
#######################################################
#                                                     #
#                        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 T0329AL586_1-D2
# Molecule2: number of CA atoms   92 (  716),  selected   92 , name T0329_D2.pdb
# PARAMETERS: T0329AL586_1-D2.T0329_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T      22      T      17          2.674
LGA    S      23      S      18          1.880
LGA    A      24      A      19          1.407
LGA    L      25      D      20          1.217
LGA    N      26      L      21          0.701
LGA    Y      27      T      22          0.525
LGA    A      28      S      23          0.596
LGA    F      29      A      24          0.917
LGA    E      30      L      25          0.772
LGA    Q      31      N      26          0.904
LGA    -       -      Y      27           -
LGA    R      35      A      28          1.927
LGA    H      36      F      29          2.070
LGA    -       -      E      30           -
LGA    -       -      Q      31           -
LGA    -       -      T      32           -
LGA    -       -      G      33           -
LGA    F      38      H      34          2.999
LGA    V      40      R      35          2.096
LGA    -       -      H      36           -
LGA    I      43      D      37          3.439
LGA    K      44      F      38          2.768
LGA    F      47      T      39          4.189
LGA    G      48      V      40          3.527
LGA    S      49      E      41          1.067
LGA    -       -      D      42           -
LGA    -       -      I      43           -
LGA    -       -      K      44           -
LGA    L      59      N      45          3.144
LGA    A      60      F      46          5.785
LGA    S      65      F      47          1.974
LGA    -       -      G      48           -
LGA    S      66      S      49          2.723
LGA    R      67      G      50          3.316
LGA    -       -      V      51           -
LGA    -       -      V      52           -
LGA    E      68      V      53          1.711
LGA    T      75      A      54          1.758
LGA    K      76      V      55          0.975
LGA    D      77      T      56          1.719
LGA    E      78      R      57          1.962
LGA    Q      79      A      58          1.628
LGA    I      80      L      59          1.172
LGA    -       -      A      60           -
LGA    -       -      Y      61           -
LGA    -       -      E      62           -
LGA    -       -      A      63           -
LGA    -       -      G      64           -
LGA    -       -      S      65           -
LGA    -       -      S      66           -
LGA    -       -      R      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      L      70           -
LGA    -       -      V      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      G      74           -
LGA    -       -      T      75           -
LGA    -       -      K      76           -
LGA    -       -      D      77           -
LGA    -       -      E      78           -
LGA    -       -      Q      79           -
LGA    -       -      I      80           -
LGA    -       -      P      81           -
LGA    -       -      E      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    V      84      T      85          3.339
LGA    -       -      Q      86           -
LGA    E      88      T      87          2.166
LGA    V      89      E      88          3.518
LGA    -       -      V      89           -
LGA    -       -      N      90           -
LGA    -       -      R      91           -
LGA    L      93      V      92          2.143
LGA    V      95      L      93          3.026
LGA    -       -      E      94           -
LGA    -       -      V      95           -
LGA    F      96      F      96          1.039
LGA    K      97      K      97          1.351
LGA    Y      99      P      98          3.075
LGA    -       -      Y      99           -
LGA    Y     100      Y     100          0.440
