
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected  132 , name T0312_D1.pdb
# PARAMETERS: T0312TS599_5-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      -       -           -
LGA    G      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    L      14      -       -           -
LGA    R      15      -       -           -
LGA    L      16      -       -           -
LGA    D      17      -       -           -
LGA    Y      18      K      10          4.530
LGA    G      19      G      11          4.761
LGA    K      20      F      12          4.360
LGA    D      21      -       -           -
LGA    L      22      -       -           -
LGA    V      23      -       -           -
LGA    R      24      L      13           #
LGA    Q      25      L      14           -
LGA    I      26      -       -           -
LGA    E      27      -       -           -
LGA    E      28      -       -           -
LGA    F      29      -       -           -
LGA    L      30      -       -           -
LGA    E      31      -       -           -
LGA    E      32      -       -           -
LGA    K      33      -       -           -
LGA    G      34      -       -           -
LGA    I      35      -       -           -
LGA    H      36      -       -           -
LGA    A      37      -       -           -
LGA    A      38      R      15          4.072
LGA    H      39      L      16          2.243
LGA    I      40      D      17           #
LGA    S      41      -       -           -
LGA    A      42      -       -           -
LGA    I      43      -       -           -
LGA    G      44      -       -           -
LGA    A      45      -       -           -
LGA    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      Y      18          3.091
LGA    K      59      G      19          0.878
LGA    E      60      K      20          3.467
LGA    Y      61      D      21          4.059
LGA    V      62      L      22           #
LGA    -       -      V      23           -
LGA    -       -      R      24           -
LGA    K      63      Q      25          1.987
LGA    K      64      I      26          2.080
LGA    E      65      E      27          3.245
LGA    L      66      E      28           -
LGA    -       -      F      29           -
LGA    -       -      L      30           -
LGA    -       -      E      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    M      67      G      34          4.846
LGA    E      68      I      35           #
LGA    P      69      H      36          4.722
LGA    L      70      A      37          2.826
LGA    E      71      A      38          0.910
LGA    I      72      H      39          0.897
LGA    L      73      I      40          1.147
LGA    S      74      S      41          0.890
LGA    L      75      A      42          1.999
LGA    S      76      I      43          1.325
LGA    G      77      G      44          2.577
LGA    N      78      A      45          2.624
LGA    -       -      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    V      79      P      69           #
LGA    S      80      -       -           -
LGA    M      81      -       -           -
LGA    K      82      -       -           -
LGA    D      83      -       -           -
LGA    S      84      -       -           -
LGA    K      85      -       -           -
LGA    P      86      -       -           -
LGA    F      87      L      70           #
LGA    C      88      E      71          3.415
LGA    H      89      I      72          3.911
LGA    I      90      L      73          2.807
LGA    H      91      S      74          1.730
LGA    V      92      L      75          1.598
LGA    L      93      S      76          1.443
LGA    L      94      G      77          2.631
LGA    G      95      N      78          0.885
LGA    K      96      V      79          0.644
LGA    D      97      S      80          2.438
LGA    -       -      M      81           -
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    -       -      P      86           -
LGA    -       -      F      87           -
LGA    G      98      C      88          2.337
LGA    E      99      H      89          1.571
LGA    V     100      I      90          1.618
LGA    Y     101      H      91          1.441
LGA    G     102      V      92          1.806
LGA    G     103      L      93          3.364
LGA    H     104      -       -           -
LGA    L     105      L      94          2.633
LGA    F     106      -       -           -
LGA    S     107      -       -           -
