
#######################################################
#                                                     #
#                        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   37 (  148),  selected   37 , name T0347AL381_4
# Molecule2: number of CA atoms  196 ( 1574),  selected  196 , name T0347.pdb
# PARAMETERS: T0347AL381_4.T0347.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      E       6           -
LGA    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    G      44      I      14          4.468
LGA    D      45      D      15           #
LGA    D      46      -       -           -
LGA    F      47      K      16          1.984
LGA    L      48      L      17          2.214
LGA    G      49      R      18          1.776
LGA    N      50      -       -           -
LGA    H      51      -       -           -
LGA    I      52      -       -           -
LGA    V      53      P      19          4.190
LGA    P      54      T      20          1.031
LGA    V      55      Q      21          2.800
LGA    V      56      I      22          2.837
LGA    A      57      A      23          2.358
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      T      39           -
LGA    -       -      R      40           -
LGA    -       -      D      46           -
LGA    -       -      F      47           -
LGA    -       -      L      48           -
LGA    -       -      G      49           -
LGA    -       -      N      50           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      V     102           -
LGA    -       -      M     103           -
LGA    -       -      D     104           -
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    -       -      L     108           -
LGA    -       -      I     109           -
LGA    -       -      Y     110           -
LGA    -       -      P     111           -
LGA    -       -      F     112           -
LGA    -       -      D     113           -
LGA    -       -      A     114           -
LGA    -       -      Q     115           -
LGA    -       -      G     116           -
LGA    -       -      L     117           -
LGA    -       -      R     118           -
LGA    -       -      R     119           -
LGA    -       -      Q     120           -
LGA    -       -      S     121           -
LGA    -       -      G     122           -
LGA    -       -      D     123           -
LGA    -       -      I     124           -
LGA    -       -      P     125           -
LGA    -       -      K     126           -
LGA    -       -      N     127           -
LGA    -       -      I     128           -
LGA    -       -      H     129           -
LGA    -       -      D     130           -
LGA    -       -      L     131           -
LGA    G      58      E     132          2.547
LGA    -       -      D     133           -
LGA    I      66      D     134          1.002
LGA    D      67      P     135          1.780
LGA    H      68      F     136           #
LGA    -       -      R     137           -
LGA    H      69      S     138          2.175
LGA    H      70      L     139          0.532
LGA    L      71      A     140          2.329
LGA    V      72      G     141          1.419
LGA    L      73      A     142          1.668
LGA    A      74      L     143          2.566
LGA    L      75      R     144          2.040
LGA    S      76      M     145          1.660
LGA    K      77      A     146          3.521
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    E      78      Y     149          1.227
LGA    G      79      A     150          2.335
LGA    V      80      K     151          1.302
LGA    E      81      V     152          3.489
LGA    -       -      I     153           -
LGA    H      82      I     154          2.863
LGA    V      83      P     155          2.565
LGA    L      84      F     156          3.467
LGA    T      85      S     157           -
LGA    S      86      E     158           -
LGA    E      87      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    -       -      D     172           -
LGA    -       -      L     173           -
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    -       -      F     178           -
LGA    -       -      D     179           -
LGA    -       -      D     180           -
LGA    -       -      A     181           -
LGA    -       -      L     182           -
LGA    -       -      A     183           -
LGA    -       -      E     184           -
