
#######################################################
#                                                     #
#                        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 T0319TS393_5
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319TS393_5.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    K       2      -       -           -
LGA    F       3      -       -           -
LGA    L       4      -       -           -
LGA    T       5      -       -           -
LGA    T       6      -       -           -
LGA    N       7      M       1           #
LGA    -       -      K       2           -
LGA    -       -      F       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    F       8      T       6           #
LGA    -       -      N       7           -
LGA    L       9      F       8           #
LGA    K      10      L       9          3.098
LGA    C      11      K      10          3.774
LGA    S      12      C      11           -
LGA    -       -      S      12           -
LGA    -       -      V      13           -
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    -       -      C      16           -
LGA    V      13      D      17          4.637
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    -       -      D      21           -
LGA    K      14      N      22          4.194
LGA    A      15      F      23          2.976
LGA    C      16      P      24          4.074
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      L      25          4.109
LGA    D      28      Q      26           -
LGA    G      29      -       -           -
LGA    S      30      -       -           -
LGA    K      31      -       -           -
LGA    C      32      -       -           -
LGA    Q      33      -       -           -
LGA    L      34      Y      27          0.838
LGA    V      35      D      28          3.143
LGA    Q      36      G      29          5.614
LGA    D      37      -       -           -
LGA    E      38      -       -           -
LGA    S      39      -       -           -
LGA    I      40      -       -           -
LGA    E      41      -       -           -
LGA    F      42      -       -           -
LGA    N      43      -       -           -
LGA    P      44      S      30          3.944
LGA    E      45      -       -           -
LGA    F      46      -       -           -
LGA    L      47      K      31          3.982
LGA    L      48      C      32           #
LGA    N      49      -       -           -
LGA    I      50      Q      33          1.999
LGA    V      51      L      34          1.392
LGA    D      52      V      35          2.908
LGA    R      53      Q      36          3.778
LGA    V      54      D      37           -
LGA    D      55      E      38           -
LGA    W      56      S      39           -
LGA    P      57      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    -       -      V      59           -
LGA    -       -      L      60           -
LGA    A      58      T      61           #
LGA    V      59      V      62          4.031
LGA    L      60      A      63          3.366
LGA    T      61      A      64          2.886
LGA    V      62      E      65          3.661
LGA    A      63      L      66           #
LGA    -       -      G      67           -
LGA    -       -      N      68           -
LGA    A      64      N      69          4.545
LGA    E      65      -       -           -
LGA    L      66      -       -           -
LGA    G      67      -       -           -
LGA    N      68      -       -           -
LGA    N      69      -       -           -
LGA    A      70      -       -           -
LGA    L      71      A      70           #
LGA    P      72      L      71           -
LGA    P      73      -       -           -
LGA    T      74      -       -           -
LGA    K      75      -       -           -
LGA    P      76      -       -           -
LGA    S      77      -       -           -
LGA    F      78      P      72           #
LGA    P      79      P      73           -
LGA    S      80      T      74           -
LGA    -       -      K      75           -
LGA    S      81      P      76           #
LGA    I      82      S      77          3.764
LGA    Q      83      F      78          0.736
LGA    E      84      P      79          4.477
LGA    L      85      S      80           -
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      D      87           -
LGA    -       -      D      88           -
LGA    T      86      D      89           #
