
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0304AL243_2-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304AL243_2-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R      17           -
LGA    -       -      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    P      67      P      67          1.236
LGA    L      68      L      68          1.362
LGA    L      69      L      69          1.421
LGA    M      70      M      70          1.282
LGA    K      71      K      71          0.812
LGA    Q      72      Q      72          0.319
LGA    L      73      L      73          0.523
LGA    E      74      E      74          0.447
LGA    L      75      L      75          0.910
LGA    M      76      M      76          1.166
LGA    L      77      L      77          1.481
LGA    T      78      T      78          1.318
LGA    S      79      S      79          1.603
LGA    G      80      G      80          2.084
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    P      84      N      83          2.382
LGA    R      85      P      84          3.426
LGA    -       -      R      85           -
LGA    H      86      H      86          3.005
LGA    Q      87      Q      87          3.721
LGA    -       -      H      88           -
LGA    H      88      T      89          3.705
LGA    T      89      V      90          1.346
LGA    V      90      T      91          1.457
LGA    T      91      L      92          1.842
LGA    L      92      Y      93          1.402
LGA    Y      93      A      94          3.288
LGA    -       -      K      95           -
LGA    A      94      G      96           #
LGA    K      95      L      97          3.210
LGA    G      96      T      98          0.824
LGA    L      97      C      99          2.263
LGA    T      98      K     100          1.551
LGA    C      99      A     101          1.753
LGA    K     100      D     102          2.022
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    A     101      C     107          4.369
LGA    D     102      D     108          5.555
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      Y     109           #
LGA    D     108      V     110           -
LGA    Y     109      -       -           -
LGA    V     110      -       -           -
LGA    Y     111      Y     111           #
LGA    L     112      L     112           -
LGA    A     113      A     113           -
LGA    V     114      V     114           -
LGA    Y     115      Y     115           -
LGA    -       -      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45  101    5.0     32    2.31    53.12     24.832     1.327

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.043126 * X  +  -0.998929 * Y  +   0.016740 * Z  +  74.977318
  Y_new =   0.676097 * X  +   0.016844 * Y  +  -0.736620 * Z  + 135.580917
  Z_new =   0.735549 * X  +   0.043086 * Y  +   0.676100 * Z  + -35.953369 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.063641   -3.077952  [ DEG:     3.6463   -176.3537 ]
  Theta =  -0.826477   -2.315115  [ DEG:   -47.3537   -132.6463 ]
  Phi   =   1.507096   -1.634497  [ DEG:    86.3503    -93.6497 ]
 
# 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: T0304AL243_2-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL243_2-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45  101   5.0   32   2.31   53.12  24.832
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL243_2-D1
REMARK Aligment from pdb entry: 1eerB
ATOM      1  N   PRO    67      54.388  19.740  40.865  1.00  0.00              
ATOM      2  CA  PRO    67      55.845  19.568  40.932  1.00  0.00              
ATOM      3  C   PRO    67      56.605  20.871  40.682  1.00  0.00              
ATOM      4  O   PRO    67      56.817  21.663  41.609  1.00  0.00              
ATOM      5  N   LEU    68      57.024  21.080  39.432  1.00  0.00              
ATOM      6  CA  LEU    68      57.732  22.298  39.046  1.00  0.00              
ATOM      7  C   LEU    68      56.793  23.441  39.417  1.00  0.00              
ATOM      8  O   LEU    68      57.201  24.597  39.566  1.00  0.00              
ATOM      9  N   LEU    69      55.525  23.083  39.570  1.00  0.00              
ATOM     10  CA  LEU    69      54.489  24.021  39.951  1.00  0.00              
ATOM     11  C   LEU    69      54.747  24.471  41.393  1.00  0.00              
ATOM     12  O   LEU    69      54.768  25.670  41.684  1.00  0.00              
ATOM     13  N   MET    70      54.953  23.506  42.288  1.00  0.00              
