
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0285AL243_5
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285AL243_5.T0285.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S       7           -
LGA    -       -      P       8           -
LGA    -       -      A       9           -
LGA    -       -      K      10           -
LGA    -       -      R      11           -
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    -       -      F      14           -
LGA    -       -      Q      15           -
LGA    -       -      M      16           -
LGA    -       -      V      17           -
LGA    -       -      G      18           -
LGA    -       -      N      19           -
LGA    I      21      A      20          1.719
LGA    N      22      I      21          4.425
LGA    R      23      N      22          2.994
LGA    N      24      R      23          3.122
LGA    T      25      N      24          2.404
LGA    Q      26      -       -           -
LGA    Q      27      -       -           -
LGA    L      28      T      25          2.467
LGA    T      29      Q      26          2.776
LGA    Q      30      Q      27          5.541
LGA    D      31      L      28           #
LGA    L      32      T      29          2.799
LGA    R      33      Q      30           -
LGA    A      34      -       -           -
LGA    M      35      -       -           -
LGA    S      39      -       -           -
LGA    L      40      D      31          3.786
LGA    R      41      L      32          3.495
LGA    F      42      R      33           -
LGA    -       -      A      34           -
LGA    -       -      M      35           -
LGA    -       -      P      36           -
LGA    -       -      N      37           -
LGA    -       -      W      38           -
LGA    -       -      S      39           -
LGA    -       -      L      40           -
LGA    V      43      R      41           #
LGA    -       -      F      42           -
LGA    -       -      V      43           -
LGA    -       -      Y      44           -
LGA    Y      44      I      45          4.692
LGA    I      45      V      46           #
LGA    V      46      D      47           -
LGA    -       -      R      48           -
LGA    -       -      N      49           -
LGA    -       -      N      50           -
LGA    -       -      Q      51           -
LGA    -       -      D      52           -
LGA    -       -      L      53           -
LGA    -       -      L      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    -       -      P      57           -
LGA    -       -      L      58           -
LGA    -       -      P      59           -
LGA    -       -      P      60           -
LGA    D      47      G      61          4.226
LGA    R      48      I      62          2.757
LGA    N      49      M      63           -
LGA    N      50      -       -           -
LGA    Q      51      -       -           -
LGA    D      52      -       -           -
LGA    L      53      V      64           #
LGA    L      54      L      65           #
LGA    -       -      A      66           -
LGA    -       -      P      67           -
LGA    -       -      R      68           -
LGA    -       -      L      69           -
LGA    -       -      T      70           -
LGA    -       -      A      71           -
LGA    -       -      K      72           -
LGA    -       -      H      73           -
LGA    -       -      P      74           -
LGA    -       -      Y      75           -
LGA    -       -      D      76           -
LGA    K      55      K      77           #
LGA    R      56      -       -           -
LGA    P      57      -       -           -
LGA    I      62      V      78          3.143
LGA    M      63      Q      79          1.446
LGA    V      64      D      80          1.667
LGA    L      65      R      81           #
LGA    A      66      N      82           #
LGA    P      67      R      83          1.622
LGA    R      68      K      84           #
LGA    -       -      L      85           -
