
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0299AL381_5-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299AL381_5-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E      23      M       1           -
LGA    L      24      T       2           -
LGA    R      25      R       3           -
LGA    Q      26      Y       4           -
LGA    E      27      A       5           -
LGA    L      28      L       6           -
LGA    T      29      L       7           -
LGA    N      30      V       8           -
LGA    L      31      -       -           -
LGA    G      32      -       -           -
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    K      35      -       -           -
LGA    V      36      R       9           #
LGA    E      37      G      10          2.444
LGA    S      38      I      11          3.609
LGA    Y      39      N      12           #
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      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      41           -
LGA    I      40      S      42           #
LGA    N      41      G      43          4.665
LGA    -       -      N      44           -
LGA    S      42      I      45          1.574
LGA    G      43      F      46          2.793
LGA    N      44      F      47          1.561
LGA    I      45      T      48          4.070
LGA    F      46      S      49           #
LGA    F      47      I      50           -
LGA    -       -      D      51           -
LGA    T      48      S      52           #
LGA    S      49      K      53          3.645
LGA    I      50      A      54          1.493
LGA    D      51      Q      55          0.888
LGA    S      52      L      56          0.500
LGA    K      53      V      57          0.469
LGA    A      54      E      58          0.496
LGA    Q      55      K      59          0.496
LGA    L      56      L      60          0.427
LGA    V      57      E      61          0.404
LGA    E      58      T      62          0.547
LGA    P      69      F      63          0.556
LGA    F      70      F      64          1.053
LGA    -       -      A      65           -
LGA    -       -      V      66           -
LGA    -       -      H      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    I      71      F      70          3.216
LGA    Q      72      I      71          2.402
LGA    -       -      Q      72           -
LGA    S      73      S      73          2.765
LGA    F      74      F      74          1.771
LGA    S      75      S      75          3.760
LGA    L      76      L      76          5.153
LGA    L      77      L      77           #
LGA    -       -      S      78           -
LGA    -       -      A     168           -
LGA    -       -      K     169           -
LGA    S      78      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)   46   91    5.0     25    2.51    24.00     20.995     0.960

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.683713 * X  +   0.239876 * Y  +  -0.689200 * Z  + -47.845150
  Y_new =   0.075194 * X  +  -0.962562 * Y  +  -0.260425 * Z  + 124.720909
  Z_new =  -0.725867 * X  +   0.126232 * Y  +  -0.676153 * Z  +  42.715118 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.957026   -0.184567  [ DEG:   169.4251    -10.5749 ]
  Theta =   0.812294    2.329299  [ DEG:    46.5410    133.4590 ]
  Phi   =   0.109538   -3.032054  [ DEG:     6.2761   -173.7239 ]
 
# 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: T0299AL381_5-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL381_5-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   91   5.0   25   2.51   24.00  20.995
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL381_5-D1
REMARK Aligment from pdb entry: 1z5nA