LGA    A     108      -       -           -
LGA    E     109      G      95          4.675
LGA    V     110      K      96           -
LGA    -       -      D      97           -
LGA    -       -      G      98           -
LGA    -       -      E      99           -
LGA    -       -      V     100           -
LGA    F     111      Y     101           #
LGA    A     112      -       -           -
LGA    C     113      -       -           -
LGA    E     114      -       -           -
LGA    V     115      -       -           -
LGA    F     116      -       -           -
LGA    V     117      G     102           #
LGA    L     118      G     103          3.698
LGA    P     119      H     104          1.801
LGA    L     120      L     105           -
LGA    S     121      F     106           -
LGA    -       -      S     107           -
LGA    -       -      A     108           -
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      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    -       -      R     127           -
LGA    -       -      A     128           -
LGA    -       -      F     129           -
LGA    -       -      D     130           -
LGA    -       -      E     131           -
LGA    -       -      Q     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    G     122      L     135          4.737
LGA    E     123      F     136           -
LGA    A     124      L     137           -
LGA    P     125      W     138           -
LGA    E     126      L     139           -
LGA    R     127      E     140           -
LGA    A     128      -       -           -
LGA    F     129      -       -           -
LGA    D     130      -       -           -
LGA    E     131      -       -           -
LGA    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     44    2.90    11.36     21.193     1.467

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.559686 * X  +  -0.625979 * Y  +  -0.543048 * Z  +  52.251827
  Y_new =   0.299920 * X  +  -0.457869 * Y  +   0.836901 * Z  +  11.236756
  Z_new =  -0.772528 * X  +  -0.631273 * Y  +  -0.068519 * Z  +  14.046413 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.678914    1.462678  [ DEG:   -96.1947     83.8053 ]
  Theta =   0.882813    2.258780  [ DEG:    50.5815    129.4185 ]
  Phi   =   0.491932   -2.649661  [ DEG:    28.1856   -151.8144 ]
 
# 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_5-D1                               
REMARK     2: T0312_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS599_5-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   44   2.90   11.36  21.193
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS599_5-D1
PFRMAT TS                                                                       
TARGET T0312                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      9  CA  GLY     9      47.246  24.092   3.763  1.00  0.00              
ATOM     10  CA  LYS    10      50.895  24.503   3.010  1.00  0.00              
ATOM     11  CA  GLY    11      53.350  22.266   4.616  1.00  0.00              
ATOM     12  CA  PHE    12      55.865  23.630   7.220  1.00  0.00              
ATOM     13  CA  LEU    13      58.779  21.452   8.466  1.00  0.00              
ATOM     14  CA  LEU    14      59.958  21.963  12.036  1.00  0.00              
ATOM     15  CA  ARG    15      63.280  20.626  13.227  1.00  0.00              
ATOM     16  CA  LEU    16      63.732  19.838  16.911  1.00  0.00              
ATOM     17  CA  ASP    17      67.250  19.932  18.517  1.00  0.00              
ATOM     18  CA  TYR    18      67.661  19.852  22.229  1.00  0.00              
ATOM     19  CA  GLY    19      66.288  22.885  24.055  1.00  0.00              
ATOM     20  CA  LYS    20      63.739  23.691  21.310  1.00  0.00              
ATOM     21  CA  ASP    21      63.176  27.312  20.404  1.00  0.00              
ATOM     22  CA  LEU    22      62.827  27.563  16.635  1.00  0.00              
ATOM     23  CA  VAL    23      60.197  24.912  16.511  1.00  0.00              
ATOM     24  CA  ARG    24      58.113  26.620  19.218  1.00  0.00              
ATOM     25  CA  GLN    25      58.308  29.948  17.313  1.00  0.00              
ATOM     26  CA  ILE    26      57.253  28.295  14.067  1.00  0.00              
ATOM     27  CA  GLU    27      54.286  26.596  15.829  1.00  0.00              
ATOM     28  CA  GLU    28      53.140  29.780  17.299  1.00  0.00              
ATOM     29  CA  PHE    29      53.388  31.566  14.019  1.00  0.00              