LGA    -       -      Y      86           -
LGA    -       -      G      87           -
LGA    -       -      R      88           -
LGA    -       -      H      89           -
LGA    -       -      I      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      N      93           -
LGA    -       -      D      94           -
LGA    -       -      G      95           -
LGA    -       -      N      96           -
LGA    -       -      S      97           -
LGA    -       -      V      98           -
LGA    -       -      K      99           -
LGA    -       -      V     100           -
LGA    -       -      V     101           -
LGA    -       -      T     102           -
LGA    -       -      I     103           -
LGA    L      69      S     104          1.672
LGA    T      70      A     105          3.759
LGA    A      71      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   99    5.0     20    3.22     5.00     12.654     0.602

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.502937 * X  +  -0.308519 * Y  +   0.807385 * Z  + -51.353073
  Y_new =  -0.612460 * X  +   0.531916 * Y  +   0.584771 * Z  + -18.225882
  Z_new =  -0.609874 * X  +  -0.788594 * Y  +   0.078565 * Z  + 102.148216 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.471498    1.670095  [ DEG:   -84.3106     95.6894 ]
  Theta =   0.655902    2.485691  [ DEG:    37.5804    142.4196 ]
  Phi   =  -0.883277    2.258316  [ DEG:   -50.6080    129.3920 ]
 
# 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: T0285AL243_5                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285AL243_5.T0285.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   99   5.0   20   3.22    5.00  12.654
REMARK  ---------------------------------------------------------- 
MOLECULE T0285AL243_5
REMARK Aligment from pdb entry: 1fviA
ATOM      1  N   ILE    21      22.283   8.249  71.575  1.00  0.00              
ATOM      2  CA  ILE    21      21.365   9.295  71.126  1.00  0.00              
ATOM      3  C   ILE    21      20.825   9.371  69.698  1.00  0.00              
ATOM      4  O   ILE    21      19.646   9.080  69.471  1.00  0.00              
ATOM      5  N   ASN    22      21.650   9.795  68.745  1.00  0.00              
ATOM      6  CA  ASN    22      21.157   9.914  67.383  1.00  0.00              
ATOM      7  C   ASN    22      21.494   8.754  66.475  1.00  0.00              
ATOM      8  O   ASN    22      21.489   8.910  65.264  1.00  0.00              
ATOM      9  N   ARG    23      21.791   7.596  67.052  1.00  0.00              
ATOM     10  CA  ARG    23      22.129   6.415  66.269  1.00  0.00              
ATOM     11  C   ARG    23      20.923   5.499  66.121  1.00  0.00              
ATOM     12  O   ARG    23      19.884   5.703  66.765  1.00  0.00              
ATOM     13  N   ASN    24      21.072   4.480  65.278  1.00  0.00              
ATOM     14  CA  ASN    24      19.997   3.521  65.064  1.00  0.00              
ATOM     15  C   ASN    24      20.012   2.462  66.161  1.00  0.00              
ATOM     16  O   ASN    24      21.030   2.275  66.841  1.00  0.00              
ATOM     17  N   THR    25      18.888   1.758  66.309  1.00  0.00              
ATOM     18  CA  THR    25      18.758   0.713  67.314  1.00  0.00              
ATOM     19  C   THR    25      19.776  -0.399  67.117  1.00  0.00              
ATOM     20  O   THR    25      20.285  -0.960  68.093  1.00  0.00              
ATOM     21  N   GLN    26      20.070  -0.718  65.858  1.00  0.00              
ATOM     22  CA  GLN    26      21.040  -1.764  65.554  1.00  0.00              
ATOM     23  C   GLN    26      22.463  -1.338  65.918  1.00  0.00              
ATOM     24  O   GLN    26      23.315  -2.175  66.215  1.00  0.00              
ATOM     25  N   GLN    27      22.712  -0.037  65.915  1.00  0.00              
ATOM     26  CA  GLN    27      24.032   0.464  66.265  1.00  0.00              
ATOM     27  C   GLN    27      24.190   0.359  67.768  1.00  0.00              
