
#######################################################
#                                                     #
#                        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   31 (  155),  selected   31 , name T0297TS239_5_2
# Molecule2: number of CA atoms  211 ( 1703),  selected  211 , name T0297.pdb
# PARAMETERS: T0297TS239_5_2.T0297.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      A       2           -
LGA    -       -      V       3           -
LGA    -       -      Q       4           -
LGA    -       -      L       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      N       8           -
LGA    -       -      W       9           -
LGA    -       -      L      10           -
LGA    -       -      L      11           -
LGA    -       -      K      12           -
LGA    -       -      E      13           -
LGA    -       -      Q      14           -
LGA    M       1      E      15          2.119
LGA    A       2      K      16          2.542
LGA    V       3      I      17          3.872
LGA    -       -      Q      18           -
LGA    -       -      T      19           -
LGA    -       -      K      20           -
LGA    -       -      Y      21           -
LGA    -       -      R      22           -
LGA    -       -      H      23           -
LGA    -       -      L      24           -
LGA    -       -      N      25           -
LGA    -       -      H      26           -
LGA    -       -      I      27           -
LGA    -       -      S      28           -
LGA    -       -      V      29           -
LGA    -       -      V      30           -
LGA    -       -      E      31           -
LGA    -       -      P      32           -
LGA    -       -      N      33           -
LGA    -       -      I      34           -
LGA    -       -      L      35           -
LGA    -       -      F      36           -
LGA    -       -      I      37           -
LGA    -       -      G      38           -
LGA    -       -      D      39           -
LGA    -       -      S      40           -
LGA    -       -      I      41           -
LGA    -       -      V      42           -
LGA    -       -      E      43           -
LGA    -       -      Y      44           -
LGA    -       -      Y      45           -
LGA    -       -      P      46           -
LGA    -       -      L      47           -
LGA    -       -      Q      48           -
LGA    -       -      E      49           -
LGA    -       -      L      50           -
LGA    -       -      F      51           -
LGA    -       -      G      52           -
LGA    -       -      T      53           -
LGA    -       -      S      54           -
LGA    -       -      K      55           -
LGA    -       -      T      56           -
LGA    -       -      I      57           -
LGA    -       -      V      58           -
LGA    -       -      N      59           -
LGA    -       -      R      60           -
LGA    -       -      G      61           -
LGA    Q       4      I      62          2.552
LGA    L       5      R      63          4.866
LGA    -       -      G      64           -
LGA    L       6      Y      65          3.318
LGA    E       7      Q      66          1.549
LGA    -       -      T      67           -
LGA    -       -      G      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      L      71           -
LGA    -       -      E      72           -
LGA    -       -      N      73           -
LGA    -       -      L      74           -
LGA    -       -      D      75           -
LGA    -       -      A      76           -
LGA    -       -      H      77           -
LGA    -       -      L      78           -
LGA    -       -      Y      79           -
LGA    -       -      G      80           -
LGA    -       -      G      81           -
LGA    -       -      A      82           -
LGA    -       -      V      83           -
LGA    -       -      D      84           -
LGA    -       -      K      85           -
LGA    -       -      I      86           -
LGA    -       -      F      87           -
LGA    -       -      L      88           -
LGA    -       -      L      89           -
LGA    -       -      I      90           -
