
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0348AL243_5
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348AL243_5.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    -       -      V      10           -
LGA    -       -      C      11           -
LGA    -       -      P      12           -
LGA    -       -      L      13           -
LGA    -       -      C      14           -
LGA    -       -      K      15           -
LGA    -       -      G      16           -
LGA    -       -      P      17           -
LGA    -       -      L      18           -
LGA    L       9      V      19          3.909
LGA    V      10      F      20          2.291
LGA    C      11      D      21          1.675
LGA    P      12      K      22          1.215
LGA    C      14      S      23          1.345
LGA    K      15      K      24          4.254
LGA    G      16      D      25          1.788
LGA    L      18      E      26          1.232
LGA    V      19      L      27          1.094
LGA    F      20      I      28          1.636
LGA    D      21      C      29          0.917
LGA    K      22      K      30          1.967
LGA    S      23      G      31          3.860
LGA    -       -      D      32           -
LGA    K      24      R      33          2.488
LGA    E      26      L      34          2.891
LGA    L      27      A      35          3.195
LGA    I      28      F      36          4.180
LGA    C      29      P      37          4.675
LGA    K      30      I      38          4.213
LGA    G      31      K      39           #
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    D      32      E      49          4.035
LGA    R      33      A      50          2.322
LGA    L      34      R      51          3.473
LGA    A      35      E      52          5.121
LGA    -       -      L      53           -
LGA    -       -      A      54           -
LGA    F      36      P      55           #
LGA    P      37      E      56           -
LGA    I      38      E      57           -
LGA    K      39      E      58           -
LGA    D      40      V      59           -
LGA    G      41      K      60           -
LGA    I      42      L      61           -
LGA    M      45      E      62           -
LGA    L      46      -       -           -
LGA    E      47      -       -           -
LGA    S      48      -       -           -
LGA    E      49      -       -           -
LGA    A      50      -       -           -
LGA    R      51      -       -           -
LGA    E      52      -       -           -
LGA    L      53      -       -           -
LGA    A      54      -       -           -
LGA    P      55      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   61    5.0     23    3.06     8.70     27.649     0.729

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.914055 * X  +  -0.265736 * Y  +   0.306410 * Z  + -82.256187
  Y_new =  -0.308963 * X  +   0.033234 * Y  +   0.950493 * Z  + -76.509590
  Z_new =  -0.262764 * X  +  -0.963473 * Y  +  -0.051725 * Z  +  46.589931 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.624431    1.517162  [ DEG:   -93.0730     86.9270 ]
  Theta =   0.265885    2.875707  [ DEG:    15.2341    164.7659 ]
  Phi   =  -0.325957    2.815636  [ DEG:   -18.6759    161.3241 ]
 
# 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: T0348AL243_5                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348AL243_5.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   61   5.0   23   3.06    8.70  27.649
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL243_5
REMARK Aligment from pdb entry: 1vf5D
ATOM      1  N   LEU     9      14.498  25.204  56.964  1.00  0.00              
ATOM      2  CA  LEU     9      15.073  24.476  55.842  1.00  0.00              
ATOM      3  C   LEU     9      14.906  25.342  54.598  1.00  0.00              
ATOM      4  O   LEU     9      13.789  25.530  54.137  1.00  0.00              
ATOM      5  N   VAL    10      15.992  25.862  54.033  1.00  0.00              
ATOM      6  CA  VAL    10      15.843  26.672  52.823  1.00  0.00              
ATOM      7  C   VAL    10      16.531  25.978  51.659  1.00  0.00              
ATOM      8  O   VAL    10      17.756  25.990  51.532  1.00  0.00              
ATOM      9  N   CYS    11      15.706  25.381  50.804  1.00  0.00              
