
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0347AL380_1-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347AL380_1-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      A      57          4.073
LGA    G      58      G      58          2.938
LGA    P      59      P      59          2.365
LGA    K      60      K      60          1.867
LGA    D      61      D      61          1.822
LGA    R      62      R      62          1.684
LGA    A      63      A      63          1.300
LGA    Y      64      Y      64          1.181
LGA    L      65      L      65          0.927
LGA    I      66      I      66          0.836
LGA    D      67      D      67          1.074
LGA    H      68      H      68          1.229
LGA    H      69      H      69          0.410
LGA    H      70      H      70          0.906
LGA    L      71      L      71          1.241
LGA    V      72      V      72          0.907
LGA    L      73      L      73          0.422
LGA    A      74      A      74          0.578
LGA    L      75      L      75          0.732
LGA    S      76      S      76          0.620
LGA    K      77      K      77          0.248
LGA    E      78      E      78          0.445
LGA    G      79      G      79          0.697
LGA    V      80      V      80          0.716
LGA    E      81      E      81          0.546
LGA    H      82      H      82          0.644
LGA    V      83      V      83          0.878
LGA    L      84      L      84          1.536
LGA    T      85      T      85          1.423
LGA    S      86      S      86          1.511
LGA    E      87      E      87          1.113
LGA    V      88      V      88          0.605
LGA    A      89      A      89          0.801
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)   33   89    5.0     33    1.39   100.00     35.314     2.207

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.195411 * X  +  -0.636483 * Y  +  -0.746126 * Z  +  43.081039
  Y_new =   0.639480 * X  +   0.494121 * Y  +  -0.588990 * Z  +  38.184910
  Z_new =   0.743559 * X  +  -0.592228 * Y  +   0.310461 * Z  +  10.639098 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.087956    2.053636  [ DEG:   -62.3353    117.6647 ]
  Theta =  -0.838378   -2.303215  [ DEG:   -48.0355   -131.9645 ]
  Phi   =   1.867362   -1.274230  [ DEG:   106.9920    -73.0080 ]
 
# 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: T0347AL380_1-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL380_1-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33   89   5.0   33   1.39  100.00  35.314
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL380_1-D1
REMARK Aligment from pdb entry: 1vk1A
ATOM      1  N   ALA    57       1.629  29.964  -0.702  1.00  0.00              
ATOM      2  CA  ALA    57       0.848  30.279   0.490  1.00  0.00              
ATOM      3  C   ALA    57       0.008  29.031   0.830  1.00  0.00              
ATOM      4  O   ALA    57      -0.780  28.573   0.014  1.00  0.00              
ATOM      5  N   GLY    58       0.187  28.463   2.034  1.00  0.00              
ATOM      6  CA  GLY    58      -0.536  27.226   2.392  1.00  0.00              
ATOM      7  C   GLY    58      -2.051  27.322   2.218  1.00  0.00              
ATOM      8  O   GLY    58      -2.653  28.361   2.507  1.00  0.00              
ATOM      9  N   PRO    59      -2.646  26.242   1.728  1.00  0.00              
ATOM     10  CA  PRO    59      -4.081  26.182   1.506  1.00  0.00              
ATOM     11  C   PRO    59      -4.575  26.900   0.254  1.00  0.00              
ATOM     12  O   PRO    59      -5.786  26.978   0.026  1.00  0.00              
ATOM     13  N   LYS    60      -3.647  27.428  -0.560  1.00  0.00              
ATOM     14  CA  LYS    60      -3.996  28.112  -1.793  1.00  0.00              
ATOM     15  C   LYS    60      -3.129  27.621  -2.911  1.00  0.00              
ATOM     16  O   LYS    60      -2.135  26.934  -2.689  1.00  0.00              
ATOM     17  N   ASP    61      -3.472  28.037  -4.126  1.00  0.00              
ATOM     18  CA  ASP    61      -2.564  27.899  -5.254  1.00  0.00              
ATOM     19  C   ASP    61      -1.956  29.271  -5.642  1.00  0.00              
ATOM     20  O   ASP    61      -1.637  29.523  -6.793  1.00  0.00              
ATOM     21  N   ARG    62      -1.769  30.125  -4.649  1.00  0.00              
ATOM     22  CA  ARG    62      -1.180  31.443  -4.821  1.00  0.00              
