
#######################################################
#                                                     #
#                        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   30 (  150),  selected   30 , name T0297TS239_4_2
# Molecule2: number of CA atoms  211 ( 1703),  selected  211 , name T0297.pdb
# PARAMETERS: T0297TS239_4_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    M       1      Q      14          1.374
LGA    -       -      E      15           -
LGA    -       -      K      16           -
LGA    A       2      I      17          2.255
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    V       3      E      43          5.363
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          1.317
LGA    L       5      R      63          4.706
LGA    -       -      G      64           -
LGA    L       6      Y      65          3.790
LGA    E       7      Q      66          0.966
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       8      N      93          3.675
LGA    W       9      D      94          3.218
LGA    -       -      I      95           -
LGA    -       -      G      96           -
LGA    -       -      K      97           -
LGA    -       -      D      98           -
LGA    L      10      V      99          1.947
LGA    L      11      P     100          0.861
LGA    K      12      V     101          0.775
LGA    E      13      N     102          0.921
LGA    -       -      E     103           -
LGA    -       -      A     104           -
LGA    Q      14      L     105          1.230
LGA    E      15      N     106          1.889
LGA    K      16      N     107          1.767
LGA    I      17      L     108          1.330
LGA    Q      18      E     109          1.400
LGA    T      19      A     110          1.530
LGA    K      20      I     111          1.283
LGA    Y      21      I     112          0.931
LGA    R      22      Q     113          1.125
LGA    H      23      S     114          1.238
LGA    L      24      V     115          1.265
LGA    N      25      A     116          0.765
LGA    H      26      R     117          1.368
LGA    I      27      D     118          1.481
LGA    S      28      Y     119          2.084
LGA    V      29      P     120          2.862
LGA    V      30      L     121           -
LGA    -       -      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)   30  211    5.0     29    2.22     3.45     11.731     1.249

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.881219 * X  +  -0.018222 * Y  +   0.472358 * Z  + -28.523079
  Y_new =  -0.230775 * X  +  -0.888669 * Y  +   0.396246 * Z  +  71.304199
  Z_new =   0.412549 * X  +  -0.458188 * Y  +  -0.787317 * Z  +  -4.563704 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.614542    0.527050  [ DEG:  -149.8022     30.1978 ]
  Theta =  -0.425250   -2.716342  [ DEG:   -24.3651   -155.6349 ]
  Phi   =  -0.256130    2.885463  [ DEG:   -14.6752    165.3248 ]
 
# 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_4_2                                
REMARK     2: T0297.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0297TS239_4_2.T0297.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30  211   5.0   29   2.22    3.45  11.731
REMARK  ---------------------------------------------------------- 
MOLECULE T0297TS239_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0297
