
#######################################################
#                                                     #
#                        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  135 (  135),  selected  135 , name T0319TS168_3
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319TS168_3.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    K       2      K       2           -
LGA    F       3      F       3           -
LGA    L       4      L       4           -
LGA    T       5      T       5           #
LGA    T       6      -       -           -
LGA    N       7      -       -           -
LGA    F       8      T       6          3.560
LGA    L       9      N       7          4.675
LGA    K      10      F       8          3.568
LGA    C      11      -       -           -
LGA    S      12      -       -           -
LGA    V      13      -       -           -
LGA    K      14      -       -           -
LGA    A      15      -       -           -
LGA    C      16      -       -           -
LGA    D      17      -       -           -
LGA    T      18      -       -           -
LGA    S      19      -       -           -
LGA    N      20      -       -           -
LGA    D      21      -       -           -
LGA    N      22      -       -           -
LGA    F      23      -       -           -
LGA    P      24      -       -           -
LGA    L      25      -       -           -
LGA    Q      26      -       -           -
LGA    Y      27      -       -           -
LGA    D      28      L       9          5.142
LGA    G      29      K      10           -
LGA    S      30      C      11           -
LGA    K      31      S      12           -
LGA    -       -      V      13           -
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    -       -      C      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    -       -      D      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    C      32      P      24           #
LGA    Q      33      L      25           -
LGA    -       -      Q      26           -
LGA    L      34      Y      27          3.985
LGA    V      35      D      28          3.630
LGA    Q      36      -       -           -
LGA    D      37      -       -           -
LGA    E      38      -       -           -
LGA    S      39      -       -           -
LGA    I      40      -       -           -
LGA    E      41      -       -           -
LGA    F      42      -       -           -
LGA    N      43      -       -           -
LGA    P      44      -       -           -
LGA    E      45      -       -           -
LGA    F      46      -       -           -
LGA    L      47      -       -           -
LGA    L      48      -       -           -
LGA    N      49      -       -           -
LGA    I      50      G      29          0.733
LGA    V      51      S      30          3.933
LGA    D      52      K      31          4.435
LGA    R      53      C      32           #
LGA    V      54      Q      33          1.440
LGA    D      55      L      34          4.849
LGA    W      56      V      35           -
LGA    P      57      Q      36           #
LGA    A      58      D      37           -
LGA    V      59      E      38           -
LGA    -       -      S      39           -
LGA    -       -      I      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      P      44           -
LGA    -       -      E      45           -
LGA    -       -      F      46           -
LGA    -       -      L      47           -
LGA    -       -      L      48           -
LGA    -       -      N      49           -
LGA    -       -      I      50           -
LGA    -       -      V      51           -
LGA    -       -      D      52           -
LGA    -       -      R      53           -
LGA    -       -      V      54           -
LGA    -       -      D      55           -
LGA    -       -      W      56           -
LGA    -       -      P      57           -
LGA    -       -      A      58           -