ATOM     30  CA  LEU    30      51.462  28.854  12.112  1.00  0.00              
ATOM     31  CA  GLU    31      48.692  28.688  14.615  1.00  0.00              
ATOM     32  CA  GLU    32      48.369  32.511  14.638  1.00  0.00              
ATOM     33  CA  LYS    33      47.950  32.681  10.911  1.00  0.00              
ATOM     34  CA  GLY    34      45.652  29.735  10.658  1.00  0.00              
ATOM     35  CA  ILE    35      47.950  27.810   8.313  1.00  0.00              
ATOM     36  CA  HIS    36      47.639  24.132   8.145  1.00  0.00              
ATOM     37  CA  ALA    37      50.242  21.535   8.027  1.00  0.00              
ATOM     38  CA  ALA    38      53.135  21.153  10.414  1.00  0.00              
ATOM     39  CA  HIS    39      55.682  18.362  10.041  1.00  0.00              
ATOM     40  CA  ILE    40      58.090  17.721  12.929  1.00  0.00              
ATOM     41  CA  SER    41      61.500  16.247  12.428  1.00  0.00              
ATOM     42  CA  ALA    42      63.499  15.249  15.455  1.00  0.00              
ATOM     43  CA  ILE    43      67.224  15.323  15.365  1.00  0.00              
ATOM     44  CA  GLY    44      69.019  14.070  18.408  1.00  0.00              
ATOM     45  CA  ALA    45      68.592  15.542  21.866  1.00  0.00              
ATOM     46  CA  VAL    46      64.867  15.965  22.285  1.00  0.00              
ATOM     47  CA  ARG    47      63.415  14.692  25.483  1.00  0.00              
ATOM     48  CA  SER    48      59.763  15.697  25.102  1.00  0.00              
ATOM     49  CA  ALA    49      59.131  16.132  21.543  1.00  0.00              
ATOM     50  CA  VAL    50      55.642  16.740  20.014  1.00  0.00              
ATOM     51  CA  ILE    51      55.220  16.281  16.317  1.00  0.00              
ATOM     52  CA  GLY    52      52.132  17.358  14.381  1.00  0.00              
ATOM     53  CA  TYR    53      51.510  15.817  11.049  1.00  0.00              
ATOM     54  CA  TYR    54      48.523  16.802   8.854  1.00  0.00              
ATOM     55  CA  ASP    55      47.348  14.379   6.318  1.00  0.00              
ATOM     56  CA  GLN    56      45.833  15.508   3.023  1.00  0.00              
ATOM     57  CA  GLU    57      48.544  14.274   0.590  1.00  0.00              
ATOM     58  CA  LYS    58      51.522  15.246   2.764  1.00  0.00              
ATOM     59  CA  LYS    59      53.920  12.349   2.578  1.00  0.00              
ATOM     60  CA  GLU    60      55.008  12.146   6.202  1.00  0.00              
ATOM     61  CA  TYR    61      58.759  12.175   5.917  1.00  0.00              
ATOM     62  CA  VAL    62      59.856  13.710   9.268  1.00  0.00              
ATOM     63  CA  LYS    63      63.349  12.655  10.285  1.00  0.00              
ATOM     64  CA  LYS    64      63.891  10.798  13.480  1.00  0.00              
ATOM     65  CA  GLU    65      67.253  10.468  15.064  1.00  0.00              
ATOM     66  CA  LEU    66      67.336   8.561  18.342  1.00  0.00              
ATOM     67  CA  MET    67      70.211   8.895  20.731  1.00  0.00              
ATOM     68  CA  GLU    68      69.531   6.234  23.344  1.00  0.00              
ATOM     69  CA  PRO    69      68.542   7.365  26.835  1.00  0.00              
ATOM     70  CA  LEU    70      64.745   7.341  26.428  1.00  0.00              
ATOM     71  CA  GLU    71      62.888  10.542  25.389  1.00  0.00              
ATOM     72  CA  ILE    72      59.263  10.508  24.608  1.00  0.00              
ATOM     73  CA  LEU    73      58.173  11.628  21.297  1.00  0.00              
ATOM     74  CA  SER    74      54.650  12.186  20.659  1.00  0.00              
ATOM     75  CA  LEU    75      53.360  12.112  17.133  1.00  0.00              
ATOM     76  CA  SER    76      50.061  13.491  16.345  1.00  0.00              
ATOM     77  CA  GLY    77      48.544  12.698  13.026  1.00  0.00              
ATOM     78  CA  ASN    78      45.485  14.499  11.868  1.00  0.00              
ATOM     79  CA  VAL    79      43.488  13.156   9.049  1.00  0.00              
ATOM     80  CA  SER    80      40.563  15.202   7.888  1.00  0.00              
ATOM     81  CA  MET    81      38.089  14.088   5.260  1.00  0.00              
ATOM     82  CA  LYS    82      37.382  16.888   2.863  1.00  0.00              
ATOM     83  CA  ASP    83      34.064  16.438   1.422  1.00  0.00              
ATOM     84  CA  SER    84      32.126  14.689   4.104  1.00  0.00              
ATOM     85  CA  LYS    85      33.597  16.301   7.240  1.00  0.00              
