
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0347AL381_4-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347AL381_4-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    H      51      K      60          0.940
LGA    I      52      D      61          2.300
LGA    V      53      R      62          1.661
LGA    P      54      A      63          2.158
LGA    V      55      Y      64          2.125
LGA    V      56      L      65          2.374
LGA    A      57      I      66          0.972
LGA    G      58      D      67          2.194
LGA    I      66      H      68          2.015
LGA    D      67      -       -           -
LGA    H      68      H      69          1.258
LGA    H      69      H      70          1.784
LGA    H      70      L      71          2.858
LGA    L      71      V      72          2.566
LGA    V      72      L      73          1.841
LGA    L      73      A      74          2.618
LGA    A      74      L      75          3.505
LGA    L      75      S      76          3.108
LGA    S      76      K      77          2.453
LGA    K      77      -       -           -
LGA    E      78      -       -           -
LGA    G      79      E      78          2.493
LGA    V      80      G      79          1.500
LGA    E      81      V      80          1.374
LGA    H      82      E      81          2.210
LGA    V      83      H      82          1.542
LGA    L      84      V      83          3.807
LGA    -       -      L      84           -
LGA    T      85      T      85          2.722
LGA    S      86      S      86          3.086
LGA    E      87      E      87          0.748
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      V     102           -
LGA    -       -      M     103           -
LGA    -       -      D     104           -
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    -       -      L     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   30   89    5.0     27    2.28    18.52     22.662     1.132

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.760921 * X  +   0.270498 * Y  +  -0.589771 * Z  +  15.191427
  Y_new =   0.264041 * X  +  -0.959381 * Y  +  -0.099355 * Z  +  99.005219
  Z_new =  -0.592690 * X  +  -0.080122 * Y  +  -0.801435 * Z  +  89.794373 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.041950    0.099642  [ DEG:  -174.2909      5.7091 ]
  Theta =   0.634395    2.507198  [ DEG:    36.3481    143.6519 ]
  Phi   =   0.334001   -2.807592  [ DEG:    19.1369   -160.8631 ]
 
# 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: T0347AL381_4-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL381_4-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30   89   5.0   27   2.28   18.52  22.662
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL381_4-D1
REMARK Aligment from pdb entry: 1a9xB
ATOM     29  N   HIS    51      -4.198  26.817   1.074  1.00  0.00              
ATOM     30  CA  HIS    51      -5.011  26.865  -0.106  1.00  0.00              
ATOM     31  C   HIS    51      -4.293  26.405  -1.296  1.00  0.00              
ATOM     32  O   HIS    51      -4.805  26.506  -2.408  1.00  0.00              
ATOM     33  N   ILE    52      -3.093  25.947  -1.015  1.00  0.00              
ATOM     34  CA  ILE    52      -2.221  25.449  -2.032  1.00  0.00              
ATOM     35  C   ILE    52      -1.759  26.475  -3.019  1.00  0.00              
ATOM     36  O   ILE    52      -1.736  26.200  -4.220  1.00  0.00              
ATOM     37  N   VAL    53      -1.370  27.649  -2.499  1.00  0.00              
ATOM     38  CA  VAL    53      -0.947  28.696  -3.393  1.00  0.00              
ATOM     39  C   VAL    53       0.535  28.943  -3.470  1.00  0.00              
ATOM     40  O   VAL    53       1.225  29.019  -2.457  1.00  0.00              
ATOM     41  N   PRO    54       0.999  29.087  -4.691  1.00  0.00              
ATOM     42  CA  PRO    54       2.403  29.371  -4.969  1.00  0.00              
ATOM     43  C   PRO    54       2.551  30.871  -4.793  1.00  0.00              
ATOM     44  O   PRO    54       1.796  31.633  -5.412  1.00  0.00              
ATOM     45  N   VAL    55       3.467  31.260  -3.908  1.00  0.00              
