
#######################################################
#                                                     #
#                        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 T0299AL243_2-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299AL243_2-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E      34      M       1           -
LGA    K      35      T       2           -
LGA    V      36      R       3           -
LGA    -       -      Y       4           -
LGA    -       -      A       5           -
LGA    -       -      L       6           -
LGA    -       -      L       7           -
LGA    -       -      V       8           -
LGA    -       -      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    E      37      N      12           #
LGA    S      38      V      13           -
LGA    Y      39      G      14           -
LGA    I      40      G      15           -
LGA    -       -      K      16           -
LGA    N      41      N      17          1.524
LGA    S      42      K      18          3.739
LGA    G      43      V      19           #
LGA    -       -      V      20           -
LGA    -       -      M      21           -
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    -       -      R      25           -
LGA    -       -      Q      26           -
LGA    -       -      E      27           -
LGA    -       -      L      28           -
LGA    -       -      T      29           -
LGA    -       -      N      30           -
LGA    -       -      L      31           -
LGA    -       -      G      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      E      37           -
LGA    -       -      S      38           -
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    N      44      N      41          4.434
LGA    I      45      S      42          3.663
LGA    F      46      G      43          2.699
LGA    F      47      N      44           #
LGA    T      48      I      45          4.782
LGA    S      49      F      46           #
LGA    -       -      F      47           -
LGA    -       -      T      48           -
LGA    -       -      S      49           -
LGA    I      50      I      50          2.127
LGA    D      51      D      51           #
LGA    S      52      -       -           -
LGA    K      53      -       -           -
LGA    A      54      -       -           -
LGA    Q      55      S      52          4.123
LGA    L      56      K      53          2.829
LGA    V      57      A      54          1.372
LGA    E      58      Q      55          2.186
LGA    K      59      L      56          2.716
LGA    L      60      V      57          2.145
LGA    E      61      E      58          1.331
LGA    -       -      K      59           -
LGA    T      62      L      60          2.171
LGA    F      63      E      61          2.166
LGA    -       -      T      62           -
LGA    F      64      F      63          1.341
LGA    A      65      F      64          2.669
LGA    V      66      A      65          2.965
LGA    H      67      V      66          2.427
LGA    Y      68      H      67          2.774
LGA    P      69      Y      68          1.299
LGA    -       -      P      69           -
LGA    -       -      F      70           -
LGA    F      70      I      71          1.659
LGA    I      71      Q      72          2.295
LGA    Q      72      S      73          3.708
LGA    S      73      F      74          1.654
LGA    F      74      S      75          0.838
LGA    S      75      L      76          1.123
LGA    L      76      L      77          4.207
LGA    L      77      S      78          1.553
LGA    S      78      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    -       -      I     174           -
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    -       -      M     177           -
LGA    -       -      L     178           -
