
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected  132 , name T0312_D1.pdb
# PARAMETERS: T0312TS599_3-D1.T0312_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G       9      G       9           -
LGA    K      10      K      10           -
LGA    G      11      G      11           -
LGA    F      12      F      12           -
LGA    L      13      L      13           -
LGA    L      14      L      14           -
LGA    R      15      R      15           -
LGA    L      16      L      16           -
LGA    D      17      D      17           -
LGA    Y      18      Y      18           -
LGA    G      19      -       -           -
LGA    K      20      -       -           -
LGA    D      21      G      19           #
LGA    -       -      K      20           -
LGA    L      22      D      21          1.459
LGA    V      23      L      22          3.886
LGA    -       -      V      23           -
LGA    R      24      R      24          1.530
LGA    Q      25      Q      25          1.882
LGA    I      26      I      26          1.339
LGA    E      27      E      27          2.139
LGA    E      28      E      28          3.000
LGA    F      29      F      29          1.299
LGA    L      30      L      30          3.175
LGA    E      31      E      31          5.259
LGA    E      32      E      32          4.688
LGA    -       -      K      33           -
LGA    K      33      G      34          4.453
LGA    G      34      I      35          2.748
LGA    -       -      H      36           -
LGA    -       -      A      37           -
LGA    I      35      A      38           #
LGA    H      36      H      39          3.588
LGA    A      37      I      40          3.643
LGA    A      38      S      41          2.835
LGA    H      39      A      42          3.196
LGA    I      40      I      43          2.309
LGA    S      41      G      44          2.846
LGA    A      42      A      45          2.229
LGA    I      43      V      46           #
LGA    G      44      R      47           -
LGA    A      45      S      48           -
LGA    V      46      A      49           -
LGA    R      47      V      50           -
LGA    S      48      I      51           -
LGA    A      49      G      52           -
LGA    V      50      Y      53           -
LGA    I      51      Y      54           -
LGA    G      52      D      55           -
LGA    Y      53      Q      56           -
LGA    Y      54      E      57           -
LGA    D      55      K      58           -
LGA    Q      56      K      59           -
LGA    E      57      E      60           -
LGA    K      58      Y      61           -
LGA    K      59      V      62           -
LGA    E      60      K      63           -
LGA    Y      61      K      64           -
LGA    V      62      E      65           -
LGA    K      63      L      66           -
LGA    K      64      M      67           -
LGA    E      65      E      68           -
LGA    L      66      -       -           -
LGA    M      67      -       -           -
LGA    E      68      -       -           -
LGA    P      69      -       -           -
LGA    L      70      -       -           -
LGA    E      71      -       -           -
LGA    I      72      -       -           -
LGA    L      73      P      69          5.652
LGA    -       -      L      70           -
LGA    S      74      E      71          1.023
LGA    L      75      I      72          1.823
LGA    -       -      L      73           -
LGA    S      76      S      74          3.945
LGA    G      77      L      75          3.181
LGA    N      78      S      76          2.760
LGA    V      79      G      77          3.776
LGA    S      80      N      78          1.578
LGA    M      81      V      79          1.381
LGA    K      82      S      80          3.196
LGA    D      83      M      81          3.132
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    -       -      P      86           -
LGA    S      84      F      87           #
LGA    K      85      C      88          3.282
LGA    P      86      H      89          2.358
LGA    F      87      I      90          1.234
LGA    C      88      H      91          1.336
LGA    H      89      V      92          1.834
LGA    I      90      L      93          1.869
LGA    H      91      L      94          1.284
LGA    V      92      G      95          2.930
LGA    L      93      K      96          1.994
LGA    L      94      D      97          1.916
LGA    G      95      -       -           -
LGA    K      96      -       -           -
LGA    D      97      -       -           -
LGA    G      98      -       -           -
LGA    E      99      -       -           -