LGA    -       -      M      90           -
LGA    -       -      A      91           -
LGA    -       -      I      92           -
LGA    D      87      L      93          2.319
LGA    D      88      N      94          3.448
LGA    -       -      D      95           -
LGA    D      89      L      96          2.024
LGA    M      90      H      97          2.471
LGA    A      91      T      98          2.128
LGA    I      92      L      99          1.386
LGA    L      93      L     100          1.111
LGA    N      94      L     101          1.212
LGA    D      95      Q     102          4.075
LGA    L      96      T     103          4.857
LGA    H      97      -       -           -
LGA    T      98      S     104          1.374
LGA    L      99      I     105          1.306
LGA    L     100      -       -           -
LGA    L     101      A     106          4.541
LGA    Q     102      E     107          3.537
LGA    T     103      G     108          3.082
LGA    S     104      E     109          4.052
LGA    I     105      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    -       -      Y     120           -
LGA    A     106      I     121           #
LGA    E     107      K     122           -
LGA    -       -      N     123           -
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    G     108      P     126           #
LGA    E     109      N     127          1.635
LGA    M     110      L     128          2.045
LGA    K     111      L     129          2.943
LGA    -       -      L     130           -
LGA    C     112      P     131          4.388
LGA    R     113      P     132          4.036
LGA    N     114      H     133          2.864
LGA    C     115      L     134           #
LGA    G     116      V     135           -
LGA    H     117      -       -           -
LGA    I     118      -       -           -
LGA    Y     119      -       -           -
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     46    3.33     4.35     18.814     1.340

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.375108 * X  +   0.509143 * Y  +   0.774640 * Z  +  17.483957
  Y_new =  -0.756618 * X  +   0.650961 * Y  +  -0.061472 * Z  +   6.506945
  Z_new =  -0.535558 * X  +  -0.563048 * Y  +   0.629408 * Z  +  10.484509 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.729806    2.411787  [ DEG:   -41.8148    138.1852 ]
  Theta =   0.565168    2.576424  [ DEG:    32.3818    147.6182 ]
  Phi   =  -1.110539    2.031054  [ DEG:   -63.6292    116.3708 ]
 
# 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: T0319TS393_5                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319TS393_5.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   46   3.33    4.35  18.814
REMARK  ---------------------------------------------------------- 
MOLECULE T0319TS393_5
PFRMAT TS
TARGET T0319
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1       9.408   8.286  -0.924  1.00 25.00           C
ATOM      2  CA  LYS     2       9.386  10.815   1.866  1.00 25.00           C
ATOM      3  CA  PHE     3      11.838  12.000   4.439  1.00 25.00           C
ATOM      4  CA  LEU     4      10.987  11.163   8.031  1.00 25.00           C
ATOM      5  CA  THR     5      12.964   9.555  10.892  1.00 25.00           C
ATOM      6  CA  THR     6      13.131   8.863  14.646  1.00 25.00           C
ATOM      7  CA  ASN     7      13.155   5.040  15.192  1.00 25.00           C
ATOM      8  CA  PHE     8      10.759   5.210  12.232  1.00 25.00           C
ATOM      9  CA  LEU     9      10.282   1.523  13.049  1.00 25.00           C
ATOM     10  CA  LYS    10       8.415  -1.233  14.843  1.00 25.00           C
ATOM     11  CA  CYS    11       9.852  -3.538  12.158  1.00 25.00           C
ATOM     12  CA  SER    12       7.977  -6.824  11.941  1.00 25.00           C
ATOM     13  CA  VAL    13       4.933  -5.121  13.501  1.00 25.00           C
ATOM     14  CA  LYS    14       2.604  -4.452  10.507  1.00 25.00           C
ATOM     15  CA  ALA    15       5.880  -3.308   8.865  1.00 25.00           C
ATOM     16  CA  CYS    16       7.441  -0.228   7.244  1.00 25.00           C
ATOM     17  CA  ASP    17       4.106   0.954   5.746  1.00 25.00           C
ATOM     18  CA  THR    18       0.945   0.164   7.709  1.00 25.00           C
ATOM     19  CA  SER    19       1.159   3.503   9.532  1.00 25.00           C
ATOM     20  CA  ASN    20       0.859   4.888   6.033  1.00 25.00           C
ATOM     21  CA  ASP    21       3.519   7.425   5.230  1.00 25.00           C
