
#######################################################
#                                                     #
#                        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   41 (  202),  selected   41 , name T0299TS102_5-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS102_5-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    T       2      T       2           -
LGA    R       3      R       3           -
LGA    -       -      Y       4           -
LGA    -       -      A       5           -
LGA    -       -      L       6           -
LGA    -       -      L       7           -
LGA    -       -      V       8           -
LGA    -       -      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    Y       4      N      12           #
LGA    A       5      V      13          3.652
LGA    L       6      -       -           -
LGA    L       7      -       -           -
LGA    V       8      G      14          2.799
LGA    R       9      G      15          3.422
LGA    G      10      K      16          2.526
LGA    I      11      N      17          3.876
LGA    N      12      K      18          3.323
LGA    V      13      -       -           -
LGA    K      18      -       -           -
LGA    V      19      V      19          5.305
LGA    V      20      V      20          2.753
LGA    M      21      M      21          2.809
LGA    A      22      A      22          4.753
LGA    E      23      E      23          3.761
LGA    L      24      L      24          1.287
LGA    R      25      R      25          1.907
LGA    Q      26      Q      26          2.140
LGA    -       -      E      27           -
LGA    E      27      L      28          1.007
LGA    L      28      T      29          3.796
LGA    T      29      N      30          4.816
LGA    -       -      L      31           -
LGA    N      30      G      32          2.789
LGA    L      31      L      33          0.551
LGA    G      32      E      34          1.745
LGA    L      33      K      35          1.507
LGA    S      78      V      36          4.026
LGA    -       -      E      37           -
LGA    -       -      S      38           -
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    -       -      S      42           -
LGA    -       -      G      43           -
LGA    T     170      N      44           #
LGA    F     171      I      45           #
LGA    D     172      -       -           -
LGA    K     173      F      46           #
LGA    I     174      F      47          4.670
LGA    G     175      T      48          3.652
LGA    -       -      S      49           -
LGA    -       -      I      50           -
LGA    -       -      D      51           -
LGA    -       -      S      52           -
LGA    -       -      K      53           -
LGA    -       -      A      54           -
LGA    -       -      Q      55           -
LGA    -       -      L      56           -
LGA    -       -      V      57           -
LGA    -       -      E      58           -
LGA    -       -      K      59           -
LGA    -       -      L      60           -
LGA    -       -      E      61           -
LGA    -       -      T      62           -
LGA    -       -      F      63           -
LGA    -       -      F      64           -
LGA    -       -      A      65           -
LGA    -       -      V      66           -
LGA    -       -      H      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      F      70           -
LGA    -       -      I      71           -
LGA    -       -      Q      72           -
LGA    -       -      S      73           -
LGA    -       -      F      74           -
LGA    -       -      S      75           -
LGA    -       -      L      76           -