LGA    A     101      A     101          0.697
LGA    H     103      D     102          2.601
LGA    C     104      H     103          4.074
LGA    -       -      C     104           -
LGA    I     106      Q     105          4.070
LGA    K     107      I     106           -
LGA    -       -      K     107           -
LGA    -       -      T     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   92    5.0     44    2.47    18.18     32.909     1.714

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.636242 * X  +   0.720918 * Y  +  -0.274722 * Z  + -24.326857
  Y_new =   0.667040 * X  +  -0.692959 * Y  +  -0.273614 * Z  +  22.219589
  Z_new =  -0.387625 * X  +  -0.009166 * Y  +  -0.921772 * Z  +  54.938435 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.131649    0.009943  [ DEG:  -179.4303      0.5697 ]
  Theta =   0.398054    2.743539  [ DEG:    22.8068    157.1932 ]
  Phi   =   0.809025   -2.332568  [ DEG:    46.3537   -133.6463 ]
 
# 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: T0329AL586_1-D2                               
REMARK     2: T0329_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329AL586_1-D2.T0329_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   92   5.0   44   2.47   18.18  32.909
REMARK  ---------------------------------------------------------- 
MOLECULE T0329AL586_1-D2
REMARK Aligment from pdb entry: 1o08_A
ATOM     45  N   THR    22      -3.690  12.137  47.936  1.00  0.00              
ATOM     46  CA  THR    22      -4.177  13.285  47.183  1.00  0.00              
ATOM     47  C   THR    22      -5.348  12.982  46.262  1.00  0.00              
ATOM     48  O   THR    22      -5.954  13.917  45.761  1.00  0.00              
ATOM     49  N   SER    23      -5.689  11.721  46.070  1.00  0.00              
ATOM     50  CA  SER    23      -6.944  11.423  45.386  1.00  0.00              
ATOM     51  C   SER    23      -8.101  12.038  46.151  1.00  0.00              
ATOM     52  O   SER    23      -9.088  12.527  45.564  1.00  0.00              
ATOM     53  N   ALA    24      -8.009  12.074  47.487  1.00  0.00              
ATOM     54  CA  ALA    24      -9.074  12.657  48.316  1.00  0.00              
ATOM     55  C   ALA    24      -9.183  14.141  47.999  1.00  0.00              
ATOM     56  O   ALA    24     -10.287  14.711  47.963  1.00  0.00              
ATOM     57  N   LEU    25      -8.039  14.790  47.807  1.00  0.00              
ATOM     58  CA  LEU    25      -8.072  16.239  47.544  1.00  0.00              
ATOM     59  C   LEU    25      -8.589  16.506  46.141  1.00  0.00              
ATOM     60  O   LEU    25      -9.370  17.455  45.899  1.00  0.00              
ATOM     61  N   ASN    26      -8.245  15.696  45.128  1.00  0.00              
ATOM     62  CA  ASN    26      -8.831  15.880  43.800  1.00  0.00              
ATOM     63  C   ASN    26     -10.342  15.715  43.855  1.00  0.00              
ATOM     64  O   ASN    26     -11.098  16.469  43.235  1.00  0.00              
ATOM     65  N   TYR    27     -10.829  14.723  44.584  1.00  0.00              
ATOM     66  CA  TYR    27     -12.276  14.499  44.750  1.00  0.00              
ATOM     67  C   TYR    27     -12.932  15.717  45.361  1.00  0.00              
ATOM     68  O   TYR    27     -13.923  16.247  44.850  1.00  0.00              
ATOM     69  N   ALA    28     -12.396  16.188  46.490  1.00  0.00              
ATOM     70  CA  ALA    28     -13.017  17.351  47.172  1.00  0.00              
ATOM     71  C   ALA    28     -13.054  18.552  46.241  1.00  0.00              
ATOM     72  O   ALA    28     -14.049  19.294  46.191  1.00  0.00              
ATOM     73  N   PHE    29     -11.978  18.767  45.509  1.00  0.00              
ATOM     74  CA  PHE    29     -11.910  19.939  44.624  1.00  0.00              
ATOM     75  C   PHE    29     -12.855  19.779  43.437  1.00  0.00              
ATOM     76  O   PHE    29     -13.547  20.755  43.056  1.00  0.00              