LGA    -       -      G      91           -
LGA    -       -      T      92           -
LGA    -       -      N      93           -
LGA    N       8      D      94          2.366
LGA    W       9      I      95          5.119
LGA    -       -      G      96           -
LGA    -       -      K      97           -
LGA    L      10      D      98          3.164
LGA    -       -      V      99           -
LGA    L      11      P     100          0.801
LGA    K      12      V     101          0.697
LGA    E      13      N     102          1.504
LGA    -       -      E     103           -
LGA    -       -      A     104           -
LGA    Q      14      L     105          1.553
LGA    E      15      N     106          1.782
LGA    K      16      N     107          1.587
LGA    I      17      L     108          1.621
LGA    Q      18      E     109          1.573
LGA    T      19      A     110          1.282
LGA    K      20      I     111          1.205
LGA    Y      21      I     112          1.267
LGA    R      22      Q     113          1.233
LGA    H      23      S     114          0.940
LGA    L      24      V     115          1.088
LGA    N      25      A     116          1.026
LGA    H      26      R     117          1.411
LGA    I      27      D     118          1.127
LGA    S      28      Y     119          1.670
LGA    V      29      P     120          2.610
LGA    V      30      L     121           -
LGA    E      31      T     122           -
LGA    -       -      E     123           -
LGA    -       -      I     124           -
LGA    -       -      K     125           -
LGA    -       -      L     126           -
LGA    -       -      L     127           -
LGA    -       -      S     128           -
LGA    -       -      I     129           -
LGA    -       -      L     130           -
LGA    -       -      P     131           -
LGA    -       -      V     132           -
LGA    -       -      N     133           -
LGA    -       -      E     134           -
LGA    -       -      R     135           -
LGA    -       -      E     136           -
LGA    -       -      E     137           -
LGA    -       -      Y     138           -
LGA    -       -      Q     139           -
LGA    -       -      Q     140           -
LGA    -       -      A     141           -
LGA    -       -      V     142           -
LGA    -       -      Y     143           -
LGA    -       -      I     144           -
LGA    -       -      R     145           -
LGA    -       -      S     146           -
LGA    -       -      N     147           -
LGA    -       -      E     148           -
LGA    -       -      K     149           -
LGA    -       -      I     150           -
LGA    -       -      Q     151           -
LGA    -       -      N     152           -
LGA    -       -      W     153           -
LGA    -       -      N     154           -
LGA    -       -      Q     155           -
LGA    -       -      A     156           -
LGA    -       -      Y     157           -
LGA    -       -      Q     158           -
LGA    -       -      E     159           -
LGA    -       -      L     160           -
LGA    -       -      A     161           -
LGA    -       -      S     162           -
LGA    -       -      A     163           -
LGA    -       -      Y     164           -
LGA    -       -      M     165           -
LGA    -       -      Q     166           -
LGA    -       -      V     167           -
LGA    -       -      E     168           -
LGA    -       -      F     169           -
LGA    -       -      V     170           -
LGA    -       -      P     171           -
LGA    -       -      V     172           -
LGA    -       -      F     173           -
LGA    -       -      D     174           -
LGA    -       -      C     175           -
LGA    -       -      L     176           -
LGA    -       -      T     177           -
LGA    -       -      D     178           -
LGA    -       -      Q     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      K     184           -
LGA    -       -      K     185           -
LGA    -       -      E     186           -
LGA    -       -      Y     187           -