LGA    -       -      K     179           -
LGA    -       -      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   91    5.0     30    2.70    20.00     23.683     1.072

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.935043 * X  +  -0.009219 * Y  +  -0.354413 * Z  +  46.674622
  Y_new =   0.336614 * X  +   0.290705 * Y  +  -0.895646 * Z  +  40.315941
  Z_new =   0.111287 * X  +  -0.956768 * Y  +  -0.268718 * Z  +  15.361826 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.844602    1.296990  [ DEG:  -105.6879     74.3121 ]
  Theta =  -0.111518   -3.030075  [ DEG:    -6.3895   -173.6105 ]
  Phi   =   2.796038   -0.345554  [ DEG:   160.2012    -19.7988 ]
 
# 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: T0299AL243_2-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL243_2-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   91   5.0   30   2.70   20.00  23.683
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL243_2-D1
REMARK Aligment from pdb entry: 1k1wA
ATOM      1  N   GLU    34      -8.269  28.505  -1.530  1.00  0.00              
ATOM      2  CA  GLU    34      -7.021  27.759  -1.385  1.00  0.00              
ATOM      3  C   GLU    34      -6.061  28.120  -2.504  1.00  0.00              
ATOM      4  O   GLU    34      -4.844  28.098  -2.315  1.00  0.00              
ATOM      5  N   LYS    35      -6.610  28.451  -3.671  1.00  0.00              
ATOM      6  CA  LYS    35      -5.777  28.833  -4.799  1.00  0.00              
ATOM      7  C   LYS    35      -5.107  30.145  -4.431  1.00  0.00              
ATOM      8  O   LYS    35      -3.967  30.410  -4.827  1.00  0.00              
ATOM      9  N   VAL    36      -5.824  30.960  -3.658  1.00  0.00              
ATOM     10  CA  VAL    36      -5.289  32.238  -3.217  1.00  0.00              
ATOM     11  C   VAL    36      -4.174  32.037  -2.195  1.00  0.00              
ATOM     12  O   VAL    36      -3.090  32.577  -2.364  1.00  0.00              
ATOM     13  N   GLU    37      -4.425  31.268  -1.139  1.00  0.00              
ATOM     14  CA  GLU    37      -3.379  31.039  -0.138  1.00  0.00              
ATOM     15  C   GLU    37      -2.123  30.527  -0.837  1.00  0.00              
ATOM     16  O   GLU    37      -0.997  30.857  -0.455  1.00  0.00              
ATOM     17  N   SER    38      -2.336  29.721  -1.871  1.00  0.00              
ATOM     18  CA  SER    38      -1.244  29.155  -2.644  1.00  0.00              
ATOM     19  C   SER    38      -0.402  30.242  -3.314  1.00  0.00              
ATOM     20  O   SER    38       0.806  30.323  -3.094  1.00  0.00              
ATOM     21  N   TYR    39      -1.059  31.067  -4.129  1.00  0.00              
ATOM     22  CA  TYR    39      -0.415  32.155  -4.861  1.00  0.00              
ATOM     23  C   TYR    39       0.233  33.189  -3.931  1.00  0.00              
ATOM     24  O   TYR    39       1.296  33.746  -4.229  1.00  0.00              
ATOM     25  N   ILE    40      -0.415  33.451  -2.804  1.00  0.00              
ATOM     26  CA  ILE    40       0.124  34.392  -1.842  1.00  0.00              
ATOM     27  C   ILE    40       1.416  33.755  -1.339  1.00  0.00              
ATOM     28  O   ILE    40       2.473  34.389  -1.321  1.00  0.00              
ATOM     29  N   ASN    41       1.319  32.484  -0.963  1.00  0.00              
ATOM     30  CA  ASN    41       2.459  31.742  -0.441  1.00  0.00              
ATOM     31  C   ASN    41       3.615  31.634  -1.430  1.00  0.00              
ATOM     32  O   ASN    41       4.769  31.481  -1.030  1.00  0.00              
ATOM     33  N   SER    42       3.313  31.711  -2.720  1.00  0.00              
ATOM     34  CA  SER    42       4.361  31.636  -3.724  1.00  0.00              
ATOM     35  C   SER    42       4.624  33.023  -4.319  1.00  0.00              
ATOM     36  O   SER    42       4.982  33.161  -5.493  1.00  0.00              
