
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0319AL588_1
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319AL588_1.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      F       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      T       6           -
LGA    -       -      N       7           -
LGA    -       -      F       8           -
LGA    -       -      L       9           -
LGA    -       -      K      10           -
LGA    -       -      C      11           -
LGA    -       -      S      12           -
LGA    -       -      V      13           -
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    -       -      C      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    -       -      D      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    -       -      P      24           -
LGA    -       -      L      25           -
LGA    -       -      Q      26           -
LGA    -       -      Y      27           -
LGA    -       -      D      28           -
LGA    -       -      G      29           -
LGA    -       -      S      30           -
LGA    -       -      K      31           -
LGA    -       -      C      32           -
LGA    -       -      Q      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      D      37           -
LGA    -       -      E      38           -
LGA    -       -      S      39           -
LGA    -       -      I      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      P      44           -
LGA    -       -      E      45           -
LGA    -       -      F      46           -
LGA    -       -      L      47           -
LGA    -       -      L      48           -
LGA    -       -      N      49           -
LGA    -       -      I      50           -
LGA    -       -      V      51           -
LGA    -       -      D      52           -
LGA    -       -      R      53           -
LGA    -       -      V      54           -
LGA    -       -      D      55           -
LGA    -       -      W      56           -
LGA    -       -      P      57           -
LGA    -       -      A      58           -
LGA    -       -      V      59           -
LGA    -       -      L      60           -
LGA    -       -      T      61           -
LGA    -       -      V      62           -
LGA    W      56      A      63          4.645
LGA    P      57      A      64          4.350
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    A      58      G      67           #
LGA    V      59      N      68          4.767
LGA    L      60      N      69          3.237
LGA    T      61      -       -           -
LGA    V      62      A      70          3.950
LGA    A      63      L      71           #
LGA    A      64      P      72           -
LGA    E      65      P      73           -
LGA    L      66      T      74           -
LGA    G      67      K      75           -
LGA    N      68      P      76           -
LGA    N      69      S      77           -
LGA    A      70      F      78           -
LGA    -       -      P      79           -
LGA    -       -      S      80           -
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    L      71      T      86          3.860
LGA    P      72      D      87          2.058
LGA    -       -      D      88           -
LGA    -       -      D      89           -
LGA    P      73      M      90          1.499
LGA    -       -      A      91           -
LGA    T      74      I      92           #
LGA    K      75      L      93          3.310
LGA    P      76      N      94          1.423
LGA    S      77      D      95          1.691
LGA    F      78      L      96          2.970
LGA    P      79      H      97          3.274
LGA    S      80      T      98          3.652
LGA    S      81      L      99          3.579
LGA    I      82      L     100          4.858
LGA    Q      83      -       -           -
LGA    E      84      L     101          4.916
LGA    -       -      Q     102           -
LGA    -       -      T     103           -
LGA    L      85      S     104          1.722
LGA    T      86      I     105          5.009
LGA    D      87      A     106          1.218
LGA    D      88      E     107          2.702
LGA    D      89      G     108          2.738
LGA    M      90      E     109           #