ATOM      1  N   GLU    23      14.447  40.103  -9.044  1.00  0.00              
ATOM      2  CA  GLU    23      14.991  41.309  -9.634  1.00  0.00              
ATOM      3  C   GLU    23      14.507  42.526  -8.839  1.00  0.00              
ATOM      4  O   GLU    23      15.243  43.503  -8.657  1.00  0.00              
ATOM      5  N   LEU    24      13.267  42.457  -8.365  1.00  0.00              
ATOM      6  CA  LEU    24      12.701  43.556  -7.604  1.00  0.00              
ATOM      7  C   LEU    24      13.402  43.689  -6.265  1.00  0.00              
ATOM      8  O   LEU    24      13.588  44.786  -5.773  1.00  0.00              
ATOM      9  N   ARG    25      13.779  42.564  -5.674  1.00  0.00              
ATOM     10  CA  ARG    25      14.465  42.573  -4.376  1.00  0.00              
ATOM     11  C   ARG    25      15.878  43.080  -4.578  1.00  0.00              
ATOM     12  O   ARG    25      16.453  43.722  -3.701  1.00  0.00              
ATOM     13  N   GLN    26      16.437  42.768  -5.744  1.00  0.00              
ATOM     14  CA  GLN    26      17.782  43.227  -6.084  1.00  0.00              
ATOM     15  C   GLN    26      17.741  44.744  -6.132  1.00  0.00              
ATOM     16  O   GLN    26      18.607  45.422  -5.572  1.00  0.00              
ATOM     17  N   GLU    27      16.732  45.282  -6.808  1.00  0.00              
ATOM     18  CA  GLU    27      16.606  46.725  -6.906  1.00  0.00              
ATOM     19  C   GLU    27      16.410  47.321  -5.514  1.00  0.00              
ATOM     20  O   GLU    27      17.084  48.277  -5.137  1.00  0.00              
ATOM     21  N   LEU    28      15.501  46.749  -4.735  1.00  0.00              
ATOM     22  CA  LEU    28      15.269  47.260  -3.395  1.00  0.00              
ATOM     23  C   LEU    28      16.588  47.352  -2.631  1.00  0.00              
ATOM     24  O   LEU    28      16.858  48.361  -1.989  1.00  0.00              
ATOM     25  N   THR    29      17.407  46.308  -2.713  1.00  0.00              
ATOM     26  CA  THR    29      18.691  46.301  -2.022  1.00  0.00              
ATOM     27  C   THR    29      19.636  47.382  -2.564  1.00  0.00              
ATOM     28  O   THR    29      20.238  48.143  -1.803  1.00  0.00              
ATOM     29  N   ASN    30      19.753  47.452  -3.884  1.00  0.00              
ATOM     30  CA  ASN    30      20.628  48.423  -4.524  1.00  0.00              
ATOM     31  C   ASN    30      20.245  49.889  -4.287  1.00  0.00              
ATOM     32  O   ASN    30      21.125  50.739  -4.138  1.00  0.00              
ATOM     33  N   LEU    31      18.949  50.194  -4.244  1.00  0.00              
ATOM     34  CA  LEU    31      18.505  51.569  -4.005  1.00  0.00              
ATOM     35  C   LEU    31      18.427  51.820  -2.495  1.00  0.00              
ATOM     36  O   LEU    31      18.146  52.929  -2.047  1.00  0.00              
ATOM     37  N   GLY    32      18.671  50.770  -1.719  1.00  0.00              
ATOM     38  CA  GLY    32      18.647  50.846  -0.259  1.00  0.00              
ATOM     39  C   GLY    32      17.335  51.363   0.354  1.00  0.00              
ATOM     40  O   GLY    32      17.345  52.179   1.294  1.00  0.00              
ATOM     41  N   LEU    33      16.213  50.872  -0.155  1.00  0.00              
ATOM     42  CA  LEU    33      14.922  51.311   0.332  1.00  0.00              
ATOM     43  C   LEU    33      14.379  50.313   1.318  1.00  0.00              
ATOM     44  O   LEU    33      14.867  49.188   1.408  1.00  0.00              
ATOM     45  N   GLU    34      13.356  50.715   2.059  1.00  0.00              
ATOM     46  CA  GLU    34      12.740  49.781   2.994  1.00  0.00              