ATOM     22  CA  ASN    22       3.138   9.129   8.594  1.00 25.00           C
ATOM     23  CA  PHE    23       6.246   9.412  10.711  1.00 25.00           C
ATOM     24  CA  PRO    24       6.289   5.569  10.653  1.00 25.00           C
ATOM     25  CA  LEU    25       8.424   6.074   7.503  1.00 25.00           C
ATOM     26  CA  GLN    26      11.008   3.283   7.579  1.00 25.00           C
ATOM     27  CA  TYR    27      14.181   1.315   8.442  1.00 25.00           C
ATOM     28  CA  ASP    28      15.529  -1.519  10.604  1.00 25.00           C
ATOM     29  CA  GLY    29      18.123  -3.377  12.622  1.00 25.00           C
ATOM     30  CA  SER    30      16.790  -2.839  16.198  1.00 25.00           C
ATOM     31  CA  LYS    31      17.380   0.815  15.346  1.00 25.00           C
ATOM     32  CA  CYS    32      17.327   3.220  12.395  1.00 25.00           C
ATOM     33  CA  GLN    33      16.437   6.231  10.158  1.00 25.00           C
ATOM     34  CA  LEU    34      14.682   7.241   6.930  1.00 25.00           C
ATOM     35  CA  VAL    35      16.404  10.613   6.952  1.00 25.00           C
ATOM     36  CA  GLN    36      15.609  14.318   6.986  1.00 25.00           C
ATOM     37  CA  ASP    37      14.528  17.523   5.273  1.00 25.00           C
ATOM     38  CA  GLU    38      12.852  20.814   6.086  1.00 25.00           C
ATOM     39  CA  SER    39      13.825  24.485   5.741  1.00 25.00           C
ATOM     40  CA  ILE    40      17.493  23.614   5.516  1.00 25.00           C
ATOM     41  CA  GLU    41      20.832  23.650   3.595  1.00 25.00           C
ATOM     42  CA  PHE    42      19.762  21.032   1.071  1.00 25.00           C
ATOM     43  CA  ASN    43      18.819  17.575  -0.313  1.00 25.00           C
ATOM     44  CA  PRO    44      21.364  14.841   0.599  1.00 25.00           C
ATOM     45  CA  GLU    45      24.443  16.690   1.929  1.00 25.00           C
ATOM     46  CA  PHE    46      22.302  18.359   4.631  1.00 25.00           C
ATOM     47  CA  LEU    47      20.858  14.954   5.626  1.00 25.00           C
ATOM     48  CA  LEU    48      24.391  13.491   5.842  1.00 25.00           C
ATOM     49  CA  ASN    49      25.499  16.427   8.036  1.00 25.00           C
ATOM     50  CA  ILE    50      22.472  15.893  10.321  1.00 25.00           C
ATOM     51  CA  VAL    51      23.307  12.165  10.596  1.00 25.00           C
ATOM     52  CA  ASP    52      26.934  13.018  11.479  1.00 25.00           C
ATOM     53  CA  ARG    53      29.658  10.409  11.527  1.00 25.00           C
ATOM     54  CA  VAL    54      28.022   7.436   9.747  1.00 25.00           C
ATOM     55  CA  ASP    55      25.587   8.495   7.070  1.00 25.00           C
ATOM     56  CA  TRP    56      22.837   7.264   9.364  1.00 25.00           C
ATOM     57  CA  PRO    57      24.330   3.855   8.460  1.00 25.00           C
ATOM     58  CA  ALA    58      20.827   2.310   8.394  1.00 25.00           C
ATOM     59  CA  VAL    59      19.597   5.136   6.122  1.00 25.00           C
ATOM     60  CA  LEU    60      22.574   4.581   3.778  1.00 25.00           C
ATOM     61  CA  THR    61      21.817   0.828   3.665  1.00 25.00           C
ATOM     62  CA  VAL    62      18.148   1.568   2.849  1.00 25.00           C
ATOM     63  CA  ALA    63      19.225   3.944   0.045  1.00 25.00           C
ATOM     64  CA  ALA    64      21.566   1.260  -1.364  1.00 25.00           C
ATOM     65  CA  GLU    65      18.722  -1.303  -1.271  1.00 25.00           C
ATOM     66  CA  LEU    66      16.416   1.152  -3.093  1.00 25.00           C
ATOM     67  CA  GLY    67      18.457   0.022  -6.117  1.00 25.00           C
ATOM     68  CA  ASN    68      21.156  -1.474  -8.395  1.00 25.00           C
ATOM     69  CA  ASN    69      23.600   1.219  -9.596  1.00 25.00           C
ATOM     70  CA  ALA    70      27.395   1.088  -9.877  1.00 25.00           C
ATOM     71  CA  LEU    71      30.117   0.097  -7.387  1.00 25.00           C
ATOM     72  CA  PRO    72      30.481  -3.513  -8.706  1.00 25.00           C
ATOM     73  CA  PRO    73      31.265  -6.378 -11.107  1.00 25.00           C
ATOM     74  CA  THR    74      31.830  -8.283  -7.842  1.00 25.00           C
ATOM     75  CA  LYS    75      32.817 -11.941  -8.175  1.00 25.00           C
ATOM     76  CA  PRO    76      31.829 -12.956  -4.645  1.00 25.00           C
ATOM     77  CA  SER    77      34.300 -10.486  -3.218  1.00 25.00           C
ATOM     78  CA  PHE    78      33.994 -12.635  -0.149  1.00 25.00           C
