.154  13.526  25.061  1.00  0.00              
ATOM     31  CA  GLU    31      73.505  12.234  23.876  1.00  0.00              
ATOM     32  CA  GLU    32      75.288  15.605  24.392  1.00  0.00              
ATOM     33  CA  LYS    33      74.133  15.950  27.935  1.00  0.00              
ATOM     34  CA  GLY    34      74.651  12.272  28.903  1.00  0.00              
ATOM     35  CA  ILE    35      70.894  11.913  29.390  1.00  0.00              
ATOM     36  CA  HIS    36      68.999   8.748  29.008  1.00  0.00              
ATOM     37  CA  ALA    37      65.525   8.824  27.625  1.00  0.00              
ATOM     38  CA  ALA    38      63.877  10.760  24.809  1.00  0.00              
ATOM     39  CA  HIS    39      60.280  10.179  23.685  1.00  0.00              
ATOM     40  CA  ILE    40      59.305  11.266  20.294  1.00  0.00              
ATOM     41  CA  SER    41      55.737  12.154  19.457  1.00  0.00              
ATOM     42  CA  ALA    42      54.803  12.655  15.900  1.00  0.00              
ATOM     43  CA  ILE    43      51.637  14.504  14.994  1.00  0.00              
ATOM     44  CA  GLY    44      50.367  14.423  11.402  1.00  0.00              
ATOM     45  CA  ALA    45      47.162  16.079  10.454  1.00  0.00              
ATOM     46  CA  VAL    46      45.542  14.727   7.300  1.00  0.00              
ATOM     47  CA  ARG    47      42.728  12.621   8.862  1.00  0.00              
ATOM     48  CA  SER    48      44.319  12.153  12.218  1.00  0.00              
ATOM     49  CA  ALA    49      47.603  10.333  12.441  1.00  0.00              
ATOM     50  CA  VAL    50      49.445  10.166  15.818  1.00  0.00              
ATOM     51  CA  ILE    51      52.663   8.323  16.074  1.00  0.00              
ATOM     52  CA  GLY    52      54.438   7.889  19.428  1.00  0.00              
ATOM     53  CA  TYR    53      58.039   6.707  19.397  1.00  0.00              
ATOM     54  CA  TYR    54      60.064   5.607  22.365  1.00  0.00              
ATOM     55  CA  ASP    55      63.880   5.760  22.041  1.00  0.00              
ATOM     56  CA  GLN    56      65.959   2.988  23.559  1.00  0.00              
ATOM     57  CA  GLU    57      67.450   1.436  20.391  1.00  0.00              
ATOM     58  CA  LYS    58      64.364   2.061  18.341  1.00  0.00              
ATOM     59  CA  LYS    59      64.915   2.955  14.777  1.00  0.00              
ATOM     60  CA  GLU    60      62.106   1.278  12.964  1.00  0.00              
ATOM     61  CA  TYR    61      61.247  -2.224  12.314  1.00  0.00              
ATOM     62  CA  VAL    62      63.533  -5.043  11.426  1.00  0.00              
ATOM     63  CA  LYS    63      62.532  -7.871  13.676  1.00  0.00              
ATOM     64  CA  LYS    64      65.326  -9.602  15.532  1.00  0.00              
ATOM     65  CA  GLU    65      64.716 -12.287  18.106  1.00  0.00              
ATOM     66  CA  LEU    66      66.945 -12.117  21.222  1.00  0.00              
ATOM     67  CA  MET    67      66.326 -13.955  24.424  1.00  0.00              
ATOM     68  CA  GLU    68      67.592 -12.376  27.580  1.00  0.00              
ATOM     69  CA  PRO    69      67.906  -9.225  29.613  1.00  0.00              
ATOM     70  CA  LEU    70      64.415  -7.716  29.154  1.00  0.00              
ATOM     71  CA  GLU    71      63.798  -4.083  28.364  1.00  0.00              
ATOM     72  CA  ILE    72      60.421  -3.111  27.287  1.00  0.00              
ATOM     73  CA  LEU    73      59.939  -0.495  24.826  1.00  0.00              
ATOM     74  CA  SER    74      56.408   0.595  24.106  1.00  0.00              
ATOM     75  CA  LEU    75      55.407   2.095  20.827  1.00  0.00              
ATOM     76  CA  SER    76      52.076   3.812  20.563  1.00  0.00              
ATOM     77  CA  GLY    77      50.325   4.201  17.259  1.00  0.00              
ATOM     78  CA  ASN    78      47.207   6.325  17.050  1.00  0.00              
ATOM     79  CA  VAL    79      45.124   6.297  14.071  1.00  0.00              
ATOM     80  CA  SER    80      41.943   8.311  14.060  1.00  0.00              
ATOM     81  CA  MET    81      38.902   7.442  11.900  1.00  0.00              
ATOM     82  CA  LYS    82      35.608   8.408  13.414  1.00  0.00              
ATOM     83  CA  ASP    83      33.923   5.086  13.867  1.00  0.00              
ATOM     84  CA  SER    84      35.621   3.928  17.004  1.00  0.00              
ATOM     85  CA  LYS    85      39.129   5.273  16.882  1.00  0.00              