ATOM     47  C   GLU    34      11.598  49.049   2.278  1.00  0.00              
ATOM     48  O   GLU    34      10.715  49.686   1.703  1.00  0.00              
ATOM     49  N   LYS    35      11.598  47.723   2.313  1.00  0.00              
ATOM     50  CA  LYS    35      10.538  46.993   1.633  1.00  0.00              
ATOM     51  C   LYS    35      10.093  45.749   2.365  1.00  0.00              
ATOM     52  O   LYS    35      10.810  45.219   3.214  1.00  0.00              
ATOM     53  N   VAL    36       8.895  45.290   2.024  1.00  0.00              
ATOM     54  CA  VAL    36       8.327  44.067   2.585  1.00  0.00              
ATOM     55  C   VAL    36       7.725  43.272   1.416  1.00  0.00              
ATOM     56  O   VAL    36       7.078  43.847   0.520  1.00  0.00              
ATOM     57  N   GLU    37       7.954  41.959   1.427  1.00  0.00              
ATOM     58  CA  GLU    37       7.462  41.054   0.400  1.00  0.00              
ATOM     59  C   GLU    37       6.359  40.219   1.047  1.00  0.00              
ATOM     60  O   GLU    37       6.488  39.804   2.181  1.00  0.00              
ATOM     61  N   SER    38       5.271  39.973   0.334  1.00  0.00              
ATOM     62  CA  SER    38       4.219  39.193   0.945  1.00  0.00              
ATOM     63  C   SER    38       2.933  39.227   0.160  1.00  0.00              
ATOM     64  O   SER    38       2.912  39.598  -1.010  1.00  0.00              
ATOM     65  N   TYR    39       1.853  38.807   0.804  1.00  0.00              
ATOM     66  CA  TYR    39       0.566  38.783   0.143  1.00  0.00              
ATOM     67  C   TYR    39       0.018  40.179   0.003  1.00  0.00              
ATOM     68  O   TYR    39       0.054  40.957   0.945  1.00  0.00              
ATOM     69  N   ILE    40      -0.466  40.509  -1.189  1.00  0.00              
ATOM     70  CA  ILE    40      -1.105  41.803  -1.402  1.00  0.00              
ATOM     71  C   ILE    40      -2.563  41.503  -1.769  1.00  0.00              
ATOM     72  O   ILE    40      -2.830  40.657  -2.639  1.00  0.00              
ATOM     73  N   ASN    41      -3.509  42.181  -1.115  1.00  0.00              
ATOM     74  CA  ASN    41      -4.929  41.934  -1.383  1.00  0.00              
ATOM     75  C   ASN    41      -5.666  43.109  -2.065  1.00  0.00              
ATOM     76  O   ASN    41      -5.411  44.272  -1.754  1.00  0.00              
ATOM     77  N   SER    42      -6.572  42.801  -3.000  1.00  0.00              
ATOM     78  CA  SER    42      -7.315  43.840  -3.693  1.00  0.00              
ATOM     79  C   SER    42      -8.826  43.705  -3.528  1.00  0.00              
ATOM     80  O   SER    42      -9.356  42.624  -3.267  1.00  0.00              
ATOM     81  N   GLY    43      -9.512  44.825  -3.707  1.00  0.00              
ATOM     82  CA  GLY    43     -10.961  44.851  -3.632  1.00  0.00              
ATOM     83  C   GLY    43     -11.411  46.144  -4.271  1.00  0.00              
ATOM     84  O   GLY    43     -10.576  46.989  -4.583  1.00  0.00              
ATOM     85  N   ASN    44     -12.711  46.314  -4.477  1.00  0.00              
ATOM     86  CA  ASN    44     -13.201  47.551  -5.065  1.00  0.00              
ATOM     87  C   ASN    44     -13.572  48.599  -4.008  1.00  0.00              
ATOM     88  O   ASN    44     -14.532  49.353  -4.164  1.00  0.00              
ATOM     89  N   ILE    45     -12.786  48.661  -2.940  1.00  0.00              
ATOM     90  CA  ILE    45     -13.052  49.630  -1.880  1.00  0.00              
ATOM     91  C   ILE    45     -11.790  50.302  -1.344  1.00  0.00              
ATOM     92  O   ILE    45     -10.741  49.673  -1.253  1.00  0.00              