ATOM     79  CA  PRO    79      33.087 -16.355  -0.568  1.00 25.00           C
ATOM     80  CA  SER    80      32.278 -16.808   3.077  1.00 25.00           C
ATOM     81  CA  SER    81      30.028 -17.968   5.911  1.00 25.00           C
ATOM     82  CA  ILE    82      32.159 -16.030   8.419  1.00 25.00           C
ATOM     83  CA  GLN    83      30.532 -15.801  11.774  1.00 25.00           C
ATOM     84  CA  GLU    84      31.045 -15.619  15.515  1.00 25.00           C
ATOM     85  CA  LEU    85      31.590 -11.923  16.093  1.00 25.00           C
ATOM     86  CA  THR    86      31.211  -8.889  13.777  1.00 25.00           C
ATOM     87  CA  ASP    87      33.091  -5.655  14.596  1.00 25.00           C
ATOM     88  CA  ASP    88      31.829  -4.069  11.347  1.00 25.00           C
ATOM     89  CA  ASP    89      28.244  -5.114  12.201  1.00 25.00           C
ATOM     90  CA  MET    90      28.608  -3.597  15.698  1.00 25.00           C
ATOM     91  CA  ALA    91      29.923  -0.339  14.174  1.00 25.00           C
ATOM     92  CA  ILE    92      26.960  -0.247  11.750  1.00 25.00           C
ATOM     93  CA  LEU    93      24.531  -0.798  14.660  1.00 25.00           C
ATOM     94  CA  ASN    94      26.194   2.042  16.618  1.00 25.00           C
ATOM     95  CA  ASP    95      25.902   4.346  13.572  1.00 25.00           C
ATOM     96  CA  LEU    96      22.196   3.445  13.216  1.00 25.00           C
ATOM     97  CA  HIS    97      21.633   4.195  16.930  1.00 25.00           C
ATOM     98  CA  THR    98      23.391   7.575  16.540  1.00 25.00           C
ATOM     99  CA  LEU    99      21.201   8.392  13.507  1.00 25.00           C
ATOM    100  CA  LEU   100      18.060   7.468  15.495  1.00 25.00           C
ATOM    101  CA  LEU   101      19.198   9.712  18.383  1.00 25.00           C
ATOM    102  CA  GLN   102      19.800  12.596  15.936  1.00 25.00           C
ATOM    103  CA  THR   103      17.466  11.795  13.056  1.00 25.00           C
ATOM    104  CA  SER   104      14.703  14.183  11.994  1.00 25.00           C
ATOM    105  CA  ILE   105      10.986  13.969  12.436  1.00 25.00           C
ATOM    106  CA  ALA   106       8.806  14.935  15.338  1.00 25.00           C
ATOM    107  CA  GLU   107       5.207  13.787  15.778  1.00 25.00           C
ATOM    108  CA  GLY   108       6.458  11.904  18.835  1.00 25.00           C
ATOM    109  CA  GLU   109       8.668   9.151  17.390  1.00 25.00           C
ATOM    110  CA  MET   110       8.333   5.496  16.639  1.00 25.00           C
ATOM    111  CA  LYS   111       9.542   3.006  19.234  1.00 25.00           C
ATOM    112  CA  CYS   112      12.540   0.624  18.929  1.00 25.00           C
ATOM    113  CA  ARG   113      13.198  -0.164  22.638  1.00 25.00           C
ATOM    114  CA  ASN   114      15.712  -2.445  24.351  1.00 25.00           C
ATOM    115  CA  CYS   115      18.011  -0.318  22.199  1.00 25.00           C
ATOM    116  CA  GLY   116      17.829   3.032  23.929  1.00 25.00           C
ATOM    117  CA  HIS   117      18.047   4.733  20.542  1.00 25.00           C
ATOM    118  CA  ILE   118      14.390   5.463  19.793  1.00 25.00           C
ATOM    119  CA  TYR   119      14.237   9.240  19.511  1.00 25.00           C
ATOM    120  CA  TYR   120      12.715  12.554  18.467  1.00 25.00           C
ATOM    121  CA  ILE   121      15.682  14.241  20.242  1.00 25.00           C
ATOM    122  CA  LYS   122      16.923  16.661  22.901  1.00 25.00           C
ATOM    123  CA  ASN   123      17.482  20.045  24.569  1.00 25.00           C
ATOM    124  CA  GLY   124      18.315  22.720  27.113  1.00 25.00           C
ATOM    125  CA  ILE   125      17.935  26.374  28.199  1.00 25.00           C
ATOM    126  CA  PRO   126      15.363  27.951  25.881  1.00 25.00           C
ATOM    127  CA  ASN   127      12.845  26.194  28.109  1.00 25.00           C
ATOM    128  CA  LEU   128      10.292  27.185  25.559  1.00 25.00           C
ATOM    129  CA  LEU   129       8.512  30.493  25.064  1.00 25.00           C
ATOM    130  CA  LEU   130       4.787  29.956  25.215  1.00 25.00           C
ATOM    131  CA  PRO   131       2.115  29.405  22.475  1.00 25.00           C
ATOM    132  CA  PRO   132       0.576  32.729  23.377  1.00 25.00           C
ATOM    133  CA  HIS   133       1.165  35.654  21.108  1.00 25.00           C
ATOM    134  CA  LEU   134      -0.124  37.821  18.201  1.00 25.00           C
ATOM    135  CA  VAL   135       3.409  39.126  17.686  1.00 25.00           C
TER
END
