
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0304AL333_4-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304AL333_4-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    R      17      G      52          5.081
LGA    P      18      L      53          4.824
LGA    W      19      F      54           #
LGA    W      20      S      55          2.574
LGA    G      21      D      56           #
LGA    L      22      -       -           -
LGA    P      23      -       -           -
LGA    C      24      A      57           #
LGA    T      25      D      58           #
LGA    V      26      A      59          2.908
LGA    T      27      Y      60          4.854
LGA    -       -      H      61           -
LGA    P      28      L      62          2.419
LGA    C      29      D      63           #
LGA    F      30      -       -           -
LGA    G      31      -       -           -
LGA    A      32      -       -           -
LGA    R      33      -       -           -
LGA    L      34      -       -           -
LGA    V      35      Q      64          5.247
LGA    Q      36      A      65          1.562
LGA    E      37      F      66          1.098
LGA    G      38      P      67          1.167
LGA    N      39      L      68          0.948
LGA    R      40      L      69          0.649
LGA    L      41      M      70          0.616
LGA    H      42      K      71          0.741
LGA    Y      43      Q      72          0.822
LGA    L      44      L      73          0.821
LGA    A      45      E      74          0.856
LGA    D      46      L      75          1.097
LGA    R      47      M      76          1.883
LGA    A      48      L      77          1.749
LGA    G      49      T      78          0.523
LGA    I      50      S      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    -       -      N      83           -
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      Y     115           -
LGA    -       -      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34  101    5.0     21    2.57     4.76     16.403     0.787

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.679821 * X  +   0.733307 * Y  +  -0.010207 * Z  +   5.416187
  Y_new =   0.640515 * X  +  -0.600461 * Y  +  -0.478734 * Z  + -12.760550
  Z_new =  -0.357188 * X  +   0.318916 * Y  +  -0.877901 * Z  +  62.541744 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.793144   -0.348448  [ DEG:   160.0354    -19.9646 ]
  Theta =   0.365256    2.776337  [ DEG:    20.9276    159.0724 ]
  Phi   =   0.755637   -2.385955  [ DEG:    43.2948   -136.7052 ]
 
# 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: T0304AL333_4-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL333_4-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34  101   5.0   21   2.57    4.76  16.403
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL333_4-D1
REMARK Aligment from pdb entry: 1glq_A
ATOM     65  N   ARG    17      35.919  15.919  30.744  1.00  0.00              
ATOM     66  CA  ARG    17      36.462  14.845  29.910  1.00  0.00              
ATOM     67  C   ARG    17      35.912  14.955  28.485  1.00  0.00              
ATOM     68  O   ARG    17      36.619  14.680  27.533  1.00  0.00              
ATOM     69  N   PRO    18      34.680  15.426  28.286  1.00  0.00              
ATOM     70  CA  PRO    18      34.095  15.604  26.965  1.00  0.00              
ATOM     71  C   PRO    18      34.920  16.600  26.183  1.00  0.00              
ATOM     72  O   PRO    18      35.349  16.315  25.066  1.00  0.00              
ATOM     73  N   TRP    19      35.197  17.788  26.764  1.00  0.00              
ATOM     74  CA  TRP    19      36.072  18.764  26.140  1.00  0.00              
ATOM     75  C   TRP    19      37.439  18.152  25.886  1.00  0.00              
ATOM     76  O   TRP    19      37.886  18.245  24.740  1.00  0.00              
ATOM     77  N   TRP    20      38.083  17.483  26.867  1.00  0.00              
ATOM     78  CA  TRP    20      39.404  16.927  26.666  1.00  0.00              
ATOM     79  C   TRP    20      39.395  15.980  25.483  1.00  0.00              
ATOM     80  O   TRP    20      40.271  16.080  24.605  1.00  0.00              
ATOM     81  N   GLY    21      48.069  21.454  22.464  1.00  0.00              
ATOM     82  CA  GLY    21      48.725  22.703  22.806  1.00  0.00              
ATOM     83  C   GLY    21      49.458  22.591  24.143  1.00  0.00              
ATOM     84  O   GLY    21      50.210  23.498  24.537  1.00  0.00              
ATOM     85  N   LEU    22      49.208  21.521  24.898  1.00  0.00              