ATOM     14  CA  MET    70      55.204  23.799  43.696  1.00  0.00              
ATOM     15  C   MET    70      56.362  24.764  43.894  1.00  0.00              
ATOM     16  O   MET    70      56.287  25.678  44.717  1.00  0.00              
ATOM     17  N   LYS    71      57.442  24.547  43.152  1.00  0.00              
ATOM     18  CA  LYS    71      58.605  25.416  43.247  1.00  0.00              
ATOM     19  C   LYS    71      58.197  26.825  42.819  1.00  0.00              
ATOM     20  O   LYS    71      58.537  27.817  43.473  1.00  0.00              
ATOM     21  N   GLN    72      57.464  26.902  41.713  1.00  0.00              
ATOM     22  CA  GLN    72      57.001  28.185  41.198  1.00  0.00              
ATOM     23  C   GLN    72      56.075  28.819  42.222  1.00  0.00              
ATOM     24  O   GLN    72      56.144  30.019  42.487  1.00  0.00              
ATOM     25  N   LEU    73      55.203  28.003  42.797  1.00  0.00              
ATOM     26  CA  LEU    73      54.279  28.493  43.805  1.00  0.00              
ATOM     27  C   LEU    73      55.115  28.976  44.985  1.00  0.00              
ATOM     28  O   LEU    73      54.868  30.047  45.545  1.00  0.00              
ATOM     29  N   GLU    74      56.119  28.175  45.337  1.00  0.00              
ATOM     30  CA  GLU    74      57.016  28.477  46.452  1.00  0.00              
ATOM     31  C   GLU    74      57.783  29.768  46.198  1.00  0.00              
ATOM     32  O   GLU    74      57.933  30.603  47.094  1.00  0.00              
ATOM     33  N   LEU    75      58.267  29.919  44.968  1.00  0.00              
ATOM     34  CA  LEU    75      59.015  31.104  44.556  1.00  0.00              
ATOM     35  C   LEU    75      58.197  32.390  44.757  1.00  0.00              
ATOM     36  O   LEU    75      58.700  33.380  45.293  1.00  0.00              
ATOM     37  N   MET    76      56.934  32.365  44.325  1.00  0.00              
ATOM     38  CA  MET    76      56.046  33.522  44.441  1.00  0.00              
ATOM     39  C   MET    76      55.631  33.816  45.874  1.00  0.00              
ATOM     40  O   MET    76      55.507  34.979  46.272  1.00  0.00              
ATOM     41  N   LEU    77      55.395  32.757  46.642  1.00  0.00              
ATOM     42  CA  LEU    77      54.999  32.896  48.039  1.00  0.00              
ATOM     43  C   LEU    77      56.187  33.417  48.822  1.00  0.00              
ATOM     44  O   LEU    77      56.080  34.401  49.558  1.00  0.00              
ATOM     45  N   THR    78      57.325  32.752  48.641  1.00  0.00              
ATOM     46  CA  THR    78      58.562  33.120  49.315  1.00  0.00              
ATOM     47  C   THR    78      58.851  34.611  49.210  1.00  0.00              
ATOM     48  O   THR    78      59.528  35.179  50.061  1.00  0.00              
ATOM     49  N   SER    79      58.334  35.244  48.162  1.00  0.00              
ATOM     50  CA  SER    79      58.551  36.669  47.953  1.00  0.00              
ATOM     51  C   SER    79      57.290  37.506  48.169  1.00  0.00              
ATOM     52  O   SER    79      57.365  38.732  48.256  1.00  0.00              
ATOM     53  N   GLY    80      56.133  36.857  48.264  1.00  0.00              
ATOM     54  CA  GLY    80      54.903  37.608  48.459  1.00  0.00              
ATOM     55  C   GLY    80      53.920  36.989  49.434  1.00  0.00              
ATOM     56  O   GLY    80      52.786  36.689  49.056  1.00  0.00              
ATOM     57  N   PRO    84      54.321  36.793  50.705  1.00  0.00              
ATOM     58  CA  PRO    84      53.446  36.199  51.723  1.00  0.00              
ATOM     59  C   PRO    84      52.329  37.122  52.197  1.00  0.00              
ATOM     60  O   PRO    84      52.501  38.341  52.258  1.00  0.00              
ATOM     61  N   ARG    85      51.187  36.518  52.520  1.00  0.00              
ATOM     62  CA  ARG    85      50.013  37.230  53.012  1.00  0.00              
ATOM     63  C   ARG    85      49.007  37.665  51.956  1.00  0.00              
ATOM     64  O   ARG    85      47.840  37.893  52.283  1.00  0.00              
ATOM     65  N   HIS    86      49.434  37.787  50.702  1.00  0.00              
ATOM     66  CA  HIS    86      48.504  38.217  49.657  1.00  0.00              
ATOM     67  C   HIS    86      48.143  37.151  48.634  1.00  0.00              
ATOM     68  O   HIS    86      48.789  36.105  48.553  1.00  0.00              
ATOM     69  N   GLN    87      47.097  37.429  47.858  1.00  0.00              
