
#######################################################
#                                                     #
#                        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   24 (  202),  selected   24 , name T0299TS389_3-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS389_3-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      T       2           -
LGA    -       -      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    -       -      N      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      V      19           -
LGA    -       -      V      20           -
LGA    -       -      M      21           -
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    Q      55      R      25          2.662
LGA    L      56      Q      26          2.508
LGA    V      57      E      27          2.978
LGA    E      58      L      28          1.746
LGA    K      59      T      29          2.956
LGA    -       -      N      30           -
LGA    -       -      L      31           -
LGA    L      60      G      32          2.491
LGA    E      61      L      33          3.726
LGA    -       -      E      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      E      37           -
LGA    -       -      S      38           -
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    -       -      S      42           -
LGA    -       -      G      43           -
LGA    -       -      N      44           -
LGA    -       -      I      45           -
LGA    T      62      F      46           #
LGA    F      63      F      47          5.843
LGA    F      64      T      48           #
LGA    A      65      S      49          4.243
LGA    V      66      I      50          3.647
LGA    H      67      D      51          3.461
LGA    Y      68      S      52          3.103
LGA    P      69      K      53          2.883
LGA    F      70      A      54          3.771
LGA    -       -      Q      55           -
LGA    I      71      L      56          1.428
LGA    -       -      V      57           -
LGA    -       -      E      58           -
LGA    Q      72      K      59          2.188
LGA    S      73      L      60          1.924
LGA    -       -      E      61           -
LGA    -       -      T      62           -
LGA    F      74      F      63          2.314
LGA    S      75      F      64          2.584
LGA    -       -      A      65           -
LGA    -       -      V      66           -
LGA    L      76      H      67          1.707
LGA    L      77      Y      68           #
LGA    S      78      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    -       -      S      78           -
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    -       -      L     178           -
LGA    -       -      K     179           -
LGA    -       -      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   91    5.0     20    3.08    10.00     14.691     0.630

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.722122 * X  +   0.670717 * Y  +   0.169346 * Z  + -19.729649
  Y_new =   0.550319 * X  +  -0.408659 * Y  +  -0.728112 * Z  +  25.454521
  Z_new =  -0.419152 * X  +   0.618980 * Y  +  -0.664210 * Z  +  -4.198357 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.391428   -0.750165  [ DEG:   137.0187    -42.9813 ]
  Theta =   0.432511    2.709081  [ DEG:    24.7811    155.2189 ]
  Phi   =   0.651191   -2.490401  [ DEG:    37.3105   -142.6895 ]
 