LGA    -       -      T     188           -
LGA    -       -      T     189           -
LGA    -       -      D     190           -
LGA    -       -      G     191           -
LGA    -       -      L     192           -
LGA    -       -      H     193           -
LGA    -       -      L     194           -
LGA    -       -      S     195           -
LGA    -       -      I     196           -
LGA    -       -      A     197           -
LGA    -       -      G     198           -
LGA    -       -      Y     199           -
LGA    -       -      Q     200           -
LGA    -       -      A     201           -
LGA    -       -      L     202           -
LGA    -       -      S     203           -
LGA    -       -      K     204           -
LGA    -       -      S     205           -
LGA    -       -      L     206           -
LGA    -       -      K     207           -
LGA    -       -      D     208           -
LGA    -       -      Y     209           -
LGA    -       -      L     210           -
LGA    -       -      Y     211           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   31  211    5.0     29    2.28     0.00     11.221     1.221

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.833176 * X  +  -0.134184 * Y  +   0.536481 * Z  + -27.238558
  Y_new =  -0.325411 * X  +  -0.903341 * Y  +   0.279433 * Z  +  77.148926
  Z_new =   0.447130 * X  +  -0.407394 * Y  +  -0.796307 * Z  +  -6.161305 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.668705    0.472888  [ DEG:  -152.9055     27.0945 ]
  Theta =  -0.463554   -2.678039  [ DEG:   -26.5597   -153.4403 ]
  Phi   =  -0.372348    2.769244  [ DEG:   -21.3340    158.6660 ]
 
# 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: T0297TS239_5_2                                
REMARK     2: T0297.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0297TS239_5_2.T0297.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31  211   5.0   29   2.28    0.00  11.221
REMARK  ---------------------------------------------------------- 
MOLECULE T0297TS239_5_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0297
PARENT 1wab
ATOM      1  N   MET     1      19.809  85.199   1.129  1.00  9.99
ATOM      2  CA  MET     1      21.039  84.722   1.823  1.00  9.99
ATOM      3  C   MET     1      20.990  84.970   3.339  1.00  9.99
ATOM      4  O   MET     1      21.791  84.340   4.056  1.00  9.99
ATOM      5  CB  MET     1      22.261  85.391   1.193  1.00  9.99
ATOM      6  N   ALA     2      20.086  85.873   3.754  1.00  9.99
ATOM      7  CA  ALA     2      20.039  86.218   5.192  1.00  9.99
ATOM      8  C   ALA     2      18.691  85.826   5.773  1.00  9.99
ATOM      9  O   ALA     2      18.479  86.249   6.934  1.00  9.99
ATOM     10  CB  ALA     2      20.418  87.689   5.386  1.00  9.99
ATOM     11  N   VAL     3      17.878  85.101   5.027  1.00  9.99
ATOM     12  CA  VAL     3      16.588  84.632   5.626  1.00  9.99
ATOM     13  C   VAL     3      16.864  83.210   6.085  1.00  9.99
ATOM     14  O   VAL     3      16.963  82.325   5.241  1.00  9.99
ATOM     15  CB  VAL     3      15.533  84.682   4.543  1.00  9.99
ATOM     16  N   GLN     4      16.862  82.975   7.386  1.00  9.99
ATOM     17  CA  GLN     4      17.261  81.631   7.870  1.00  9.99
ATOM     18  C   GLN     4      16.283  80.584   7.393  1.00  9.99
ATOM     19  O   GLN     4      15.068  80.798   7.509  1.00  9.99
ATOM     20  CB  GLN     4      17.361  81.766   9.394  1.00  9.99
ATOM     21  N   LEU     5      16.815  79.481   6.878  1.00  9.99
ATOM     22  CA  LEU     5      15.939  78.409   6.398  1.00  9.99
ATOM     23  C   LEU     5      16.732  77.124   6.424  1.00  9.99
ATOM     24  O   LEU     5      17.967  77.165   6.186  1.00  9.99
ATOM     25  CB  LEU     5      15.384  78.728   4.966  1.00  9.99
ATOM     26  N   LEU     6      16.088  76.051   6.799  1.00  9.99
ATOM     27  CA  LEU     6      16.761  74.763   6.817  1.00  9.99
ATOM     28  C   LEU     6      16.838  74.217   5.403  1.00  9.99
ATOM     29  O   LEU     6      16.120  74.695   4.510  1.00  9.99
ATOM     30  CB  LEU     6      15.907  73.880   7.733  1.00  9.99