LGA    -       -      L      77           -
LGA    Q     176      S      78          2.767
LGA    -       -      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    -       -      I     174           -
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    -       -      M     177           -
LGA    M     177      L     178          2.293
LGA    L     178      K     179          4.345
LGA    K     179      K     180           #
LGA    K     180      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   91    5.0     27    3.28    33.33     17.865     0.799

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.449006 * X  +  -0.771122 * Y  +  -0.451404 * Z  +  -6.549768
  Y_new =  -0.891411 * X  +   0.351815 * Y  +   0.285678 * Z  +  45.552624
  Z_new =  -0.061482 * X  +   0.530658 * Y  +  -0.845353 * Z  +  -5.573316 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.581029   -0.560563  [ DEG:   147.8821    -32.1179 ]
  Theta =   0.061521    3.080072  [ DEG:     3.5249    176.4751 ]
  Phi   =  -2.037401    1.104192  [ DEG:  -116.7345     63.2655 ]
 
# 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: T0299TS102_5-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS102_5-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   91   5.0   27   3.28   33.33  17.865
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS102_5-D1
PFRMAT TS
TARGET T0299
MODEL 5
PARENT 1wh8_A
ATOM      1  N   MET     1       8.707  45.018  -8.064  1.00  1.00
ATOM      2  CA  MET     1       7.898  43.840  -7.765  1.00  1.00
ATOM      3  C   MET     1       8.675  42.558  -8.063  1.00  1.00
ATOM      4  O   MET     1       8.639  41.620  -7.272  1.00  1.00
ATOM      5  CB  MET     1       6.540  43.909  -8.509  1.00  1.00
ATOM      6  N   THR     2       9.409  42.506  -9.178  1.00  1.00
ATOM      7  CA  THR     2      10.021  41.262  -9.616  1.00  1.00
ATOM      8  C   THR     2      11.111  40.790  -8.645  1.00  1.00
ATOM      9  O   THR     2      11.395  39.598  -8.573  1.00  1.00
ATOM     10  CB  THR     2      10.534  41.409 -11.059  1.00  1.00
ATOM     11  N   ARG     3      11.688  41.700  -7.864  1.00  1.00
ATOM     12  CA  ARG     3      12.683  41.408  -6.851  1.00  1.00
ATOM     13  C   ARG     3      12.034  40.977  -5.531  1.00  1.00
ATOM     14  O   ARG     3      12.630  40.209  -4.780  1.00  1.00
ATOM     15  CB  ARG     3      13.536  42.664  -6.684  1.00  1.00
ATOM     16  N   TYR     4      10.811  41.420  -5.239  1.00  1.00
ATOM     17  CA  TYR     4      10.017  40.888  -4.135  1.00  1.00
ATOM     18  C   TYR     4       9.675  39.436  -4.478  1.00  1.00
ATOM     19  O   TYR     4       9.940  38.525  -3.691  1.00  1.00
ATOM     20  CB  TYR     4       8.761  41.764  -3.917  1.00  1.00
ATOM     21  N   ALA     5       9.146  39.223  -5.685  1.00  1.00
ATOM     22  CA  ALA     5       8.795  37.924  -6.242  1.00  1.00
ATOM     23  C   ALA     5      10.016  36.996  -6.249  1.00  1.00
ATOM     24  O   ALA     5       9.871  35.794  -6.026  1.00  1.00
ATOM     25  CB  ALA     5       8.254  38.137  -7.670  1.00  1.00
ATOM     26  N   LEU     6      11.212  37.535  -6.498  1.00  1.00
ATOM     27  CA  LEU     6      12.438  36.747  -6.551  1.00  1.00
ATOM     28  C   LEU     6      12.655  36.024  -5.226  1.00  1.00
ATOM     29  O   LEU     6      12.953  34.831  -5.192  1.00  1.00
ATOM     30  CB  LEU     6      13.637  37.660  -6.831  1.00  1.00
ATOM     31  N   LEU     7      12.490  36.772  -4.139  1.00  1.00
ATOM     32  CA  LEU     7      12.719  36.318  -2.782  1.00  1.00
ATOM     33  C   LEU     7      11.573  35.427  -2.283  1.00  1.00
ATOM     34  O   LEU     7      11.739  34.704  -1.300  1.00  1.00
ATOM     35  CB  LEU     7      12.826  37.550  -1.878  1.00  1.00