LGA    A      91      M     110           -
LGA    -       -      K     111           -
LGA    -       -      C     112           -
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    -       -      H     117           -
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    I      92      Y     120          3.196
LGA    L      93      I     121          3.295
LGA    -       -      K     122           -
LGA    -       -      N     123           -
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    N      94      P     126          2.594
LGA    D      95      N     127          1.818
LGA    L      96      L     128          4.198
LGA    -       -      L     129           -
LGA    -       -      L     130           -
LGA    -       -      P     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      V     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41  135    5.0     27    3.40     3.70     11.294     0.770

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.619610 * X  +   0.645848 * Y  +  -0.446054 * Z  + 100.663818
  Y_new =   0.317820 * X  +  -0.726054 * Y  +  -0.609784 * Z  +  87.412056
  Z_new =  -0.717687 * X  +   0.236063 * Y  +  -0.655134 * Z  +  10.444263 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.795747   -0.345846  [ DEG:   160.1845    -19.8155 ]
  Theta =   0.800475    2.341118  [ DEG:    45.8638    134.1362 ]
  Phi   =   0.473942   -2.667650  [ DEG:    27.1549   -152.8451 ]
 
# 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: T0319AL588_1                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319AL588_1.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41  135   5.0   27   3.40    3.70  11.294
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL588_1
REMARK Aligment from pdb entry: 1b35_D
ATOM      1  N   TRP    56      24.889  -2.116   7.114  1.00  0.00              
ATOM      2  CA  TRP    56      23.800  -2.420   6.132  1.00  0.00              
ATOM      3  C   TRP    56      23.504  -1.198   5.268  1.00  0.00              
ATOM      4  O   TRP    56      23.624  -1.254   4.038  1.00  0.00              
ATOM      5  N   PRO    57      23.112  -0.097   5.905  1.00  0.00              
ATOM      6  CA  PRO    57      22.824   1.134   5.173  1.00  0.00              
ATOM      7  C   PRO    57      24.026   1.489   4.293  1.00  0.00              
ATOM      8  O   PRO    57      23.874   1.846   3.125  1.00  0.00              
ATOM      9  N   ALA    58      25.215   1.376   4.882  1.00  0.00              
ATOM     10  CA  ALA    58      26.481   1.677   4.225  1.00  0.00              
ATOM     11  C   ALA    58      26.668   0.814   2.980  1.00  0.00              
ATOM     12  O   ALA    58      27.042   1.313   1.912  1.00  0.00              
ATOM     13  N   VAL    59      26.399  -0.481   3.122  1.00  0.00              
ATOM     14  CA  VAL    59      26.525  -1.419   2.012  1.00  0.00              
ATOM     15  C   VAL    59      25.497  -1.155   0.913  1.00  0.00              
ATOM     16  O   VAL    59      25.815  -1.232  -0.272  1.00  0.00              
ATOM     17  N   LEU    60      24.260  -0.857   1.302  1.00  0.00              
ATOM     18  CA  LEU    60      23.218  -0.568   0.323  1.00  0.00              
ATOM     19  C   LEU    60      23.629   0.651  -0.504  1.00  0.00              
ATOM     20  O   LEU    60      23.426   0.688  -1.720  1.00  0.00              
ATOM     21  N   THR    61      24.209   1.646   0.164  1.00  0.00              
ATOM     22  CA  THR    61      24.645   2.875  -0.502  1.00  0.00              
ATOM     23  C   THR    61      25.748   2.615  -1.531  1.00  0.00              
ATOM     24  O   THR    61      25.653   3.059  -2.678  1.00  0.00              
ATOM     25  N   VAL    62      26.788   1.891  -1.121  1.00  0.00              
ATOM     26  CA  VAL    62      27.906   1.576  -2.009  1.00  0.00              
ATOM     27  C   VAL    62      27.437   0.741  -3.199  1.00  0.00              
ATOM     28  O   VAL    62      27.943   0.890  -4.314  1.00  0.00              
ATOM     29  N   ALA    63      26.472  -0.140  -2.957  1.00  0.00              
ATOM     30  CA  ALA    63      25.948  -0.993  -4.015  1.00  0.00              
ATOM     31  C   ALA    63      25.289  -0.165  -5.120  1.00  0.00              
