
#######################################################
#                                                     #
#                        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   29 (  145),  selected   29 , name T0320TS239_5_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS239_5_1-D1.T0320_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    Q       2      -       -           -
LGA    S       4      -       -           -
LGA    K       5      M       1          5.203
LGA    A       6      Q       2           -
LGA    A       7      L       3           -
LGA    E       8      S       4           #
LGA    M       9      K       5          2.012
LGA    C      10      A       6          4.554
LGA    Y      11      A       7          1.468
LGA    -       -      E       8           -
LGA    -       -      M       9           -
LGA    -       -      C      10           -
LGA    E      12      Y      11          1.898
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    I      13      T      14          2.882
LGA    -       -      N      15           -
LGA    T      14      S      16          4.184
LGA    N      15      Y      17          3.241
LGA    -       -      L      18           -
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      S      29           -
LGA    -       -      T      30           -
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    S      16      A      33           #
LGA    T      30      I      34          1.243
LGA    Q      31      R      35          1.264
LGA    E      32      L      36          1.815
LGA    A      33      T      37          1.576
LGA    I      34      R      38          0.694
LGA    R      35      K      39          0.988
LGA    L      36      Y      40          1.145
LGA    T      37      L      41          1.194
LGA    R      38      L      42          0.924
LGA    K      39      S      43          1.586
LGA    Y      40      E      44          2.445
LGA    L      41      I      45          2.452
LGA    -       -      F      46           -
LGA    L      42      V      47          0.707
LGA    S      43      R      48          2.088
LGA    -       -      W      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      L      52           -
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      F      58           -
LGA    -       -      S      59           -
LGA    -       -      Y      60           -
LGA    -       -      N      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      K      64           -
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    -       -      Q      67           -
LGA    -       -      V      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      L      71           -
LGA    -       -      L      72           -
LGA    -       -      Y      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      C      76           -
LGA    -       -      L      77           -
LGA    -       -      W      78           -
LGA    -       -      E      79           -
LGA    -       -      Y      80           -
LGA    -       -      F      81           -
LGA    -       -      F      82           -
LGA    -       -      I      83           -
LGA    -       -      K      84           -
LGA    -       -      A      85           -
LGA    -       -      Q      86           -
LGA    -       -      N      87           -
LGA    -       -      S      88           -
LGA    -       -      F      97           -
LGA    -       -      P      98           -
LGA    -       -      M      99           -
LGA    -       -      Q     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      P     103           -
LGA    -       -      T     104           -
LGA    -       -      V     105           -
LGA    -       -      F     106           -
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    -       -      E     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      S     124           -
LGA    -       -      E     125           -
LGA    -       -      R     126           -
LGA    -       -      Y     127           -
LGA    -       -      C     128           -
LGA    -       -      L     129           -
LGA    -       -      S     130           -
LGA    -       -      L     131           -
LGA    -       -      Y     132           -
LGA    -       -      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    -       -      A     145           -