LGA    L      60      V      59           #
LGA    T      61      -       -           -
LGA    V      62      -       -           -
LGA    A      63      -       -           -
LGA    A      64      -       -           -
LGA    E      65      L      60          1.993
LGA    L      66      T      61          4.470
LGA    G      67      V      62           -
LGA    N      68      A      63           -
LGA    N      69      A      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      G      67           -
LGA    -       -      N      68           -
LGA    -       -      N      69           -
LGA    -       -      A      70           -
LGA    -       -      L      71           -
LGA    A      70      P      72           #
LGA    L      71      P      73           #
LGA    P      72      T      74           #
LGA    P      73      K      75           -
LGA    T      74      P      76           -
LGA    K      75      -       -           -
LGA    P      76      -       -           -
LGA    S      77      -       -           -
LGA    F      78      -       -           -
LGA    P      79      -       -           -
LGA    S      80      S      77           #
LGA    S      81      F      78          3.234
LGA    -       -      P      79           -
LGA    -       -      S      80           -
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    I      82      L      85          4.897
LGA    -       -      T      86           -
LGA    -       -      D      87           -
LGA    -       -      D      88           -
LGA    Q      83      D      89          3.652
LGA    E      84      M      90          3.450
LGA    L      85      A      91          2.989
LGA    -       -      I      92           -
LGA    T      86      L      93          1.444
LGA    D      87      N      94          1.580
LGA    D      88      D      95          1.345
LGA    D      89      L      96          0.871
LGA    M      90      H      97          1.034
LGA    A      91      T      98          1.064
LGA    I      92      L      99          0.749
LGA    L      93      L     100          1.388
LGA    N      94      L     101          3.318
LGA    D      95      Q     102          4.974
LGA    L      96      T     103          4.227
LGA    H      97      S     104          3.208
LGA    T      98      -       -           -
LGA    L      99      I     105          0.649
LGA    L     100      -       -           -
LGA    L     101      A     106          4.560
LGA    Q     102      E     107          3.614
LGA    T     103      G     108          3.181
LGA    S     104      E     109          2.593
LGA    -       -      M     110           -
LGA    -       -      K     111           -
LGA    -       -      C     112           -
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    -       -      H     117           -
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    I     105      Y     120          1.693
LGA    A     106      I     121          4.014
LGA    E     107      K     122           #
LGA    -       -      N     123           -
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    G     108      P     126          4.696
LGA    E     109      N     127          2.516
LGA    M     110      L     128           #
LGA    K     111      -       -           -
LGA    C     112      L     129          4.792
LGA    R     113      L     130          2.379
LGA    -       -      P     131           -
LGA    N     114      P     132          3.817
LGA    C     115      H     133           #
LGA    G     116      -       -           -
LGA    H     117      -       -           -
LGA    I     118      L     134           #
LGA    Y     119      V     135           -
LGA    Y     120      -       -           -
LGA    I     121      -       -           -
LGA    K     122      -       -           -
LGA    N     123      -       -           -
LGA    G     124      -       -           -
LGA    I     125      -       -           -
LGA    P     126      -       -           -
