
#######################################################
#                                                     #
#                        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 T0312TS168_4-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected  132 , name T0312_D1.pdb
# PARAMETERS: T0312TS168_4-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      -       -           -
LGA    L      13      -       -           -
LGA    L      14      -       -           -
LGA    R      15      -       -           -
LGA    L      16      -       -           -
LGA    D      17      -       -           -
LGA    Y      18      -       -           -
LGA    G      19      -       -           -
LGA    K      20      -       -           -
LGA    D      21      -       -           -
LGA    L      22      -       -           -
LGA    V      23      -       -           -
LGA    R      24      -       -           -
LGA    Q      25      G       9          3.060
LGA    I      26      K      10          1.386
LGA    E      27      G      11          5.090
LGA    E      28      -       -           -
LGA    F      29      -       -           -
LGA    L      30      F      12           #
LGA    E      31      L      13           -
LGA    E      32      L      14           -
LGA    K      33      R      15           -
LGA    G      34      L      16           -
LGA    I      35      D      17           -
LGA    -       -      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    -       -      R      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      E      27           -
LGA    -       -      E      28           -
LGA    -       -      F      29           -
LGA    -       -      L      30           -
LGA    -       -      E      31           -
LGA    -       -      E      32           -
LGA    H      36      K      33          5.257
LGA    A      37      G      34           #
LGA    A      38      -       -           -
LGA    H      39      -       -           -
LGA    I      40      I      35          1.761
LGA    S      41      H      36          3.026
LGA    A      42      A      37           -
LGA    I      43      A      38           -
LGA    G      44      H      39           -
LGA    A      45      I      40           -
LGA    V      46      S      41           -
LGA    R      47      A      42           -
LGA    S      48      I      43           -
LGA    A      49      G      44           -
LGA    V      50      A      45           -
LGA    I      51      V      46           -
LGA    G      52      R      47           -
LGA    Y      53      S      48           -
LGA    Y      54      A      49           -
LGA    D      55      V      50           -
LGA    -       -      I      51           -
LGA    -       -      G      52           -
LGA    -       -      Y      53           -
LGA    Q      56      Y      54          4.107
LGA    E      57      D      55          1.352
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    K      58      K      59          2.179
LGA    K      59      E      60          1.265
LGA    E      60      Y      61          1.544
LGA    Y      61      V      62          4.300
LGA    V      62      K      63          5.189
LGA    K      63      K      64           -
LGA    K      64      E      65           -
LGA    E      65      L      66           -
LGA    L      66      M      67           -
LGA    M      67      E      68           -
LGA    E      68      P      69           -
LGA    P      69      L      70           -
LGA    L      70      E      71           -
LGA    E      71      I      72           -
LGA    I      72      L      73           -
LGA    L      73      S      74           -
LGA    S      74      L      75           -
LGA    -       -      S      76           -
LGA    -       -      G      77           -
LGA    -       -      N      78           -
LGA    -       -      V      79           -
LGA    -       -      S      80           -
LGA    -       -      M      81           -
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    -       -      P      86           -
LGA    L      75      F      87          3.458
LGA    S      76      C      88          2.319
LGA    G      77      H      89          1.379
LGA    N      78      I      90          3.302
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    V      79      L     105          2.452