LGA    V     100      G      98          2.368
LGA    Y     101      E      99          2.926
LGA    G     102      V     100          2.547
LGA    G     103      Y     101          1.487
LGA    H     104      G     102          1.964
LGA    L     105      -       -           -
LGA    F     106      -       -           -
LGA    S     107      -       -           -
LGA    A     108      G     103          2.205
LGA    E     109      H     104           #
LGA    V     110      -       -           -
LGA    F     111      L     105          2.874
LGA    A     112      F     106          3.084
LGA    C     113      -       -           -
LGA    E     114      S     107           #
LGA    V     115      A     108           -
LGA    F     116      E     109           -
LGA    V     117      V     110           -
LGA    L     118      F     111           -
LGA    -       -      A     112           -
LGA    -       -      C     113           -
LGA    -       -      E     114           -
LGA    -       -      V     115           -
LGA    -       -      F     116           -
LGA    -       -      V     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      L     120           -
LGA    -       -      S     121           -
LGA    -       -      G     122           -
LGA    -       -      E     123           -
LGA    -       -      A     124           -
LGA    -       -      P     125           -
LGA    -       -      E     126           -
LGA    P     119      R     127           #
LGA    L     120      A     128          5.433
LGA    S     121      -       -           -
LGA    G     122      -       -           -
LGA    E     123      F     129          2.608
LGA    A     124      D     130          5.237
LGA    -       -      E     131           -
LGA    -       -      Q     132           -
LGA    -       -      T     133           -
LGA    P     125      G     134           #
LGA    E     126      L     135          5.673
LGA    R     127      -       -           -
LGA    A     128      F     136           #
LGA    F     129      L     137           -
LGA    D     130      W     138           -
LGA    E     131      L     139           -
LGA    Q     132      E     140           -
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     53    3.03    24.53     26.195     1.691

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.126636 * X  +  -0.327621 * Y  +   0.936284 * Z  +  52.958702
  Y_new =   0.656732 * X  +   0.735083 * Y  +   0.168392 * Z  +   5.852518
  Z_new =  -0.743415 * X  +   0.593563 * Y  +   0.308247 * Z  +  14.455721 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.091816   -2.049777  [ DEG:    62.5564   -117.4436 ]
  Theta =   0.838163    2.303430  [ DEG:    48.0232    131.9768 ]
  Phi   =   1.380307   -1.761285  [ DEG:    79.0858   -100.9142 ]
 
# 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_3-D1                               
REMARK     2: T0312_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS599_3-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   53   3.03   24.53  26.195
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS599_3-D1
PFRMAT TS                                                                       
TARGET T0312                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      9  CA  GLY     9      75.718  -3.052  24.035  1.00  0.00              
ATOM     10  CA  LYS    10      73.288  -5.562  22.616  1.00  0.00              
ATOM     11  CA  GLY    11      72.666  -5.775  18.909  1.00  0.00              
ATOM     12  CA  PHE    12      69.344  -4.560  17.459  1.00  0.00              
ATOM     13  CA  LEU    13      68.564  -4.996  13.887  1.00  0.00              
ATOM     14  CA  LEU    14      66.067  -2.740  12.245  1.00  0.00              
ATOM     15  CA  ARG    15      64.612  -3.675   8.971  1.00  0.00              
ATOM     16  CA  LEU    16      62.616  -1.174   7.028  1.00  0.00              
ATOM     17  CA  ASP    17      60.075  -2.204   4.425  1.00  0.00              
ATOM     18  CA  TYR    18      59.724  -0.521   1.211  1.00  0.00              
ATOM     19  CA  GLY    19      58.370   2.833   1.672  1.00  0.00              
ATOM     20  CA  LYS    20      59.111   3.588   5.356  1.00  0.00              
ATOM     21  CA  ASP    21      60.285   7.139   5.085  1.00  0.00              
ATOM     22  CA  LEU    22      58.310   8.851   7.781  1.00  0.00              
ATOM     23  CA  VAL    23      59.075   6.419  10.536  1.00  0.00              
ATOM     24  CA  ARG    24      62.760   6.491   9.778  1.00  0.00              
ATOM     25  CA  GLN    25      63.050  10.223   9.546  1.00  0.00              
