
#######################################################
#                                                     #
#                        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 T0360AL381_3-D1
# Molecule2: number of CA atoms   97 (  785),  selected   97 , name T0360_D1.pdb
# PARAMETERS: T0360AL381_3-D1.T0360_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      K      20           -
LGA    -       -      K      21           -
LGA    -       -      K      22           -
LGA    -       -      Q      23           -
LGA    -       -      T      24           -
LGA    -       -      E      25           -
LGA    -       -      M      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      D      29           -
LGA    -       -      H      30           -
LGA    -       -      I      31           -
LGA    -       -      Y      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    -       -      Y      35           -
LGA    -       -      D      36           -
LGA    -       -      V      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      R      40           -
LGA    -       -      F      41           -
LGA    -       -      K      42           -
LGA    -       -      P      43           -
LGA    C      72      L      44          3.311
LGA    R      73      A      45          2.752
LGA    -       -      L      46           -
LGA    -       -      G      47           -
LGA    R      74      I      48          2.469
LGA    P      75      D      49          3.586
LGA    R      76      Q      50          3.531
LGA    Y      77      D      51          1.928
LGA    L      78      L      52          1.766
LGA    K      79      I      53          2.071
LGA    A      80      A      54          1.323
LGA    L      81      A      55          4.534
LGA    A      82      L      56           #
LGA    R      83      P      57          4.194
LGA    G      84      Q      58          2.800
LGA    G      85      Y      59          2.502
LGA    K      86      D      60          4.538
LGA    -       -      A      61           -
LGA    -       -      A      62           -
LGA    R      87      L      63          3.973
LGA    F      88      I      64          1.796
LGA    -       -      A      65           -
LGA    -       -      R      66           -
LGA    D      89      V      67          1.741
LGA    L      90      L      68          2.029
LGA    -       -      A      69           -
LGA    N      91      N      70          2.348
LGA    N      92      H      71          2.258
LGA    R      93      C      72          2.423
LGA    -       -      R      73           -
LGA    -       -      R      74           -
LGA    F      94      P      75          4.256
LGA    K      95      R      76          3.429
LGA    -       -      Y      77           -
LGA    G      96      L      78          1.632
LGA    E      97      K      79          1.963
LGA    -       -      A      80           -
LGA    V      98      L      81          4.226
LGA    T      99      A      82          4.232
LGA    P     100      -       -           -
LGA    E     101      R      83          3.553
LGA    E     102      -       -           -
LGA    Q     103      -       -           -
LGA    A     104      -       -           -
LGA    I     105      -       -           -
LGA    A     106      -       -           -
LGA    Q     107      -       -           -
LGA    N     108      -       -           -
LGA    H     109      -       -           -
LGA    P     110      -       -           -
LGA    F     111      -       -           -
LGA    V     112      -       -           -
LGA    Q     113      G      84           #
LGA    -       -      G      85           -
LGA    -       -      K      86           -
LGA    -       -      R      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -
LGA    -       -      L      90           -