ATOM     70  CA  GLN    87      46.624  36.509  46.827  1.00  0.00              
ATOM     71  C   GLN    87      47.516  36.603  45.595  1.00  0.00              
ATOM     72  O   GLN    87      47.581  37.642  44.945  1.00  0.00              
ATOM     73  N   HIS    88      48.208  35.513  45.285  1.00  0.00              
ATOM     74  CA  HIS    88      49.106  35.486  44.144  1.00  0.00              
ATOM     75  C   HIS    88      48.551  34.646  43.008  1.00  0.00              
ATOM     76  O   HIS    88      48.178  33.489  43.193  1.00  0.00              
ATOM     77  N   THR    89      48.511  35.239  41.824  1.00  0.00              
ATOM     78  CA  THR    89      48.020  34.545  40.649  1.00  0.00              
ATOM     79  C   THR    89      49.131  34.515  39.623  1.00  0.00              
ATOM     80  O   THR    89      49.884  35.475  39.493  1.00  0.00              
ATOM     81  N   VAL    90      49.242  33.417  38.892  1.00  0.00              
ATOM     82  CA  VAL    90      50.275  33.333  37.883  1.00  0.00              
ATOM     83  C   VAL    90      49.892  32.368  36.780  1.00  0.00              
ATOM     84  O   VAL    90      49.011  31.517  36.950  1.00  0.00              
ATOM     85  N   THR    91      50.547  32.537  35.636  1.00  0.00              
ATOM     86  CA  THR    91      50.329  31.705  34.469  1.00  0.00              
ATOM     87  C   THR    91      51.705  31.282  33.975  1.00  0.00              
ATOM     88  O   THR    91      52.676  32.023  34.115  1.00  0.00              
ATOM     89  N   LEU    92      51.794  30.090  33.403  1.00  0.00              
ATOM     90  CA  LEU    92      53.069  29.620  32.904  1.00  0.00              
ATOM     91  C   LEU    92      53.069  29.501  31.388  1.00  0.00              
ATOM     92  O   LEU    92      54.087  29.735  30.741  1.00  0.00              
ATOM     93  N   TYR    93      51.919  29.152  30.822  1.00  0.00              
ATOM     94  CA  TYR    93      51.798  28.992  29.378  1.00  0.00              
ATOM     95  C   TYR    93      50.684  29.851  28.775  1.00  0.00              
ATOM     96  O   TYR    93      50.228  29.586  27.661  1.00  0.00              
ATOM     97  N   ALA    94      50.256  30.872  29.512  1.00  0.00              
ATOM     98  CA  ALA    94      49.200  31.781  29.068  1.00  0.00              
ATOM     99  C   ALA    94      47.894  31.050  28.799  1.00  0.00              
ATOM    100  O   ALA    94      46.857  31.678  28.584  1.00  0.00              
ATOM    101  N   LYS    95      47.948  29.722  28.814  1.00  0.00              
ATOM    102  CA  LYS    95      46.767  28.893  28.582  1.00  0.00              
ATOM    103  C   LYS    95      46.225  28.460  29.938  1.00  0.00              
ATOM    104  O   LYS    95      45.149  27.869  30.036  1.00  0.00              
ATOM    105  N   GLY    96      46.987  28.777  30.979  1.00  0.00              
ATOM    106  CA  GLY    96      46.648  28.406  32.344  1.00  0.00              
ATOM    107  C   GLY    96      46.711  29.588  33.299  1.00  0.00              
ATOM    108  O   GLY    96      47.291  30.619  32.985  1.00  0.00              
ATOM    109  N   LEU    97      46.123  29.413  34.477  1.00  0.00              
ATOM    110  CA  LEU    97      46.123  30.439  35.507  1.00  0.00              
ATOM    111  C   LEU    97      45.783  29.834  36.851  1.00  0.00              
ATOM    112  O   LEU    97      44.804  29.096  36.986  1.00  0.00              
ATOM    113  N   THR    98      46.591  30.164  37.849  1.00  0.00              
ATOM    114  CA  THR    98      46.375  29.660  39.193  1.00  0.00              
ATOM    115  C   THR    98      46.498  30.762  40.226  1.00  0.00              
ATOM    116  O   THR    98      47.525  31.439  40.329  1.00  0.00              
ATOM    117  N   CYS    99      45.432  30.941  40.990  1.00  0.00              
ATOM    118  CA  CYS    99      45.418  31.927  42.050  1.00  0.00              
ATOM    119  C   CYS    99      45.413  31.128  43.336  1.00  0.00              
ATOM    120  O   CYS    99      44.695  30.134  43.459  1.00  0.00              
ATOM    121  N   LYS   100      46.210  31.557  44.298  1.00  0.00              
ATOM    122  CA  LYS   100      46.280  30.836  45.539  1.00  0.00              
ATOM    123  C   LYS   100      46.721  31.720  46.671  1.00  0.00              
ATOM    124  O   LYS   100      46.934  32.919  46.499  1.00  0.00              