ATOM     28  O   GLN    27      25.166  -0.201  68.267  1.00  0.00              
ATOM     29  N   LEU    28      23.192   0.882  68.478  1.00  0.00              
ATOM     30  CA  LEU    28      23.150   0.846  69.933  1.00  0.00              
ATOM     31  C   LEU    28      23.308  -0.605  70.400  1.00  0.00              
ATOM     32  O   LEU    28      24.130  -0.898  71.256  1.00  0.00              
ATOM     33  N   THR    29      22.539  -1.509  69.797  1.00  0.00              
ATOM     34  CA  THR    29      22.575  -2.924  70.146  1.00  0.00              
ATOM     35  C   THR    29      23.963  -3.552  70.080  1.00  0.00              
ATOM     36  O   THR    29      24.351  -4.289  70.977  1.00  0.00              
ATOM     37  N   GLN    30      24.708  -3.247  69.021  1.00  0.00              
ATOM     38  CA  GLN    30      26.041  -3.797  68.836  1.00  0.00              
ATOM     39  C   GLN    30      27.076  -3.141  69.734  1.00  0.00              
ATOM     40  O   GLN    30      28.061  -3.771  70.104  1.00  0.00              
ATOM     41  N   ASP    31      26.878  -1.875  70.074  1.00  0.00              
ATOM     42  CA  ASP    31      27.826  -1.192  70.953  1.00  0.00              
ATOM     43  C   ASP    31      27.703  -1.727  72.390  1.00  0.00              
ATOM     44  O   ASP    31      28.701  -2.017  73.045  1.00  0.00              
ATOM     45  N   LEU    32      26.466  -1.889  72.847  1.00  0.00              
ATOM     46  CA  LEU    32      26.168  -2.384  74.194  1.00  0.00              
ATOM     47  C   LEU    32      26.373  -3.893  74.326  1.00  0.00              
ATOM     48  O   LEU    32      26.976  -4.380  75.289  1.00  0.00              
ATOM     49  N   ARG    33      25.870  -4.621  73.340  1.00  0.00              
ATOM     50  CA  ARG    33      25.912  -6.068  73.367  1.00  0.00              
ATOM     51  C   ARG    33      27.150  -6.763  72.844  1.00  0.00              
ATOM     52  O   ARG    33      27.240  -7.989  72.909  1.00  0.00              
ATOM     53  N   ALA    34      28.101  -6.005  72.321  1.00  0.00              
ATOM     54  CA  ALA    34      29.331  -6.626  71.844  1.00  0.00              
ATOM     55  C   ALA    34      30.373  -6.429  72.936  1.00  0.00              
ATOM     56  O   ALA    34      30.489  -5.340  73.502  1.00  0.00              
ATOM     57  N   MET    35      31.110  -7.498  73.236  1.00  0.00              
ATOM     58  CA  MET    35      32.118  -7.465  74.280  1.00  0.00              
ATOM     59  C   MET    35      33.346  -6.614  74.044  1.00  0.00              
ATOM     60  O   MET    35      34.460  -7.134  74.054  1.00  0.00              
ATOM     61  N   SER    39      33.161   6.029  72.470  1.00  0.00              
ATOM     62  CA  SER    39      32.009   6.756  71.946  1.00  0.00              
ATOM     63  C   SER    39      31.083   7.151  73.065  1.00  0.00              
ATOM     64  O   SER    39      30.957   6.444  74.068  1.00  0.00              
ATOM     65  N   LEU    40      30.433   8.290  72.875  1.00  0.00              
ATOM     66  CA  LEU    40      29.494   8.812  73.845  1.00  0.00              
ATOM     67  C   LEU    40      28.188   8.009  73.767  1.00  0.00              
ATOM     68  O   LEU    40      27.837   7.464  72.714  1.00  0.00              
ATOM     69  N   ARG    41      27.513   7.882  74.904  1.00  0.00              
ATOM     70  CA  ARG    41      26.244   7.169  74.983  1.00  0.00              
ATOM     71  C   ARG    41      25.442   7.729  76.149  1.00  0.00              
ATOM     72  O   ARG    41      25.941   8.502  76.968  1.00  0.00              
ATOM     73  N   PHE    42      24.181   7.350  76.216  1.00  0.00              
ATOM     74  CA  PHE    42      23.327   7.845  77.275  1.00  0.00              
ATOM     75  C   PHE    42      22.699   6.708  78.064  1.00  0.00              
ATOM     76  O   PHE    42      22.757   5.548  77.662  1.00  0.00              
ATOM     77  N   VAL    43      22.156   7.045  79.226  1.00  0.00              