# 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: T0299TS389_3-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS389_3-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   91   5.0   20   3.08   10.00  14.691
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS389_3-D1
PFRMAT TS
TARGET T0299
MODEL  3
PARENT N/A
ATOM      2  N   GLN    55     -11.734  34.281  -2.773  1.00  0.00
ATOM      3  CA  GLN    55     -12.015  35.290  -3.783  1.00  0.00
ATOM      4  CB  GLN    55     -12.069  34.657  -5.175  1.00  0.00
ATOM      5  CG  GLN    55     -10.717  34.197  -5.699  1.00  0.00
ATOM      6  CD  GLN    55     -10.824  33.473  -7.027  1.00  0.00
ATOM      7  OE1 GLN    55     -11.921  33.229  -7.526  1.00  0.00
ATOM      8  NE2 GLN    55      -9.678  33.127  -7.604  1.00  0.00
ATOM      9  O   GLN    55     -13.501  37.190  -3.690  1.00  0.00
ATOM     10  C   GLN    55     -13.352  35.971  -3.524  1.00  0.00
ATOM     11  N   LEU    56     -14.351  35.208  -3.097  1.00  0.00
ATOM     12  CA  LEU    56     -15.667  35.770  -2.780  1.00  0.00
ATOM     13  CB  LEU    56     -16.676  34.653  -2.504  1.00  0.00
ATOM     14  CG  LEU    56     -17.080  33.795  -3.705  1.00  0.00
ATOM     15  CD1 LEU    56     -17.939  32.620  -3.261  1.00  0.00
ATOM     16  CD2 LEU    56     -17.879  34.615  -4.707  1.00  0.00
ATOM     17  O   LEU    56     -16.174  37.757  -1.533  1.00  0.00
ATOM     18  C   LEU    56     -15.596  36.658  -1.552  1.00  0.00
ATOM     19  N   VAL    57     -14.847  36.231  -0.536  1.00  0.00
ATOM     20  CA  VAL    57     -14.694  37.059   0.658  1.00  0.00
ATOM     21  CB  VAL    57     -13.899  36.326   1.755  1.00  0.00
ATOM     22  CG1 VAL    57     -13.595  37.268   2.910  1.00  0.00
ATOM     23  CG2 VAL    57     -14.696  35.146   2.290  1.00  0.00
ATOM     24  O   VAL    57     -14.267  39.389   0.913  1.00  0.00
ATOM     25  C   VAL    57     -13.949  38.347   0.318  1.00  0.00
ATOM     26  N   GLU    58     -13.005  38.324  -0.624  1.00  0.00
ATOM     27  CA  GLU    58     -12.339  39.564  -1.037  1.00  0.00
ATOM     28  CB  GLU    58     -11.255  39.268  -2.077  1.00  0.00
ATOM     29  CG  GLU    58     -10.039  38.547  -1.517  1.00  0.00
ATOM     30  CD  GLU    58      -9.044  38.164  -2.593  1.00  0.00
ATOM     31  OE1 GLU    58      -9.338  38.395  -3.785  1.00  0.00
ATOM     32  OE2 GLU    58      -7.969  37.630  -2.247  1.00  0.00
ATOM     33  O   GLU    58     -13.357  41.717  -1.365  1.00  0.00
ATOM     34  C   GLU    58     -13.362  40.507  -1.644  1.00  0.00
ATOM     35  N   LYS    59     -14.259  40.001  -2.482  1.00  0.00
ATOM     36  CA  LYS    59     -15.322  40.825  -3.047  1.00  0.00
ATOM     37  CB  LYS    59     -16.176  40.007  -4.017  1.00  0.00
ATOM     38  CG  LYS    59     -17.287  40.800  -4.687  1.00  0.00
ATOM     39  CD  LYS    59     -18.049  39.946  -5.688  1.00  0.00
ATOM     40  CE  LYS    59     -19.190  40.724  -6.322  1.00  0.00
ATOM     41  NZ  LYS    59     -19.960  39.893  -7.287  1.00  0.00
ATOM     42  O   LYS    59     -16.583  42.555  -1.934  1.00  0.00
ATOM     43  C   LYS    59     -16.225  41.359  -1.941  1.00  0.00
ATOM     44  N   LEU    60     -16.632  40.506  -1.014  1.00  0.00
ATOM     45  CA  LEU    60     -17.498  40.915   0.087  1.00  0.00
ATOM     46  CB  LEU    60     -17.843  39.714   0.970  1.00  0.00
ATOM     47  CG  LEU    60     -18.739  39.996   2.179  1.00  0.00
ATOM     48  CD1 LEU    60     -20.092  40.527   1.733  1.00  0.00