ATOM     86  CA  PRO    86      41.839   2.884  16.211  1.00  0.00              
ATOM     87  CA  PHE    87      44.649   2.807  18.799  1.00  0.00              
ATOM     88  CA  CYS    88      47.642   0.604  18.195  1.00  0.00              
ATOM     89  CA  HIS    89      50.039  -0.417  20.875  1.00  0.00              
ATOM     90  CA  ILE    90      53.270  -2.018  19.824  1.00  0.00              
ATOM     91  CA  HIS    91      55.405  -3.806  22.237  1.00  0.00              
ATOM     92  CA  VAL    92      59.105  -4.015  21.536  1.00  0.00              
ATOM     93  CA  LEU    93      61.367  -6.137  23.702  1.00  0.00              
ATOM     94  CA  LEU    94      65.005  -5.154  23.998  1.00  0.00              
ATOM     95  CA  GLY    95      67.553  -7.708  25.444  1.00  0.00              
ATOM     96  CA  LYS    96      70.686  -6.527  27.301  1.00  0.00              
ATOM     97  CA  ASP    97      72.884  -7.673  24.380  1.00  0.00              
ATOM     98  CA  GLY    98      71.018  -5.417  21.908  1.00  0.00              
ATOM     99  CA  GLU    99      68.988  -8.114  20.303  1.00  0.00              
ATOM    100  CA  VAL   100      65.669  -6.778  19.334  1.00  0.00              
ATOM    101  CA  TYR   101      62.627  -8.795  19.716  1.00  0.00              
ATOM    102  CA  GLY   102      59.569  -7.752  17.791  1.00  0.00              
ATOM    103  CA  GLY   103      56.342  -9.572  18.377  1.00  0.00              
ATOM    104  CA  HIS   104      53.182  -9.029  16.447  1.00  0.00              
ATOM    105  CA  LEU   105      52.214  -5.549  17.679  1.00  0.00              
ATOM    106  CA  PHE   106      55.730  -4.123  16.961  1.00  0.00              
ATOM    107  CA  SER   107      56.582  -5.642  13.558  1.00  0.00              
ATOM    108  CA  ALA   108      53.131  -4.860  12.161  1.00  0.00              
ATOM    109  CA  GLU   109      53.189  -1.240  13.373  1.00  0.00              
ATOM    110  CA  VAL   110      56.462   0.287  12.111  1.00  0.00              
ATOM    111  CA  PHE   111      56.109  -1.069   8.582  1.00  0.00              
ATOM    112  CA  ALA   112      52.463   0.019   8.347  1.00  0.00              
ATOM    113  CA  CYS   113      53.019   3.617   9.543  1.00  0.00              
ATOM    114  CA  GLU   114      55.889   4.067   7.078  1.00  0.00              
ATOM    115  CA  VAL   115      53.893   2.602   4.117  1.00  0.00              
ATOM    116  CA  PHE   116      50.855   4.884   4.840  1.00  0.00              
ATOM    117  CA  VAL   117      52.258   8.244   5.824  1.00  0.00              
ATOM    118  CA  LEU   118      50.078  11.097   7.001  1.00  0.00              
ATOM    119  CA  PRO   119      51.214  14.695   6.579  1.00  0.00              
ATOM    120  CA  LEU   120      48.711  17.474   6.387  1.00  0.00              
ATOM    121  CA  SER   121      49.522  20.188   3.951  1.00  0.00              
ATOM    122  CA  GLY   122      47.661  19.019   0.912  1.00  0.00              
ATOM    123  CA  GLU   123      49.018  15.428   0.710  1.00  0.00              
ATOM    124  CA  ALA   124      46.561  12.584   0.210  1.00  0.00              
ATOM    125  CA  PRO   125      48.042   9.665   2.132  1.00  0.00              
ATOM    126  CA  GLU   126      48.055   7.003  -0.591  1.00  0.00              
ATOM    127  CA  ARG   127      49.481   9.590  -3.035  1.00  0.00              
ATOM    128  CA  ALA   128      52.302  10.806  -0.808  1.00  0.00              
ATOM    129  CA  PHE   129      53.408   7.266   0.142  1.00  0.00              
ATOM    130  CA  ASP   130      53.423   5.473  -3.156  1.00  0.00              
ATOM    131  CA  GLU   131      50.204   3.415  -3.103  1.00  0.00              
ATOM    132  CA  GLN   132      51.828   0.537  -4.907  1.00  0.00              
ATOM    133  CA  THR   133      54.547   0.215  -2.230  1.00  0.00              
ATOM    134  CA  GLY   134      52.201   0.885   0.715  1.00  0.00              
ATOM    135  CA  LEU   135      51.568  -2.468   1.997  1.00  0.00              
ATOM    136  CA  PHE   136      51.867  -3.184   5.614  1.00  0.00              
ATOM    137  CA  LEU   137      51.997  -6.904   6.069  1.00  0.00              
ATOM    138  CA  TRP   138      54.012  -8.678   8.751  1.00  0.00              
ATOM    139  CA  LEU   139      54.144 -12.506   8.611  1.00  0.00              
ATOM    140  CA  GLU   140      52.876 -13.193  12.136  1.00  0.00              
TER                                                                             
END