ATOM     93  N   PHE    46     -11.892  51.588  -1.015  1.00  0.00              
ATOM     94  CA  PHE    46     -10.767  52.286  -0.433  1.00  0.00              
ATOM     95  C   PHE    46     -10.918  52.099   1.082  1.00  0.00              
ATOM     96  O   PHE    46     -11.809  52.660   1.689  1.00  0.00              
ATOM     97  N   PHE    47     -10.053  51.265   1.660  1.00  0.00              
ATOM     98  CA  PHE    47     -10.062  50.952   3.084  1.00  0.00              
ATOM     99  C   PHE    47      -9.735  52.199   3.882  1.00  0.00              
ATOM    100  O   PHE    47      -8.728  52.886   3.616  1.00  0.00              
ATOM    101  N   THR    48     -10.579  52.452   4.876  1.00  0.00              
ATOM    102  CA  THR    48     -10.495  53.639   5.713  1.00  0.00              
ATOM    103  C   THR    48     -10.738  53.268   7.178  1.00  0.00              
ATOM    104  O   THR    48     -11.544  53.899   7.855  1.00  0.00              
ATOM    105  N   SER    49     -10.044  52.244   7.665  1.00  0.00              
ATOM    106  CA  SER    49     -10.229  51.825   9.041  1.00  0.00              
ATOM    107  C   SER    49     -11.603  51.228   9.300  1.00  0.00              
ATOM    108  O   SER    49     -12.298  50.796   8.372  1.00  0.00              
ATOM    109  N   ILE    50     -11.993  51.193  10.572  1.00  0.00              
ATOM    110  CA  ILE    50     -13.286  50.655  10.985  1.00  0.00              
ATOM    111  C   ILE    50     -13.456  49.188  10.567  1.00  0.00              
ATOM    112  O   ILE    50     -12.508  48.401  10.614  1.00  0.00              
ATOM    113  N   ASP    51     -14.669  48.826  10.166  1.00  0.00              
ATOM    114  CA  ASP    51     -14.993  47.462   9.759  1.00  0.00              
ATOM    115  C   ASP    51     -14.202  46.964   8.533  1.00  0.00              
ATOM    116  O   ASP    51     -13.700  45.827   8.520  1.00  0.00              
ATOM    117  N   SER    52     -14.108  47.806   7.505  1.00  0.00              
ATOM    118  CA  SER    52     -13.380  47.424   6.303  1.00  0.00              
ATOM    119  C   SER    52     -12.017  46.875   6.662  1.00  0.00              
ATOM    120  O   SER    52     -11.692  45.729   6.336  1.00  0.00              
ATOM    121  N   LYS    53     -11.226  47.686   7.354  1.00  0.00              
ATOM    122  CA  LYS    53      -9.897  47.282   7.765  1.00  0.00              
ATOM    123  C   LYS    53      -9.874  46.014   8.617  1.00  0.00              
ATOM    124  O   LYS    53      -9.112  45.085   8.343  1.00  0.00              
ATOM    125  N   ALA    54     -10.701  45.969   9.653  1.00  0.00              
ATOM    126  CA  ALA    54     -10.705  44.812  10.549  1.00  0.00              
ATOM    127  C   ALA    54     -11.098  43.496   9.873  1.00  0.00              
ATOM    128  O   ALA    54     -10.594  42.437  10.235  1.00  0.00              
ATOM    129  N   GLN    55     -12.002  43.566   8.900  1.00  0.00              
ATOM    130  CA  GLN    55     -12.433  42.375   8.185  1.00  0.00              
ATOM    131  C   GLN    55     -11.232  41.823   7.420  1.00  0.00              
ATOM    132  O   GLN    55     -10.961  40.625   7.463  1.00  0.00              
ATOM    133  N   LEU    56     -10.530  42.704   6.709  1.00  0.00              
ATOM    134  CA  LEU    56      -9.345  42.302   5.954  1.00  0.00              
ATOM    135  C   LEU    56      -8.292  41.669   6.887  1.00  0.00              
ATOM    136  O   LEU    56      -7.774  40.576   6.627  1.00  0.00              
ATOM    137  N   VAL    57      -7.971  42.363   7.966  1.00  0.00              
ATOM    138  CA  VAL    57      -6.970  41.858   8.911  1.00  0.00              