LGA    -       -      N      91           -
LGA    -       -      N      92           -
LGA    -       -      R      93           -
LGA    -       -      F      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      E      97           -
LGA    -       -      V      98           -
LGA    -       -      T      99           -
LGA    -       -      P     100           -
LGA    -       -      E     101           -
LGA    -       -      E     102           -
LGA    -       -      Q     103           -
LGA    -       -      A     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    -       -      Q     107           -
LGA    -       -      N     108           -
LGA    -       -      H     109           -
LGA    -       -      P     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      Q     113           -
LGA    -       -      Q     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   97    5.0     28    3.07    14.29     18.899     0.885

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.228482 * X  +  -0.782040 * Y  +   0.579835 * Z  + -103.627724
  Y_new =  -0.555271 * X  +   0.384534 * Y  +   0.737433 * Z  +   4.729427
  Z_new =  -0.799669 * X  +  -0.490456 * Y  +  -0.346385 * Z  +  39.595924 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.185706    0.955887  [ DEG:  -125.2317     54.7683 ]
  Theta =   0.926744    2.214849  [ DEG:    53.0985    126.9015 ]
  Phi   =  -1.180434    1.961158  [ DEG:   -67.6339    112.3661 ]
 
# 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: T0360AL381_3-D1                               
REMARK     2: T0360_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0360AL381_3-D1.T0360_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   97   5.0   28   3.07   14.29  18.899
REMARK  ---------------------------------------------------------- 
MOLECULE T0360AL381_3-D1
REMARK Aligment from pdb entry: 1p6bA
ATOM      1  N   CYS    72     -71.768  -0.497 -19.742  1.00  0.00              
ATOM      2  CA  CYS    72     -71.778  -0.991 -21.107  1.00  0.00              
ATOM      3  C   CYS    72     -72.129   0.130 -22.067  1.00  0.00              
ATOM      4  O   CYS    72     -72.846   1.061 -21.676  1.00  0.00              
ATOM      5  N   ARG    73     -71.647   0.000 -23.325  1.00  0.00              
ATOM      6  CA  ARG    73     -71.911   0.978 -24.371  1.00  0.00              
ATOM      7  C   ARG    73     -73.074   0.600 -25.263  1.00  0.00              
ATOM      8  O   ARG    73     -73.545   1.404 -26.089  1.00  0.00              
ATOM      9  N   ARG    74     -73.529  -0.635 -25.087  1.00  0.00              
ATOM     10  CA  ARG    74     -74.611  -1.171 -25.892  1.00  0.00              
ATOM     11  C   ARG    74     -75.949  -0.484 -25.718  1.00  0.00              
ATOM     12  O   ARG    74     -76.802  -0.904 -24.922  1.00  0.00              
ATOM     13  N   PRO    75     -76.166   0.585 -26.465  1.00  0.00              
ATOM     14  CA  PRO    75     -77.436   1.251 -26.295  1.00  0.00              
ATOM     15  C   PRO    75     -78.580   0.340 -26.641  1.00  0.00              
ATOM     16  O   PRO    75     -79.708   0.575 -26.213  1.00  0.00              
ATOM     17  N   ARG    76     -78.300  -0.705 -27.435  1.00  0.00              
ATOM     18  CA  ARG    76     -79.403  -1.585 -27.809  1.00  0.00              
ATOM     19  C   ARG    76     -79.965  -2.401 -26.635  1.00  0.00              
ATOM     20  O   ARG    76     -81.173  -2.642 -26.537  1.00  0.00              
ATOM     21  N   TYR    77     -79.071  -2.808 -25.738  1.00  0.00              
ATOM     22  CA  TYR    77     -79.445  -3.550 -24.552  1.00  0.00              
ATOM     23  C   TYR    77     -80.317  -2.624 -23.689  1.00  0.00              
ATOM     24  O   TYR    77     -81.466  -2.887 -23.332  1.00  0.00              
ATOM     25  N   LEU    78     -79.756  -1.473 -23.393  1.00  0.00              