ATOM     23  C   ARG    62       0.205  31.448  -4.175  1.00  0.00              
ATOM     24  O   ARG    62       0.525  30.576  -3.356  1.00  0.00              
ATOM     25  N   ALA    63       1.002  32.452  -4.526  1.00  0.00              
ATOM     26  CA  ALA    63       2.369  32.571  -4.069  1.00  0.00              
ATOM     27  C   ALA    63       2.627  33.894  -3.387  1.00  0.00              
ATOM     28  O   ALA    63       2.211  34.957  -3.869  1.00  0.00              
ATOM     29  N   TYR    64       3.337  33.823  -2.271  1.00  0.00              
ATOM     30  CA  TYR    64       4.000  34.960  -1.679  1.00  0.00              
ATOM     31  C   TYR    64       5.151  35.381  -2.559  1.00  0.00              
ATOM     32  O   TYR    64       5.994  34.567  -2.895  1.00  0.00              
ATOM     33  N   LEU    65       5.208  36.668  -2.908  1.00  0.00              
ATOM     34  CA  LEU    65       6.398  37.229  -3.508  1.00  0.00              
ATOM     35  C   LEU    65       7.425  37.359  -2.388  1.00  0.00              
ATOM     36  O   LEU    65       7.239  38.115  -1.464  1.00  0.00              
ATOM     37  N   ILE    66       8.514  36.616  -2.504  1.00  0.00              
ATOM     38  CA  ILE    66       9.632  36.707  -1.558  1.00  0.00              
ATOM     39  C   ILE    66      10.532  37.848  -2.030  1.00  0.00              
ATOM     40  O   ILE    66      10.863  38.728  -1.275  1.00  0.00              
ATOM     41  N   ASP    67      10.913  37.808  -3.302  1.00  0.00              
ATOM     42  CA  ASP    67      11.725  38.830  -3.915  1.00  0.00              
ATOM     43  C   ASP    67      11.229  39.090  -5.319  1.00  0.00              
ATOM     44  O   ASP    67      10.994  38.157  -6.074  1.00  0.00              
ATOM     45  N   HIS    68      11.098  40.364  -5.659  1.00  0.00              
ATOM     46  CA  HIS    68      10.712  40.777  -7.006  1.00  0.00              
ATOM     47  C   HIS    68       9.444  41.601  -7.115  1.00  0.00              
ATOM     48  O   HIS    68       8.807  41.603  -8.161  1.00  0.00              
ATOM     49  N   HIS    69       9.087  42.363  -6.089  1.00  0.00              
ATOM     50  CA  HIS    69       7.897  43.202  -6.150  1.00  0.00              
ATOM     51  C   HIS    69       7.913  44.180  -7.310  1.00  0.00              
ATOM     52  O   HIS    69       6.909  44.352  -7.990  1.00  0.00              
ATOM     53  N   HIS    70       9.042  44.840  -7.539  1.00  0.00              
ATOM     54  CA  HIS    70       9.118  45.833  -8.597  1.00  0.00              
ATOM     55  C   HIS    70       9.088  45.191  -9.967  1.00  0.00              
ATOM     56  O   HIS    70       8.487  45.756 -10.901  1.00  0.00              
ATOM     57  N   LEU    71       9.702  44.018 -10.099  1.00  0.00              
ATOM     58  CA  LEU    71       9.635  43.235 -11.337  1.00  0.00              
ATOM     59  C   LEU    71       8.222  42.769 -11.652  1.00  0.00              
ATOM     60  O   LEU    71       7.725  42.943 -12.768  1.00  0.00              
ATOM     61  N   VAL    72       7.532  42.225 -10.654  1.00  0.00              
ATOM     62  CA  VAL    72       6.137  41.808 -10.808  1.00  0.00              
ATOM     63  C   VAL    72       5.243  42.978 -11.177  1.00  0.00              
ATOM     64  O   VAL    72       4.471  42.909 -12.143  1.00  0.00              
ATOM     65  N   LEU    73       5.358  44.073 -10.441  1.00  0.00              
ATOM     66  CA  LEU    73       4.495  45.210 -10.668  1.00  0.00              
ATOM     67  C   LEU    73       4.799  45.864 -12.018  1.00  0.00              
ATOM     68  O   LEU    73       3.885  46.311 -12.714  1.00  0.00              
ATOM     69  N   ALA    74       6.076  45.923 -12.397  1.00  0.00              
ATOM     70  CA  ALA    74       6.442  46.482 -13.685  1.00  0.00              
ATOM     71  C   ALA    74       5.919  45.648 -14.839  1.00  0.00              
ATOM     72  O   ALA    74       5.390  46.182 -15.818  1.00  0.00              
ATOM     73  N   LEU    75       6.037  44.336 -14.721  1.00  0.00              
ATOM     74  CA  LEU    75       5.505  43.449 -15.733  1.00  0.00              
ATOM     75  C   LEU    75       3.987  43.566 -15.837  1.00  0.00              
ATOM     76  O   LEU    75       3.442  43.554 -16.941  1.00  0.00              
ATOM     77  N   SER    76       3.300  43.647 -14.708  1.00  0.00              