ATOM     10  CA  CYS    11      16.160  24.639  49.637  1.00  0.00              
ATOM     11  C   CYS    11      16.825  25.562  48.623  1.00  0.00              
ATOM     12  O   CYS    11      16.234  26.553  48.192  1.00  0.00              
ATOM     13  N   PRO    12      18.080  25.255  48.247  1.00  0.00              
ATOM     14  CA  PRO    12      18.841  26.052  47.281  1.00  0.00              
ATOM     15  C   PRO    12      18.567  25.707  45.811  1.00  0.00              
ATOM     16  O   PRO    12      18.499  26.599  44.964  1.00  0.00              
ATOM     17  N   CYS    14      18.397  24.419  45.522  1.00  0.00              
ATOM     18  CA  CYS    14      18.150  23.954  44.154  1.00  0.00              
ATOM     19  C   CYS    14      17.135  24.777  43.377  1.00  0.00              
ATOM     20  O   CYS    14      17.377  25.137  42.221  1.00  0.00              
ATOM     21  N   LYS    15      15.992  25.058  43.997  1.00  0.00              
ATOM     22  CA  LYS    15      14.957  25.817  43.311  1.00  0.00              
ATOM     23  C   LYS    15      14.178  26.826  44.172  1.00  0.00              
ATOM     24  O   LYS    15      13.109  27.282  43.772  1.00  0.00              
ATOM     25  N   GLY    16      14.711  27.160  45.350  1.00  0.00              
ATOM     26  CA  GLY    16      14.090  28.147  46.230  1.00  0.00              
ATOM     27  C   GLY    16      12.928  27.800  47.157  1.00  0.00              
ATOM     28  O   GLY    16      12.037  28.631  47.363  1.00  0.00              
ATOM     29  N   LEU    18      12.946  26.605  47.748  1.00  0.00              
ATOM     30  CA  LEU    18      11.890  26.186  48.672  1.00  0.00              
ATOM     31  C   LEU    18      12.355  26.443  50.096  1.00  0.00              
ATOM     32  O   LEU    18      13.436  26.020  50.492  1.00  0.00              
ATOM     33  N   VAL    19      11.526  27.132  50.866  1.00  0.00              
ATOM     34  CA  VAL    19      11.871  27.471  52.236  1.00  0.00              
ATOM     35  C   VAL    19      11.011  26.715  53.237  1.00  0.00              
ATOM     36  O   VAL    19       9.814  26.517  53.015  1.00  0.00              
ATOM     37  N   PHE    20      11.639  26.286  54.329  1.00  0.00              
ATOM     38  CA  PHE    20      10.978  25.534  55.393  1.00  0.00              
ATOM     39  C   PHE    20      11.377  26.069  56.769  1.00  0.00              
ATOM     40  O   PHE    20      12.131  27.034  56.867  1.00  0.00              
ATOM     41  N   ASP    21      10.845  25.454  57.823  1.00  0.00              
ATOM     42  CA  ASP    21      11.120  25.874  59.191  1.00  0.00              
ATOM     43  C   ASP    21      11.930  24.847  59.992  1.00  0.00              
ATOM     44  O   ASP    21      12.735  24.103  59.441  1.00  0.00              
ATOM     45  N   LYS    22      11.719  24.828  61.301  1.00  0.00              
ATOM     46  CA  LYS    22      12.420  23.928  62.205  1.00  0.00              
ATOM     47  C   LYS    22      11.831  22.512  62.240  1.00  0.00              
ATOM     48  O   LYS    22      12.559  21.515  62.316  1.00  0.00              
ATOM     49  N   SER    23      10.508  22.440  62.155  1.00  0.00              
ATOM     50  CA  SER    23       9.788  21.176  62.212  1.00  0.00              
ATOM     51  C   SER    23       9.331  20.706  60.829  1.00  0.00              
ATOM     52  O   SER    23       8.425  19.885  60.714  1.00  0.00              
ATOM     53  N   LYS    24       9.952  21.235  59.780  1.00  0.00              
ATOM     54  CA  LYS    24       9.588  20.840  58.428  1.00  0.00              
ATOM     55  C   LYS    24       8.587  21.798  57.822  1.00  0.00              
ATOM     56  O   LYS    24       8.163  21.647  56.679  1.00  0.00              
ATOM     57  N   GLU    26       8.229  22.806  58.606  1.00  0.00              
ATOM     58  CA  GLU    26       7.257  23.815  58.208  1.00  0.00              
ATOM     59  C   GLU    26       7.737  24.744  57.097  1.00  0.00              
ATOM     60  O   GLU    26       8.538  25.643  57.350  1.00  0.00              
ATOM     61  N   LEU    27       7.206  24.562  55.889  1.00  0.00              
ATOM     62  CA  LEU    27       7.570  25.407  54.747  1.00  0.00              