LGA    S      80      F     106          4.089
LGA    M      81      S     107           -
LGA    K      82      A     108           -
LGA    D      83      E     109           -
LGA    S      84      V     110           -
LGA    K      85      F     111           -
LGA    P      86      A     112           -
LGA    F      87      C     113           -
LGA    C      88      E     114           -
LGA    H      89      V     115           #
LGA    I      90      F     116           -
LGA    H      91      V     117           -
LGA    V      92      L     118           -
LGA    L      93      P     119           -
LGA    L      94      L     120           -
LGA    G      95      S     121           -
LGA    K      96      G     122           -
LGA    D      97      E     123           -
LGA    G      98      -       -           -
LGA    E      99      -       -           -
LGA    V     100      -       -           -
LGA    Y     101      A     124          4.713
LGA    G     102      -       -           -
LGA    G     103      -       -           -
LGA    H     104      -       -           -
LGA    L     105      -       -           -
LGA    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      P     125          3.039
LGA    F     116      E     126          3.686
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      R     127          4.183
LGA    A     128      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     129      F     136           #
LGA    D     130      L     137          4.294
LGA    E     131      W     138           #
LGA    Q     132      L     139           -
LGA    T     133      E     140           -
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     24    3.44    12.50     10.763     0.678

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.365766 * X  +  -0.088584 * Y  +  -0.926481 * Z  +  60.738087
  Y_new =  -0.818922 * X  +   0.442384 * Y  +  -0.365600 * Z  +   6.094898
  Z_new =   0.442247 * X  +   0.892440 * Y  +   0.089266 * Z  +  20.808630 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.471103   -1.670489  [ DEG:    84.2880    -95.7120 ]
  Theta =  -0.458102   -2.683490  [ DEG:   -26.2473   -153.7527 ]
  Phi   =  -1.150737    1.990856  [ DEG:   -65.9324    114.0676 ]
 
# 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: T0312TS168_4-D1                               
REMARK     2: T0312_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS168_4-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   24   3.44   12.50  10.763
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS168_4-D1
PFRMAT TS
TARGET T0312
MODEL 4
PARENT N/A
ATOM      9  CA  GLY     9      54.085  17.628  13.781  1.00 25.00           C
ATOM     10  CA  LYS    10      57.396  16.741  12.064  1.00 25.00           C
ATOM     11  CA  GLY    11      58.790  13.936  14.158  1.00 25.00           C
ATOM     12  CA  PHE    12      62.158  14.072  15.945  1.00 25.00           C
ATOM     13  CA  LEU    13      61.209  10.952  17.891  1.00 25.00           C
ATOM     14  CA  LEU    14      63.241  10.988  21.133  1.00 25.00           C
ATOM     15  CA  ARG    15      63.645   8.947  24.242  1.00 25.00           C
ATOM     16  CA  LEU    16      63.770   9.262  27.980  1.00 25.00           C
ATOM     17  CA  ASP    17      65.315  11.732  30.400  1.00 25.00           C
ATOM     18  CA  TYR    18      67.594  12.095  33.420  1.00 25.00           C
ATOM     19  CA  GLY    19      67.453  14.124  36.648  1.00 25.00           C
ATOM     20  CA  LYS    20      65.177  17.124  36.249  1.00 25.00           C
ATOM     21  CA  ASP    21      68.366  19.111  35.505  1.00 25.00           C
ATOM     22  CA  LEU    22      68.571  17.527  32.024  1.00 25.00           C
ATOM     23  CA  VAL    23      64.905  18.426  31.373  1.00 25.00           C
ATOM     24  CA  ARG    24      65.568  22.032  32.476  1.00 25.00           C
ATOM     25  CA  GLN    25      68.598  22.216  30.140  1.00 25.00           C
ATOM     26  CA  ILE    26      66.477  20.880  27.244  1.00 25.00           C
ATOM     27  CA  GLU    27      63.778  23.496  27.981  1.00 25.00           C
ATOM     28  CA  GLU    28      66.430  26.258  28.017  1.00 25.00           C
ATOM     29  CA  PHE    29      67.802  25.018  24.664  1.00 25.00           C
ATOM     30  CA  LEU    30      64.267  25.021  23.188  1.00 25.00           C