ATOM     78  CA  SER    76       1.855  43.835 -14.743  1.00  0.00              
ATOM     79  C   SER    76       1.505  45.143 -15.427  1.00  0.00              
ATOM     80  O   SER    76       0.599  45.182 -16.270  1.00  0.00              
ATOM     81  N   LYS    77       2.232  46.209 -15.111  1.00  0.00              
ATOM     82  CA  LYS    77       1.975  47.521 -15.730  1.00  0.00              
ATOM     83  C   LYS    77       2.181  47.465 -17.241  1.00  0.00              
ATOM     84  O   LYS    77       1.442  48.122 -18.004  1.00  0.00              
ATOM     85  N   GLU    78       3.159  46.682 -17.689  1.00  0.00              
ATOM     86  CA  GLU    78       3.442  46.525 -19.118  1.00  0.00              
ATOM     87  C   GLU    78       2.443  45.616 -19.840  1.00  0.00              
ATOM     88  O   GLU    78       2.456  45.532 -21.073  1.00  0.00              
ATOM     89  N   GLY    79       1.595  44.930 -19.095  1.00  0.00              
ATOM     90  CA  GLY    79       0.603  44.025 -19.661  1.00  0.00              
ATOM     91  C   GLY    79       1.076  42.593 -19.875  1.00  0.00              
ATOM     92  O   GLY    79       0.432  41.847 -20.593  1.00  0.00              
ATOM     93  N   VAL    80       2.166  42.182 -19.217  1.00  0.00              
ATOM     94  CA  VAL    80       2.653  40.830 -19.335  1.00  0.00              
ATOM     95  C   VAL    80       1.769  39.875 -18.548  1.00  0.00              
ATOM     96  O   VAL    80       0.920  40.311 -17.760  1.00  0.00              
ATOM     97  N   GLU    81       2.000  38.588 -18.744  1.00  0.00              
ATOM     98  CA  GLU    81       1.202  37.537 -18.140  1.00  0.00              
ATOM     99  C   GLU    81       1.933  36.652 -17.155  1.00  0.00              
ATOM    100  O   GLU    81       1.308  36.131 -16.252  1.00  0.00              
ATOM    101  N   HIS    82       3.236  36.442 -17.351  1.00  0.00              
ATOM    102  CA  HIS    82       3.971  35.465 -16.570  1.00  0.00              
ATOM    103  C   HIS    82       5.372  35.967 -16.292  1.00  0.00              
ATOM    104  O   HIS    82       5.836  36.903 -16.949  1.00  0.00              
ATOM    105  N   VAL    83       6.044  35.342 -15.329  1.00  0.00              
ATOM    106  CA  VAL    83       7.444  35.635 -15.102  1.00  0.00              
ATOM    107  C   VAL    83       8.167  34.372 -14.665  1.00  0.00              
ATOM    108  O   VAL    83       7.625  33.560 -13.913  1.00  0.00              
ATOM    109  N   LEU    84       9.424  34.208 -15.092  1.00  0.00              
ATOM    110  CA  LEU    84      10.248  33.112 -14.595  1.00  0.00              
ATOM    111  C   LEU    84      10.524  33.261 -13.103  1.00  0.00              
ATOM    112  O   LEU    84      10.861  34.353 -12.647  1.00  0.00              
ATOM    113  N   THR    85      10.370  32.161 -12.385  1.00  0.00              
ATOM    114  CA  THR    85      10.334  32.148 -10.948  1.00  0.00              
ATOM    115  C   THR    85      11.064  30.935 -10.367  1.00  0.00              
ATOM    116  O   THR    85      11.082  29.858 -10.947  1.00  0.00              
ATOM    117  N   SER    86      11.615  31.137  -9.183  1.00  0.00              
ATOM    118  CA  SER    86      12.165  30.063  -8.374  1.00  0.00              
ATOM    119  C   SER    86      11.222  29.909  -7.201  1.00  0.00              
ATOM    120  O   SER    86      10.936  30.884  -6.514  1.00  0.00              
ATOM    121  N   GLU    87      10.747  28.691  -6.970  1.00  0.00              
ATOM    122  CA  GLU    87       9.809  28.390  -5.903  1.00  0.00              
ATOM    123  C   GLU    87      10.583  27.831  -4.693  1.00  0.00              
ATOM    124  O   GLU    87      11.283  26.833  -4.817  1.00  0.00              
ATOM    125  N   VAL    88      10.461  28.500  -3.561  1.00  0.00              
ATOM    126  CA  VAL    88      11.162  28.207  -2.324  1.00  0.00              
ATOM    127  C   VAL    88      10.203  27.600  -1.306  1.00  0.00              
ATOM    128  O   VAL    88       8.987  27.842  -1.355  1.00  0.00              
ATOM    129  N   ALA    89      10.751  26.824  -0.369  1.00  0.00              
ATOM    130  CA  ALA    89      10.047  26.502   0.867  1.00  0.00              
ATOM    131  C   ALA    89      10.400  27.621   1.837  1.00  0.00              
ATOM    132  O   ALA    89      11.521  27.688   2.314  1.00  0.00              
END