ATOM     32  O   ALA    63      25.301  -0.559  -6.290  1.00  0.00              
ATOM     33  N   ALA    64      24.727   0.984  -4.757  1.00  0.00              
ATOM     34  CA  ALA    64      24.078   1.849  -5.740  1.00  0.00              
ATOM     35  C   ALA    64      25.084   2.673  -6.549  1.00  0.00              
ATOM     36  O   ALA    64      24.984   2.754  -7.765  1.00  0.00              
ATOM     37  N   GLU    65      26.048   3.276  -5.860  1.00  0.00              
ATOM     38  CA  GLU    65      27.071   4.115  -6.489  1.00  0.00              
ATOM     39  C   GLU    65      27.946   3.371  -7.500  1.00  0.00              
ATOM     40  O   GLU    65      28.260   3.890  -8.570  1.00  0.00              
ATOM     41  N   LEU    66      28.347   2.157  -7.151  1.00  0.00              
ATOM     42  CA  LEU    66      29.191   1.355  -8.026  1.00  0.00              
ATOM     43  C   LEU    66      28.376   0.325  -8.798  1.00  0.00              
ATOM     44  O   LEU    66      28.909  -0.356  -9.668  1.00  0.00              
ATOM     45  N   GLY    67      27.079   0.246  -8.499  1.00  0.00              
ATOM     46  CA  GLY    67      26.196  -0.758  -9.090  1.00  0.00              
ATOM     47  C   GLY    67      26.947  -2.079  -9.174  1.00  0.00              
ATOM     48  O   GLY    67      27.079  -2.693 -10.235  1.00  0.00              
ATOM     49  N   ASN    68      47.288 -14.080   3.196  1.00  0.00              
ATOM     50  CA  ASN    68      47.601 -15.257   4.003  1.00  0.00              
ATOM     51  C   ASN    68      47.704 -15.008   5.511  1.00  0.00              
ATOM     52  O   ASN    68      47.306 -15.862   6.312  1.00  0.00              
ATOM     53  N   ASN    69      48.239 -13.854   5.898  1.00  0.00              
ATOM     54  CA  ASN    69      48.397 -13.529   7.316  1.00  0.00              
ATOM     55  C   ASN    69      47.216 -12.760   7.901  1.00  0.00              
ATOM     56  O   ASN    69      47.127 -12.587   9.115  1.00  0.00              
ATOM     57  N   ALA    70      46.312 -12.305   7.039  1.00  0.00              
ATOM     58  CA  ALA    70      45.143 -11.545   7.473  1.00  0.00              
ATOM     59  C   ALA    70      44.231 -12.316   8.425  1.00  0.00              
ATOM     60  O   ALA    70      43.774 -13.410   8.113  1.00  0.00              
ATOM     61  N   LEU    71      43.963 -11.730   9.588  1.00  0.00              
ATOM     62  CA  LEU    71      43.081 -12.352  10.571  1.00  0.00              
ATOM     63  C   LEU    71      41.922 -11.403  10.879  1.00  0.00              
ATOM     64  O   LEU    71      42.110 -10.355  11.499  1.00  0.00              
ATOM     65  N   PRO    72      40.704 -11.757  10.436  1.00  0.00              
ATOM     66  CA  PRO    72      39.519 -10.927  10.670  1.00  0.00              
ATOM     67  C   PRO    72      39.043 -10.924  12.125  1.00  0.00              
ATOM     68  O   PRO    72      39.103 -11.946  12.816  1.00  0.00              
ATOM     69  N   PRO    73      38.577  -9.766  12.582  1.00  0.00              
ATOM     70  CA  PRO    73      38.072  -9.628  13.945  1.00  0.00              
ATOM     71  C   PRO    73      36.610  -9.177  13.897  1.00  0.00              
ATOM     72  O   PRO    73      36.190  -8.501  12.960  1.00  0.00              
ATOM     73  N   THR    74      35.835  -9.558  14.908  1.00  0.00              
ATOM     74  CA  THR    74      34.416  -9.215  14.962  1.00  0.00              
ATOM     75  C   THR    74      34.067  -7.730  14.788  1.00  0.00              
ATOM     76  O   THR    74      33.037  -7.403  14.201  1.00  0.00              
ATOM     77  N   LYS    75      34.911  -6.830  15.289  1.00  0.00              
ATOM     78  CA  LYS    75      34.629  -5.407  15.153  1.00  0.00              
ATOM     79  C   LYS    75      35.223  -4.825  13.884  1.00  0.00              
ATOM     80  O   LYS    75      36.445  -4.792  13.738  1.00  0.00              
ATOM     81  N   PRO    76      34.376  -4.357  12.969  1.00  0.00              
ATOM     82  CA  PRO    76      34.861  -3.801  11.705  1.00  0.00              
ATOM     83  C   PRO    76      34.113  -2.556  11.235  1.00  0.00              
ATOM     84  O   PRO    76      33.420  -1.888  12.004  1.00  0.00              