ATOM     49  CD2 LEU    60     -18.966  38.730   2.988  1.00  0.00
ATOM     50  O   LEU    60     -17.490  42.966   1.301  1.00  0.00
ATOM     51  C   LEU    60     -16.842  41.963   0.969  1.00  0.00
ATOM     52  N   GLU    61     -15.603  41.736   1.374  1.00  0.00
ATOM     53  CA  GLU    61     -14.864  42.692   2.192  1.00  0.00
ATOM     54  CB  GLU    61     -13.448  42.181   2.467  1.00  0.00
ATOM     55  CG  GLU    61     -13.390  40.996   3.417  1.00  0.00
ATOM     56  CD  GLU    61     -11.988  40.438   3.568  1.00  0.00
ATOM     57  OE1 GLU    61     -11.074  40.933   2.874  1.00  0.00
ATOM     58  OE2 GLU    61     -11.801  39.509   4.380  1.00  0.00
ATOM     59  O   GLU    61     -14.964  45.097   2.115  1.00  0.00
ATOM     60  C   GLU    61     -14.762  44.031   1.486  1.00  0.00
ATOM     61  N   THR    62     -14.516  44.089   0.192  1.00  0.00
ATOM     62  CA  THR    62     -14.443  45.314  -0.587  1.00  0.00
ATOM     63  CB  THR    62     -14.137  45.023  -2.068  1.00  0.00
ATOM     64  CG2 THR    62     -14.108  46.316  -2.869  1.00  0.00
ATOM     65  OG1 THR    62     -12.861  44.380  -2.179  1.00  0.00
ATOM     66  O   THR    62     -15.801  47.291  -0.305  1.00  0.00
ATOM     67  C   THR    62     -15.770  46.065  -0.517  1.00  0.00
ATOM     68  N   PHE    63     -16.883  45.357  -0.692  1.00  0.00
ATOM     69  CA  PHE    63     -18.189  46.003  -0.617  1.00  0.00
ATOM     70  CB  PHE    63     -19.292  45.032  -1.047  1.00  0.00
ATOM     71  CG  PHE    63     -19.382  44.838  -2.534  1.00  0.00
ATOM     72  CD1 PHE    63     -18.843  43.714  -3.133  1.00  0.00
ATOM     73  CD2 PHE    63     -20.006  45.781  -3.332  1.00  0.00
ATOM     74  CE1 PHE    63     -18.928  43.535  -4.502  1.00  0.00
ATOM     75  CE2 PHE    63     -20.090  45.602  -4.701  1.00  0.00
ATOM     76  CZ  PHE    63     -19.553  44.485  -5.286  1.00  0.00
ATOM     77  O   PHE    63     -19.035  47.581   0.975  1.00  0.00
ATOM     78  C   PHE    63     -18.493  46.464   0.796  1.00  0.00
ATOM     79  N   PHE    64     -18.172  45.700   1.819  1.00  0.00
ATOM     80  CA  PHE    64     -18.441  46.073   3.201  1.00  0.00
ATOM     81  CB  PHE    64     -18.028  44.947   4.149  1.00  0.00
ATOM     82  CG  PHE    64     -18.266  45.256   5.600  1.00  0.00
ATOM     83  CD1 PHE    64     -19.534  45.150   6.146  1.00  0.00
ATOM     84  CD2 PHE    64     -17.225  45.656   6.419  1.00  0.00
ATOM     85  CE1 PHE    64     -19.754  45.434   7.481  1.00  0.00
ATOM     86  CE2 PHE    64     -17.445  45.941   7.753  1.00  0.00
ATOM     87  CZ  PHE    64     -18.704  45.833   8.284  1.00  0.00
ATOM     88  O   PHE    64     -18.148  48.213   4.273  1.00  0.00
ATOM     89  C   PHE    64     -17.657  47.325   3.555  1.00  0.00
ATOM     90  N   ALA    65     -16.422  47.421   3.059  1.00  0.00
ATOM     91  CA  ALA    65     -15.585  48.601   3.276  1.00  0.00
ATOM     92  CB  ALA    65     -14.182  48.362   2.743  1.00  0.00
ATOM     93  O   ALA    65     -16.228  50.906   3.177  1.00  0.00
ATOM     94  C   ALA    65     -16.159  49.812   2.570  1.00  0.00
ATOM     95  N   VAL    66     -16.617  49.693   1.343  1.00  0.00
ATOM     96  CA  VAL    66     -17.230  50.804   0.629  1.00  0.00
ATOM     97  CB  VAL    66     -17.690  50.385  -0.780  1.00  0.00
ATOM     98  CG1 VAL    66     -18.499  51.496  -1.429  1.00  0.00
ATOM     99  CG2 VAL    66     -16.488  50.086  -1.664  1.00  0.00
ATOM    100  O   VAL    66     -18.656  52.515   1.555  1.00  0.00