ATOM     77  N   GLU    30     -12.946  18.586  42.834  1.00  0.00              
ATOM     78  CA  GLU    30     -13.890  18.414  41.743  1.00  0.00              
ATOM     79  C   GLU    30     -15.322  18.522  42.212  1.00  0.00              
ATOM     80  O   GLU    30     -16.128  19.107  41.478  1.00  0.00              
ATOM     81  N   GLN    31     -15.603  17.994  43.388  1.00  0.00              
ATOM     82  CA  GLN    31     -16.983  18.101  43.912  1.00  0.00              
ATOM     83  C   GLN    31     -17.351  19.552  44.131  1.00  0.00              
ATOM     84  O   GLN    31     -18.446  19.997  43.793  1.00  0.00              
ATOM     85  N   ARG    35     -16.155  22.184  42.606  1.00  0.00              
ATOM     86  CA  ARG    35     -16.337  22.824  41.301  1.00  0.00              
ATOM     87  C   ARG    35     -17.706  22.510  40.745  1.00  0.00              
ATOM     88  O   ARG    35     -18.465  23.352  40.302  1.00  0.00              
ATOM     89  N   HIS    36     -18.027  21.219  40.718  1.00  0.00              
ATOM     90  CA  HIS    36     -19.291  20.742  40.175  1.00  0.00              
ATOM     91  C   HIS    36     -20.446  21.437  40.873  1.00  0.00              
ATOM     92  O   HIS    36     -21.385  21.968  40.231  1.00  0.00              
ATOM     93  N   PHE    38     -21.299  24.929  39.808  1.00  0.00              
ATOM     94  CA  PHE    38     -22.058  25.017  38.535  1.00  0.00              
ATOM     95  C   PHE    38     -23.361  24.213  38.550  1.00  0.00              
ATOM     96  O   PHE    38     -23.923  23.936  37.481  1.00  0.00              
ATOM     97  N   VAL    40     -24.074  21.108  39.495  1.00  0.00              
ATOM     98  CA  VAL    40     -23.996  19.664  39.188  1.00  0.00              
ATOM     99  C   VAL    40     -23.706  18.948  40.513  1.00  0.00              
ATOM    100  O   VAL    40     -22.624  19.162  41.033  1.00  0.00              
ATOM    101  N   ILE    43     -21.315  14.521  41.784  1.00  0.00              
ATOM    102  CA  ILE    43     -19.961  14.047  42.097  1.00  0.00              
ATOM    103  C   ILE    43     -19.904  13.592  43.549  1.00  0.00              
ATOM    104  O   ILE    43     -19.507  14.317  44.465  1.00  0.00              
ATOM    105  N   LYS    44     -20.357  12.366  43.755  1.00  0.00              
ATOM    106  CA  LYS    44     -20.190  11.725  45.061  1.00  0.00              
ATOM    107  C   LYS    44     -19.079  10.685  44.937  1.00  0.00              
ATOM    108  O   LYS    44     -18.405  10.522  43.900  1.00  0.00              
ATOM    109  N   PHE    47     -19.428   8.186  42.027  1.00  0.00              
ATOM    110  CA  PHE    47     -19.148   8.767  40.707  1.00  0.00              
ATOM    111  C   PHE    47     -17.670   9.042  40.542  1.00  0.00              
ATOM    112  O   PHE    47     -17.089   8.847  39.465  1.00  0.00              
ATOM    113  N   GLY    48     -17.023   9.439  41.641  1.00  0.00              
ATOM    114  CA  GLY    48     -15.617   9.827  41.592  1.00  0.00              
ATOM    115  C   GLY    48     -14.745   8.656  41.191  1.00  0.00              
ATOM    116  O   GLY    48     -13.630   8.900  40.710  1.00  0.00              
ATOM    117  N   SER    49     -15.200   7.394  41.330  1.00  0.00              
ATOM    118  CA  SER    49     -14.335   6.289  40.838  1.00  0.00              
ATOM    119  C   SER    49     -14.137   6.399  39.340  1.00  0.00              
ATOM    120  O   SER    49     -13.104   5.914  38.833  1.00  0.00              
ATOM    121  N   LEU    59     -13.621   9.249  37.835  1.00  0.00              
ATOM    122  CA  LEU    59     -12.713  10.376  37.691  1.00  0.00              
ATOM    123  C   LEU    59     -11.278  10.048  38.119  1.00  0.00              
ATOM    124  O   LEU    59     -10.367  10.746  37.653  1.00  0.00              
ATOM    125  N   ALA    60     -11.093   9.036  38.982  1.00  0.00              