ATOM     63  C   LEU    27       7.320  26.884  55.077  1.00  0.00              
ATOM     64  O   LEU    27       6.478  27.197  55.912  1.00  0.00              
ATOM     65  N   ILE    28       8.056  27.790  54.433  1.00  0.00              
ATOM     66  CA  ILE    28       7.908  29.228  54.689  1.00  0.00              
ATOM     67  C   ILE    28       6.931  29.873  53.704  1.00  0.00              
ATOM     68  O   ILE    28       5.998  30.578  54.096  1.00  0.00              
ATOM     69  N   CYS    29       7.174  29.635  52.424  1.00  0.00              
ATOM     70  CA  CYS    29       6.360  30.160  51.334  1.00  0.00              
ATOM     71  C   CYS    29       6.606  29.234  50.151  1.00  0.00              
ATOM     72  O   CYS    29       6.268  28.052  50.207  1.00  0.00              
ATOM     73  N   LYS    30       8.709  26.423  47.785  1.00  0.00              
ATOM     74  CA  LYS    30       8.580  25.302  48.719  1.00  0.00              
ATOM     75  C   LYS    30       7.143  24.769  48.622  1.00  0.00              
ATOM     76  O   LYS    30       6.199  25.465  48.998  1.00  0.00              
ATOM     77  N   GLY    31       6.959  23.519  48.144  1.00  0.00              
ATOM     78  CA  GLY    31       5.600  22.966  48.020  1.00  0.00              
ATOM     79  C   GLY    31       4.744  22.896  49.294  1.00  0.00              
ATOM     80  O   GLY    31       3.724  23.581  49.380  1.00  0.00              
ATOM     81  N   ASP    32       5.147  22.081  50.271  1.00  0.00              
ATOM     82  CA  ASP    32       4.404  21.943  51.536  1.00  0.00              
ATOM     83  C   ASP    32       5.311  21.666  52.737  1.00  0.00              
ATOM     84  O   ASP    32       6.535  21.669  52.625  1.00  0.00              
ATOM     85  N   ARG    33       4.692  21.433  53.889  1.00  0.00              
ATOM     86  CA  ARG    33       5.425  21.151  55.117  1.00  0.00              
ATOM     87  C   ARG    33       6.091  19.780  55.079  1.00  0.00              
ATOM     88  O   ARG    33       5.473  18.787  54.695  1.00  0.00              
ATOM     89  N   LEU    34       7.352  19.731  55.500  1.00  0.00              
ATOM     90  CA  LEU    34       8.136  18.497  55.506  1.00  0.00              
ATOM     91  C   LEU    34       7.582  17.374  56.400  1.00  0.00              
ATOM     92  O   LEU    34       6.978  17.636  57.438  1.00  0.00              
ATOM     93  N   ALA    35       7.313  14.312  59.053  1.00  0.00              
ATOM     94  CA  ALA    35       7.850  14.112  60.401  1.00  0.00              
ATOM     95  C   ALA    35       8.056  12.632  60.710  1.00  0.00              
ATOM     96  O   ALA    35       7.614  11.761  59.958  1.00  0.00              
ATOM     97  N   PHE    36       8.749  12.367  61.816  1.00  0.00              
ATOM     98  CA  PHE    36       9.028  11.007  62.259  1.00  0.00              
ATOM     99  C   PHE    36       8.729  10.892  63.762  1.00  0.00              
ATOM    100  O   PHE    36       8.108  11.785  64.344  1.00  0.00              
ATOM    101  N   PRO    37       9.169   9.794  64.379  1.00  0.00              
ATOM    102  CA  PRO    37       8.954   9.552  65.809  1.00  0.00              
ATOM    103  C   PRO    37      10.299   9.592  66.542  1.00  0.00              
ATOM    104  O   PRO    37      11.315   9.960  65.952  1.00  0.00              
ATOM    105  N   ILE    38      10.311   9.233  67.825  1.00  0.00              
ATOM    106  CA  ILE    38      11.551   9.267  68.602  1.00  0.00              
ATOM    107  C   ILE    38      11.825   8.015  69.429  1.00  0.00              
ATOM    108  O   ILE    38      11.266   7.864  70.515  1.00  0.00              
ATOM    109  N   LYS    39      12.680   7.125  68.917  1.00  0.00              
ATOM    110  CA  LYS    39      13.029   5.886  69.627  1.00  0.00              
ATOM    111  C   LYS    39      14.326   5.168  69.167  1.00  0.00              
ATOM    112  O   LYS    39      14.838   5.440  68.078  1.00  0.00              
ATOM    113  N   ASP    40      18.715  -1.187  70.774  1.00  0.00              
ATOM    114  CA  ASP    40      20.029  -1.859  70.836  1.00  0.00              
ATOM    115  C   ASP    40      21.105  -1.248  69.932  1.00  0.00              