PARENT 1wab
ATOM      1  N   MET     1      17.128  85.414   2.385  1.00  9.99
ATOM      2  CA  MET     1      18.430  85.075   3.028  1.00  9.99
ATOM      3  C   MET     1      18.385  85.228   4.557  1.00  9.99
ATOM      4  O   MET     1      19.284  84.677   5.221  1.00  9.99
ATOM      5  CB  MET     1      19.531  85.943   2.418  1.00  9.99
ATOM      6  N   ALA     2      17.376  85.970   5.040  1.00  9.99
ATOM      7  CA  ALA     2      17.318  86.224   6.497  1.00  9.99
ATOM      8  C   ALA     2      16.052  85.615   7.076  1.00  9.99
ATOM      9  O   ALA     2      15.813  85.938   8.264  1.00  9.99
ATOM     10  CB  ALA     2      17.494  87.720   6.771  1.00  9.99
ATOM     11  N   VAL     3      15.329  84.827   6.302  1.00  9.99
ATOM     12  CA  VAL     3      14.132  84.150   6.895  1.00  9.99
ATOM     13  C   VAL     3      14.612  82.756   7.263  1.00  9.99
ATOM     14  O   VAL     3      14.812  81.943   6.366  1.00  9.99
ATOM     15  CB  VAL     3      13.052  84.113   5.835  1.00  9.99
ATOM     16  N   GLN     4      14.676  82.450   8.548  1.00  9.99
ATOM     17  CA  GLN     4      15.269  81.149   8.944  1.00  9.99
ATOM     18  C   GLN     4      14.434  80.005   8.422  1.00  9.99
ATOM     19  O   GLN     4      13.205  80.040   8.571  1.00  9.99
ATOM     20  CB  GLN     4      15.388  81.210  10.471  1.00  9.99
ATOM     21  N   LEU     5      15.100  79.018   7.833  1.00  9.99
ATOM     22  CA  LEU     5      14.369  77.864   7.305  1.00  9.99
ATOM     23  C   LEU     5      15.332  76.703   7.240  1.00  9.99
ATOM     24  O   LEU     5      16.544  76.929   6.985  1.00  9.99
ATOM     25  CB  LEU     5      13.739  78.183   5.904  1.00  9.99
ATOM     26  N   LEU     6      14.853  75.530   7.562  1.00  9.99
ATOM     27  CA  LEU     6      15.698  74.350   7.492  1.00  9.99
ATOM     28  C   LEU     6      15.814  73.901   6.047  1.00  9.99
ATOM     29  O   LEU     6      15.014  74.324   5.196  1.00  9.99
ATOM     30  CB  LEU     6      14.997  73.306   8.368  1.00  9.99
ATOM     31  N   GLU     7      16.812  73.060   5.791  1.00  9.99
ATOM     32  CA  GLU     7      16.830  72.430   4.426  1.00  9.99
ATOM     33  C   GLU     7      15.790  71.326   4.404  1.00  9.99
ATOM     34  O   GLU     7      15.790  70.384   5.225  1.00  9.99
ATOM     35  CB  GLU     7      18.254  71.989   4.116  1.00  9.99
ATOM     36  N   ASN     8      14.977  71.389   3.357  1.00  9.99
ATOM     37  CA  ASN     8      13.915  70.372   3.148  1.00  9.99
ATOM     38  C   ASN     8      14.566  69.119   2.565  1.00  9.99
ATOM     39  O   ASN     8      15.350  69.267   1.597  1.00  9.99
ATOM     40  CB  ASN     8      12.912  70.935   2.131  1.00  9.99
ATOM     41  N   TRP     9      14.187  67.966   3.096  1.00  9.99
ATOM     42  CA  TRP     9      14.779  66.712   2.617  1.00  9.99
ATOM     43  C   TRP     9      14.035  66.311   1.320  1.00  9.99
ATOM     44  O   TRP     9      12.831  65.935   1.461  1.00  9.99
ATOM     45  CB  TRP     9      14.730  65.620   3.676  1.00  9.99
ATOM     46  N   LEU    10      14.710  66.454   0.184  1.00  9.99
ATOM     47  CA  LEU    10      14.035  65.926  -1.038  1.00  9.99
ATOM     48  C   LEU    10      14.728  64.671  -1.560  1.00  9.99
ATOM     49  O   LEU    10      14.482  64.329  -2.744  1.00  9.99
ATOM     50  CB  LEU    10      13.947  67.009  -2.111  1.00  9.99