ATOM     78  CA  VAL    43      21.480   6.071  80.060  1.00  0.00              
ATOM     79  C   VAL    43      20.278   6.771  80.662  1.00  0.00              
ATOM     80  O   VAL    43      20.426   7.712  81.453  1.00  0.00              
ATOM     81  N   TYR    44      19.093   6.376  80.199  1.00  0.00              
ATOM     82  CA  TYR    44      17.848   6.936  80.703  1.00  0.00              
ATOM     83  C   TYR    44      17.522   6.130  81.960  1.00  0.00              
ATOM     84  O   TYR    44      17.180   4.942  81.877  1.00  0.00              
ATOM     85  N   ILE    45      17.681   6.775  83.112  1.00  0.00              
ATOM     86  CA  ILE    45      17.461   6.152  84.418  1.00  0.00              
ATOM     87  C   ILE    45      16.033   6.375  84.840  1.00  0.00              
ATOM     88  O   ILE    45      15.673   7.474  85.244  1.00  0.00              
ATOM     89  N   VAL    46      15.211   5.334  84.745  1.00  0.00              
ATOM     90  CA  VAL    46      13.804   5.478  85.094  1.00  0.00              
ATOM     91  C   VAL    46      13.302   4.870  86.406  1.00  0.00              
ATOM     92  O   VAL    46      12.159   5.131  86.803  1.00  0.00              
ATOM     93  N   ASP    47      14.133   4.059  87.067  1.00  0.00              
ATOM     94  CA  ASP    47      13.740   3.462  88.337  1.00  0.00              
ATOM     95  C   ASP    47      14.934   3.233  89.253  1.00  0.00              
ATOM     96  O   ASP    47      16.076   3.188  88.803  1.00  0.00              
ATOM     97  N   ARG    48      14.637   3.073  90.538  1.00  0.00              
ATOM     98  CA  ARG    48      15.637   2.898  91.587  1.00  0.00              
ATOM     99  C   ARG    48      15.017   2.128  92.739  1.00  0.00              
ATOM    100  O   ARG    48      14.189   2.685  93.471  1.00  0.00              
ATOM    101  N   ASN    49      13.643  -1.950  99.416  1.00  0.00              
ATOM    102  CA  ASN    49      12.293  -2.477  99.360  1.00  0.00              
ATOM    103  C   ASN    49      11.535  -2.242  98.061  1.00  0.00              
ATOM    104  O   ASN    49      11.077  -1.137  97.801  1.00  0.00              
ATOM    105  N   ASN    50      11.357  -3.303  97.248  1.00  0.00              
ATOM    106  CA  ASN    50      10.635  -3.208  95.971  1.00  0.00              
ATOM    107  C   ASN    50       9.162  -2.832  96.168  1.00  0.00              
ATOM    108  O   ASN    50       8.499  -2.368  95.241  1.00  0.00              
ATOM    109  N   GLN    51       8.658  -3.022  97.386  1.00  0.00              
ATOM    110  CA  GLN    51       7.281  -2.686  97.685  1.00  0.00              
ATOM    111  C   GLN    51       7.090  -1.189  97.863  1.00  0.00              
ATOM    112  O   GLN    51       5.958  -0.718  97.905  1.00  0.00              
ATOM    113  N   ASP    52       8.187  -0.438  97.982  1.00  0.00              
ATOM    114  CA  ASP    52       8.088   1.014  98.096  1.00  0.00              
ATOM    115  C   ASP    52       7.361   1.515  96.835  1.00  0.00              
ATOM    116  O   ASP    52       7.649   1.060  95.730  1.00  0.00              
ATOM    117  N   LEU    53       6.390   2.409  97.008  1.00  0.00              
ATOM    118  CA  LEU    53       5.612   2.949  95.882  1.00  0.00              
ATOM    119  C   LEU    53       6.459   3.638  94.818  1.00  0.00              
ATOM    120  O   LEU    53       7.401   4.362  95.139  1.00  0.00              
ATOM    121  N   LEU    54       6.087   3.432  93.555  1.00  0.00              
ATOM    122  CA  LEU    54       6.790   4.020  92.416  1.00  0.00              
ATOM    123  C   LEU    54       7.150   5.506  92.557  1.00  0.00              
ATOM    124  O   LEU    54       8.302   5.880  92.308  1.00  0.00              
ATOM    125  N   LYS    55       6.188   6.352  92.934  1.00  0.00              
ATOM    126  CA  LYS    55       6.475   7.779  93.104  1.00  0.00              