ATOM    139  C   VAL    57      -7.356  40.483   9.439  1.00  0.00              
ATOM    140  O   VAL    57      -6.509  39.620   9.606  1.00  0.00              
ATOM    141  N   GLU    58      -8.645  40.290   9.681  1.00  0.00              
ATOM    142  CA  GLU    58      -9.161  39.027  10.171  1.00  0.00              
ATOM    143  C   GLU    58      -9.005  37.925   9.133  1.00  0.00              
ATOM    144  O   GLU    58      -8.495  36.852   9.432  1.00  0.00              
ATOM    145  N   PRO    69      -9.433  38.193   7.905  1.00  0.00              
ATOM    146  CA  PRO    69      -9.367  37.186   6.853  1.00  0.00              
ATOM    147  C   PRO    69      -7.997  36.966   6.236  1.00  0.00              
ATOM    148  O   PRO    69      -7.698  35.876   5.766  1.00  0.00              
ATOM    149  N   PHE    70      -7.164  37.995   6.228  1.00  0.00              
ATOM    150  CA  PHE    70      -5.846  37.870   5.614  1.00  0.00              
ATOM    151  C   PHE    70      -4.774  38.462   6.543  1.00  0.00              
ATOM    152  O   PHE    70      -4.155  39.498   6.251  1.00  0.00              
ATOM    153  N   ILE    71      -1.860  37.687   7.074  1.00  0.00              
ATOM    154  CA  ILE    71      -0.539  37.806   6.479  1.00  0.00              
ATOM    155  C   ILE    71      -0.497  38.830   5.360  1.00  0.00              
ATOM    156  O   ILE    71       0.564  39.050   4.762  1.00  0.00              
ATOM    157  N   GLN    72      -1.637  39.450   5.049  1.00  0.00              
ATOM    158  CA  GLN    72      -1.676  40.449   3.973  1.00  0.00              
ATOM    159  C   GLN    72      -0.803  41.604   4.432  1.00  0.00              
ATOM    160  O   GLN    72      -0.960  42.099   5.552  1.00  0.00              
ATOM    161  N   SER    73       0.121  42.031   3.578  1.00  0.00              
ATOM    162  CA  SER    73       1.018  43.116   3.948  1.00  0.00              
ATOM    163  C   SER    73       0.554  44.467   3.450  1.00  0.00              
ATOM    164  O   SER    73       1.102  45.494   3.843  1.00  0.00              
ATOM    165  N   PHE    74      -0.446  44.471   2.580  1.00  0.00              
ATOM    166  CA  PHE    74      -0.942  45.720   2.000  1.00  0.00              
ATOM    167  C   PHE    74      -2.232  45.470   1.228  1.00  0.00              
ATOM    168  O   PHE    74      -2.504  44.341   0.804  1.00  0.00              
ATOM    169  N   SER    75      -3.002  46.535   1.011  1.00  0.00              
ATOM    170  CA  SER    75      -4.265  46.424   0.312  1.00  0.00              
ATOM    171  C   SER    75      -4.401  47.541  -0.723  1.00  0.00              
ATOM    172  O   SER    75      -4.007  48.680  -0.475  1.00  0.00              
ATOM    173  N   LEU    76      -4.933  47.204  -1.893  1.00  0.00              
ATOM    174  CA  LEU    76      -5.179  48.205  -2.925  1.00  0.00              
ATOM    175  C   LEU    76      -6.339  47.746  -3.807  1.00  0.00              
ATOM    176  O   LEU    76      -7.139  46.903  -3.380  1.00  0.00              
ATOM    177  N   LEU    77      -6.440  48.247  -5.034  1.00  0.00              
ATOM    178  CA  LEU    77      -7.619  47.928  -5.841  1.00  0.00              
ATOM    179  C   LEU    77      -7.506  47.377  -7.265  1.00  0.00              
ATOM    180  O   LEU    77      -8.543  47.289  -7.950  1.00  0.00              
ATOM    181  N   SER    78      -6.295  47.040  -7.734  1.00  0.00              
ATOM    182  CA  SER    78      -6.135  46.482  -9.091  1.00  0.00              
ATOM    183  C   SER    78      -5.243  45.247  -9.230  1.00  0.00              
ATOM    184  O   SER    78      -5.433  44.426 -10.141  1.00  0.00              
END