ATOM     26  CA  ILE    26      61.078  10.886  12.742  1.00  0.00              
ATOM     27  CA  GLU    27      63.094   8.400  14.634  1.00  0.00              
ATOM     28  CA  GLU    28      66.408   9.613  13.636  1.00  0.00              
ATOM     29  CA  PHE    29      65.728  13.184  14.454  1.00  0.00              
ATOM     30  CA  LEU    30      64.468  12.224  17.788  1.00  0.00              
ATOM     31  CA  GLU    31      67.391  10.016  18.731  1.00  0.00              
ATOM     32  CA  GLU    32      70.098  12.360  17.699  1.00  0.00              
ATOM     33  CA  LYS    33      68.790  15.208  19.593  1.00  0.00              
ATOM     34  CA  GLY    34      67.738  13.321  22.754  1.00  0.00              
ATOM     35  CA  ILE    35      64.135  14.324  22.064  1.00  0.00              
ATOM     36  CA  HIS    36      60.867  12.708  22.730  1.00  0.00              
ATOM     37  CA  ALA    37      58.878  13.238  19.522  1.00  0.00              
ATOM     38  CA  ALA    38      55.154  13.271  18.951  1.00  0.00              
ATOM     39  CA  HIS    39      53.789  12.982  15.440  1.00  0.00              
ATOM     40  CA  ILE    40      50.237  13.862  14.785  1.00  0.00              
ATOM     41  CA  SER    41      48.739  13.185  11.392  1.00  0.00              
ATOM     42  CA  ALA    42      45.283  14.425  10.604  1.00  0.00              
ATOM     43  CA  ILE    43      43.680  13.528   7.351  1.00  0.00              
ATOM     44  CA  GLY    44      40.285  15.036   6.410  1.00  0.00              
ATOM     45  CA  ALA    45      38.520  13.988   3.262  1.00  0.00              
ATOM     46  CA  VAL    46      35.757  16.254   1.921  1.00  0.00              
ATOM     47  CA  ARG    47      37.763  18.522  -0.435  1.00  0.00              
ATOM     48  CA  SER    48      41.201  17.534   0.763  1.00  0.00              
ATOM     49  CA  ALA    49      42.463  18.718   4.096  1.00  0.00              
ATOM     50  CA  VAL    50      45.776  17.462   5.343  1.00  0.00              
ATOM     51  CA  ILE    51      46.995  18.352   8.817  1.00  0.00              
ATOM     52  CA  GLY    52      50.435  17.469   9.934  1.00  0.00              
ATOM     53  CA  TYR    53      51.504  18.114  13.514  1.00  0.00              
ATOM     54  CA  TYR    54      55.037  17.370  14.522  1.00  0.00              
ATOM     55  CA  ASP    55      56.115  17.744  18.000  1.00  0.00              
ATOM     56  CA  GLN    56      59.628  18.762  19.017  1.00  0.00              
ATOM     57  CA  GLU    57      61.325  20.947  16.376  1.00  0.00              
ATOM     58  CA  LYS    58      58.140  21.620  14.393  1.00  0.00              
ATOM     59  CA  LYS    59      58.831  20.097  11.039  1.00  0.00              
ATOM     60  CA  GLU    60      55.730  18.570   9.542  1.00  0.00              
ATOM     61  CA  TYR    61      52.813  20.952   9.663  1.00  0.00              
ATOM     62  CA  VAL    62      51.186  21.395   6.290  1.00  0.00              
ATOM     63  CA  LYS    63      47.789  22.852   6.954  1.00  0.00              
ATOM     64  CA  LYS    64      44.928  22.077   4.520  1.00  0.00              
ATOM     65  CA  GLU    65      41.498  23.554   4.981  1.00  0.00              
ATOM     66  CA  LEU    66      38.643  21.036   4.529  1.00  0.00              
ATOM     67  CA  MET    67      35.353  22.304   3.225  1.00  0.00              
ATOM     68  CA  GLU    68      32.684  19.735   2.840  1.00  0.00              
ATOM     69  CA  PRO    69      31.053  16.959   4.741  1.00  0.00              
ATOM     70  CA  LEU    70      33.766  14.947   6.074  1.00  0.00              
ATOM     71  CA  GLU    71      35.659  12.058   7.147  1.00  0.00              
ATOM     72  CA  ILE    72      38.269  12.611   9.680  1.00  0.00              
ATOM     73  CA  LEU    73      41.093  10.387   9.915  1.00  0.00              
ATOM     74  CA  SER    74      43.387  10.894  12.833  1.00  0.00              
ATOM     75  CA  LEU    75      46.765   9.328  13.026  1.00  0.00              
ATOM     76  CA  SER    76      48.797   9.844  16.127  1.00  0.00              
ATOM     77  CA  GLY    77      52.337   8.664  16.282  1.00  0.00              
ATOM     78  CA  ASN    78      54.203   8.585  19.537  1.00  0.00              
ATOM     79  CA  VAL    79      57.860   8.095  19.523  1.00  0.00              
ATOM     80  CA  SER    80      59.695   7.761  22.780  1.00  0.00              
ATOM     81  CA  MET    81      63.541   7.574  22.843  1.00  0.00              
ATOM     82  CA  LYS    82      64.886   5.382  25.569  1.00  0.00              
ATOM     83  CA  ASP    83      67.661   3.408  23.979  1.00  0.00              