ATOM    126  CA  ALA    60      -9.734   8.766  39.443  1.00  0.00              
ATOM    127  C   ALA    60      -8.849   8.403  38.245  1.00  0.00              
ATOM    128  O   ALA    60      -9.225   7.600  37.385  1.00  0.00              
ATOM    129  N   SER    65      -8.013  10.154  35.653  1.00  0.00              
ATOM    130  CA  SER    65      -8.411  10.829  34.432  1.00  0.00              
ATOM    131  C   SER    65      -7.864  12.240  34.404  1.00  0.00              
ATOM    132  O   SER    65      -7.800  12.905  35.466  1.00  0.00              
ATOM    133  N   SER    66      -7.469  12.747  33.229  1.00  0.00              
ATOM    134  CA  SER    66      -6.821  14.048  33.147  1.00  0.00              
ATOM    135  C   SER    66      -7.736  15.168  33.640  1.00  0.00              
ATOM    136  O   SER    66      -8.933  14.969  33.820  1.00  0.00              
ATOM    137  N   ARG    67      -7.149  16.350  33.821  1.00  0.00              
ATOM    138  CA  ARG    67      -7.929  17.502  34.257  1.00  0.00              
ATOM    139  C   ARG    67      -9.113  17.775  33.332  1.00  0.00              
ATOM    140  O   ARG    67     -10.276  17.913  33.766  1.00  0.00              
ATOM    141  N   GLU    68      -8.831  17.897  32.027  1.00  0.00              
ATOM    142  CA  GLU    68      -9.884  18.261  31.049  1.00  0.00              
ATOM    143  C   GLU    68     -10.856  17.111  30.908  1.00  0.00              
ATOM    144  O   GLU    68     -12.053  17.298  30.721  1.00  0.00              
ATOM    145  N   THR    75     -11.656  14.938  33.203  1.00  0.00              
ATOM    146  CA  THR    75     -12.446  14.972  34.420  1.00  0.00              
ATOM    147  C   THR    75     -13.567  16.000  34.316  1.00  0.00              
ATOM    148  O   THR    75     -14.725  15.663  34.602  1.00  0.00              
ATOM    149  N   LYS    76     -13.163  17.227  33.917  1.00  0.00              
ATOM    150  CA  LYS    76     -14.206  18.260  33.788  1.00  0.00              
ATOM    151  C   LYS    76     -15.285  17.824  32.811  1.00  0.00              
ATOM    152  O   LYS    76     -16.482  17.985  33.053  1.00  0.00              
ATOM    153  N   ASP    77     -14.876  17.212  31.668  1.00  0.00              
ATOM    154  CA  ASP    77     -15.919  16.878  30.701  1.00  0.00              
ATOM    155  C   ASP    77     -16.792  15.751  31.223  1.00  0.00              
ATOM    156  O   ASP    77     -17.995  15.757  30.922  1.00  0.00              
ATOM    157  N   GLU    78     -16.265  14.780  31.980  1.00  0.00              
ATOM    158  CA  GLU    78     -17.098  13.728  32.553  1.00  0.00              
ATOM    159  C   GLU    78     -18.139  14.359  33.483  1.00  0.00              
ATOM    160  O   GLU    78     -19.277  13.908  33.528  1.00  0.00              
ATOM    161  N   GLN    79     -17.770  15.395  34.225  1.00  0.00              
ATOM    162  CA  GLN    79     -18.725  16.101  35.122  1.00  0.00              
ATOM    163  C   GLN    79     -19.719  16.869  34.270  1.00  0.00              
ATOM    164  O   GLN    79     -20.918  16.778  34.525  1.00  0.00              
ATOM    165  N   ILE    80     -19.250  17.563  33.230  1.00  0.00              
ATOM    166  CA  ILE    80     -20.197  18.329  32.379  1.00  0.00              
ATOM    167  C   ILE    80     -21.132  17.408  31.621  1.00  0.00              
ATOM    168  O   ILE    80     -22.257  17.796  31.270  1.00  0.00              
ATOM    169  N   VAL    84     -21.411  24.279  28.420  1.00  0.00              
ATOM    170  CA  VAL    84     -20.738  25.517  28.793  1.00  0.00              
ATOM    171  C   VAL    84     -19.939  26.016  27.567  1.00  0.00              
ATOM    172  O   VAL    84     -19.606  25.199  26.656  1.00  0.00              
ATOM    173  N   GLU    88     -15.788  29.290  29.347  1.00  0.00              
ATOM    174  CA  GLU    88     -16.102  28.812  30.703  1.00  0.00              
ATOM    175  C   GLU    88     -15.399  27.500  30.960  1.00  0.00              