ATOM     31  N   GLU     7      17.713  73.233   5.220  1.00  9.99
ATOM     32  CA  GLU     7      17.667  72.526   3.895  1.00  9.99
ATOM     33  C   GLU     7      16.483  71.577   3.909  1.00  9.99
ATOM     34  O   GLU     7      16.338  70.695   4.782  1.00  9.99
ATOM     35  CB  GLU     7      19.021  71.874   3.647  1.00  9.99
ATOM     36  N   ASN     8      15.705  71.689   2.840  1.00  9.99
ATOM     37  CA  ASN     8      14.516  70.818   2.662  1.00  9.99
ATOM     38  C   ASN     8      14.995  69.454   2.167  1.00  9.99
ATOM     39  O   ASN     8      15.809  69.435   1.213  1.00  9.99
ATOM     40  CB  ASN     8      13.619  71.452   1.590  1.00  9.99
ATOM     41  N   TRP     9      14.450  68.398   2.753  1.00  9.99
ATOM     42  CA  TRP     9      14.869  67.048   2.361  1.00  9.99
ATOM     43  C   TRP     9      14.099  66.678   1.071  1.00  9.99
ATOM     44  O   TRP     9      12.852  66.481   1.202  1.00  9.99
ATOM     45  CB  TRP     9      14.650  66.039   3.479  1.00  9.99
ATOM     46  N   LEU    10      14.807  66.658  -0.054  1.00  9.99
ATOM     47  CA  LEU    10      14.086  66.157  -1.261  1.00  9.99
ATOM     48  C   LEU    10      14.606  64.789  -1.693  1.00  9.99
ATOM     49  O   LEU    10      14.334  64.414  -2.862  1.00  9.99
ATOM     50  CB  LEU    10      14.169  67.175  -2.395  1.00  9.99
ATOM     51  N   LEU    11      15.370  64.143  -0.817  1.00  9.99
ATOM     52  CA  LEU    11      16.017  62.851  -1.195  1.00  9.99
ATOM     53  C   LEU    11      15.324  61.787  -0.355  1.00  9.99
ATOM     54  O   LEU    11      15.031  60.662  -0.867  1.00  9.99
ATOM     55  CB  LEU    11      17.533  62.884  -1.014  1.00  9.99
ATOM     56  N   LYS    12      15.183  61.999   0.954  1.00  9.99
ATOM     57  CA  LYS    12      14.324  61.106   1.780  1.00  9.99
ATOM     58  C   LYS    12      15.030  60.498   2.965  1.00  9.99
ATOM     59  O   LYS    12      14.320  59.876   3.826  1.00  9.99
ATOM     60  CB  LYS    12      13.751  59.991   0.888  1.00  9.99
ATOM     61  N   GLU    13      16.334  60.719   3.159  1.00  9.99
ATOM     62  CA  GLU    13      17.062  60.051   4.250  1.00  9.99
ATOM     63  C   GLU    13      17.319  61.009   5.440  1.00  9.99
ATOM     64  O   GLU    13      17.943  60.507   6.425  1.00  9.99
ATOM     65  CB  GLU    13      18.346  59.418   3.697  1.00  9.99
ATOM     66  N   GLN    14      16.914  62.258   5.331  1.00  9.99
ATOM     67  CA  GLN    14      16.934  63.147   6.534  1.00  9.99
ATOM     68  C   GLN    14      18.358  63.461   6.979  1.00  9.99
ATOM     69  O   GLN    14      18.516  63.871   8.178  1.00  9.99
ATOM     70  CB  GLN    14      16.144  62.488   7.677  1.00  9.99
ATOM     71  N   GLU    15      19.383  63.423   6.120  1.00  9.99
ATOM     72  CA  GLU    15      20.748  63.519   6.630  1.00  9.99
ATOM     73  C   GLU    15      21.065  64.917   7.170  1.00  9.99
ATOM     74  O   GLU    15      21.842  64.994   8.135  1.00  9.99
ATOM     75  CB  GLU    15      21.786  63.152   5.521  1.00  9.99
ATOM     76  N   LYS    16      20.559  65.945   6.485  1.00  9.99
ATOM     77  CA  LYS    16      20.918  67.308   6.957  1.00  9.99
ATOM     78  C   LYS    16      20.381  67.557   8.357  1.00  9.99
ATOM     79  O   LYS    16      21.141  68.066   9.220  1.00  9.99
ATOM     80  CB  LYS    16      20.351  68.314   5.947  1.00  9.99
ATOM     81  N   ILE    17      19.140  67.164   8.591  1.00  9.99
ATOM     82  CA  ILE    17      18.564  67.347   9.968  1.00  9.99
ATOM     83  C   ILE    17      19.275  66.421  10.950  1.00  9.99
ATOM     84  O   ILE    17      19.463  66.860  12.098  1.00  9.99
ATOM     85  CB  ILE    17      17.070  67.161   9.904  1.00  9.99
ATOM     86  N   GLN    18      19.720  65.233  10.555  1.00  9.99
ATOM     87  CA  GLN    18      20.510  64.401  11.460  1.00  9.99
ATOM     88  C   GLN    18      21.797  65.097  11.919  1.00  9.99
ATOM     89  O   GLN    18      22.201  64.995  13.086  1.00  9.99
ATOM     90  CB  GLN    18      20.824  63.044  10.839  1.00  9.99
ATOM     91  N   THR    19      22.470  65.696  10.928  1.00  9.99
ATOM     92  CA  THR    19      23.691  66.456  11.240  1.00  9.99
ATOM     93  C   THR    19      23.400  67.608  12.208  1.00  9.99