ATOM     31  CA  GLU    31      63.718  28.595  24.452  1.00 25.00           C
ATOM     32  CA  GLU    32      67.038  29.686  22.884  1.00 25.00           C
ATOM     33  CA  LYS    33      70.808  29.201  22.994  1.00 25.00           C
ATOM     34  CA  GLY    34      72.385  25.868  22.216  1.00 25.00           C
ATOM     35  CA  ILE    35      71.433  22.206  22.063  1.00 25.00           C
ATOM     36  CA  HIS    36      72.193  18.520  21.767  1.00 25.00           C
ATOM     37  CA  ALA    37      69.111  16.232  21.740  1.00 25.00           C
ATOM     38  CA  ALA    38      65.524  15.288  22.810  1.00 25.00           C
ATOM     39  CA  HIS    39      66.502  12.446  25.204  1.00 25.00           C
ATOM     40  CA  ILE    40      69.135  11.290  22.669  1.00 25.00           C
ATOM     41  CA  SER    41      71.587   9.597  20.340  1.00 25.00           C
ATOM     42  CA  ALA    42      70.788  12.099  17.580  1.00 25.00           C
ATOM     43  CA  ILE    43      67.688  13.623  15.931  1.00 25.00           C
ATOM     44  CA  GLY    44      67.713  15.571  12.670  1.00 25.00           C
ATOM     45  CA  ALA    45      65.814  13.196  10.323  1.00 25.00           C
ATOM     46  CA  VAL    46      62.217  12.247   9.466  1.00 25.00           C
ATOM     47  CA  ARG    47      63.523   9.874   6.799  1.00 25.00           C
ATOM     48  CA  SER    48      60.966   7.393   5.610  1.00 25.00           C
ATOM     49  CA  ALA    49      61.227   3.637   5.716  1.00 25.00           C
ATOM     50  CA  VAL    50      62.588   0.553   7.483  1.00 25.00           C
ATOM     51  CA  ILE    51      62.163   0.335  11.258  1.00 25.00           C
ATOM     52  CA  GLY    52      60.865  -1.176  14.442  1.00 25.00           C
ATOM     53  CA  TYR    53      60.269  -3.919  17.071  1.00 25.00           C
ATOM     54  CA  TYR    54      56.665  -4.528  18.212  1.00 25.00           C
ATOM     55  CA  ASP    55      54.626  -7.217  20.061  1.00 25.00           C
ATOM     56  CA  GLN    56      53.716  -9.989  22.457  1.00 25.00           C
ATOM     57  CA  GLU    57      51.423 -12.359  20.452  1.00 25.00           C
ATOM     58  CA  LYS    58      53.916 -15.215  19.868  1.00 25.00           C
ATOM     59  CA  LYS    59      55.362 -13.736  16.743  1.00 25.00           C
ATOM     60  CA  GLU    60      54.216 -10.824  14.505  1.00 25.00           C
ATOM     61  CA  TYR    61      54.508  -7.146  13.582  1.00 25.00           C
ATOM     62  CA  VAL    62      55.764  -5.641  10.322  1.00 25.00           C
ATOM     63  CA  LYS    63      57.093  -2.225   9.545  1.00 25.00           C
ATOM     64  CA  LYS    64      57.765   1.444   8.901  1.00 25.00           C
ATOM     65  CA  GLU    65      59.401   4.621  10.283  1.00 25.00           C
ATOM     66  CA  LEU    66      63.026   5.822  10.157  1.00 25.00           C
ATOM     67  CA  MET    67      65.651   5.352   7.364  1.00 25.00           C
ATOM     68  CA  GLU    68      68.196   5.793   4.561  1.00 25.00           C
ATOM     69  CA  PRO    69      69.772   9.206   5.157  1.00 25.00           C
ATOM     70  CA  LEU    70      68.838  12.863   5.418  1.00 25.00           C
ATOM     71  CA  GLU    71      70.529  13.784   8.716  1.00 25.00           C
ATOM     72  CA  ILE    72      71.080  11.846  11.924  1.00 25.00           C
ATOM     73  CA  LEU    73      69.002   8.654  11.619  1.00 25.00           C
ATOM     74  CA  SER    74      67.951   4.981  12.104  1.00 25.00           C
ATOM     75  CA  LEU    75      65.047   4.225  14.499  1.00 25.00           C
ATOM     76  CA  SER    76      61.528   3.757  15.896  1.00 25.00           C
ATOM     77  CA  GLY    77      60.037   1.730  18.799  1.00 25.00           C
ATOM     78  CA  ASN    78      56.916   1.872  16.628  1.00 25.00           C
ATOM     79  CA  VAL    79      53.913  -0.396  16.027  1.00 25.00           C
ATOM     80  CA  SER    80      52.650  -2.050  12.877  1.00 25.00           C
ATOM     81  CA  MET    81      49.047  -2.681  11.998  1.00 25.00           C
ATOM     82  CA  LYS    82      45.808  -4.265  10.830  1.00 25.00           C
ATOM     83  CA  ASP    83      43.348  -1.470  10.233  1.00 25.00           C
ATOM     84  CA  SER    84      44.552  -0.039  13.591  1.00 25.00           C
ATOM     85  CA  LYS    85      47.737   0.911  15.512  1.00 25.00           C