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      D     150           -
LGA    -       -      F     151           -
LGA    -       -      I     152           -
LGA    -       -      K     153           -
LGA    -       -      I     154           -
LGA    -       -      Y     155           -
LGA    -       -      P     156           -
LGA    -       -      E     157           -
LGA    -       -      T     158           -
LGA    -       -      E     159           -
LGA    -       -      A     160           -
LGA    -       -      I     161           -
LGA    -       -      V     162           -
LGA    -       -      I     163           -
LGA    -       -      G     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      H     167           -
LGA    -       -      T     168           -
LGA    -       -      D     169           -
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
LGA    -       -      I     178           -
LGA    -       -      Q     179           -
LGA    -       -      R     180           -
LGA    -       -      T     181           -
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    -       -      F     188           -
LGA    -       -      M     189           -
LGA    -       -      R     190           -
LGA    -       -      L     191           -
LGA    -       -      Q     192           -
LGA    -       -      P     193           -
LGA    -       -      L     194           -
LGA    -       -      L     195           -
LGA    -       -      H     196           -
LGA    -       -      W     197           -
LGA    -       -      D     198           -
LGA    -       -      L     199           -
LGA    -       -      T     200           -
LGA    -       -      N     201           -
LGA    -       -      I     202           -
LGA    -       -      W     203           -
LGA    -       -      S     204           -
LGA    -       -      F     205           -
LGA    -       -      L     206           -
LGA    -       -      L     207           -
LGA    -       -      Y     208           -
LGA    -       -      S     209           -
LGA    -       -      N     210           -
LGA    -       -      E     211           -
LGA    -       -      P     212           -
LGA    -       -      I     213           -
LGA    -       -      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    -       -      Y     217           -
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      I     224           -
LGA    -       -      G     225           -
LGA    -       -      G     226           -
LGA    -       -      I     227           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   29  214    5.0     22    2.41     0.00      7.870     0.878

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.546321 * X  +   0.692961 * Y  +  -0.470467 * Z  + -18.571606
  Y_new =   0.092993 * X  +  -0.508044 * Y  +  -0.856296 * Z  + 104.715034
  Z_new =  -0.832398 * X  +  -0.511562 * Y  +   0.213115 * Z  +  76.498482 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.176066    1.965527  [ DEG:   -67.3836    112.6164 ]
  Theta =   0.983420    2.158172  [ DEG:    56.3458    123.6542 ]
  Phi   =   2.972991   -0.168601  [ DEG:   170.3399     -9.6601 ]
 
# 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: T0320TS239_5_1-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS239_5_1-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29  214   5.0   22   2.41    0.00   7.870
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS239_5_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 2nsy_A
ATOM      1  N   MET     1      -1.248  41.254  16.989  1.00  9.99
ATOM      2  CA  MET     1      -1.067  41.594  18.418  1.00  9.99
ATOM      3  C   MET     1      -1.322  40.325  19.237  1.00  9.99
ATOM      4  O   MET     1      -0.630  40.212  20.273  1.00  9.99
ATOM      5  CB  MET     1      -1.972  42.722  18.858  1.00  9.99
ATOM      6  N   GLN     2      -2.129  39.408  18.766  1.00  9.99
ATOM      7  CA  GLN     2      -2.317  38.148  19.484  1.00  9.99
ATOM      8  C   GLN     2      -1.015  37.412  19.654  1.00  9.99
ATOM      9  O   GLN     2      -0.642  36.897  20.745  1.00  9.99
ATOM     10  CB  GLN     2      -3.439  37.327  18.835  1.00  9.99
ATOM     11  N   SER     4      -0.279  37.244  18.566  1.00  9.99
ATOM     12  CA  SER     4       1.007  36.578  18.568  1.00  9.99
ATOM     13  C   SER     4       2.002  37.293  19.432  1.00  9.99