ATOM     84  CA  SER    84      65.385   0.732  22.383  1.00  0.00              
ATOM     85  CA  LYS    85      62.785   2.942  20.802  1.00  0.00              
ATOM     86  CA  PRO    86      59.307   2.774  22.021  1.00  0.00              
ATOM     87  CA  PHE    87      56.915   3.392  19.225  1.00  0.00              
ATOM     88  CA  CYS    88      53.231   3.753  19.852  1.00  0.00              
ATOM     89  CA  HIS    89      50.867   4.282  16.985  1.00  0.00              
ATOM     90  CA  ILE    90      47.406   5.597  17.613  1.00  0.00              
ATOM     91  CA  HIS    91      44.788   5.357  14.987  1.00  0.00              
ATOM     92  CA  VAL    92      41.566   7.389  15.415  1.00  0.00              
ATOM     93  CA  LEU    93      38.828   7.210  12.827  1.00  0.00              
ATOM     94  CA  LEU    94      36.013   9.721  12.925  1.00  0.00              
ATOM     95  CA  GLY    95      33.078   9.325  10.555  1.00  0.00              
ATOM     96  CA  LYS    96      31.207  12.424   9.307  1.00  0.00              
ATOM     97  CA  ASP    97      28.431  11.629  11.810  1.00  0.00              
ATOM     98  CA  GLY    98      30.649  11.781  14.825  1.00  0.00              
ATOM     99  CA  GLU    99      30.953   8.064  15.663  1.00  0.00              
ATOM    100  CA  VAL   100      34.406   7.490  16.832  1.00  0.00              
ATOM    101  CA  TYR   101      36.321   4.459  15.833  1.00  0.00              
ATOM    102  CA  GLY   102      39.474   3.587  17.667  1.00  0.00              
ATOM    103  CA  GLY   103      42.175   1.555  16.056  1.00  0.00              
ATOM    104  CA  HIS   104      44.470  -0.266  18.259  1.00  0.00              
ATOM    105  CA  LEU   105      44.871  -3.376  16.033  1.00  0.00              
ATOM    106  CA  PHE   106      45.612  -1.405  12.865  1.00  0.00              
ATOM    107  CA  SER   107      48.278   0.847  14.480  1.00  0.00              
ATOM    108  CA  ALA   108      50.126  -1.930  16.193  1.00  0.00              
ATOM    109  CA  GLU   109      50.130  -3.799  12.877  1.00  0.00              
ATOM    110  CA  VAL   110      50.944  -1.210  10.189  1.00  0.00              
ATOM    111  CA  PHE   111      53.751   0.837  11.779  1.00  0.00              
ATOM    112  CA  ALA   112      55.349  -2.405  13.064  1.00  0.00              
ATOM    113  CA  CYS   113      55.277  -4.337   9.744  1.00  0.00              
ATOM    114  CA  GLU   114      56.811  -1.427   7.793  1.00  0.00              
ATOM    115  CA  VAL   115      59.477  -1.316  10.493  1.00  0.00              
ATOM    116  CA  PHE   116      60.798  -4.710  11.524  1.00  0.00              
ATOM    117  CA  VAL   117      62.815  -4.870  14.596  1.00  0.00              
ATOM    118  CA  LEU   118      65.130  -7.833  15.415  1.00  0.00              
ATOM    119  CA  PRO   119      66.874  -7.843  18.748  1.00  0.00              
ATOM    120  CA  LEU   120      70.049  -9.762  19.279  1.00  0.00              
ATOM    121  CA  SER   121      71.526  -9.406  22.738  1.00  0.00              
ATOM    122  CA  GLY   122      68.479  -9.581  24.944  1.00  0.00              
ATOM    123  CA  GLU   123      66.051  -7.463  22.996  1.00  0.00              
ATOM    124  CA  ALA   124      63.165  -8.890  21.137  1.00  0.00              
ATOM    125  CA  PRO   125      61.591  -6.810  18.528  1.00  0.00              
ATOM    126  CA  GLU   126      59.335  -9.244  16.591  1.00  0.00              
ATOM    127  CA  ARG   127      58.373 -10.838  19.939  1.00  0.00              
ATOM    128  CA  ALA   128      57.386  -7.523  21.556  1.00  0.00              
ATOM    129  CA  PHE   129      55.268  -6.588  18.512  1.00  0.00              
ATOM    130  CA  ASP   130      53.405  -9.916  18.122  1.00  0.00              
ATOM    131  CA  GLU   131      51.825 -10.035  21.568  1.00  0.00              
ATOM    132  CA  GLN   132      48.259 -10.655  20.300  1.00  0.00              
ATOM    133  CA  THR   133      48.642  -7.748  17.868  1.00  0.00              
ATOM    134  CA  GLY   134      49.987  -5.426  20.637  1.00  0.00              
ATOM    135  CA  LEU   135      47.476  -2.803  20.227  1.00  0.00              
ATOM    136  CA  PHE   136      45.473  -1.275  23.033  1.00  0.00              
ATOM    137  CA  LEU   137      42.770   1.113  21.756  1.00  0.00              
ATOM    138  CA  TRP   138      39.077   0.571  22.100  1.00  0.00              
ATOM    139  CA  LEU   139      36.248   2.203  20.406  1.00  0.00              
ATOM    140  CA  GLU   140      34.081   2.890  23.484  1.00  0.00              
TER                                                                             
END