ATOM     46  CA  VAL    55       3.711  32.665  -3.613  1.00  0.00              
ATOM     47  C   VAL    55       5.188  33.017  -3.366  1.00  0.00              
ATOM     48  O   VAL    55       6.006  32.343  -2.766  1.00  0.00              
ATOM     49  N   VAL    56       5.560  34.148  -3.835  1.00  0.00              
ATOM     50  CA  VAL    56       6.904  34.560  -3.660  1.00  0.00              
ATOM     51  C   VAL    56       6.903  35.907  -2.909  1.00  0.00              
ATOM     52  O   VAL    56       5.977  36.717  -3.034  1.00  0.00              
ATOM     53  N   ALA    57       7.919  36.133  -2.091  1.00  0.00              
ATOM     54  CA  ALA    57       8.109  37.380  -1.335  1.00  0.00              
ATOM     55  C   ALA    57       9.532  37.759  -1.626  1.00  0.00              
ATOM     56  O   ALA    57      10.211  36.974  -2.287  1.00  0.00              
ATOM     57  N   GLY    58       9.937  38.945  -1.170  1.00  0.00              
ATOM     58  CA  GLY    58      11.271  39.509  -1.324  1.00  0.00              
ATOM     59  C   GLY    58      11.690  39.931  -2.689  1.00  0.00              
ATOM     60  O   GLY    58      12.878  39.928  -2.989  1.00  0.00              
ATOM     61  N   ILE    66      10.755  40.294  -3.525  1.00  0.00              
ATOM     62  CA  ILE    66      11.218  40.721  -4.826  1.00  0.00              
ATOM     63  C   ILE    66      10.913  42.218  -5.022  1.00  0.00              
ATOM     64  O   ILE    66      10.111  42.813  -4.312  1.00  0.00              
ATOM     65  N   ASP    67      11.545  42.838  -5.996  1.00  0.00              
ATOM     66  CA  ASP    67      11.317  44.234  -6.216  1.00  0.00              
ATOM     67  C   ASP    67      10.052  44.396  -6.980  1.00  0.00              
ATOM     68  O   ASP    67      10.062  44.435  -8.205  1.00  0.00              
ATOM     69  N   HIS    68       8.968  44.475  -6.233  1.00  0.00              
ATOM     70  CA  HIS    68       7.669  44.644  -6.827  1.00  0.00              
ATOM     71  C   HIS    68       7.529  45.935  -7.613  1.00  0.00              
ATOM     72  O   HIS    68       6.669  46.081  -8.496  1.00  0.00              
ATOM     73  N   HIS    69       8.385  46.912  -7.285  1.00  0.00              
ATOM     74  CA  HIS    69       8.304  48.200  -7.947  1.00  0.00              
ATOM     75  C   HIS    69       8.792  48.106  -9.390  1.00  0.00              
ATOM     76  O   HIS    69       8.185  48.588 -10.350  1.00  0.00              
ATOM     77  N   HIS    70       9.928  47.445  -9.511  1.00  0.00              
ATOM     78  CA  HIS    70      10.510  47.183 -10.794  1.00  0.00              
ATOM     79  C   HIS    70       9.484  46.447 -11.693  1.00  0.00              
ATOM     80  O   HIS    70       9.326  46.723 -12.894  1.00  0.00              
ATOM     81  N   LEU    71       8.792  45.490 -11.069  1.00  0.00              
ATOM     82  CA  LEU    71       7.773  44.669 -11.719  1.00  0.00              
ATOM     83  C   LEU    71       6.629  45.513 -12.213  1.00  0.00              
ATOM     84  O   LEU    71       6.250  45.452 -13.391  1.00  0.00              
ATOM     85  N   VAL    72       6.074  46.309 -11.288  1.00  0.00              
ATOM     86  CA  VAL    72       4.977  47.191 -11.644  1.00  0.00              
ATOM     87  C   VAL    72       5.413  48.160 -12.756  1.00  0.00              
ATOM     88  O   VAL    72       4.699  48.446 -13.697  1.00  0.00              
ATOM     89  N   LEU    73       6.617  48.672 -12.642  1.00  0.00              
ATOM     90  CA  LEU    73       7.069  49.579 -13.654  1.00  0.00              
ATOM     91  C   LEU    73       7.149  48.919 -15.042  1.00  0.00              
ATOM     92  O   LEU    73       6.870  49.495 -16.081  1.00  0.00              
ATOM     93  N   ALA    74       7.538  47.675 -15.077  1.00  0.00              
ATOM     94  CA  ALA    74       7.663  46.963 -16.333  1.00  0.00              
ATOM     95  C   ALA    74       6.280  46.726 -16.969  1.00  0.00              
ATOM     96  O   ALA    74       6.017  46.954 -18.152  1.00  0.00              