ATOM    101  C   VAL    66     -18.448  51.301   1.404  1.00  0.00
ATOM    102  N   HIS    67     -19.295  50.386   1.869  1.00  0.00
ATOM    103  CA  HIS    67     -20.508  50.783   2.560  1.00  0.00
ATOM    104  CB  HIS    67     -21.434  49.580   2.751  1.00  0.00
ATOM    105  CG  HIS    67     -22.057  49.090   1.481  1.00  0.00
ATOM    106  CD2 HIS    67     -21.983  47.868   0.695  1.00  0.00
ATOM    107  ND1 HIS    67     -22.939  49.847   0.745  1.00  0.00
ATOM    108  CE1 HIS    67     -23.325  49.143  -0.334  1.00  0.00
ATOM    109  NE2 HIS    67     -22.755  47.954  -0.371  1.00  0.00
ATOM    110  O   HIS    67     -21.016  52.329   4.284  1.00  0.00
ATOM    111  C   HIS    67     -20.298  51.371   3.937  1.00  0.00
ATOM    112  N   TYR    68     -19.410  50.834   4.745  1.00  0.00
ATOM    113  CA  TYR    68     -19.257  51.164   6.137  1.00  0.00
ATOM    114  CB  TYR    68     -19.334  49.902   6.998  1.00  0.00
ATOM    115  CG  TYR    68     -20.648  49.164   6.888  1.00  0.00
ATOM    116  CD1 TYR    68     -20.766  48.035   6.086  1.00  0.00
ATOM    117  CD2 TYR    68     -21.767  49.598   7.587  1.00  0.00
ATOM    118  CE1 TYR    68     -21.964  47.354   5.980  1.00  0.00
ATOM    119  CE2 TYR    68     -22.974  48.930   7.493  1.00  0.00
ATOM    120  CZ  TYR    68     -23.065  47.800   6.680  1.00  0.00
ATOM    121  OH  TYR    68     -24.259  47.124   6.576  1.00  0.00
ATOM    122  O   TYR    68     -17.869  52.320   7.667  1.00  0.00
ATOM    123  C   TYR    68     -17.961  51.839   6.539  1.00  0.00
ATOM    124  N   PRO    69     -16.956  51.779   5.676  1.00  0.00
ATOM    125  CA  PRO    69     -15.656  52.351   5.999  1.00  0.00
ATOM    126  CB  PRO    69     -15.992  53.587   6.836  1.00  0.00
ATOM    127  CG  PRO    69     -17.241  53.218   7.561  1.00  0.00
ATOM    128  CD  PRO    69     -18.042  52.373   6.610  1.00  0.00
ATOM    129  O   PRO    69     -13.623  51.699   7.077  1.00  0.00
ATOM    130  C   PRO    69     -14.783  51.383   6.783  1.00  0.00
ATOM    131  N   PHE    70     -15.309  50.216   7.141  1.00  0.00
ATOM    132  CA  PHE    70     -14.560  49.229   7.898  1.00  0.00
ATOM    133  CB  PHE    70     -15.511  48.335   8.695  1.00  0.00
ATOM    134  CG  PHE    70     -16.202  49.040   9.829  1.00  0.00
ATOM    135  CD1 PHE    70     -17.475  49.558   9.666  1.00  0.00
ATOM    136  CD2 PHE    70     -15.579  49.187  11.054  1.00  0.00
ATOM    137  CE1 PHE    70     -18.111  50.206  10.707  1.00  0.00
ATOM    138  CE2 PHE    70     -16.214  49.836  12.096  1.00  0.00
ATOM    139  CZ  PHE    70     -17.475  50.345  11.926  1.00  0.00
ATOM    140  O   PHE    70     -14.245  47.802   5.984  1.00  0.00
ATOM    141  C   PHE    70     -13.734  48.341   6.968  1.00  0.00
ATOM    142  N   ILE    71     -12.474  48.159   7.337  1.00  0.00
ATOM    143  CA  ILE    71     -11.566  47.300   6.587  1.00  0.00
ATOM    144  CB  ILE    71     -10.175  47.941   6.441  1.00  0.00
ATOM    145  CG1 ILE    71     -10.269  49.244   5.647  1.00  0.00
ATOM    146  CG2 ILE    71      -9.228  46.999   5.712  1.00  0.00
ATOM    147  CD1 ILE    71      -9.001  50.071   5.676  1.00  0.00
ATOM    148  O   ILE    71     -11.457  45.881   8.548  1.00  0.00
ATOM    149  C   ILE    71     -11.420  45.972   7.323  1.00  0.00
ATOM    150  N   GLN    72     -11.328  44.896   6.552  1.00  0.00
ATOM    151  CA  GLN    72     -11.185  43.556   7.114  1.00  0.00