ATOM     36  N   VAL     8      10.406  35.503  -2.932  1.00  1.00
ATOM     37  CA  VAL     8       9.166  34.916  -2.453  1.00  1.00
ATOM     38  C   VAL     8       9.299  33.398  -2.284  1.00  1.00
ATOM     39  O   VAL     8       9.944  32.743  -3.119  1.00  1.00
ATOM     40  CB  VAL     8       8.056  35.258  -3.454  1.00  1.00
ATOM     41  N   ARG     9       8.634  32.831  -1.265  1.00  1.00
ATOM     42  CA  ARG     9       8.378  31.406  -1.176  1.00  1.00
ATOM     43  C   ARG     9       7.313  31.018  -2.209  1.00  1.00
ATOM     44  O   ARG     9       6.795  31.868  -2.944  1.00  1.00
ATOM     45  CB  ARG     9       7.923  31.183   0.266  1.00  1.00
ATOM     46  N   GLY    10       7.004  29.725  -2.280  1.00  1.00
ATOM     47  CA  GLY    10       5.969  29.181  -3.141  1.00  1.00
ATOM     48  C   GLY    10       4.597  29.703  -2.711  1.00  1.00
ATOM     49  O   GLY    10       4.034  29.273  -1.699  1.00  1.00
ATOM     50  N   ILE    11       4.071  30.666  -3.459  1.00  1.00
ATOM     51  CA  ILE    11       2.768  31.273  -3.241  1.00  1.00
ATOM     52  C   ILE    11       1.740  30.478  -4.023  1.00  1.00
ATOM     53  O   ILE    11       1.668  30.587  -5.245  1.00  1.00
ATOM     54  CB  ILE    11       2.818  32.748  -3.626  1.00  1.00
ATOM     55  N   ASN    12       0.988  29.646  -3.298  1.00  1.00
ATOM     56  CA  ASN    12      -0.031  28.746  -3.827  1.00  1.00
ATOM     57  C   ASN    12      -1.035  29.509  -4.671  1.00  1.00
ATOM     58  O   ASN    12      -1.943  30.157  -4.142  1.00  1.00
ATOM     59  CB  ASN    12      -0.770  28.026  -2.703  1.00  1.00
ATOM     60  N   VAL    13      -0.842  29.481  -5.984  1.00  1.00
ATOM     61  CA  VAL    13      -1.577  30.330  -6.893  1.00  1.00
ATOM     62  C   VAL    13      -3.068  30.055  -6.733  1.00  1.00
ATOM     63  O   VAL    13      -3.842  31.002  -6.621  1.00  1.00
ATOM     64  CB  VAL    13      -1.057  30.140  -8.325  1.00  1.00
ATOM     65  N   LYS    18      -3.459  28.777  -6.664  1.00  1.00
ATOM     66  CA  LYS    18      -4.834  28.375  -6.516  1.00  1.00
ATOM     67  C   LYS    18      -5.474  28.983  -5.277  1.00  1.00
ATOM     68  O   LYS    18      -6.446  29.722  -5.413  1.00  1.00
ATOM     69  CB  LYS    18      -4.927  26.854  -6.506  1.00  1.00
ATOM     70  N   VAL    19      -4.934  28.702  -4.092  1.00  1.00
ATOM     71  CA  VAL    19      -5.470  29.151  -2.816  1.00  1.00
ATOM     72  C   VAL    19      -5.585  30.677  -2.783  1.00  1.00
ATOM     73  O   VAL    19      -6.611  31.197  -2.348  1.00  1.00
ATOM     74  CB  VAL    19      -4.563  28.603  -1.704  1.00  1.00
ATOM     75  N   VAL    20      -4.591  31.396  -3.317  1.00  1.00
ATOM     76  CA  VAL    20      -4.631  32.849  -3.444  1.00  1.00
ATOM     77  C   VAL    20      -5.791  33.206  -4.383  1.00  1.00
ATOM     78  O   VAL    20      -6.670  33.940  -3.953  1.00  1.00
ATOM     79  CB  VAL    20      -3.243  33.358  -3.909  1.00  1.00
ATOM     80  N   MET    21      -5.873  32.689  -5.619  1.00  1.00
ATOM     81  CA  MET    21      -6.972  33.043  -6.529  1.00  1.00
ATOM     82  C   MET    21      -8.339  32.788  -5.899  1.00  1.00
ATOM     83  O   MET    21      -9.238  33.607  -6.042  1.00  1.00
ATOM     84  CB  MET    21      -6.898  32.325  -7.890  1.00  1.00
ATOM     85  N   ALA    22      -8.484  31.661  -5.202  1.00  1.00
ATOM     86  CA  ALA    22      -9.677  31.303  -4.459  1.00  1.00
ATOM     87  C   ALA    22     -10.007  32.405  -3.458  1.00  1.00
ATOM     88  O   ALA    22     -11.045  33.046  -3.576  1.00  1.00
ATOM     89  CB  ALA    22      -9.485  29.948  -3.757  1.00  1.00
ATOM     90  N   GLU    23      -9.115  32.669  -2.509  1.00  1.00
ATOM     91  CA  GLU    23      -9.349  33.638  -1.453  1.00  1.00