ATOM     26  CA  LEU    78     -80.392  -0.467 -22.560  1.00  0.00              
ATOM     27  C   LEU    78     -81.811  -0.042 -22.892  1.00  0.00              
ATOM     28  O   LEU    78     -82.680  -0.015 -22.009  1.00  0.00              
ATOM     29  N   LYS    79     -82.052   0.305 -24.170  1.00  0.00              
ATOM     30  CA  LYS    79     -83.373   0.753 -24.627  1.00  0.00              
ATOM     31  C   LYS    79     -84.386  -0.370 -24.623  1.00  0.00              
ATOM     32  O   LYS    79     -85.598  -0.154 -24.493  1.00  0.00              
ATOM     33  N   ALA    80     -83.852  -1.579 -24.761  1.00  0.00              
ATOM     34  CA  ALA    80     -84.672  -2.769 -24.720  1.00  0.00              
ATOM     35  C   ALA    80     -85.296  -2.912 -23.308  1.00  0.00              
ATOM     36  O   ALA    80     -86.501  -3.134 -23.122  1.00  0.00              
ATOM     37  N   LEU    81     -84.473  -2.756 -22.279  1.00  0.00              
ATOM     38  CA  LEU    81     -85.002  -2.847 -20.936  1.00  0.00              
ATOM     39  C   LEU    81     -85.882  -1.661 -20.601  1.00  0.00              
ATOM     40  O   LEU    81     -86.945  -1.822 -19.976  1.00  0.00              
ATOM     41  N   ALA    82     -85.434  -0.466 -21.023  1.00  0.00              
ATOM     42  CA  ALA    82     -86.188   0.737 -20.744  1.00  0.00              
ATOM     43  C   ALA    82     -87.574   0.664 -21.340  1.00  0.00              
ATOM     44  O   ALA    82     -88.573   1.117 -20.749  1.00  0.00              
ATOM     45  N   ARG    83     -87.615   0.087 -22.543  1.00  0.00              
ATOM     46  CA  ARG    83     -88.862  -0.043 -23.253  1.00  0.00              
ATOM     47  C   ARG    83     -89.853  -0.929 -22.511  1.00  0.00              
ATOM     48  O   ARG    83     -91.066  -0.798 -22.680  1.00  0.00              
ATOM     49  N   GLY    84     -89.322  -1.821 -21.662  1.00  0.00              
ATOM     50  CA  GLY    84     -90.147  -2.720 -20.863  1.00  0.00              
ATOM     51  C   GLY    84     -90.692  -2.165 -19.569  1.00  0.00              
ATOM     52  O   GLY    84     -91.604  -2.764 -18.993  1.00  0.00              
ATOM     53  N   GLY    85     -90.138  -1.035 -19.121  1.00  0.00              
ATOM     54  CA  GLY    85     -90.623  -0.405 -17.891  1.00  0.00              
ATOM     55  C   GLY    85     -89.608  -0.424 -16.758  1.00  0.00              
ATOM     56  O   GLY    85     -89.864   0.104 -15.674  1.00  0.00              
ATOM     57  N   LYS    86     -88.453  -1.029 -17.024  1.00  0.00              
ATOM     58  CA  LYS    86     -87.442  -1.103 -16.005  1.00  0.00              
ATOM     59  C   LYS    86     -86.776   0.213 -15.839  1.00  0.00              
ATOM     60  O   LYS    86     -86.749   1.033 -16.763  1.00  0.00              
ATOM     61  N   ARG    87     -86.217   0.371 -14.648  1.00  0.00              
ATOM     62  CA  ARG    87     -85.481   1.555 -14.363  1.00  0.00              
ATOM     63  C   ARG    87     -84.046   1.172 -14.653  1.00  0.00              
ATOM     64  O   ARG    87     -83.661   0.029 -14.414  1.00  0.00              
ATOM     65  N   PHE    88     -83.288   2.091 -15.243  1.00  0.00              
ATOM     66  CA  PHE    88     -81.903   1.869 -15.630  1.00  0.00              
ATOM     67  C   PHE    88     -80.961   2.599 -14.697  1.00  0.00              
ATOM     68  O   PHE    88     -80.986   3.831 -14.616  1.00  0.00              
ATOM     69  N   ASP    89     -80.151   1.823 -13.983  1.00  0.00              
ATOM     70  CA  ASP    89     -79.222   2.419 -13.053  1.00  0.00              
ATOM     71  C   ASP    89     -77.853   2.761 -13.641  1.00  0.00              
ATOM     72  O   ASP    89     -77.009   1.881 -13.860  1.00  0.00              