ATOM     94  O   THR    19      24.103  67.703  13.227  1.00  9.99
ATOM     95  CB  THR    19      24.284  66.958   9.911  1.00  9.99
ATOM     96  N   LYS    20      22.411  68.405  11.891  1.00  9.99
ATOM     97  CA  LYS    20      22.006  69.511  12.784  1.00  9.99
ATOM     98  C   LYS    20      21.736  68.988  14.197  1.00  9.99
ATOM     99  O   LYS    20      22.255  69.534  15.183  1.00  9.99
ATOM    100  CB  LYS    20      20.787  70.236  12.199  1.00  9.99
ATOM    101  N   TYR    21      20.954  67.920  14.250  1.00  9.99
ATOM    102  CA  TYR    21      20.626  67.343  15.598  1.00  9.99
ATOM    103  C   TYR    21      21.845  66.818  16.321  1.00  9.99
ATOM    104  O   TYR    21      21.942  66.986  17.574  1.00  9.99
ATOM    105  CB  TYR    21      19.515  66.280  15.525  1.00  9.99
ATOM    106  N   ARG    22      22.798  66.241  15.589  1.00  9.99
ATOM    107  CA  ARG    22      24.050  65.803  16.212  1.00  9.99
ATOM    108  C   ARG    22      24.772  66.994  16.845  1.00  9.99
ATOM    109  O   ARG    22      25.301  66.933  17.947  1.00  9.99
ATOM    110  CB  ARG    22      24.994  65.051  15.279  1.00  9.99
ATOM    111  N   HIS    23      24.859  68.100  16.074  1.00  9.99
ATOM    112  CA  HIS    23      25.556  69.304  16.541  1.00  9.99
ATOM    113  C   HIS    23      24.876  69.932  17.749  1.00  9.99
ATOM    114  O   HIS    23      25.587  70.388  18.665  1.00  9.99
ATOM    115  CB  HIS    23      25.608  70.292  15.349  1.00  9.99
ATOM    116  N   LEU    24      23.552  69.941  17.719  1.00  9.99
ATOM    117  CA  LEU    24      22.751  70.439  18.851  1.00  9.99
ATOM    118  C   LEU    24      23.154  69.602  20.080  1.00  9.99
ATOM    119  O   LEU    24      23.404  70.157  21.165  1.00  9.99
ATOM    120  CB  LEU    24      21.258  70.419  18.565  1.00  9.99
ATOM    121  N   ASN    25      23.178  68.307  19.884  1.00  9.99
ATOM    122  CA  ASN    25      23.559  67.408  21.014  1.00  9.99
ATOM    123  C   ASN    25      24.974  67.674  21.474  1.00  9.99
ATOM    124  O   ASN    25      25.274  67.627  22.687  1.00  9.99
ATOM    125  CB  ASN    25      23.292  65.949  20.622  1.00  9.99
ATOM    126  N   HIS    26      25.894  67.923  20.556  1.00  9.99
ATOM    127  CA  HIS    26      27.296  68.250  20.834  1.00  9.99
ATOM    128  C   HIS    26      27.377  69.476  21.745  1.00  9.99
ATOM    129  O   HIS    26      28.106  69.480  22.765  1.00  9.99
ATOM    130  CB  HIS    26      28.090  68.498  19.566  1.00  9.99
ATOM    131  N   ILE    27      26.620  70.503  21.337  1.00  9.99
ATOM    132  CA  ILE    27      26.646  71.758  22.120  1.00  9.99
ATOM    133  C   ILE    27      25.996  71.540  23.488  1.00  9.99
ATOM    134  O   ILE    27      26.465  72.187  24.458  1.00  9.99
ATOM    135  CB  ILE    27      25.961  72.901  21.363  1.00  9.99
ATOM    136  N   SER    28      24.991  70.707  23.563  1.00  9.99
ATOM    137  CA  SER    28      24.298  70.437  24.839  1.00  9.99
ATOM    138  C   SER    28      25.287  69.772  25.799  1.00  9.99
ATOM    139  O   SER    28      25.371  70.148  26.994  1.00  9.99
ATOM    140  CB  SER    28      23.033  69.632  24.682  1.00  9.99
ATOM    141  N   VAL    29      26.103  68.872  25.278  1.00  9.99
ATOM    142  CA  VAL    29      26.914  67.963  26.103  1.00  9.99
ATOM    143  C   VAL    29      28.338  68.457  26.271  1.00  9.99
ATOM    144  O   VAL    29      28.996  68.101  27.287  1.00  9.99
ATOM    145  CB  VAL    29      26.717  66.546  25.485  1.00  9.99
ATOM    146  N   VAL    30      28.874  69.366  25.463  1.00  9.99
ATOM    147  CA  VAL    30      30.267  69.769  25.490  1.00  9.99
ATOM    148  C   VAL    30      30.478  71.223  25.871  1.00  9.99
ATOM    149  O   VAL    30      29.517  72.002  25.888  1.00  9.99
ATOM    150  CB  VAL    30      30.953  69.596  24.119  1.00  9.99
ATOM    151  N   GLU    31      31.736  71.603  26.035  1.00  9.99
ATOM    152  CA  GLU    31      32.068  72.993  26.386  1.00  9.99
ATOM    153  C   GLU    31      33.228  73.516  25.588  1.00  9.99
ATOM    154  O   GLU    31      34.337  73.804  26.062  1.00  9.99
ATOM    155  CB  GLU    31      32.361  73.110  27.899  1.00  9.99
TER
END