LGA    N     127      -       -           -
LGA    L     128      -       -           -
LGA    L     129      -       -           -
LGA    L     130      -       -           -
LGA    P     131      -       -           -
LGA    P     132      -       -           -
LGA    H     133      -       -           -
LGA    L     134      -       -           -
LGA    V     135      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  135  135    5.0     42    3.36     4.76     17.771     1.214

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.387051 * X  +   0.868636 * Y  +   0.309296 * Z  +  17.961559
  Y_new =  -0.914207 * X  +   0.317839 * Y  +   0.251404 * Z  +   4.815354
  Z_new =   0.120072 * X  +  -0.380067 * Y  +   0.917132 * Z  +  10.780144 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.392865    2.748728  [ DEG:   -22.5095    157.4905 ]
  Theta =  -0.120363   -3.021230  [ DEG:    -6.8963   -173.1037 ]
  Phi   =  -1.170305    1.971288  [ DEG:   -67.0535    112.9465 ]
 
# 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: T0319TS168_3                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319TS168_3.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  135  135   5.0   42   3.36    4.76  17.771
REMARK  ---------------------------------------------------------- 
MOLECULE T0319TS168_3
PFRMAT TS
TARGET T0319
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1       3.527  13.952  17.940  1.00 25.00           C
ATOM      2  CA  LYS     2       5.252  12.063  15.179  1.00 25.00           C
ATOM      3  CA  PHE     3       7.226   9.635  13.047  1.00 25.00           C
ATOM      4  CA  LEU     4       9.595   7.135  11.503  1.00 25.00           C
ATOM      5  CA  THR     5      12.135   4.257  11.465  1.00 25.00           C
ATOM      6  CA  THR     6      13.286   4.596   7.797  1.00 25.00           C
ATOM      7  CA  ASN     7      13.049   1.001   6.460  1.00 25.00           C
ATOM      8  CA  PHE     8      14.585  -0.016   9.821  1.00 25.00           C
ATOM      9  CA  LEU     9      11.907  -2.567  10.613  1.00 25.00           C
ATOM     10  CA  LYS    10      12.431  -5.387  13.121  1.00 25.00           C
ATOM     11  CA  CYS    11       9.664  -3.754  15.202  1.00 25.00           C
ATOM     12  CA  SER    12       7.981  -7.021  16.164  1.00 25.00           C
ATOM     13  CA  VAL    13       8.585  -8.557  12.697  1.00 25.00           C
ATOM     14  CA  LYS    14       4.775  -8.576  12.450  1.00 25.00           C
ATOM     15  CA  ALA    15       5.462  -6.255   9.520  1.00 25.00           C
ATOM     16  CA  CYS    16       5.928  -2.811  10.947  1.00 25.00           C
ATOM     17  CA  ASP    17       2.297  -2.547  11.910  1.00 25.00           C
ATOM     18  CA  THR    18       1.265   0.431   9.774  1.00 25.00           C
ATOM     19  CA  SER    19       1.937   0.463   6.029  1.00 25.00           C
ATOM     20  CA  ASN    20       2.884  -3.165   5.822  1.00 25.00           C
ATOM     21  CA  ASP    21       6.421  -4.378   4.922  1.00 25.00           C
ATOM     22  CA  ASN    22       7.405  -0.732   5.556  1.00 25.00           C
ATOM     23  CA  PHE    23       8.171   2.625   7.272  1.00 25.00           C
ATOM     24  CA  PRO    24       7.726   1.889  10.949  1.00 25.00           C
ATOM     25  CA  LEU    25       6.905   2.728  14.625  1.00 25.00           C
ATOM     26  CA  GLN    26      10.453   1.398  15.217  1.00 25.00           C
ATOM     27  CA  TYR    27      13.699  -0.423  14.772  1.00 25.00           C
ATOM     28  CA  ASP    28      14.650  -0.751  18.485  1.00 25.00           C
ATOM     29  CA  GLY    29      17.926  -1.785  20.116  1.00 25.00           C
ATOM     30  CA  SER    30      19.562  -2.120  16.698  1.00 25.00           C
ATOM     31  CA  LYS    31      18.923   1.203  15.090  1.00 25.00           C
ATOM     32  CA  CYS    32      17.489   3.493  12.439  1.00 25.00           C
ATOM     33  CA  GLN    33      16.301   7.136  12.479  1.00 25.00           C