ATOM     86  CA  PRO    86      50.276   2.538  17.830  1.00 25.00           C
ATOM     87  CA  PHE    87      52.904   5.003  16.527  1.00 25.00           C
ATOM     88  CA  CYS    88      54.276   8.164  14.899  1.00 25.00           C
ATOM     89  CA  HIS    89      57.972   8.729  14.367  1.00 25.00           C
ATOM     90  CA  ILE    90      61.685   9.302  13.513  1.00 25.00           C
ATOM     91  CA  HIS    91      65.185   9.246  14.985  1.00 25.00           C
ATOM     92  CA  VAL    92      66.926   9.007  18.363  1.00 25.00           C
ATOM     93  CA  LEU    93      69.648   7.113  16.397  1.00 25.00           C
ATOM     94  CA  LEU    94      73.344   6.194  16.262  1.00 25.00           C
ATOM     95  CA  GLY    95      74.983   9.602  16.449  1.00 25.00           C
ATOM     96  CA  LYS    96      77.830   8.219  18.534  1.00 25.00           C
ATOM     97  CA  ASP    97      78.343   4.473  18.821  1.00 25.00           C
ATOM     98  CA  GLY    98      76.760   4.711  22.247  1.00 25.00           C
ATOM     99  CA  GLU    99      73.692   2.524  22.831  1.00 25.00           C
ATOM    100  CA  VAL   100      71.124   4.272  20.683  1.00 25.00           C
ATOM    101  CA  TYR   101      68.451   5.838  22.972  1.00 25.00           C
ATOM    102  CA  GLY   102      65.903   4.418  20.551  1.00 25.00           C
ATOM    103  CA  GLY   103      62.408   6.005  20.387  1.00 25.00           C
ATOM    104  CA  HIS   104      59.332   7.605  22.048  1.00 25.00           C
ATOM    105  CA  LEU   105      57.568   6.245  19.004  1.00 25.00           C
ATOM    106  CA  PHE   106      54.560   8.448  19.887  1.00 25.00           C
ATOM    107  CA  SER   107      50.848   8.982  19.488  1.00 25.00           C
ATOM    108  CA  ALA   108      51.211  12.168  21.501  1.00 25.00           C
ATOM    109  CA  GLU   109      51.119  11.036  25.148  1.00 25.00           C
ATOM    110  CA  VAL   110      51.886   7.404  24.184  1.00 25.00           C
ATOM    111  CA  PHE   111      54.494   5.494  26.236  1.00 25.00           C
ATOM    112  CA  ALA   112      56.491   3.744  23.508  1.00 25.00           C
ATOM    113  CA  CYS   113      59.539   4.019  25.795  1.00 25.00           C
ATOM    114  CA  GLU   114      62.904   2.889  24.276  1.00 25.00           C
ATOM    115  CA  VAL   115      66.366   1.826  25.490  1.00 25.00           C
ATOM    116  CA  PHE   116      67.247  -0.138  22.332  1.00 25.00           C
ATOM    117  CA  VAL   117      70.582  -0.901  20.666  1.00 25.00           C
ATOM    118  CA  LEU   118      70.988   0.545  17.171  1.00 25.00           C
ATOM    119  CA  PRO   119      74.147  -1.441  16.606  1.00 25.00           C
ATOM    120  CA  LEU   120      73.643  -0.435  13.018  1.00 25.00           C
ATOM    121  CA  SER   121      76.052  -2.717  11.062  1.00 25.00           C
ATOM    122  CA  GLY   122      74.542  -6.016  10.064  1.00 25.00           C
ATOM    123  CA  GLU   123      71.243  -4.517  11.207  1.00 25.00           C
ATOM    124  CA  ALA   124      68.434  -3.755  13.679  1.00 25.00           C
ATOM    125  CA  PRO   125      67.714  -3.520  17.338  1.00 25.00           C
ATOM    126  CA  GLU   126      66.379  -4.820  20.624  1.00 25.00           C
ATOM    127  CA  ARG   127      63.353  -4.171  22.798  1.00 25.00           C
ATOM    128  CA  ALA   128      60.146  -2.182  22.113  1.00 25.00           C
ATOM    129  CA  PHE   129      58.528  -2.866  25.474  1.00 25.00           C
ATOM    130  CA  ASP   130      59.817  -5.723  27.629  1.00 25.00           C
ATOM    131  CA  GLU   131      59.414  -8.625  29.968  1.00 25.00           C
ATOM    132  CA  GLN   132      58.871  -7.161  33.384  1.00 25.00           C
ATOM    133  CA  THR   133      55.389  -5.707  32.923  1.00 25.00           C
ATOM    134  CA  GLY   134      53.463  -3.180  30.836  1.00 25.00           C
ATOM    135  CA  LEU   135      50.425  -5.025  32.221  1.00 25.00           C
ATOM    136  CA  PHE   136      47.714  -5.796  34.689  1.00 25.00           C
ATOM    137  CA  LEU   137      44.882  -3.726  36.135  1.00 25.00           C
ATOM    138  CA  TRP   138      41.261  -2.629  36.798  1.00 25.00           C
ATOM    139  CA  LEU   139      38.854  -3.536  39.658  1.00 25.00           C
ATOM    140  CA  GLU   140      35.657  -2.911  41.620  1.00 25.00           C
TER
END