ATOM    116  O   ASP    40      21.651  -1.922  69.051  1.00  0.00              
ATOM    117  N   GLY    41      21.410   0.027  70.156  1.00  0.00              
ATOM    118  CA  GLY    41      22.403   0.740  69.355  1.00  0.00              
ATOM    119  C   GLY    41      21.973   0.719  67.884  1.00  0.00              
ATOM    120  O   GLY    41      22.762   1.005  66.979  1.00  0.00              
ATOM    121  N   ILE    42      18.660   2.328  66.300  1.00  0.00              
ATOM    122  CA  ILE    42      17.452   3.156  66.432  1.00  0.00              
ATOM    123  C   ILE    42      16.285   2.657  65.570  1.00  0.00              
ATOM    124  O   ILE    42      16.507   2.161  64.465  1.00  0.00              
ATOM    125  N   MET    45      15.049   2.785  66.072  1.00  0.00              
ATOM    126  CA  MET    45      13.860   2.323  65.333  1.00  0.00              
ATOM    127  C   MET    45      12.732   3.327  65.056  1.00  0.00              
ATOM    128  O   MET    45      11.974   3.694  65.946  1.00  0.00              
ATOM    129  N   LEU    46      12.608   3.727  63.798  1.00  0.00              
ATOM    130  CA  LEU    46      11.560   4.635  63.353  1.00  0.00              
ATOM    131  C   LEU    46      10.680   3.668  62.542  1.00  0.00              
ATOM    132  O   LEU    46      11.123   2.558  62.241  1.00  0.00              
ATOM    133  N   GLU    47       0.891   7.011  58.433  1.00  0.00              
ATOM    134  CA  GLU    47       0.184   7.704  59.524  1.00  0.00              
ATOM    135  C   GLU    47       0.037   9.245  59.555  1.00  0.00              
ATOM    136  O   GLU    47       0.716   9.966  58.831  1.00  0.00              
ATOM    137  N   SER    48      -0.865   9.716  60.426  1.00  0.00              
ATOM    138  CA  SER    48      -1.205  11.138  60.636  1.00  0.00              
ATOM    139  C   SER    48      -0.136  12.046  61.282  1.00  0.00              
ATOM    140  O   SER    48       0.749  11.565  61.987  1.00  0.00              
ATOM    141  N   GLU    49      -0.229  13.353  61.015  1.00  0.00              
ATOM    142  CA  GLU    49       0.685  14.381  61.557  1.00  0.00              
ATOM    143  C   GLU    49       0.004  15.480  62.401  1.00  0.00              
ATOM    144  O   GLU    49      -1.040  16.013  62.012  1.00  0.00              
ATOM    145  N   ALA    50       0.606  15.812  63.548  1.00  0.00              
ATOM    146  CA  ALA    50       0.083  16.830  64.482  1.00  0.00              
ATOM    147  C   ALA    50       0.365  18.312  64.175  1.00  0.00              
ATOM    148  O   ALA    50      -0.316  19.191  64.710  1.00  0.00              
ATOM    149  N   ARG    51       1.361  18.595  63.339  1.00  0.00              
ATOM    150  CA  ARG    51       1.712  19.982  63.021  1.00  0.00              
ATOM    151  C   ARG    51       0.541  20.759  62.425  1.00  0.00              
ATOM    152  O   ARG    51       0.461  21.979  62.580  1.00  0.00              
ATOM    153  N   GLU    52      -0.360  20.052  61.744  1.00  0.00              
ATOM    154  CA  GLU    52      -1.524  20.679  61.118  1.00  0.00              
ATOM    155  C   GLU    52      -2.838  20.106  61.686  1.00  0.00              
ATOM    156  O   GLU    52      -3.876  20.778  61.670  1.00  0.00              
ATOM    157  N   LEU    53      -2.789  18.869  62.184  1.00  0.00              
ATOM    158  CA  LEU    53      -3.966  18.263  62.788  1.00  0.00              
ATOM    159  C   LEU    53      -4.830  17.284  62.004  1.00  0.00              
ATOM    160  O   LEU    53      -5.572  16.500  62.613  1.00  0.00              
ATOM    161  N   ALA    54      -4.762  17.323  60.674  1.00  0.00              
ATOM    162  CA  ALA    54      -5.567  16.422  59.840  1.00  0.00              
ATOM    163  C   ALA    54      -4.841  15.131  59.472  1.00  0.00              
ATOM    164  O   ALA    54      -3.663  14.955  59.786  1.00  0.00              
ATOM    165  N   PRO    55      -5.562  14.224  58.819  1.00  0.00              
ATOM    166  CA  PRO    55      -4.978  12.967  58.378  1.00  0.00              
ATOM    167  C   PRO    55      -3.744  13.335  57.540  1.00  0.00              
ATOM    168  O   PRO    55      -3.699  14.400  56.920  1.00  0.00              
END