ATOM     34  CA  LEU    34      16.103   9.002   9.150  1.00 25.00           C
ATOM     35  CA  VAL    35      12.650   9.736   7.588  1.00 25.00           C
ATOM     36  CA  GLN    36      10.026  11.763   5.707  1.00 25.00           C
ATOM     37  CA  ASP    37       9.234  15.123   4.106  1.00 25.00           C
ATOM     38  CA  GLU    38       6.869  14.946   1.160  1.00 25.00           C
ATOM     39  CA  SER    39       6.971  17.675  -1.509  1.00 25.00           C
ATOM     40  CA  ILE    40      10.656  16.843  -1.799  1.00 25.00           C
ATOM     41  CA  GLU    41       9.835  15.250  -5.172  1.00 25.00           C
ATOM     42  CA  PHE    42      13.466  14.004  -4.859  1.00 25.00           C
ATOM     43  CA  ASN    43      13.710  10.272  -5.730  1.00 25.00           C
ATOM     44  CA  PRO    44      12.971   7.583  -3.130  1.00 25.00           C
ATOM     45  CA  GLU    45      11.917  10.621  -1.050  1.00 25.00           C
ATOM     46  CA  PHE    46      12.872   8.781   2.169  1.00 25.00           C
ATOM     47  CA  LEU    47      16.282   7.887   0.675  1.00 25.00           C
ATOM     48  CA  LEU    48      16.832  11.543  -0.322  1.00 25.00           C
ATOM     49  CA  ASN    49      15.919  12.673   3.221  1.00 25.00           C
ATOM     50  CA  ILE    50      18.375  10.129   4.692  1.00 25.00           C
ATOM     51  CA  VAL    51      21.125  11.388   2.341  1.00 25.00           C
ATOM     52  CA  ASP    52      20.402  14.999   3.391  1.00 25.00           C
ATOM     53  CA  ARG    53      21.980  17.205   6.113  1.00 25.00           C
ATOM     54  CA  VAL    54      21.700  14.478   8.750  1.00 25.00           C
ATOM     55  CA  ASP    55      24.329  12.804   6.556  1.00 25.00           C
ATOM     56  CA  TRP    56      23.129   9.242   6.903  1.00 25.00           C
ATOM     57  CA  PRO    57      25.201   6.149   7.803  1.00 25.00           C
ATOM     58  CA  ALA    58      21.999   4.199   8.583  1.00 25.00           C
ATOM     59  CA  VAL    59      20.502   5.265   5.223  1.00 25.00           C
ATOM     60  CA  LEU    60      23.688   4.140   3.420  1.00 25.00           C
ATOM     61  CA  THR    61      23.542   0.761   5.216  1.00 25.00           C
ATOM     62  CA  VAL    62      19.870   0.355   4.206  1.00 25.00           C
ATOM     63  CA  ALA    63      20.756   1.170   0.570  1.00 25.00           C
ATOM     64  CA  ALA    64      23.583  -1.412   0.654  1.00 25.00           C
ATOM     65  CA  GLU    65      21.179  -4.035   2.071  1.00 25.00           C
ATOM     66  CA  LEU    66      18.650  -3.247  -0.695  1.00 25.00           C
ATOM     67  CA  GLY    67      19.416  -4.698  -4.081  1.00 25.00           C
ATOM     68  CA  ASN    68      22.254  -6.343  -5.979  1.00 25.00           C
ATOM     69  CA  ASN    69      24.653  -4.202  -7.951  1.00 25.00           C
ATOM     70  CA  ALA    70      27.272  -6.330  -6.109  1.00 25.00           C
ATOM     71  CA  LEU    71      25.919  -9.690  -4.840  1.00 25.00           C
ATOM     72  CA  PRO    72      28.362 -12.580  -5.221  1.00 25.00           C
ATOM     73  CA  PRO    73      28.122 -16.077  -3.672  1.00 25.00           C
ATOM     74  CA  THR    74      31.486 -16.900  -5.261  1.00 25.00           C
ATOM     75  CA  LYS    75      35.067 -15.702  -5.269  1.00 25.00           C
ATOM     76  CA  PRO    76      35.908 -17.337  -1.882  1.00 25.00           C
ATOM     77  CA  SER    77      38.220 -17.103   1.121  1.00 25.00           C
ATOM     78  CA  PHE    78      36.086 -15.024   3.492  1.00 25.00           C
ATOM     79  CA  PRO    79      35.729 -18.197   5.652  1.00 25.00           C
ATOM     80  CA  SER    80      33.052 -18.966   8.252  1.00 25.00           C
ATOM     81  CA  SER    81      34.020 -16.060  10.476  1.00 25.00           C
ATOM     82  CA  ILE    82      33.116 -14.085  13.582  1.00 25.00           C
ATOM     83  CA  GLN    83      36.709 -12.878  13.584  1.00 25.00           C
ATOM     84  CA  GLU    84      35.685  -9.821  15.561  1.00 25.00           C