ATOM     37  N   GLY    43       4.426  34.042  -3.482  1.00  0.00              
ATOM     38  CA  GLY    43       4.657  35.429  -3.856  1.00  0.00              
ATOM     39  C   GLY    43       4.055  35.987  -5.132  1.00  0.00              
ATOM     40  O   GLY    43       4.662  36.847  -5.757  1.00  0.00              
ATOM     41  N   ASN    44       2.872  35.531  -5.525  1.00  0.00              
ATOM     42  CA  ASN    44       2.249  36.045  -6.741  1.00  0.00              
ATOM     43  C   ASN    44       1.140  37.064  -6.457  1.00  0.00              
ATOM     44  O   ASN    44       0.661  37.758  -7.360  1.00  0.00              
ATOM     45  N   ILE    45       0.750  37.169  -5.193  1.00  0.00              
ATOM     46  CA  ILE    45      -0.304  38.095  -4.808  1.00  0.00              
ATOM     47  C   ILE    45      -0.005  38.885  -3.550  1.00  0.00              
ATOM     48  O   ILE    45       0.663  38.397  -2.643  1.00  0.00              
ATOM     49  N   PHE    46      -0.488  40.126  -3.530  1.00  0.00              
ATOM     50  CA  PHE    46      -0.417  41.005  -2.357  1.00  0.00              
ATOM     51  C   PHE    46      -1.888  41.362  -2.173  1.00  0.00              
ATOM     52  O   PHE    46      -2.519  41.883  -3.099  1.00  0.00              
ATOM     53  N   PHE    47      -2.443  41.062  -1.005  1.00  0.00              
ATOM     54  CA  PHE    47      -3.846  41.368  -0.770  1.00  0.00              
ATOM     55  C   PHE    47      -4.014  42.842  -0.452  1.00  0.00              
ATOM     56  O   PHE    47      -3.375  43.372   0.457  1.00  0.00              
ATOM     57  N   THR    48      -4.857  43.496  -1.240  1.00  0.00              
ATOM     58  CA  THR    48      -5.172  44.904  -1.064  1.00  0.00              
ATOM     59  C   THR    48      -6.500  44.879  -0.322  1.00  0.00              
ATOM     60  O   THR    48      -7.409  44.115  -0.672  1.00  0.00              
ATOM     61  N   SER    49      -6.614  45.716   0.698  1.00  0.00              
ATOM     62  CA  SER    49      -7.812  45.732   1.529  1.00  0.00              
ATOM     63  C   SER    49      -8.637  47.024   1.386  1.00  0.00              
ATOM     64  O   SER    49      -8.335  47.866   0.547  1.00  0.00              
ATOM     65  N   ILE    50     -17.813  50.206   1.423  1.00  0.00              
ATOM     66  CA  ILE    50     -18.553  51.449   1.615  1.00  0.00              
ATOM     67  C   ILE    50     -17.651  52.548   1.046  1.00  0.00              
ATOM     68  O   ILE    50     -16.466  52.320   0.779  1.00  0.00              
ATOM     69  N   ASP    51     -18.207  53.727   0.824  1.00  0.00              
ATOM     70  CA  ASP    51     -17.379  54.821   0.365  1.00  0.00              
ATOM     71  C   ASP    51     -16.898  55.353   1.703  1.00  0.00              
ATOM     72  O   ASP    51     -17.661  55.970   2.461  1.00  0.00              
ATOM     73  N   SER    52     -19.412  57.013   9.060  1.00  0.00              
ATOM     74  CA  SER    52     -18.788  57.491  10.301  1.00  0.00              
ATOM     75  C   SER    52     -17.341  57.014  10.526  1.00  0.00              
ATOM     76  O   SER    52     -16.990  55.863  10.222  1.00  0.00              
ATOM     77  N   LYS    53     -16.523  57.907  11.080  1.00  0.00              
ATOM     78  CA  LYS    53     -15.119  57.634  11.370  1.00  0.00              
ATOM     79  C   LYS    53     -14.925  56.292  12.095  1.00  0.00              
ATOM     80  O   LYS    53     -14.017  55.520  11.763  1.00  0.00              
ATOM     81  N   ALA    54     -15.778  56.012  13.079  1.00  0.00              
ATOM     82  CA  ALA    54     -15.680  54.774  13.847  1.00  0.00              
ATOM     83  C   ALA    54     -16.043  53.539  13.039  1.00  0.00              
ATOM     84  O   ALA    54     -15.586  52.436  13.345  1.00  0.00              