ATOM    127  C   LYS    55       7.616   7.991  94.097  1.00  0.00              
ATOM    128  O   LYS    55       8.401   8.933  93.965  1.00  0.00              
ATOM    129  N   ARG    56       7.644   7.147  95.127  1.00  0.00              
ATOM    130  CA  ARG    56       8.640   7.225  96.180  1.00  0.00              
ATOM    131  C   ARG    56      10.032   6.798  95.730  1.00  0.00              
ATOM    132  O   ARG    56      11.036   7.389  96.141  1.00  0.00              
ATOM    133  N   PRO    57      10.100   5.755  94.908  1.00  0.00              
ATOM    134  CA  PRO    57      11.384   5.296  94.382  1.00  0.00              
ATOM    135  C   PRO    57      11.929   6.392  93.456  1.00  0.00              
ATOM    136  O   PRO    57      13.125   6.621  93.407  1.00  0.00              
ATOM    137  N   ILE    62      11.040   7.069  92.733  1.00  0.00              
ATOM    138  CA  ILE    62      11.440   8.147  91.842  1.00  0.00              
ATOM    139  C   ILE    62      12.041   9.279  92.673  1.00  0.00              
ATOM    140  O   ILE    62      13.040   9.881  92.276  1.00  0.00              
ATOM    141  N   MET    63      11.440   9.546  93.833  1.00  0.00              
ATOM    142  CA  MET    63      11.931  10.580  94.735  1.00  0.00              
ATOM    143  C   MET    63      13.305  10.200  95.284  1.00  0.00              
ATOM    144  O   MET    63      14.135  11.065  95.548  1.00  0.00              
ATOM    145  N   VAL    64      13.532   8.901  95.472  1.00  0.00              
ATOM    146  CA  VAL    64      14.833   8.411  95.926  1.00  0.00              
ATOM    147  C   VAL    64      15.893   8.763  94.863  1.00  0.00              
ATOM    148  O   VAL    64      16.987   9.241  95.189  1.00  0.00              
ATOM    149  N   LEU    65      15.565   8.493  93.598  1.00  0.00              
ATOM    150  CA  LEU    65      16.456   8.782  92.471  1.00  0.00              
ATOM    151  C   LEU    65      16.741  10.269  92.446  1.00  0.00              
ATOM    152  O   LEU    65      17.890  10.681  92.314  1.00  0.00              
ATOM    153  N   ALA    66      15.694  11.073  92.606  1.00  0.00              
ATOM    154  CA  ALA    66      15.841  12.523  92.583  1.00  0.00              
ATOM    155  C   ALA    66      16.792  13.012  93.664  1.00  0.00              
ATOM    156  O   ALA    66      17.708  13.806  93.381  1.00  0.00              
ATOM    157  N   PRO    67      16.589  12.504  94.882  1.00  0.00              
ATOM    158  CA  PRO    67      17.417  12.874  96.023  1.00  0.00              
ATOM    159  C   PRO    67      18.852  12.413  95.871  1.00  0.00              
ATOM    160  O   PRO    67      19.781  13.158  96.197  1.00  0.00              
ATOM    161  N   ARG    68      19.041  11.216  95.324  1.00  0.00              
ATOM    162  CA  ARG    68      20.389  10.706  95.129  1.00  0.00              
ATOM    163  C   ARG    68      21.133  11.689  94.229  1.00  0.00              
ATOM    164  O   ARG    68      22.272  12.057  94.522  1.00  0.00              
ATOM    165  N   LEU    69      20.457  12.151  93.172  1.00  0.00              
ATOM    166  CA  LEU    69      21.041  13.103  92.213  1.00  0.00              
ATOM    167  C   LEU    69      21.375  14.447  92.872  1.00  0.00              
ATOM    168  O   LEU    69      22.335  15.115  92.498  1.00  0.00              
ATOM    169  N   THR    70      20.564  14.834  93.848  1.00  0.00              
ATOM    170  CA  THR    70      20.767  16.067  94.597  1.00  0.00              
ATOM    171  C   THR    70      22.059  15.967  95.403  1.00  0.00              
ATOM    172  O   THR    70      22.755  16.957  95.589  1.00  0.00              
ATOM    173  N   ALA    71      22.354  14.765  95.897  1.00  0.00              
ATOM    174  CA  ALA    71      23.553  14.506  96.698  1.00  0.00              
ATOM    175  C   ALA    71      24.769  14.352  95.781  1.00  0.00              
ATOM    176  O   ALA    71      25.892  14.671  96.173  1.00  0.00              
END