ATOM    152  CB  GLN    72     -12.281  42.630   6.578  1.00  0.00
ATOM    153  CG  GLN    72     -13.694  43.103   6.878  1.00  0.00
ATOM    154  CD  GLN    72     -13.997  43.127   8.363  1.00  0.00
ATOM    155  OE1 GLN    72     -13.743  42.155   9.075  1.00  0.00
ATOM    156  NE2 GLN    72     -14.542  44.242   8.836  1.00  0.00
ATOM    157  O   GLN    72      -9.365  43.311   5.618  1.00  0.00
ATOM    158  C   GLN    72      -9.817  43.008   6.718  1.00  0.00
ATOM    159  N   SER    73      -9.199  42.233   7.593  1.00  0.00
ATOM    160  CA  SER    73      -7.941  41.563   7.295  1.00  0.00
ATOM    161  CB  SER    73      -6.964  41.714   8.462  1.00  0.00
ATOM    162  OG  SER    73      -5.764  40.997   8.220  1.00  0.00
ATOM    163  O   SER    73      -8.791  39.454   7.983  1.00  0.00
ATOM    164  C   SER    73      -8.290  40.091   7.069  1.00  0.00
ATOM    165  N   PHE    74      -8.056  39.599   5.862  1.00  0.00
ATOM    166  CA  PHE    74      -8.398  38.233   5.500  1.00  0.00
ATOM    167  CB  PHE    74      -8.915  38.174   4.061  1.00  0.00
ATOM    168  CG  PHE    74      -9.267  36.789   3.599  1.00  0.00
ATOM    169  CD1 PHE    74     -10.463  36.202   3.973  1.00  0.00
ATOM    170  CD2 PHE    74      -8.401  36.071   2.791  1.00  0.00
ATOM    171  CE1 PHE    74     -10.787  34.926   3.548  1.00  0.00
ATOM    172  CE2 PHE    74      -8.725  34.796   2.367  1.00  0.00
ATOM    173  CZ  PHE    74      -9.912  34.223   2.742  1.00  0.00
ATOM    174  O   PHE    74      -6.131  37.599   5.088  1.00  0.00
ATOM    175  C   PHE    74      -7.205  37.285   5.592  1.00  0.00
ATOM    176  N   SER    75      -7.451  36.121   6.155  1.00  0.00
ATOM    177  CA  SER    75      -6.511  35.017   6.154  1.00  0.00
ATOM    178  CB  SER    75      -6.022  34.727   7.573  1.00  0.00
ATOM    179  OG  SER    75      -7.088  34.297   8.402  1.00  0.00
ATOM    180  O   SER    75      -8.497  33.772   5.633  1.00  0.00
ATOM    181  C   SER    75      -7.256  33.795   5.585  1.00  0.00
ATOM    182  N   LEU    76      -6.521  32.796   5.112  1.00  0.00
ATOM    183  CA  LEU    76      -7.211  31.628   4.556  1.00  0.00
ATOM    184  CB  LEU    76      -7.468  31.820   3.059  1.00  0.00
ATOM    185  CG  LEU    76      -6.233  32.043   2.184  1.00  0.00
ATOM    186  CD1 LEU    76      -5.610  30.714   1.786  1.00  0.00
ATOM    187  CD2 LEU    76      -6.604  32.792   0.913  1.00  0.00
ATOM    188  O   LEU    76      -5.176  30.407   4.861  1.00  0.00
ATOM    189  C   LEU    76      -6.416  30.344   4.715  1.00  0.00
ATOM    190  N   LEU    77      -7.119  29.235   4.705  1.00  0.00
ATOM    191  CA  LEU    77      -6.475  27.922   4.771  1.00  0.00
ATOM    192  CB  LEU    77      -5.747  27.748   6.105  1.00  0.00
ATOM    193  CG  LEU    77      -6.630  27.558   7.341  1.00  0.00
ATOM    194  CD1 LEU    77      -5.814  27.029   8.509  1.00  0.00
ATOM    195  CD2 LEU    77      -7.262  28.876   7.759  1.00  0.00
ATOM    196  O   LEU    77      -8.751  27.249   4.477  1.00  0.00
ATOM    197  C   LEU    77      -7.570  26.877   4.633  1.00  0.00
ATOM    198  N   SER    78      -7.241  25.596   4.627  1.00  0.00
ATOM    199  CA  SER    78      -8.231  24.539   4.583  1.00  0.00
ATOM    200  CB  SER    78      -7.553  23.175   4.439  1.00  0.00
ATOM    201  OG  SER    78      -6.805  22.852   5.598  1.00  0.00
ATOM    202  O   SER    78      -8.476  24.947   6.940  1.00  0.00
ATOM    203  C   SER    78      -9.028  24.580   5.884  1.00  0.00
TER
END