LGA    -       -      A     185           -
LGA    -       -      M     186           -
LGA    -       -      K     187           -
LGA    -       -      L     188           -
LGA    -       -      A     189           -
LGA    -       -      K     190           -
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    -       -      A     194           -
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    -       -      V     203           -
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37  196    5.0     28    2.47     7.14      9.810     1.088

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.336343 * X  +  -0.427453 * Y  +   0.839141 * Z  + -50.314503
  Y_new =   0.724045 * X  +  -0.452404 * Y  +  -0.520663 * Z  +  98.508354
  Z_new =   0.602190 * X  +   0.782697 * Y  +   0.157332 * Z  + -86.036140 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.372427   -1.769165  [ DEG:    78.6343   -101.3657 ]
  Theta =  -0.646241   -2.495352  [ DEG:   -37.0269   -142.9731 ]
  Phi   =   1.135922   -2.005671  [ DEG:    65.0835   -114.9165 ]
 
# 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: T0347AL381_4                                  
REMARK     2: T0347.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL381_4.T0347.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37  196   5.0   28   2.47    7.14   9.810
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL381_4
REMARK Aligment from pdb entry: 1a9xB
ATOM      1  N   GLY    44      -2.059  41.041 -11.060  1.00  0.00              
ATOM      2  CA  GLY    44      -0.866  40.913 -10.276  1.00  0.00              
ATOM      3  C   GLY    44      -1.108  40.703  -8.816  1.00  0.00              
ATOM      4  O   GLY    44      -0.452  39.851  -8.254  1.00  0.00              
ATOM      5  N   ASP    45      -2.002  41.454  -8.184  1.00  0.00              
ATOM      6  CA  ASP    45      -2.227  41.210  -6.764  1.00  0.00              
ATOM      7  C   ASP    45      -2.624  39.744  -6.497  1.00  0.00              
ATOM      8  O   ASP    45      -2.056  39.059  -5.644  1.00  0.00              
ATOM      9  N   ASP    46      -3.581  39.270  -7.289  1.00  0.00              
ATOM     10  CA  ASP    46      -4.042  37.897  -7.196  1.00  0.00              
ATOM     11  C   ASP    46      -2.902  36.970  -7.377  1.00  0.00              
ATOM     12  O   ASP    46      -2.782  35.971  -6.713  1.00  0.00              
ATOM     13  N   PHE    47      -2.055  37.303  -8.312  1.00  0.00              
ATOM     14  CA  PHE    47      -0.924  36.436  -8.569  1.00  0.00              
ATOM     15  C   PHE    47       0.021  36.313  -7.387  1.00  0.00              
ATOM     16  O   PHE    47       0.481  35.216  -7.055  1.00  0.00              
ATOM     17  N   LEU    48       0.347  37.442  -6.757  1.00  0.00              
ATOM     18  CA  LEU    48       1.249  37.486  -5.603  1.00  0.00              
ATOM     19  C   LEU    48       0.641  36.703  -4.455  1.00  0.00              
ATOM     20  O   LEU    48       1.283  35.928  -3.782  1.00  0.00              
ATOM     21  N   GLY    49      -0.626  36.952  -4.246  1.00  0.00              
ATOM     22  CA  GLY    49      -1.334  36.267  -3.191  1.00  0.00              
ATOM     23  C   GLY    49      -1.274  34.788  -3.377  1.00  0.00              
ATOM     24  O   GLY    49      -0.963  34.060  -2.445  1.00  0.00              
ATOM     25  N   ASN    50      -1.570  34.385  -4.602  1.00  0.00              
ATOM     26  CA  ASN    50      -1.543  33.000  -5.040  1.00  0.00              
ATOM     27  C   ASN    50      -0.152  32.401  -4.849  1.00  0.00              
ATOM     28  O   ASN    50       0.022  31.213  -4.608  1.00  0.00              
ATOM     29  N   HIS    51       0.878  33.214  -4.954  1.00  0.00              
ATOM     30  CA  HIS    51       2.176  32.620  -4.808  1.00  0.00              
ATOM     31  C   HIS    51       2.726  32.808  -3.465  1.00  0.00              
ATOM     32  O   HIS    51       3.881  32.472  -3.215  1.00  0.00              
ATOM     33  N   ILE    52       1.875  33.387  -2.648  1.00  0.00              
ATOM     34  CA  ILE    52       2.210  33.666  -1.287  1.00  0.00              
ATOM     35  C   ILE    52       3.300  34.677  -1.104  1.00  0.00              
ATOM     36  O   ILE    52       4.183  34.478  -0.269  1.00  0.00              
ATOM     37  N   VAL    53       3.214  35.770  -1.877  1.00  0.00              