ATOM     73  N   LEU    90     -77.634   4.069 -13.884  1.00  0.00              
ATOM     74  CA  LEU    90     -76.362   4.611 -14.383  1.00  0.00              
ATOM     75  C   LEU    90     -75.658   5.173 -13.141  1.00  0.00              
ATOM     76  O   LEU    90     -75.642   6.369 -12.872  1.00  0.00              
ATOM     77  N   ASN    91     -75.129   4.278 -12.308  1.00  0.00              
ATOM     78  CA  ASN    91     -74.581   4.601 -10.988  1.00  0.00              
ATOM     79  C   ASN    91     -73.091   4.636 -10.771  1.00  0.00              
ATOM     80  O   ASN    91     -72.667   4.789  -9.632  1.00  0.00              
ATOM     81  N   ASN    92     -72.276   4.454 -11.805  1.00  0.00              
ATOM     82  CA  ASN    92     -70.837   4.480 -11.571  1.00  0.00              
ATOM     83  C   ASN    92     -70.124   5.546 -12.404  1.00  0.00              
ATOM     84  O   ASN    92     -68.982   5.371 -12.839  1.00  0.00              
ATOM     85  N   ARG    93     -70.794   6.668 -12.627  1.00  0.00              
ATOM     86  CA  ARG    93     -70.242   7.752 -13.442  1.00  0.00              
ATOM     87  C   ARG    93     -68.763   8.105 -13.205  1.00  0.00              
ATOM     88  O   ARG    93     -67.960   8.165 -14.154  1.00  0.00              
ATOM     89  N   PHE    94     -68.360   8.353 -11.943  1.00  0.00              
ATOM     90  CA  PHE    94     -66.958   8.706 -11.746  1.00  0.00              
ATOM     91  C   PHE    94     -65.958   7.567 -11.864  1.00  0.00              
ATOM     92  O   PHE    94     -64.762   7.805 -11.769  1.00  0.00              
ATOM     93  N   LYS    95     -66.416   6.339 -12.034  1.00  0.00              
ATOM     94  CA  LYS    95     -65.512   5.193 -12.150  1.00  0.00              
ATOM     95  C   LYS    95     -64.724   5.193 -13.463  1.00  0.00              
ATOM     96  O   LYS    95     -65.277   5.030 -14.556  1.00  0.00              
ATOM     97  N   GLY    96     -63.416   5.395 -13.357  1.00  0.00              
ATOM     98  CA  GLY    96     -62.529   5.412 -14.510  1.00  0.00              
ATOM     99  C   GLY    96     -61.065   5.264 -14.102  1.00  0.00              
ATOM    100  O   GLY    96     -60.614   5.951 -13.184  1.00  0.00              
ATOM    101  N   GLU    97     -60.324   4.351 -14.766  1.00  0.00              
ATOM    102  CA  GLU    97     -58.902   4.144 -14.460  1.00  0.00              
ATOM    103  C   GLU    97     -58.028   4.816 -15.513  1.00  0.00              
ATOM    104  O   GLU    97     -56.831   4.588 -15.556  1.00  0.00              
ATOM    105  N   VAL    98     -58.631   5.635 -16.377  1.00  0.00              
ATOM    106  CA  VAL    98     -57.865   6.332 -17.399  1.00  0.00              
ATOM    107  C   VAL    98     -56.734   7.083 -16.702  1.00  0.00              
ATOM    108  O   VAL    98     -56.949   7.831 -15.750  1.00  0.00              
ATOM    109  N   THR    99     -55.506   6.851 -17.130  1.00  0.00              
ATOM    110  CA  THR    99     -54.387   7.495 -16.461  1.00  0.00              
ATOM    111  C   THR    99     -53.782   6.567 -15.391  1.00  0.00              
ATOM    112  O   THR    99     -52.565   6.524 -15.160  1.00  0.00              
ATOM    113  N   PRO   100     -54.663   5.807 -14.737  1.00  0.00              
ATOM    114  CA  PRO   100     -54.282   4.851 -13.709  1.00  0.00              
ATOM    115  C   PRO   100     -54.051   3.489 -14.368  1.00  0.00              
ATOM    116  O   PRO   100     -54.168   2.434 -13.750  1.00  0.00              
ATOM    117  N   GLU   101     -53.739   3.516 -15.662  1.00  0.00              
ATOM    118  CA  GLU   101     -53.504   2.300 -16.426  1.00  0.00              
ATOM    119  C   GLU   101     -52.257   1.592 -15.963  1.00  0.00              
ATOM    120  O   GLU   101     -51.916   0.497 -16.410  1.00  0.00              