ATOM     85  N   GLN    55     -16.869  53.714  12.009  1.00  0.00              
ATOM     86  CA  GLN    55     -17.260  52.583  11.169  1.00  0.00              
ATOM     87  C   GLN    55     -16.164  52.192  10.179  1.00  0.00              
ATOM     88  O   GLN    55     -16.037  51.030   9.810  1.00  0.00              
ATOM     89  N   LEU    56     -15.358  53.161   9.763  1.00  0.00              
ATOM     90  CA  LEU    56     -14.279  52.868   8.838  1.00  0.00              
ATOM     91  C   LEU    56     -13.341  51.882   9.487  1.00  0.00              
ATOM     92  O   LEU    56     -13.083  50.814   8.922  1.00  0.00              
ATOM     93  N   VAL    57     -12.838  52.246  10.672  1.00  0.00              
ATOM     94  CA  VAL    57     -11.931  51.395  11.435  1.00  0.00              
ATOM     95  C   VAL    57     -12.419  49.962  11.448  1.00  0.00              
ATOM     96  O   VAL    57     -11.666  49.045  11.129  1.00  0.00              
ATOM     97  N   GLU    58     -13.682  49.766  11.810  1.00  0.00              
ATOM     98  CA  GLU    58     -14.235  48.426  11.858  1.00  0.00              
ATOM     99  C   GLU    58     -14.259  47.835  10.468  1.00  0.00              
ATOM    100  O   GLU    58     -13.734  46.743  10.273  1.00  0.00              
ATOM    101  N   LYS    59     -14.858  48.553   9.509  1.00  0.00              
ATOM    102  CA  LYS    59     -14.956  48.092   8.114  1.00  0.00              
ATOM    103  C   LYS    59     -13.595  47.648   7.581  1.00  0.00              
ATOM    104  O   LYS    59     -13.452  46.522   7.106  1.00  0.00              
ATOM    105  N   LEU    60     -12.593  48.521   7.664  1.00  0.00              
ATOM    106  CA  LEU    60     -11.260  48.162   7.182  1.00  0.00              
ATOM    107  C   LEU    60     -10.710  46.946   7.944  1.00  0.00              
ATOM    108  O   LEU    60     -10.331  45.942   7.333  1.00  0.00              
ATOM    109  N   GLU    61     -10.683  47.034   9.274  1.00  0.00              
ATOM    110  CA  GLU    61     -10.201  45.944  10.129  1.00  0.00              
ATOM    111  C   GLU    61     -10.851  44.591   9.834  1.00  0.00              
ATOM    112  O   GLU    61     -10.212  43.551   9.942  1.00  0.00              
ATOM    113  N   THR    62      -9.187  43.516   6.766  1.00  0.00              
ATOM    114  CA  THR    62      -7.782  43.385   7.120  1.00  0.00              
ATOM    115  C   THR    62      -7.566  42.041   7.828  1.00  0.00              
ATOM    116  O   THR    62      -6.496  41.417   7.719  1.00  0.00              
ATOM    117  N   PHE    63      -8.598  41.595   8.543  1.00  0.00              
ATOM    118  CA  PHE    63      -8.541  40.338   9.278  1.00  0.00              
ATOM    119  C   PHE    63      -8.768  39.150   8.351  1.00  0.00              
ATOM    120  O   PHE    63      -8.245  38.058   8.567  1.00  0.00              
ATOM    121  N   PHE    64      -9.548  39.363   7.305  1.00  0.00              
ATOM    122  CA  PHE    64      -9.823  38.285   6.370  1.00  0.00              
ATOM    123  C   PHE    64      -8.520  37.959   5.660  1.00  0.00              
ATOM    124  O   PHE    64      -8.121  36.799   5.576  1.00  0.00              
ATOM    125  N   ALA    65      -7.863  39.000   5.153  1.00  0.00              
ATOM    126  CA  ALA    65      -6.604  38.845   4.443  1.00  0.00              
ATOM    127  C   ALA    65      -5.610  38.086   5.308  1.00  0.00              
ATOM    128  O   ALA    65      -4.889  37.213   4.815  1.00  0.00              
ATOM    129  N   VAL    66      -5.563  38.416   6.596  1.00  0.00              
ATOM    130  CA  VAL    66      -4.644  37.720   7.487  1.00  0.00              
ATOM    131  C   VAL    66      -4.953  36.227   7.504  1.00  0.00              
ATOM    132  O   VAL    66      -4.045  35.408   7.439  1.00  0.00              