ATOM     38  CA  VAL    53       4.248  36.769  -1.782  1.00  0.00              
ATOM     39  C   VAL    53       3.889  38.024  -1.035  1.00  0.00              
ATOM     40  O   VAL    53       2.828  38.608  -1.235  1.00  0.00              
ATOM     41  N   PRO    54       4.808  38.433  -0.187  1.00  0.00              
ATOM     42  CA  PRO    54       4.661  39.651   0.602  1.00  0.00              
ATOM     43  C   PRO    54       5.084  40.780  -0.320  1.00  0.00              
ATOM     44  O   PRO    54       6.187  40.725  -0.881  1.00  0.00              
ATOM     45  N   VAL    55       4.179  41.738  -0.511  1.00  0.00              
ATOM     46  CA  VAL    55       4.430  42.876  -1.385  1.00  0.00              
ATOM     47  C   VAL    55       3.846  44.208  -0.881  1.00  0.00              
ATOM     48  O   VAL    55       2.773  44.368  -0.326  1.00  0.00              
ATOM     49  N   VAL    56       4.577  45.236  -1.097  1.00  0.00              
ATOM     50  CA  VAL    56       4.124  46.507  -0.667  1.00  0.00              
ATOM     51  C   VAL    56       4.055  47.436  -1.896  1.00  0.00              
ATOM     52  O   VAL    56       4.825  47.301  -2.854  1.00  0.00              
ATOM     53  N   ALA    57       3.104  48.357  -1.893  1.00  0.00              
ATOM     54  CA  ALA    57       2.921  49.359  -2.954  1.00  0.00              
ATOM     55  C   ALA    57       2.818  50.656  -2.204  1.00  0.00              
ATOM     56  O   ALA    57       2.805  50.607  -0.975  1.00  0.00              
ATOM     57  N   GLY    58       2.785  51.767  -2.939  1.00  0.00              
ATOM     58  CA  GLY    58       2.676  53.127  -2.428  1.00  0.00              
ATOM     59  C   GLY    58       3.846  53.687  -1.697  1.00  0.00              
ATOM     60  O   GLY    58       3.675  54.552  -0.846  1.00  0.00              
ATOM     61  N   ILE    66       5.029  53.225  -2.002  1.00  0.00              
ATOM     62  CA  ILE    66       6.131  53.823  -1.284  1.00  0.00              
ATOM     63  C   ILE    66       7.026  54.607  -2.263  1.00  0.00              
ATOM     64  O   ILE    66       6.962  54.437  -3.474  1.00  0.00              
ATOM     65  N   ASP    67       7.875  55.468  -1.743  1.00  0.00              
ATOM     66  CA  ASP    67       8.720  56.239  -2.603  1.00  0.00              
ATOM     67  C   ASP    67       9.876  55.400  -3.015  1.00  0.00              
ATOM     68  O   ASP    67      10.915  55.404  -2.364  1.00  0.00              
ATOM     69  N   HIS    68       9.668  54.675  -4.095  1.00  0.00              
ATOM     70  CA  HIS    68      10.696  53.819  -4.624  1.00  0.00              
ATOM     71  C   HIS    68      11.941  54.570  -5.060  1.00  0.00              
ATOM     72  O   HIS    68      13.046  54.015  -5.162  1.00  0.00              
ATOM     73  N   HIS    69      11.768  55.870  -5.339  1.00  0.00              
ATOM     74  CA  HIS    69      12.886  56.666  -5.806  1.00  0.00              
ATOM     75  C   HIS    69      13.883  56.926  -4.680  1.00  0.00              
ATOM     76  O   HIS    69      15.103  56.782  -4.799  1.00  0.00              
ATOM     77  N   HIS    70      13.307  57.311  -3.557  1.00  0.00              
ATOM     78  CA  HIS    70      14.067  57.531  -2.362  1.00  0.00              
ATOM     79  C   HIS    70      14.878  56.255  -2.016  1.00  0.00              
ATOM     80  O   HIS    70      16.054  56.297  -1.619  1.00  0.00              
ATOM     81  N   LEU    71      14.203  55.114  -2.175  1.00  0.00              
ATOM     82  CA  LEU    71      14.767  53.793  -1.909  1.00  0.00              
ATOM     83  C   LEU    71      15.937  53.511  -2.813  1.00  0.00              
ATOM     84  O   LEU    71      17.033  53.161  -2.351  1.00  0.00              
ATOM     85  N   VAL    72      15.690  53.664  -4.122  1.00  0.00              
ATOM     86  CA  VAL    72      16.744  53.445  -5.096  1.00  0.00              
ATOM     87  C   VAL    72      17.923  54.395  -4.826  1.00  0.00              
ATOM     88  O   VAL    72      19.084  54.041  -4.899  1.00  0.00              
ATOM     89  N   LEU    73      17.614  55.630  -4.504  1.00  0.00              
ATOM     90  CA  LEU    73      18.678  56.552  -4.243  1.00  0.00              
ATOM     91  C   LEU    73      19.538  56.130  -3.038  1.00  0.00              
ATOM     92  O   LEU    73      20.746  56.289  -2.983  1.00  0.00              
ATOM     93  N   ALA    74      18.912  55.573  -2.039  1.00  0.00              