ATOM     86  CA  LEU    22      49.863  21.273  26.169  1.00  0.00              
ATOM     87  C   LEU    22      51.249  20.739  25.881  1.00  0.00              
ATOM     88  O   LEU    22      51.371  19.811  25.079  1.00  0.00              
ATOM     89  N   PRO    23      52.299  21.275  26.520  1.00  0.00              
ATOM     90  CA  PRO    23      53.683  20.882  26.217  1.00  0.00              
ATOM     91  C   PRO    23      53.914  19.374  26.196  1.00  0.00              
ATOM     92  O   PRO    23      54.460  18.817  25.248  1.00  0.00              
ATOM     93  N   CYS    24      53.526  18.710  27.277  1.00  0.00              
ATOM     94  CA  CYS    24      53.672  17.264  27.345  1.00  0.00              
ATOM     95  C   CYS    24      52.332  16.541  27.077  1.00  0.00              
ATOM     96  O   CYS    24      52.168  15.400  27.535  1.00  0.00              
ATOM     97  N   THR    25      51.330  17.198  26.470  1.00  0.00              
ATOM     98  CA  THR    25      49.985  16.658  26.212  1.00  0.00              
ATOM     99  C   THR    25      49.157  16.386  27.463  1.00  0.00              
ATOM    100  O   THR    25      48.194  15.623  27.415  1.00  0.00              
ATOM    101  N   VAL    26      49.443  16.983  28.625  1.00  0.00              
ATOM    102  CA  VAL    26      48.723  16.647  29.852  1.00  0.00              
ATOM    103  C   VAL    26      48.457  17.891  30.649  1.00  0.00              
ATOM    104  O   VAL    26      49.047  18.941  30.351  1.00  0.00              
ATOM    105  N   THR    27      47.569  17.771  31.643  1.00  0.00              
ATOM    106  CA  THR    27      47.234  18.823  32.581  1.00  0.00              
ATOM    107  C   THR    27      47.762  18.431  33.969  1.00  0.00              
ATOM    108  O   THR    27      47.898  17.225  34.184  1.00  0.00              
ATOM    109  N   PRO    28      48.035  19.285  34.976  1.00  0.00              
ATOM    110  CA  PRO    28      47.690  20.725  34.972  1.00  0.00              
ATOM    111  C   PRO    28      48.448  21.698  34.073  1.00  0.00              
ATOM    112  O   PRO    28      49.580  21.450  33.658  1.00  0.00              
ATOM    113  N   CYS    29      47.778  22.777  33.710  1.00  0.00              
ATOM    114  CA  CYS    29      48.411  23.874  33.012  1.00  0.00              
ATOM    115  C   CYS    29      48.245  25.028  34.000  1.00  0.00              
ATOM    116  O   CYS    29      47.194  25.140  34.653  1.00  0.00              
ATOM    117  N   PHE    30      49.246  25.894  34.190  1.00  0.00              
ATOM    118  CA  PHE    30      49.166  26.966  35.176  1.00  0.00              
ATOM    119  C   PHE    30      49.633  28.270  34.530  1.00  0.00              
ATOM    120  O   PHE    30      50.627  28.258  33.800  1.00  0.00              
ATOM    121  N   GLY    31      52.307  36.232  32.824  1.00  0.00              
ATOM    122  CA  GLY    31      52.992  35.994  31.560  1.00  0.00              
ATOM    123  C   GLY    31      53.536  34.571  31.355  1.00  0.00              
ATOM    124  O   GLY    31      53.818  34.149  30.231  1.00  0.00              
ATOM    125  N   ALA    32      53.763  33.863  32.458  1.00  0.00              
ATOM    126  CA  ALA    32      54.380  32.547  32.461  1.00  0.00              
ATOM    127  C   ALA    32      53.361  31.399  32.472  1.00  0.00              
ATOM    128  O   ALA    32      52.511  31.295  33.364  1.00  0.00              
ATOM    129  N   ARG    33      53.482  30.517  31.491  1.00  0.00              
ATOM    130  CA  ARG    33      52.641  29.344  31.404  1.00  0.00              
ATOM    131  C   ARG    33      53.549  28.190  31.772  1.00  0.00              
ATOM    132  O   ARG    33      54.641  28.030  31.223  1.00  0.00              
ATOM    133  N   LEU    34      53.122  27.415  32.749  1.00  0.00              
ATOM    134  CA  LEU    34      53.880  26.274  33.209  1.00  0.00              
ATOM    135  C   LEU    34      53.044  25.011  33.087  1.00  0.00              
ATOM    136  O   LEU    34      51.799  25.057  33.055  1.00  0.00              
ATOM    137  N   VAL    35      53.761  23.905  32.912  1.00  0.00              
ATOM    138  CA  VAL    35      53.186  22.560  32.967  1.00  0.00              
ATOM    139  C   VAL    35      54.012  21.872  34.038  1.00  0.00              
ATOM    140  O   VAL    35      55.063  22.395  34.440  1.00  0.00              
ATOM    141  N   GLN    36      53.561  20.669  34.434  1.00  0.00              
ATOM    142  CA  GLN    36      54.154  19.798  35.451  1.00  0.00              
ATOM    143  C   GLN    36      53.829  20.268  36.867  1.00  0.00              