ATOM    133  N   HIS    67      -6.233  35.874   7.568  1.00  0.00              
ATOM    134  CA  HIS    67      -6.625  34.469   7.560  1.00  0.00              
ATOM    135  C   HIS    67      -6.313  33.833   6.215  1.00  0.00              
ATOM    136  O   HIS    67      -6.321  32.609   6.090  1.00  0.00              
ATOM    137  N   TYR    68      -6.057  34.659   5.204  1.00  0.00              
ATOM    138  CA  TYR    68      -5.712  34.148   3.884  1.00  0.00              
ATOM    139  C   TYR    68      -4.202  34.009   3.836  1.00  0.00              
ATOM    140  O   TYR    68      -3.642  33.449   2.888  1.00  0.00              
ATOM    141  N   PRO    69      -3.542  34.544   4.862  1.00  0.00              
ATOM    142  CA  PRO    69      -2.098  34.448   4.943  1.00  0.00              
ATOM    143  C   PRO    69      -1.292  35.695   4.642  1.00  0.00              
ATOM    144  O   PRO    69      -0.071  35.667   4.752  1.00  0.00              
ATOM    145  N   PHE    70      -1.943  36.793   4.277  1.00  0.00              
ATOM    146  CA  PHE    70      -1.206  38.015   3.960  1.00  0.00              
ATOM    147  C   PHE    70      -1.437  39.130   4.988  1.00  0.00              
ATOM    148  O   PHE    70      -2.508  39.232   5.584  1.00  0.00              
ATOM    149  N   ILE    71      -0.425  39.963   5.194  1.00  0.00              
ATOM    150  CA  ILE    71      -0.545  41.090   6.108  1.00  0.00              
ATOM    151  C   ILE    71      -0.688  42.325   5.226  1.00  0.00              
ATOM    152  O   ILE    71       0.310  42.941   4.832  1.00  0.00              
ATOM    153  N   GLN    72      -1.936  42.670   4.909  1.00  0.00              
ATOM    154  CA  GLN    72      -2.236  43.804   4.046  1.00  0.00              
ATOM    155  C   GLN    72      -1.713  45.116   4.588  1.00  0.00              
ATOM    156  O   GLN    72      -1.818  45.393   5.786  1.00  0.00              
ATOM    157  N   SER    73      -1.144  45.918   3.693  1.00  0.00              
ATOM    158  CA  SER    73      -0.600  47.221   4.049  1.00  0.00              
ATOM    159  C   SER    73      -1.184  48.302   3.143  1.00  0.00              
ATOM    160  O   SER    73      -0.911  49.494   3.326  1.00  0.00              
ATOM    161  N   PHE    74      -1.999  47.888   2.175  1.00  0.00              
ATOM    162  CA  PHE    74      -2.585  48.860   1.270  1.00  0.00              
ATOM    163  C   PHE    74      -4.094  48.802   1.166  1.00  0.00              
ATOM    164  O   PHE    74      -4.716  47.772   1.415  1.00  0.00              
ATOM    165  N   SER    75      -4.692  49.919   0.782  1.00  0.00              
ATOM    166  CA  SER    75      -6.133  49.989   0.641  1.00  0.00              
ATOM    167  C   SER    75      -6.628  50.512  -0.705  1.00  0.00              
ATOM    168  O   SER    75      -6.196  51.567  -1.165  1.00  0.00              
ATOM    169  N   LEU    76      -7.531  49.766  -1.340  1.00  0.00              
ATOM    170  CA  LEU    76      -8.129  50.211  -2.592  1.00  0.00              
ATOM    171  C   LEU    76      -9.224  51.191  -2.184  1.00  0.00              
ATOM    172  O   LEU    76     -10.162  50.832  -1.473  1.00  0.00              
ATOM    173  N   LEU    77      -9.094  52.440  -2.600  1.00  0.00              
ATOM    174  CA  LEU    77     -10.112  53.410  -2.261  1.00  0.00              
ATOM    175  C   LEU    77     -11.350  53.096  -3.093  1.00  0.00              
ATOM    176  O   LEU    77     -11.327  53.220  -4.313  1.00  0.00              
ATOM    177  N   SER    78     -12.432  52.686  -2.440  1.00  0.00              
ATOM    178  CA  SER    78     -13.655  52.378  -3.165  1.00  0.00              
ATOM    179  C   SER    78     -14.127  53.577  -3.985  1.00  0.00              
ATOM    180  O   SER    78     -14.261  54.689  -3.468  1.00  0.00              
END