ATOM    125  N   ALA   101      46.179  30.381  59.384  1.00  0.00              
ATOM    126  CA  ALA   101      44.961  30.172  60.151  1.00  0.00              
ATOM    127  C   ALA   101      44.390  28.813  59.750  1.00  0.00              
ATOM    128  O   ALA   101      43.882  28.654  58.635  1.00  0.00              
ATOM    129  N   ASP   102      44.479  27.841  60.657  1.00  0.00              
ATOM    130  CA  ASP   102      43.986  26.483  60.404  1.00  0.00              
ATOM    131  C   ASP   102      42.857  26.079  61.357  1.00  0.00              
ATOM    132  O   ASP   102      42.421  26.882  62.182  1.00  0.00              
ATOM    133  N   THR   103      42.388  24.837  61.233  1.00  0.00              
ATOM    134  CA  THR   103      41.312  24.296  62.074  1.00  0.00              
ATOM    135  C   THR   103      40.031  25.143  62.068  1.00  0.00              
ATOM    136  O   THR   103      40.023  26.283  62.540  1.00  0.00              
ATOM    137  N   LEU   104      38.943  24.571  61.551  1.00  0.00              
ATOM    138  CA  LEU   104      37.681  25.293  61.475  1.00  0.00              
ATOM    139  C   LEU   104      37.506  25.860  60.075  1.00  0.00              
ATOM    140  O   LEU   104      36.402  26.220  59.647  1.00  0.00              
ATOM    141  N   SER   105      38.627  25.939  59.365  1.00  0.00              
ATOM    142  CA  SER   105      38.669  26.435  57.998  1.00  0.00              
ATOM    143  C   SER   105      38.472  25.249  57.054  1.00  0.00              
ATOM    144  O   SER   105      39.440  24.674  56.555  1.00  0.00              
ATOM    145  N   SER   106      37.215  24.885  56.822  1.00  0.00              
ATOM    146  CA  SER   106      36.919  23.762  55.952  1.00  0.00              
ATOM    147  C   SER   106      36.999  24.108  54.480  1.00  0.00              
ATOM    148  O   SER   106      37.338  25.237  54.128  1.00  0.00              
ATOM    149  N   ASP   108      36.688  23.157  53.587  1.00  0.00              
ATOM    150  CA  ASP   108      36.745  23.422  52.147  1.00  0.00              
ATOM    151  C   ASP   108      35.702  24.448  51.697  1.00  0.00              
ATOM    152  O   ASP   108      35.823  25.044  50.625  1.00  0.00              
ATOM    153  N   TYR   109      34.678  24.651  52.518  1.00  0.00              
ATOM    154  CA  TYR   109      33.644  25.618  52.183  1.00  0.00              
ATOM    155  C   TYR   109      33.838  26.897  52.973  1.00  0.00              
ATOM    156  O   TYR   109      32.911  27.692  53.156  1.00  0.00              
ATOM    157  N   VAL   110      35.063  27.094  53.445  1.00  0.00              
ATOM    158  CA  VAL   110      35.407  28.265  54.233  1.00  0.00              
ATOM    159  C   VAL   110      35.512  29.504  53.359  1.00  0.00              
ATOM    160  O   VAL   110      35.383  30.633  53.844  1.00  0.00              
ATOM    161  N   TYR   111      35.742  29.290  52.068  1.00  0.00              
ATOM    162  CA  TYR   111      35.890  30.404  51.141  1.00  0.00              
ATOM    163  C   TYR   111      35.185  30.192  49.818  1.00  0.00              
ATOM    164  O   TYR   111      35.062  29.057  49.344  1.00  0.00              
ATOM    165  N   LEU   112      34.722  31.302  49.237  1.00  0.00              
ATOM    166  CA  LEU   112      34.050  31.301  47.938  1.00  0.00              
ATOM    167  C   LEU   112      34.920  32.105  46.951  1.00  0.00              
ATOM    168  O   LEU   112      35.239  33.272  47.200  1.00  0.00              
ATOM    169  N   ALA   113      35.310  31.477  45.842  1.00  0.00              
ATOM    170  CA  ALA   113      36.157  32.130  44.836  1.00  0.00              
ATOM    171  C   ALA   113      35.455  32.552  43.536  1.00  0.00              
ATOM    172  O   ALA   113      35.266  31.737  42.622  1.00  0.00              
ATOM    173  N   VAL   114      35.101  33.831  43.447  1.00  0.00              
ATOM    174  CA  VAL   114      34.434  34.369  42.265  1.00  0.00              
ATOM    175  C   VAL   114      35.377  35.147  41.345  1.00  0.00              
ATOM    176  O   VAL   114      36.335  35.780  41.801  1.00  0.00              
ATOM    177  N   TYR   115      35.095  35.095  40.046  1.00  0.00              
ATOM    178  CA  TYR   115      35.894  35.812  39.047  1.00  0.00              
ATOM    179  C   TYR   115      35.045  36.286  37.877  1.00  0.00              
ATOM    180  O   TYR   115      34.026  35.679  37.542  1.00  0.00              
END