ATOM     14  O   SER     4       2.792  36.688  20.189  1.00  9.99
ATOM     15  CB  SER     4       1.579  36.495  17.134  1.00  9.99
ATOM     16  N   LYS     5       2.014  38.605  19.456  1.00  9.99
ATOM     17  CA  LYS     5       2.887  39.414  20.245  1.00  9.99
ATOM     18  C   LYS     5       2.572  39.142  21.728  1.00  9.99
ATOM     19  O   LYS     5       3.468  38.950  22.555  1.00  9.99
ATOM     20  CB  LYS     5       2.805  40.883  19.957  1.00  9.99
ATOM     21  N   ALA     6       1.311  39.228  22.141  1.00  9.99
ATOM     22  CA  ALA     6       0.940  39.044  23.542  1.00  9.99
ATOM     23  C   ALA     6       1.248  37.623  23.981  1.00  9.99
ATOM     24  O   ALA     6       1.822  37.441  25.079  1.00  9.99
ATOM     25  CB  ALA     6      -0.555  39.313  23.714  1.00  9.99
ATOM     26  N   ALA     7       1.050  36.632  23.123  1.00  9.99
ATOM     27  CA  ALA     7       1.429  35.261  23.436  1.00  9.99
ATOM     28  C   ALA     7       2.875  35.188  23.739  1.00  9.99
ATOM     29  O   ALA     7       3.347  34.501  24.678  1.00  9.99
ATOM     30  CB  ALA     7       1.169  34.372  22.231  1.00  9.99
ATOM     31  N   GLU     8       3.757  35.804  22.930  1.00  9.99
ATOM     32  CA  GLU     8       5.197  35.764  23.134  1.00  9.99
ATOM     33  C   GLU     8       5.574  36.458  24.400  1.00  9.99
ATOM     34  O   GLU     8       6.403  36.027  25.247  1.00  9.99
ATOM     35  CB  GLU     8       5.965  36.354  21.921  1.00  9.99
ATOM     36  N   MET     9       4.991  37.629  24.662  1.00  9.99
ATOM     37  CA  MET     9       5.317  38.439  25.813  1.00  9.99
ATOM     38  C   MET     9       4.929  37.706  27.111  1.00  9.99
ATOM     39  O   MET     9       5.625  37.920  28.118  1.00  9.99
ATOM     40  CB  MET     9       4.677  39.835  25.728  1.00  9.99
ATOM     41  N   CYS    10       3.843  36.993  27.093  1.00  9.99
ATOM     42  CA  CYS    10       3.361  36.302  28.311  1.00  9.99
ATOM     43  C   CYS    10       3.904  34.892  28.387  1.00  9.99
ATOM     44  O   CYS    10       3.510  34.143  29.320  1.00  9.99
ATOM     45  CB  CYS    10       1.840  36.368  28.349  1.00  9.99
ATOM     46  N   TYR    11       4.718  34.470  27.415  1.00  9.99
ATOM     47  CA  TYR    11       5.388  33.146  27.463  1.00  9.99
ATOM     48  C   TYR    11       4.434  32.040  27.256  1.00  9.99
ATOM     49  O   TYR    11       4.612  30.892  27.837  1.00  9.99
ATOM     50  CB  TYR    11       6.332  33.070  28.663  1.00  9.99
ATOM     51  N   GLU    12       3.337  32.047  26.527  1.00  9.99
ATOM     52  CA  GLU    12       2.335  31.079  26.385  1.00  9.99
ATOM     53  C   GLU    12       2.497  30.038  25.243  1.00  9.99
ATOM     54  O   GLU    12       2.750  30.457  24.086  1.00  9.99
ATOM     55  CB  GLU    12       0.930  31.661  26.150  1.00  9.99
ATOM     56  N   ILE    13       2.294  28.756  25.447  1.00  9.99
ATOM     57  CA  ILE    13       2.228  27.723  24.393  1.00  9.99
ATOM     58  C   ILE    13       0.852  27.346  23.997  1.00  9.99
ATOM     59  O   ILE    13      -0.038  27.229  24.787  1.00  9.99
ATOM     60  CB  ILE    13       2.753  26.366  24.957  1.00  9.99
ATOM     61  N   THR    14       0.617  27.033  22.697  1.00  9.99
ATOM     62  CA  THR    14      -0.651  26.623  22.170  1.00  9.99
ATOM     63  C   THR    14      -0.945  25.205  22.691  1.00  9.99
ATOM     64  O   THR    14      -2.031  24.837  22.921  1.00  9.99
ATOM     65  CB  THR    14      -0.531  26.477  20.632  1.00  9.99
ATOM     66  N   ASN    15       0.282  24.604  22.838  1.00  9.99
ATOM     67  CA  ASN    15       0.630  23.260  23.151  1.00  9.99
ATOM     68  C   ASN    15       1.790  23.012  24.201  1.00  9.99
ATOM     69  O   ASN    15       2.926  23.407  23.979  1.00  9.99
ATOM     70  CB  ASN    15       1.112  22.528  21.853  1.00  9.99
ATOM     71  N   SER    16       1.280  22.279  25.182  1.00  9.99
ATOM     72  CA  SER    16       2.142  21.809  26.287  1.00  9.99
ATOM     73  C   SER    16       1.894  20.279  26.525  1.00  9.99
ATOM     74  O   SER    16       0.965  19.522  26.293  1.00  9.99
ATOM     75  CB  SER    16       1.898  22.583  27.606  1.00  9.99
ATOM     76  N   THR    30       2.977  19.875  27.231  1.00  9.99
ATOM     77  CA  THR    30       3.114  18.490  27.784  1.00  9.99
ATOM     78  C   THR    30       3.011  18.710  29.297  1.00  9.99
ATOM     79  O   THR    30       3.949  19.270  29.918  1.00  9.99