ATOM     51  N   LEU    11      15.596  64.090  -0.738  1.00  9.99
ATOM     52  CA  LEU    11      16.406  62.925  -1.203  1.00  9.99
ATOM     53  C   LEU    11      15.888  61.728  -0.416  1.00  9.99
ATOM     54  O   LEU    11      15.741  60.604  -0.989  1.00  9.99
ATOM     55  CB  LEU    11      17.907  63.158  -1.046  1.00  9.99
ATOM     56  N   LYS    12      15.752  61.843   0.905  1.00  9.99
ATOM     57  CA  LYS    12      15.046  60.794   1.691  1.00  9.99
ATOM     58  C   LYS    12      15.859  60.224   2.826  1.00  9.99
ATOM     59  O   LYS    12      15.264  59.462   3.660  1.00  9.99
ATOM     60  CB  LYS    12      14.611  59.663   0.745  1.00  9.99
ATOM     61  N   GLU    13      17.124  60.614   3.010  1.00  9.99
ATOM     62  CA  GLU    13      17.965  59.994   4.047  1.00  9.99
ATOM     63  C   GLU    13      18.118  60.908   5.287  1.00  9.99
ATOM     64  O   GLU    13      18.829  60.444   6.230  1.00  9.99
ATOM     65  CB  GLU    13      19.310  59.578   3.436  1.00  9.99
ATOM     66  N   GLN    14      17.541  62.093   5.260  1.00  9.99
ATOM     67  CA  GLN    14      17.468  62.907   6.513  1.00  9.99
ATOM     68  C   GLN    14      18.846  63.391   6.952  1.00  9.99
ATOM     69  O   GLN    14      18.976  63.750   8.170  1.00  9.99
ATOM     70  CB  GLN    14      16.807  62.080   7.628  1.00  9.99
ATOM     71  N   GLU    15      19.844  63.544   6.075  1.00  9.99
ATOM     72  CA  GLU    15      21.196  63.802   6.566  1.00  9.99
ATOM     73  C   GLU    15      21.330  65.197   7.183  1.00  9.99
ATOM     74  O   GLU    15      22.112  65.327   8.137  1.00  9.99
ATOM     75  CB  GLU    15      22.246  63.646   5.419  1.00  9.99
ATOM     76  N   LYS    16      20.669  66.182   6.569  1.00  9.99
ATOM     77  CA  LYS    16      20.848  67.553   7.116  1.00  9.99
ATOM     78  C   LYS    16      20.317  67.644   8.536  1.00  9.99
ATOM     79  O   LYS    16      21.021  68.204   9.416  1.00  9.99
ATOM     80  CB  LYS    16      20.122  68.525   6.177  1.00  9.99
ATOM     81  N   ILE    17      19.149  67.070   8.768  1.00  9.99
ATOM     82  CA  ILE    17      18.588  67.091  10.163  1.00  9.99
ATOM     83  C   ILE    17      19.445  66.219  11.076  1.00  9.99
ATOM     84  O   ILE    17      19.599  66.615  12.245  1.00  9.99
ATOM     85  CB  ILE    17      17.133  66.703  10.114  1.00  9.99
ATOM     86  N   GLN    18      20.040  65.129  10.604  1.00  9.99
ATOM     87  CA  GLN    18      20.960  64.366  11.443  1.00  9.99
ATOM     88  C   GLN    18      22.149  65.208  11.921  1.00  9.99
ATOM     89  O   GLN    18      22.593  65.097  13.073  1.00  9.99
ATOM     90  CB  GLN    18      21.443  63.103  10.737  1.00  9.99
ATOM     91  N   THR    19      22.708  65.950  10.956  1.00  9.99
ATOM     92  CA  THR    19      23.820  66.854  11.292  1.00  9.99
ATOM     93  C   THR    19      23.397  67.898  12.332  1.00  9.99
ATOM     94  O   THR    19      24.106  68.031  13.342  1.00  9.99
ATOM     95  CB  THR    19      24.304  67.508   9.985  1.00  9.99
ATOM     96  N   LYS    20      22.300  68.566  12.079  1.00  9.99
ATOM     97  CA  LYS    20      21.768  69.552  13.044  1.00  9.99
ATOM     98  C   LYS    20      21.609  68.916  14.427  1.00  9.99
ATOM     99  O   LYS    20      22.072  69.473  15.435  1.00  9.99
ATOM    100  CB  LYS    20      20.446  70.131  12.524  1.00  9.99