ATOM     97  N   LEU    75       5.360  46.261 -16.135  1.00  0.00              
ATOM     98  CA  LEU    75       4.000  45.988 -16.547  1.00  0.00              
ATOM     99  C   LEU    75       3.315  47.256 -17.033  1.00  0.00              
ATOM    100  O   LEU    75       2.545  47.256 -18.009  1.00  0.00              
ATOM    101  N   SER    76       3.577  48.357 -16.337  1.00  0.00              
ATOM    102  CA  SER    76       2.954  49.605 -16.721  1.00  0.00              
ATOM    103  C   SER    76       3.492  50.028 -18.053  1.00  0.00              
ATOM    104  O   SER    76       2.763  50.343 -18.974  1.00  0.00              
ATOM    105  N   LYS    77       4.807  50.012 -18.140  1.00  0.00              
ATOM    106  CA  LYS    77       5.499  50.435 -19.345  1.00  0.00              
ATOM    107  C   LYS    77       5.270  49.561 -20.546  1.00  0.00              
ATOM    108  O   LYS    77       4.919  50.039 -21.621  1.00  0.00              
ATOM    109  N   GLU    78       5.522  48.277 -20.377  1.00  0.00              
ATOM    110  CA  GLU    78       5.379  47.410 -21.504  1.00  0.00              
ATOM    111  C   GLU    78       4.046  46.679 -21.604  1.00  0.00              
ATOM    112  O   GLU    78       3.801  45.965 -22.570  1.00  0.00              
ATOM    113  N   GLY    79       3.153  46.872 -20.637  1.00  0.00              
ATOM    114  CA  GLY    79       1.857  46.206 -20.664  1.00  0.00              
ATOM    115  C   GLY    79       1.900  44.837 -19.976  1.00  0.00              
ATOM    116  O   GLY    79       2.952  44.319 -19.567  1.00  0.00              
ATOM    117  N   VAL    80       0.734  44.249 -19.819  1.00  0.00              
ATOM    118  CA  VAL    80       0.616  42.946 -19.179  1.00  0.00              
ATOM    119  C   VAL    80       1.454  41.846 -19.853  1.00  0.00              
ATOM    120  O   VAL    80       1.722  41.860 -21.067  1.00  0.00              
ATOM    121  N   GLU    81       1.880  40.896 -19.024  1.00  0.00              
ATOM    122  CA  GLU    81       2.691  39.804 -19.462  1.00  0.00              
ATOM    123  C   GLU    81       2.325  38.594 -18.678  1.00  0.00              
ATOM    124  O   GLU    81       1.892  38.668 -17.541  1.00  0.00              
ATOM    125  N   HIS    82       2.511  37.479 -19.336  1.00  0.00              
ATOM    126  CA  HIS    82       2.247  36.238 -18.719  1.00  0.00              
ATOM    127  C   HIS    82       3.528  35.877 -18.051  1.00  0.00              
ATOM    128  O   HIS    82       4.619  36.241 -18.562  1.00  0.00              
ATOM    129  N   VAL    83       3.389  35.134 -16.933  1.00  0.00              
ATOM    130  CA  VAL    83       4.587  34.726 -16.205  1.00  0.00              
ATOM    131  C   VAL    83       4.432  33.377 -15.490  1.00  0.00              
ATOM    132  O   VAL    83       3.413  32.677 -15.602  1.00  0.00              
ATOM    133  N   LEU    84       5.479  33.042 -14.718  1.00  0.00              
ATOM    134  CA  LEU    84       5.439  31.811 -13.976  1.00  0.00              
ATOM    135  C   LEU    84       6.339  31.878 -12.780  1.00  0.00              
ATOM    136  O   LEU    84       7.511  32.364 -12.841  1.00  0.00              
ATOM    137  N   THR    85       5.758  31.351 -11.717  1.00  0.00              
ATOM    138  CA  THR    85       6.462  31.267 -10.454  1.00  0.00              
ATOM    139  C   THR    85       6.727  29.817 -10.134  1.00  0.00              
ATOM    140  O   THR    85       5.833  28.985 -10.150  1.00  0.00              
ATOM    141  N   SER    86       7.952  29.550  -9.777  1.00  0.00              
ATOM    142  CA  SER    86       8.314  28.249  -9.368  1.00  0.00              
ATOM    143  C   SER    86       8.855  28.398  -7.945  1.00  0.00              
ATOM    144  O   SER    86       9.784  29.150  -7.690  1.00  0.00              
ATOM    145  N   GLU    87       8.282  27.682  -6.991  1.00  0.00              
ATOM    146  CA  GLU    87       8.811  27.759  -5.642  1.00  0.00              
ATOM    147  C   GLU    87       9.321  26.371  -5.308  1.00  0.00              
ATOM    148  O   GLU    87       8.536  25.437  -5.297  1.00  0.00              
END