ATOM     92  C   GLU    23      -9.625  35.025  -2.039  1.00  1.00
ATOM     93  O   GLU    23     -10.523  35.716  -1.584  1.00  1.00
ATOM     94  CB  GLU    23      -8.126  33.579  -0.525  1.00  1.00
ATOM     95  N   LEU    24      -8.914  35.417  -3.093  1.00  1.00
ATOM     96  CA  LEU    24      -9.061  36.685  -3.794  1.00  1.00
ATOM     97  C   LEU    24     -10.468  36.795  -4.393  1.00  1.00
ATOM     98  O   LEU    24     -11.149  37.793  -4.173  1.00  1.00
ATOM     99  CB  LEU    24      -7.932  36.782  -4.843  1.00  1.00
ATOM    100  N   ARG    25     -10.920  35.784  -5.145  1.00  1.00
ATOM    101  CA  ARG    25     -12.274  35.736  -5.704  1.00  1.00
ATOM    102  C   ARG    25     -13.301  35.932  -4.605  1.00  1.00
ATOM    103  O   ARG    25     -14.256  36.682  -4.786  1.00  1.00
ATOM    104  CB  ARG    25     -12.507  34.358  -6.334  1.00  1.00
ATOM    105  N   GLN    26     -13.113  35.244  -3.487  1.00  1.00
ATOM    106  CA  GLN    26     -14.072  35.236  -2.394  1.00  1.00
ATOM    107  C   GLN    26     -14.126  36.595  -1.724  1.00  1.00
ATOM    108  O   GLN    26     -15.195  37.051  -1.339  1.00  1.00
ATOM    109  CB  GLN    26     -13.722  34.090  -1.431  1.00  1.00
ATOM    110  N   GLU    27     -12.991  37.272  -1.613  1.00  1.00
ATOM    111  CA  GLU    27     -12.931  38.673  -1.185  1.00  1.00
ATOM    112  C   GLU    27     -13.674  39.572  -2.184  1.00  1.00
ATOM    113  O   GLU    27     -14.431  40.439  -1.743  1.00  1.00
ATOM    114  CB  GLU    27     -11.478  39.126  -0.923  1.00  1.00
ATOM    115  N   LEU    28     -13.499  39.392  -3.501  1.00  1.00
ATOM    116  CA  LEU    28     -14.238  40.182  -4.485  1.00  1.00
ATOM    117  C   LEU    28     -15.737  39.954  -4.318  1.00  1.00
ATOM    118  O   LEU    28     -16.477  40.929  -4.240  1.00  1.00
ATOM    119  CB  LEU    28     -13.820  39.919  -5.945  1.00  1.00
ATOM    120  N   THR    29     -16.181  38.699  -4.259  1.00  1.00
ATOM    121  CA  THR    29     -17.579  38.335  -4.108  1.00  1.00
ATOM    122  C   THR    29     -18.148  38.865  -2.790  1.00  1.00
ATOM    123  O   THR    29     -19.255  39.401  -2.818  1.00  1.00
ATOM    124  CB  THR    29     -17.717  36.812  -4.309  1.00  1.00
ATOM    125  N   ASN    30     -17.442  38.763  -1.656  1.00  1.00
ATOM    126  CA  ASN    30     -17.970  39.204  -0.356  1.00  1.00
ATOM    127  C   ASN    30     -18.347  40.676  -0.438  1.00  1.00
ATOM    128  O   ASN    30     -19.451  41.090  -0.099  1.00  1.00
ATOM    129  CB  ASN    30     -16.940  39.015   0.775  1.00  1.00
ATOM    130  N   LEU    31     -17.412  41.459  -0.972  1.00  1.00
ATOM    131  CA  LEU    31     -17.508  42.898  -1.123  1.00  1.00
ATOM    132  C   LEU    31     -18.250  43.300  -2.405  1.00  1.00
ATOM    133  O   LEU    31     -18.324  44.489  -2.713  1.00  1.00
ATOM    134  CB  LEU    31     -16.079  43.446  -1.076  1.00  1.00
ATOM    135  N   GLY    32     -18.812  42.335  -3.148  1.00  1.00
ATOM    136  CA  GLY    32     -19.547  42.472  -4.416  1.00  1.00
ATOM    137  C   GLY    32     -18.811  43.232  -5.531  1.00  1.00
ATOM    138  O   GLY    32     -19.411  43.693  -6.509  1.00  1.00
ATOM    139  N   LEU    33     -17.490  43.296  -5.425  1.00  1.00
ATOM    140  CA  LEU    33     -16.562  43.948  -6.333  1.00  1.00
ATOM    141  C   LEU    33     -16.542  43.250  -7.693  1.00  1.00
ATOM    142  O   LEU    33     -16.932  42.086  -7.839  1.00  1.00
ATOM    143  CB  LEU    33     -15.166  43.869  -5.703  1.00  1.00
ATOM    144  N   SER    78     -16.003  43.954  -8.685  1.00  1.00
ATOM    145  CA  SER    78     -15.895  43.557 -10.077  1.00  1.00
ATOM    146  C   SER    78     -14.445  43.276 -10.428  1.00  1.00