ATOM    101  N   TYR    21      20.983  67.749  14.430  1.00  9.99
ATOM    102  CA  TYR    21      20.773  67.056  15.747  1.00  9.99
ATOM    103  C   TYR    21      22.071  66.666  16.416  1.00  9.99
ATOM    104  O   TYR    21      22.175  66.775  17.675  1.00  9.99
ATOM    105  CB  TYR    21      19.818  65.854  15.630  1.00  9.99
ATOM    106  N   ARG    22      23.075  66.270  15.634  1.00  9.99
ATOM    107  CA  ARG    22      24.391  65.977  16.209  1.00  9.99
ATOM    108  C   ARG    22      24.957  67.219  16.899  1.00  9.99
ATOM    109  O   ARG    22      25.518  67.170  17.987  1.00  9.99
ATOM    110  CB  ARG    22      25.407  65.418  15.217  1.00  9.99
ATOM    111  N   HIS    23      24.871  68.368  16.195  1.00  9.99
ATOM    112  CA  HIS    23      25.406  69.629  16.720  1.00  9.99
ATOM    113  C   HIS    23      24.677  70.086  17.975  1.00  9.99
ATOM    114  O   HIS    23      25.341  70.585  18.905  1.00  9.99
ATOM    115  CB  HIS    23      25.291  70.680  15.589  1.00  9.99
ATOM    116  N   LEU    24      23.364  69.913  17.968  1.00  9.99
ATOM    117  CA  LEU    24      22.530  70.229  19.141  1.00  9.99
ATOM    118  C   LEU    24      23.077  69.388  20.311  1.00  9.99
ATOM    119  O   LEU    24      23.275  69.910  21.423  1.00  9.99
ATOM    120  CB  LEU    24      21.048  70.017  18.881  1.00  9.99
ATOM    121  N   ASN    25      23.275  68.123  20.038  1.00  9.99
ATOM    122  CA  ASN    25      23.805  67.223  21.106  1.00  9.99
ATOM    123  C   ASN    25      25.180  67.657  21.556  1.00  9.99
ATOM    124  O   ASN    25      25.515  67.584  22.760  1.00  9.99
ATOM    125  CB  ASN    25      23.732  65.766  20.633  1.00  9.99
ATOM    126  N   HIS    26      26.033  68.084  20.640  1.00  9.99
ATOM    127  CA  HIS    26      27.384  68.587  20.912  1.00  9.99
ATOM    128  C   HIS    26      27.317  69.758  21.893  1.00  9.99
ATOM    129  O   HIS    26      28.064  69.806  22.899  1.00  9.99
ATOM    130  CB  HIS    26      28.103  69.015  19.648  1.00  9.99
ATOM    131  N   ILE    27      26.416  70.691  21.560  1.00  9.99
ATOM    132  CA  ILE    27      26.287  71.891  22.416  1.00  9.99
ATOM    133  C   ILE    27      25.708  71.507  23.779  1.00  9.99
ATOM    134  O   ILE    27      26.108  72.158  24.778  1.00  9.99
ATOM    135  CB  ILE    27      25.432  72.969  21.741  1.00  9.99
ATOM    136  N   SER    28      24.830  70.540  23.822  1.00  9.99
ATOM    137  CA  SER    28      24.214  70.103  25.091  1.00  9.99
ATOM    138  C   SER    28      25.309  69.530  25.993  1.00  9.99
ATOM    139  O   SER    28      25.371  69.845  27.206  1.00  9.99
ATOM    140  CB  SER    28      23.069  69.140  24.909  1.00  9.99
ATOM    141  N   VAL    29      26.229  68.784  25.405  1.00  9.99
ATOM    142  CA  VAL    29      27.178  67.952  26.160  1.00  9.99
ATOM    143  C   VAL    29      28.524  68.628  26.333  1.00  9.99
ATOM    144  O   VAL    29      29.250  68.311  27.315  1.00  9.99
ATOM    145  CB  VAL    29      27.164  66.558  25.463  1.00  9.99
ATOM    146  N   VAL    30      28.909  69.648  25.572  1.00  9.99
ATOM    147  CA  VAL    30      30.233  70.239  25.599  1.00  9.99
ATOM    148  C   VAL    30      30.250  71.684  26.062  1.00  9.99
ATOM    149  O   VAL    30      29.191  72.320  26.142  1.00  9.99
ATOM    150  CB  VAL    30      30.901  70.242  24.208  1.00  9.99
TER
END