ATOM    176  O   GLU    88     -14.923  27.297  32.110  1.00  0.00              
ATOM    177  N   VAL    89     -15.326  26.574  29.985  1.00  0.00              
ATOM    178  CA  VAL    89     -14.645  25.320  30.190  1.00  0.00              
ATOM    179  C   VAL    89     -13.233  25.573  30.695  1.00  0.00              
ATOM    180  O   VAL    89     -12.758  24.980  31.676  1.00  0.00              
ATOM    181  N   LEU    93     -13.151  26.923  34.274  1.00  0.00              
ATOM    182  CA  LEU    93     -13.515  25.951  35.273  1.00  0.00              
ATOM    183  C   LEU    93     -12.337  25.037  35.598  1.00  0.00              
ATOM    184  O   LEU    93     -12.099  24.705  36.763  1.00  0.00              
ATOM    185  N   VAL    95      -9.944  26.980  37.678  1.00  0.00              
ATOM    186  CA  VAL    95     -10.519  27.249  38.980  1.00  0.00              
ATOM    187  C   VAL    95     -10.296  26.083  39.900  1.00  0.00              
ATOM    188  O   VAL    95      -9.841  26.189  41.044  1.00  0.00              
ATOM    189  N   PHE    96     -10.649  24.893  39.394  1.00  0.00              
ATOM    190  CA  PHE    96     -10.392  23.670  40.149  1.00  0.00              
ATOM    191  C   PHE    96      -8.908  23.505  40.464  1.00  0.00              
ATOM    192  O   PHE    96      -8.537  23.140  41.596  1.00  0.00              
ATOM    193  N   LYS    97      -8.052  23.712  39.466  1.00  0.00              
ATOM    194  CA  LYS    97      -6.628  23.495  39.713  1.00  0.00              
ATOM    195  C   LYS    97      -6.098  24.489  40.746  1.00  0.00              
ATOM    196  O   LYS    97      -5.301  24.110  41.626  1.00  0.00              
ATOM    197  N   TYR    99      -7.642  25.792  43.228  1.00  0.00              
ATOM    198  CA  TYR    99      -8.130  25.343  44.554  1.00  0.00              
ATOM    199  C   TYR    99      -7.317  24.150  45.013  1.00  0.00              
ATOM    200  O   TYR    99      -6.810  24.103  46.145  1.00  0.00              
ATOM    201  N   TYR   100      -7.167  23.154  44.144  1.00  0.00              
ATOM    202  CA  TYR   100      -6.382  21.974  44.452  1.00  0.00              
ATOM    203  C   TYR   100      -4.960  22.312  44.835  1.00  0.00              
ATOM    204  O   TYR   100      -4.378  21.785  45.809  1.00  0.00              
ATOM    205  N   ALA   101      -4.299  23.210  44.096  1.00  0.00              
ATOM    206  CA  ALA   101      -2.928  23.620  44.377  1.00  0.00              
ATOM    207  C   ALA   101      -2.846  24.275  45.754  1.00  0.00              
ATOM    208  O   ALA   101      -1.904  24.036  46.521  1.00  0.00              
ATOM    209  N   HIS   103      -4.840  23.438  48.274  1.00  0.00              
ATOM    210  CA  HIS   103      -5.080  22.345  49.210  1.00  0.00              
ATOM    211  C   HIS   103      -3.781  21.570  49.490  1.00  0.00              
ATOM    212  O   HIS   103      -3.636  21.044  50.582  1.00  0.00              
ATOM    213  N   CYS   104      -2.900  21.473  48.493  1.00  0.00              
ATOM    214  CA  CYS   104      -1.730  20.600  48.676  1.00  0.00              
ATOM    215  C   CYS   104      -0.512  21.363  49.183  1.00  0.00              
ATOM    216  O   CYS   104       0.569  20.772  49.294  1.00  0.00              
ATOM    217  N   ILE   106       1.275  19.578  52.185  1.00  0.00              
ATOM    218  CA  ILE   106       1.693  18.177  52.114  1.00  0.00              
ATOM    219  C   ILE   106       3.159  18.079  52.551  1.00  0.00              
ATOM    220  O   ILE   106       3.982  18.944  52.197  1.00  0.00              
ATOM    221  N   LYS   107       3.486  17.040  53.303  1.00  0.00              
ATOM    222  CA  LYS   107       4.848  16.891  53.837  1.00  0.00              
ATOM    223  C   LYS   107       5.300  15.457  53.802  1.00  0.00              
ATOM    224  O   LYS   107       4.495  14.543  53.466  1.00  0.00              
END