ATOM     86  CA  PRO    86      35.033  13.474   9.264  1.00  0.00              
ATOM     87  CA  PHE    87      38.129  14.191  11.189  1.00  0.00              
ATOM     88  CA  CYS    88      40.396  11.384  12.203  1.00  0.00              
ATOM     89  CA  HIS    89      42.937  11.884  14.851  1.00  0.00              
ATOM     90  CA  ILE    90      45.775   9.446  15.157  1.00  0.00              
ATOM     91  CA  HIS    91      47.999   9.430  18.167  1.00  0.00              
ATOM     92  CA  VAL    92      51.382   7.875  17.848  1.00  0.00              
ATOM     93  CA  LEU    93      53.734   7.504  20.758  1.00  0.00              
ATOM     94  CA  LEU    94      57.397   6.949  20.152  1.00  0.00              
ATOM     95  CA  GLY    95      59.775   5.843  22.821  1.00  0.00              
ATOM     96  CA  LYS    96      63.495   6.696  22.585  1.00  0.00              
ATOM     97  CA  ASP    97      64.316   2.984  22.466  1.00  0.00              
ATOM     98  CA  GLY    98      62.314   2.559  19.280  1.00  0.00              
ATOM     99  CA  GLU    99      59.152   0.938  20.380  1.00  0.00              
ATOM    100  CA  VAL   100      56.064   2.337  18.754  1.00  0.00              
ATOM    101  CA  TYR   101      53.027   2.724  20.713  1.00  0.00              
ATOM    102  CA  GLY   102      49.820   3.333  18.913  1.00  0.00              
ATOM    103  CA  GLY   103      46.908   5.000  20.607  1.00  0.00              
ATOM    104  CA  HIS   104      43.347   4.428  19.422  1.00  0.00              
ATOM    105  CA  LEU   105      43.050   6.473  16.180  1.00  0.00              
ATOM    106  CA  PHE   106      46.466   5.171  15.010  1.00  0.00              
ATOM    107  CA  SER   107      45.313   1.524  15.329  1.00  0.00              
ATOM    108  CA  ALA   108      42.305   2.300  13.072  1.00  0.00              
ATOM    109  CA  GLU   109      44.460   4.215  10.554  1.00  0.00              
ATOM    110  CA  VAL   110      47.379   2.005   9.638  1.00  0.00              
ATOM    111  CA  PHE   111      45.461  -1.528   9.032  1.00  0.00              
ATOM    112  CA  ALA   112      43.013   0.541   7.092  1.00  0.00              
ATOM    113  CA  CYS   113      45.670   2.363   5.064  1.00  0.00              
ATOM    114  CA  GLU   114      47.533  -0.619   3.792  1.00  0.00              
ATOM    115  CA  VAL   115      48.215  -2.574   6.963  1.00  0.00              
ATOM    116  CA  PHE   116      49.219   0.626   9.254  1.00  0.00              
ATOM    117  CA  VAL   117      51.162  -1.275  11.970  1.00  0.00              
ATOM    118  CA  LEU   118      51.705   0.046  15.522  1.00  0.00              
ATOM    119  CA  PRO   119      54.111  -1.524  17.926  1.00  0.00              
ATOM    120  CA  LEU   120      53.532  -1.371  21.633  1.00  0.00              
ATOM    121  CA  SER   121      56.385  -2.814  23.616  1.00  0.00              
ATOM    122  CA  GLY   122      57.530  -5.663  21.385  1.00  0.00              
ATOM    123  CA  GLU   123      54.152  -6.532  19.868  1.00  0.00              
ATOM    124  CA  ALA   124      53.961  -6.140  16.109  1.00  0.00              
ATOM    125  CA  PRO   125      50.909  -5.044  14.241  1.00  0.00              
ATOM    126  CA  GLU   126      50.823  -7.043  11.017  1.00  0.00              
ATOM    127  CA  ARG   127      51.270 -10.168  13.198  1.00  0.00              
ATOM    128  CA  ALA   128      48.481  -9.300  15.636  1.00  0.00              
ATOM    129  CA  PHE   129      45.946  -8.448  12.897  1.00  0.00              
ATOM    130  CA  ASP   130      46.181 -11.210  10.412  1.00  0.00              
ATOM    131  CA  GLU   131      48.072  -9.777   7.481  1.00  0.00              
ATOM    132  CA  GLN   132      46.016 -11.450   4.957  1.00  0.00              
ATOM    133  CA  THR   133      42.630 -10.236   5.971  1.00  0.00              
ATOM    134  CA  GLY   134      43.833  -6.603   6.691  1.00  0.00              
ATOM    135  CA  LEU   135      42.709  -6.637  10.271  1.00  0.00              
ATOM    136  CA  PHE   136      41.188  -3.283  11.002  1.00  0.00              
ATOM    137  CA  LEU   137      40.417  -2.582  14.600  1.00  0.00              
ATOM    138  CA  TRP   138      41.588   0.266  16.722  1.00  0.00              
ATOM    139  CA  LEU   139      38.854   0.607  19.345  1.00  0.00              
ATOM    140  CA  GLU   140      38.459  -3.148  19.794  1.00  0.00              
TER                                                                             
END