ATOM     80  CB  THR    30       4.488  18.007  27.380  1.00  9.99
ATOM     81  N   GLN    31       2.013  18.205  29.949  1.00  9.99
ATOM     82  CA  GLN    31       1.754  18.502  31.364  1.00  9.99
ATOM     83  C   GLN    31       2.853  17.996  32.260  1.00  9.99
ATOM     84  O   GLN    31       3.266  18.730  33.172  1.00  9.99
ATOM     85  CB  GLN    31       0.421  17.839  31.729  1.00  9.99
ATOM     86  N   GLU    32       3.417  16.807  32.053  1.00  9.99
ATOM     87  CA  GLU    32       4.452  16.298  32.909  1.00  9.99
ATOM     88  C   GLU    32       5.685  17.148  32.763  1.00  9.99
ATOM     89  O   GLU    32       6.390  17.408  33.727  1.00  9.99
ATOM     90  CB  GLU    32       4.733  14.807  32.601  1.00  9.99
ATOM     91  N   ALA    33       6.053  17.563  31.540  1.00  9.99
ATOM     92  CA  ALA    33       7.206  18.392  31.350  1.00  9.99
ATOM     93  C   ALA    33       7.005  19.766  32.034  1.00  9.99
ATOM     94  O   ALA    33       7.947  20.306  32.554  1.00  9.99
ATOM     95  CB  ALA    33       7.598  18.572  29.866  1.00  9.99
ATOM     96  N   ILE    34       5.793  20.311  31.909  1.00  9.99
ATOM     97  CA  ILE    34       5.522  21.623  32.557  1.00  9.99
ATOM     98  C   ILE    34       5.776  21.545  34.073  1.00  9.99
ATOM     99  O   ILE    34       6.366  22.440  34.637  1.00  9.99
ATOM    100  CB  ILE    34       4.090  22.084  32.291  1.00  9.99
ATOM    101  N   ARG    35       5.284  20.451  34.660  1.00  9.99
ATOM    102  CA  ARG    35       5.511  20.261  36.116  1.00  9.99
ATOM    103  C   ARG    35       6.957  20.149  36.465  1.00  9.99
ATOM    104  O   ARG    35       7.485  20.813  37.330  1.00  9.99
ATOM    105  CB  ARG    35       4.713  19.034  36.596  1.00  9.99
ATOM    106  N   LEU    36       7.707  19.345  35.659  1.00  9.99
ATOM    107  CA  LEU    36       9.130  19.222  35.866  1.00  9.99
ATOM    108  C   LEU    36       9.861  20.538  35.767  1.00  9.99
ATOM    109  O   LEU    36      10.696  20.953  36.529  1.00  9.99
ATOM    110  CB  LEU    36       9.694  18.201  34.870  1.00  9.99
ATOM    111  N   THR    37       9.521  21.320  34.708  1.00  9.99
ATOM    112  CA  THR    37      10.184  22.568  34.467  1.00  9.99
ATOM    113  C   THR    37       9.953  23.584  35.635  1.00  9.99
ATOM    114  O   THR    37      10.784  24.330  36.005  1.00  9.99
ATOM    115  CB  THR    37       9.702  23.217  33.169  1.00  9.99
ATOM    116  N   ARG    38       8.706  23.566  36.137  1.00  9.99
ATOM    117  CA  ARG    38       8.306  24.581  37.134  1.00  9.99
ATOM    118  C   ARG    38       8.849  24.217  38.511  1.00  9.99
ATOM    119  O   ARG    38       9.347  25.079  39.225  1.00  9.99
ATOM    120  CB  ARG    38       6.798  24.813  37.022  1.00  9.99
ATOM    121  N   LYS    39       8.837  22.911  38.820  1.00  9.99
ATOM    122  CA  LYS    39       9.527  22.467  40.042  1.00  9.99
ATOM    123  C   LYS    39      11.030  22.756  39.918  1.00  9.99
ATOM    124  O   LYS    39      11.646  23.257  40.848  1.00  9.99
ATOM    125  CB  LYS    39       9.277  20.969  40.274  1.00  9.99
ATOM    126  N   TYR    40      11.604  22.479  38.735  1.00  9.99
ATOM    127  CA  TYR    40      13.043  22.700  38.565  1.00  9.99
ATOM    128  C   TYR    40      13.414  24.163  38.679  1.00  9.99
ATOM    129  O   TYR    40      14.439  24.502  39.236  1.00  9.99
ATOM    130  CB  TYR    40      13.522  22.126  37.241  1.00  9.99
ATOM    131  N   LEU    41      12.529  25.064  38.214  1.00  9.99
ATOM    132  CA  LEU    41      12.744  26.480  38.396  1.00  9.99
ATOM    133  C   LEU    41      12.776  26.882  39.848  1.00  9.99
ATOM    134  O   LEU    41      13.668  27.595  40.308  1.00  9.99
ATOM    135  CB  LEU    41      11.613  27.238  37.674  1.00  9.99
ATOM    136  N   LEU    42      11.795  26.385  40.634  1.00  9.99
ATOM    137  CA  LEU    42      11.772  26.690  42.058  1.00  9.99
ATOM    138  C   LEU    42      13.054  26.216  42.701  1.00  9.99
ATOM    139  O   LEU    42      13.658  26.890  43.529  1.00  9.99
ATOM    140  CB  LEU    42      10.550  26.120  42.746  1.00  9.99
ATOM    141  N   SER    43      13.515  24.989  42.385  1.00  9.99
ATOM    142  CA  SER    43      14.767  24.481  42.954  1.00  9.99
ATOM    143  C   SER    43      15.979  25.300  42.479  1.00  9.99
ATOM    144  O   SER    43      16.818  25.573  43.351  1.00  9.99
ATOM    145  CB  SER    43      14.937  23.013  42.535  1.00  9.99
TER
END