ATOM     94  CA  ALA    74      19.624  55.152  -0.848  1.00  0.00              
ATOM     95  C   ALA    74      20.549  53.959  -1.156  1.00  0.00              
ATOM     96  O   ALA    74      21.727  53.891  -0.801  1.00  0.00              
ATOM     97  N   LEU    75      19.983  52.988  -1.859  1.00  0.00              
ATOM     98  CA  LEU    75      20.697  51.792  -2.253  1.00  0.00              
ATOM     99  C   LEU    75      21.874  52.135  -3.154  1.00  0.00              
ATOM    100  O   LEU    75      22.964  51.545  -3.066  1.00  0.00              
ATOM    101  N   SER    76      21.655  53.090  -4.051  1.00  0.00              
ATOM    102  CA  SER    76      22.717  53.467  -4.959  1.00  0.00              
ATOM    103  C   SER    76      23.818  54.117  -4.179  1.00  0.00              
ATOM    104  O   SER    76      24.978  53.771  -4.289  1.00  0.00              
ATOM    105  N   LYS    77      23.418  55.071  -3.363  1.00  0.00              
ATOM    106  CA  LYS    77      24.357  55.837  -2.563  1.00  0.00              
ATOM    107  C   LYS    77      25.081  55.048  -1.509  1.00  0.00              
ATOM    108  O   LYS    77      26.305  55.087  -1.416  1.00  0.00              
ATOM    109  N   GLU    78      24.317  54.368  -0.676  1.00  0.00              
ATOM    110  CA  GLU    78      24.951  53.649   0.384  1.00  0.00              
ATOM    111  C   GLU    78      25.204  52.171   0.113  1.00  0.00              
ATOM    112  O   GLU    78      25.803  51.484   0.932  1.00  0.00              
ATOM    113  N   GLY    79      24.791  51.668  -1.048  1.00  0.00              
ATOM    114  CA  GLY    79      24.996  50.263  -1.376  1.00  0.00              
ATOM    115  C   GLY    79      23.836  49.384  -0.895  1.00  0.00              
ATOM    116  O   GLY    79      22.905  49.818  -0.196  1.00  0.00              
ATOM    117  N   VAL    80      23.873  48.133  -1.296  1.00  0.00              
ATOM    118  CA  VAL    80      22.838  47.180  -0.922  1.00  0.00              
ATOM    119  C   VAL    80      22.647  47.035   0.598  1.00  0.00              
ATOM    120  O   VAL    80      23.576  47.212   1.407  1.00  0.00              
ATOM    121  N   GLU    81      21.408  46.726   0.969  1.00  0.00              
ATOM    122  CA  GLU    81      21.033  46.573   2.339  1.00  0.00              
ATOM    123  C   GLU    81      20.004  45.503   2.435  1.00  0.00              
ATOM    124  O   GLU    81      19.236  45.262   1.519  1.00  0.00              
ATOM    125  N   HIS    82      20.025  44.869   3.579  1.00  0.00              
ATOM    126  CA  HIS    82      19.087  43.850   3.844  1.00  0.00              
ATOM    127  C   HIS    82      17.923  44.564   4.437  1.00  0.00              
ATOM    128  O   HIS    82      18.115  45.601   5.125  1.00  0.00              
ATOM    129  N   VAL    83      16.727  43.986   4.198  1.00  0.00              
ATOM    130  CA  VAL    83      15.522  44.609   4.741  1.00  0.00              
ATOM    131  C   VAL    83      14.418  43.599   5.081  1.00  0.00              
ATOM    132  O   VAL    83      14.583  42.373   4.980  1.00  0.00              
ATOM    133  N   LEU    84      13.262  44.162   5.467  1.00  0.00              
ATOM    134  CA  LEU    84      12.143  43.317   5.787  1.00  0.00              
ATOM    135  C   LEU    84      10.849  44.053   5.612  1.00  0.00              
ATOM    136  O   LEU    84      10.687  45.244   6.027  1.00  0.00              
ATOM    137  N   THR    85       9.946  43.295   5.018  1.00  0.00              
ATOM    138  CA  THR    85       8.603  43.787   4.786  1.00  0.00              
ATOM    139  C   THR    85       7.639  43.008   5.645  1.00  0.00              
ATOM    140  O   THR    85       7.624  41.787   5.643  1.00  0.00              
ATOM    141  N   SER    86       6.794  43.737   6.320  1.00  0.00              
ATOM    142  CA  SER    86       5.783  43.133   7.096  1.00  0.00              
ATOM    143  C   SER    86       4.462  43.667   6.541  1.00  0.00              
ATOM    144  O   SER    86       4.230  44.865   6.481  1.00  0.00              
ATOM    145  N   GLU    87       3.568  42.783   6.125  1.00  0.00              
ATOM    146  CA  GLU    87       2.282  43.257   5.647  1.00  0.00              
ATOM    147  C   GLU    87       1.245  42.702   6.602  1.00  0.00              
ATOM    148  O   GLU    87       1.126  41.492   6.710  1.00  0.00              
END