ATOM    121  N   GLU   102     -51.577   2.265 -15.059  1.00  0.00              
ATOM    122  CA  GLU   102     -50.374   1.754 -14.462  1.00  0.00              
ATOM    123  C   GLU   102     -50.776   0.546 -13.606  1.00  0.00              
ATOM    124  O   GLU   102     -50.185  -0.542 -13.672  1.00  0.00              
ATOM    125  N   GLN   103     -51.835   0.794 -12.819  1.00  0.00              
ATOM    126  CA  GLN   103     -52.456  -0.123 -11.882  1.00  0.00              
ATOM    127  C   GLN   103     -53.388  -1.165 -12.527  1.00  0.00              
ATOM    128  O   GLN   103     -54.469  -0.883 -13.080  1.00  0.00              
ATOM    129  N   ALA   104     -52.960  -2.416 -12.442  1.00  0.00              
ATOM    130  CA  ALA   104     -53.736  -3.514 -12.998  1.00  0.00              
ATOM    131  C   ALA   104     -55.049  -3.787 -12.234  1.00  0.00              
ATOM    132  O   ALA   104     -56.100  -4.010 -12.856  1.00  0.00              
ATOM    133  N   ILE   105     -54.982  -3.758 -10.883  1.00  0.00              
ATOM    134  CA  ILE   105     -56.137  -3.969 -10.022  1.00  0.00              
ATOM    135  C   ILE   105     -57.215  -2.903 -10.237  1.00  0.00              
ATOM    136  O   ILE   105     -58.379  -3.227 -10.486  1.00  0.00              
ATOM    137  N   ALA   106     -56.803  -1.630 -10.150  1.00  0.00              
ATOM    138  CA  ALA   106     -57.673  -0.486 -10.360  1.00  0.00              
ATOM    139  C   ALA   106     -58.238  -0.487 -11.770  1.00  0.00              
ATOM    140  O   ALA   106     -59.415  -0.222 -12.003  1.00  0.00              
ATOM    141  N   GLN   107     -57.373  -0.784 -12.743  1.00  0.00              
ATOM    142  CA  GLN   107     -57.861  -0.798 -14.097  1.00  0.00              
ATOM    143  C   GLN   107     -58.991  -1.795 -14.252  1.00  0.00              
ATOM    144  O   GLN   107     -59.969  -1.524 -14.945  1.00  0.00              
ATOM    145  N   ASN   108     -58.848  -2.950 -13.591  1.00  0.00              
ATOM    146  CA  ASN   108     -59.827  -4.033 -13.630  1.00  0.00              
ATOM    147  C   ASN   108     -61.190  -3.683 -13.019  1.00  0.00              
ATOM    148  O   ASN   108     -62.248  -4.093 -13.504  1.00  0.00              
ATOM    149  N   HIS   109     -61.148  -2.917 -11.940  1.00  0.00              
ATOM    150  CA  HIS   109     -62.339  -2.511 -11.215  1.00  0.00              
ATOM    151  C   HIS   109     -63.004  -1.287 -11.835  1.00  0.00              
ATOM    152  O   HIS   109     -64.205  -1.269 -12.084  1.00  0.00              
ATOM    153  N   PRO   110     -62.196  -0.263 -12.090  1.00  0.00              
ATOM    154  CA  PRO   110     -62.695   0.988 -12.632  1.00  0.00              
ATOM    155  C   PRO   110     -63.002   1.041 -14.092  1.00  0.00              
ATOM    156  O   PRO   110     -63.898   1.784 -14.509  1.00  0.00              
ATOM    157  N   PHE   111     -62.250   0.286 -14.879  1.00  0.00              
ATOM    158  CA  PHE   111     -62.479   0.329 -16.302  1.00  0.00              
ATOM    159  C   PHE   111     -61.615   1.416 -16.956  1.00  0.00              
ATOM    160  O   PHE   111     -60.818   2.101 -16.301  1.00  0.00              
ATOM    161  N   VAL   112     -61.784   1.567 -18.272  1.00  0.00              
ATOM    162  CA  VAL   112     -61.027   2.541 -19.048  1.00  0.00              
ATOM    163  C   VAL   112     -61.862   3.447 -19.917  1.00  0.00              
ATOM    164  O   VAL   112     -61.354   4.083 -20.843  1.00  0.00              
ATOM    165  N   GLN   113     -63.149   3.481 -19.614  1.00  0.00              
ATOM    166  CA  GLN   113     -64.056   4.363 -20.290  1.00  0.00              
ATOM    167  C   GLN   113     -63.980   5.636 -19.448  1.00  0.00              
ATOM    168  O   GLN   113     -63.804   5.523 -18.239  1.00  0.00              
END