ATOM    144  O   GLN    36      54.400  21.257  37.369  1.00  0.00              
ATOM    145  N   GLU    37      52.950  19.534  37.596  1.00  0.00              
ATOM    146  CA  GLU    37      52.494  19.939  38.913  1.00  0.00              
ATOM    147  C   GLU    37      53.599  20.223  39.921  1.00  0.00              
ATOM    148  O   GLU    37      53.499  21.187  40.690  1.00  0.00              
ATOM    149  N   GLY    38      54.702  19.478  39.938  1.00  0.00              
ATOM    150  CA  GLY    38      55.738  19.780  40.921  1.00  0.00              
ATOM    151  C   GLY    38      56.584  20.972  40.505  1.00  0.00              
ATOM    152  O   GLY    38      57.113  21.650  41.374  1.00  0.00              
ATOM    153  N   ASN    39      56.694  21.254  39.197  1.00  0.00              
ATOM    154  CA  ASN    39      57.382  22.462  38.742  1.00  0.00              
ATOM    155  C   ASN    39      56.573  23.689  39.168  1.00  0.00              
ATOM    156  O   ASN    39      57.121  24.707  39.576  1.00  0.00              
ATOM    157  N   ARG    40      55.240  23.623  39.068  1.00  0.00              
ATOM    158  CA  ARG    40      54.346  24.681  39.520  1.00  0.00              
ATOM    159  C   ARG    40      54.453  24.840  41.037  1.00  0.00              
ATOM    160  O   ARG    40      54.535  25.981  41.529  1.00  0.00              
ATOM    161  N   LEU    41      54.476  23.755  41.824  1.00  0.00              
ATOM    162  CA  LEU    41      54.677  23.879  43.259  1.00  0.00              
ATOM    163  C   LEU    41      56.015  24.512  43.627  1.00  0.00              
ATOM    164  O   LEU    41      56.075  25.357  44.521  1.00  0.00              
ATOM    165  N   HIS    42      57.104  24.097  42.974  1.00  0.00              
ATOM    166  CA  HIS    42      58.419  24.679  43.235  1.00  0.00              
ATOM    167  C   HIS    42      58.428  26.146  42.802  1.00  0.00              
ATOM    168  O   HIS    42      58.970  26.970  43.522  1.00  0.00              
ATOM    169  N   TYR    43      57.777  26.529  41.708  1.00  0.00              
ATOM    170  CA  TYR    43      57.686  27.913  41.285  1.00  0.00              
ATOM    171  C   TYR    43      57.009  28.761  42.373  1.00  0.00              
ATOM    172  O   TYR    43      57.477  29.850  42.731  1.00  0.00              
ATOM    173  N   LEU    44      55.879  28.295  42.907  1.00  0.00              
ATOM    174  CA  LEU    44      55.167  29.029  43.945  1.00  0.00              
ATOM    175  C   LEU    44      55.984  29.082  45.231  1.00  0.00              
ATOM    176  O   LEU    44      55.996  30.103  45.926  1.00  0.00              
ATOM    177  N   ALA    45      56.751  28.040  45.540  1.00  0.00              
ATOM    178  CA  ALA    45      57.608  28.031  46.721  1.00  0.00              
ATOM    179  C   ALA    45      58.677  29.096  46.560  1.00  0.00              
ATOM    180  O   ALA    45      58.939  29.873  47.470  1.00  0.00              
ATOM    181  N   ASP    46      59.262  29.205  45.381  1.00  0.00              
ATOM    182  CA  ASP    46      60.323  30.168  45.086  1.00  0.00              
ATOM    183  C   ASP    46      59.756  31.582  45.110  1.00  0.00              
ATOM    184  O   ASP    46      60.211  32.429  45.882  1.00  0.00              
ATOM    185  N   ARG    47      58.666  31.835  44.394  1.00  0.00              
ATOM    186  CA  ARG    47      58.179  33.181  44.314  1.00  0.00              
ATOM    187  C   ARG    47      57.470  33.664  45.546  1.00  0.00              
ATOM    188  O   ARG    47      57.418  34.877  45.740  1.00  0.00              
ATOM    189  N   ALA    48      56.911  32.811  46.406  1.00  0.00              
ATOM    190  CA  ALA    48      56.201  33.295  47.565  1.00  0.00              
ATOM    191  C   ALA    48      57.018  33.107  48.833  1.00  0.00              
ATOM    192  O   ALA    48      56.524  33.338  49.937  1.00  0.00              
ATOM    193  N   GLY    49      58.285  32.711  48.723  1.00  0.00              
ATOM    194  CA  GLY    49      59.144  32.586  49.878  1.00  0.00              
ATOM    195  C   GLY    49      58.869  31.368  50.747  1.00  0.00              
ATOM    196  O   GLY    49      59.013  31.393  51.970  1.00  0.00              
ATOM    197  N   ILE    50      58.560  30.246  50.121  1.00  0.00              
ATOM    198  CA  ILE    50      58.250  28.995  50.793  1.00  0.00              
ATOM    199  C   ILE    50      59.227  27.916  50.415  1.00  0.00              
ATOM    200  O   ILE    50      58.809  26.762  50.238  1.00  0.00              
END