ATOM    147  O   SER    78     -13.631  44.193 -10.334  1.00  1.00
ATOM    148  CB  SER    78     -16.395  44.717 -10.957  1.00  1.00
ATOM    386  N   THR   170      -6.960  47.082   2.018  1.00  1.00
ATOM    387  CA  THR   170      -6.934  46.592   0.652  1.00  1.00
ATOM    388  C   THR   170      -8.230  46.889  -0.095  1.00  1.00
ATOM    389  O   THR   170      -8.194  47.520  -1.156  1.00  1.00
ATOM    390  CB  THR   170      -6.638  45.085   0.676  1.00  1.00
ATOM    391  N   PHE   171      -9.365  46.441   0.431  1.00  1.00
ATOM    392  CA  PHE   171     -10.678  46.629  -0.133  1.00  1.00
ATOM    393  C   PHE   171     -11.065  48.097  -0.016  1.00  1.00
ATOM    394  O   PHE   171     -11.675  48.621  -0.939  1.00  1.00
ATOM    395  CB  PHE   171     -11.673  45.698   0.584  1.00  1.00
ATOM    396  N   ASP   172     -10.667  48.773   1.061  1.00  1.00
ATOM    397  CA  ASP   172     -10.917  50.198   1.252  1.00  1.00
ATOM    398  C   ASP   172     -10.407  50.989   0.054  1.00  1.00
ATOM    399  O   ASP   172     -11.177  51.694  -0.600  1.00  1.00
ATOM    400  CB  ASP   172     -10.245  50.713   2.529  1.00  1.00
ATOM    401  N   LYS   173      -9.113  50.849  -0.246  1.00  1.00
ATOM    402  CA  LYS   173      -8.482  51.534  -1.368  1.00  1.00
ATOM    403  C   LYS   173      -9.108  51.078  -2.682  1.00  1.00
ATOM    404  O   LYS   173      -9.278  51.905  -3.580  1.00  1.00
ATOM    405  CB  LYS   173      -6.959  51.298  -1.345  1.00  1.00
ATOM    406  N   ILE   174      -9.479  49.798  -2.794  1.00  1.00
ATOM    407  CA  ILE   174     -10.064  49.258  -4.011  1.00  1.00
ATOM    408  C   ILE   174     -11.461  49.828  -4.272  1.00  1.00
ATOM    409  O   ILE   174     -11.764  50.196  -5.405  1.00  1.00
ATOM    410  CB  ILE   174     -10.097  47.724  -3.948  1.00  1.00
ATOM    411  N   GLY   175     -12.333  49.907  -3.261  1.00  1.00
ATOM    412  CA  GLY   175     -13.643  50.530  -3.429  1.00  1.00
ATOM    413  C   GLY   175     -13.441  51.995  -3.762  1.00  1.00
ATOM    414  O   GLY   175     -14.142  52.512  -4.624  1.00  1.00
ATOM    415  N   GLN   176     -12.468  52.653  -3.128  1.00  1.00
ATOM    416  CA  GLN   176     -12.208  54.080  -3.292  1.00  1.00
ATOM    417  C   GLN   176     -11.913  54.471  -4.742  1.00  1.00
ATOM    418  O   GLN   176     -12.159  55.606  -5.144  1.00  1.00
ATOM    419  CB  GLN   176     -11.049  54.511  -2.391  1.00  1.00
ATOM    420  N   MET   177     -11.457  53.515  -5.553  1.00  1.00
ATOM    421  CA  MET   177     -11.284  53.682  -6.989  1.00  1.00
ATOM    422  C   MET   177     -12.612  54.032  -7.660  1.00  1.00
ATOM    423  O   MET   177     -12.692  54.967  -8.451  1.00  1.00
ATOM    424  CB  MET   177     -10.800  52.372  -7.600  1.00  1.00
ATOM    425  N   LEU   178     -13.653  53.246  -7.369  1.00  1.00
ATOM    426  CA  LEU   178     -15.000  53.423  -7.899  1.00  1.00
ATOM    427  C   LEU   178     -15.701  54.570  -7.170  1.00  1.00
ATOM    428  O   LEU   178     -16.493  55.294  -7.773  1.00  1.00
ATOM    429  CB  LEU   178     -15.781  52.108  -7.710  1.00  1.00
ATOM    430  N   LYS   179     -15.405  54.698  -5.868  1.00  1.00
ATOM    431  CA  LYS   179     -16.113  55.446  -4.852  1.00  1.00
ATOM    432  C   LYS   179     -17.613  55.416  -5.155  1.00  1.00
ATOM    433  O   LYS   179     -18.142  54.335  -5.429  1.00  1.00
ATOM    434  CB  LYS   179     -15.440  56.818  -4.651  1.00  1.00
ATOM    435  N   LYS   180     -18.304  56.551  -5.078  1.00  1.00
ATOM    436  CA  LYS   180     -19.674  56.670  -5.555  1.00  1.00
ATOM    437  C   LYS   180     -19.589  57.031  -7.035  1.00  1.00
ATOM    438  O   LYS   180     -18.726  57.828  -7.411  1.00  1.00
ATOM    439  CB  LYS   180     -20.421  57.762  -4.783  1.00  1.00
TER
END