ATOM     85  CA  LEU    85      36.800  -7.664  12.620  1.00 25.00           C
ATOM     86  CA  THR    86      33.425  -6.241  11.703  1.00 25.00           C
ATOM     87  CA  ASP    87      34.834  -2.689  11.943  1.00 25.00           C
ATOM     88  CA  ASP    88      32.490  -1.542   9.141  1.00 25.00           C
ATOM     89  CA  ASP    89      29.512  -3.134  10.948  1.00 25.00           C
ATOM     90  CA  MET    90      30.508  -1.369  14.197  1.00 25.00           C
ATOM     91  CA  ALA    91      30.758   1.970  12.337  1.00 25.00           C
ATOM     92  CA  ILE    92      27.292   1.404  10.808  1.00 25.00           C
ATOM     93  CA  LEU    93      25.863   0.622  14.274  1.00 25.00           C
ATOM     94  CA  ASN    94      27.443   3.818  15.673  1.00 25.00           C
ATOM     95  CA  ASP    95      25.941   5.850  12.795  1.00 25.00           C
ATOM     96  CA  LEU    96      22.500   4.308  13.470  1.00 25.00           C
ATOM     97  CA  HIS    97      22.815   5.171  17.187  1.00 25.00           C
ATOM     98  CA  THR    98      23.763   8.773  16.296  1.00 25.00           C
ATOM     99  CA  LEU    99      20.737   9.018  13.962  1.00 25.00           C
ATOM    100  CA  LEU   100      18.458   7.690  16.739  1.00 25.00           C
ATOM    101  CA  LEU   101      19.894  10.266  19.183  1.00 25.00           C
ATOM    102  CA  GLN   102      19.291  13.058  16.632  1.00 25.00           C
ATOM    103  CA  THR   103      16.631  12.475  13.908  1.00 25.00           C
ATOM    104  CA  SER   104      13.556  12.765  11.710  1.00 25.00           C
ATOM    105  CA  ILE   105      10.079  13.766  13.004  1.00 25.00           C
ATOM    106  CA  ALA   106      10.646  13.774  16.807  1.00 25.00           C
ATOM    107  CA  GLU   107       8.290  14.256  19.712  1.00 25.00           C
ATOM    108  CA  GLY   108       8.401  10.441  20.056  1.00 25.00           C
ATOM    109  CA  GLU   109       9.836   8.388  17.237  1.00 25.00           C
ATOM    110  CA  MET   110      12.867   7.064  15.393  1.00 25.00           C
ATOM    111  CA  LYS   111      14.656   3.860  16.454  1.00 25.00           C
ATOM    112  CA  CYS   112      12.315   3.689  19.487  1.00 25.00           C
ATOM    113  CA  ARG   113      13.413   2.057  22.773  1.00 25.00           C
ATOM    114  CA  ASN   114      14.773   0.739  26.077  1.00 25.00           C
ATOM    115  CA  CYS   115      18.103   1.060  24.230  1.00 25.00           C
ATOM    116  CA  GLY   116      21.224   3.108  25.217  1.00 25.00           C
ATOM    117  CA  HIS   117      21.032   5.214  22.036  1.00 25.00           C
ATOM    118  CA  ILE   118      18.361   3.529  19.882  1.00 25.00           C
ATOM    119  CA  TYR   119      16.327   6.683  20.501  1.00 25.00           C
ATOM    120  CA  TYR   120      13.767   9.436  19.924  1.00 25.00           C
ATOM    121  CA  ILE   121      15.416  12.756  20.635  1.00 25.00           C
ATOM    122  CA  LYS   122      16.827  14.698  23.529  1.00 25.00           C
ATOM    123  CA  ASN   123      18.915  17.055  25.745  1.00 25.00           C
ATOM    124  CA  GLY   124      18.123  18.910  28.921  1.00 25.00           C
ATOM    125  CA  ILE   125      19.398  22.472  29.274  1.00 25.00           C
ATOM    126  CA  PRO   126      17.167  24.282  31.790  1.00 25.00           C
ATOM    127  CA  ASN   127      13.593  24.848  30.861  1.00 25.00           C
ATOM    128  CA  LEU   128      14.098  27.618  28.339  1.00 25.00           C
ATOM    129  CA  LEU   129      16.777  29.452  26.401  1.00 25.00           C
ATOM    130  CA  LEU   130      15.780  31.805  23.542  1.00 25.00           C
ATOM    131  CA  PRO   131      18.219  32.081  20.651  1.00 25.00           C
ATOM    132  CA  PRO   132      18.524  33.641  17.196  1.00 25.00           C
ATOM    133  CA  HIS   133      14.880  32.971  16.623  1.00 25.00           C
ATOM    134  CA  LEU   134      11.674  33.696  18.441  1.00 25.00           C
ATOM    135  CA  VAL   135       9.446  32.192  15.809  1.00 25.00           C
TER
END