ATOM     85  N   SER    77      34.262  -2.277   9.943  1.00  0.00              
ATOM     86  CA  SER    77      33.632  -1.138   9.289  1.00  0.00              
ATOM     87  C   SER    77      32.125  -1.336   9.101  1.00  0.00              
ATOM     88  O   SER    77      31.376  -0.366   9.016  1.00  0.00              
ATOM     89  N   PHE    78      31.682  -2.589   9.035  1.00  0.00              
ATOM     90  CA  PHE    78      30.259  -2.874   8.853  1.00  0.00              
ATOM     91  C   PHE    78      29.600  -3.472  10.095  1.00  0.00              
ATOM     92  O   PHE    78      28.446  -3.897  10.048  1.00  0.00              
ATOM     93  N   PRO    79      30.324  -3.497  11.207  1.00  0.00              
ATOM     94  CA  PRO    79      29.790  -4.059  12.443  1.00  0.00              
ATOM     95  C   PRO    79      28.822  -3.154  13.219  1.00  0.00              
ATOM     96  O   PRO    79      28.077  -3.636  14.079  1.00  0.00              
ATOM     97  N   SER    80      28.823  -1.857  12.915  1.00  0.00              
ATOM     98  CA  SER    80      27.954  -0.904  13.614  1.00  0.00              
ATOM     99  C   SER    80      26.801  -0.364  12.762  1.00  0.00              
ATOM    100  O   SER    80      27.005   0.466  11.876  1.00  0.00              
ATOM    101  N   SER    81      25.569  -0.829  13.026  1.00  0.00              
ATOM    102  CA  SER    81      24.404  -0.364  12.261  1.00  0.00              
ATOM    103  C   SER    81      24.110   1.135  12.417  1.00  0.00              
ATOM    104  O   SER    81      24.167   1.686  13.516  1.00  0.00              
ATOM    105  N   ILE    82      23.795   1.780  11.298  1.00  0.00              
ATOM    106  CA  ILE    82      23.521   3.213  11.252  1.00  0.00              
ATOM    107  C   ILE    82      22.385   3.775  12.119  1.00  0.00              
ATOM    108  O   ILE    82      22.362   4.975  12.379  1.00  0.00              
ATOM    109  N   GLN    83      21.447   2.942  12.567  1.00  0.00              
ATOM    110  CA  GLN    83      20.346   3.456  13.385  1.00  0.00              
ATOM    111  C   GLN    83      20.755   3.802  14.815  1.00  0.00              
ATOM    112  O   GLN    83      19.981   4.418  15.556  1.00  0.00              
ATOM    113  N   GLU    84      21.967   3.414  15.204  1.00  0.00              
ATOM    114  CA  GLU    84      22.448   3.697  16.552  1.00  0.00              
ATOM    115  C   GLU    84      23.114   5.067  16.625  1.00  0.00              
ATOM    116  O   GLU    84      24.347   5.169  16.638  1.00  0.00              
ATOM    117  N   LEU    85      22.303   6.124  16.659  1.00  0.00              
ATOM    118  CA  LEU    85      22.845   7.477  16.743  1.00  0.00              
ATOM    119  C   LEU    85      21.855   8.432  17.391  1.00  0.00              
ATOM    120  O   LEU    85      20.656   8.161  17.436  1.00  0.00              
ATOM    121  N   THR    86      22.365   9.560  17.879  1.00  0.00              
ATOM    122  CA  THR    86      21.536  10.559  18.539  1.00  0.00              
ATOM    123  C   THR    86      21.530  11.911  17.832  1.00  0.00              
ATOM    124  O   THR    86      21.159  12.925  18.426  1.00  0.00              
ATOM    125  N   ASP    87      21.946  11.940  16.573  1.00  0.00              
ATOM    126  CA  ASP    87      21.938  13.197  15.835  1.00  0.00              
ATOM    127  C   ASP    87      20.490  13.685  15.757  1.00  0.00              
ATOM    128  O   ASP    87      19.567  12.885  15.592  1.00  0.00              
ATOM    129  N   ASP    88      20.293  14.993  15.897  1.00  0.00              
ATOM    130  CA  ASP    88      18.956  15.587  15.872  1.00  0.00              
ATOM    131  C   ASP    88      17.990  14.939  14.877  1.00  0.00              
ATOM    132  O   ASP    88      16.917  14.479  15.260  1.00  0.00              
ATOM    133  N   ASP    89      18.375  14.899  13.606  1.00  0.00              
ATOM    134  CA  ASP    89      17.533  14.315  12.562  1.00  0.00              
ATOM    135  C   ASP    89      17.096  12.877  12.856  1.00  0.00              
ATOM    136  O   ASP    89      15.936  12.525  12.638  1.00  0.00              
ATOM    137  N   MET    90      18.021  12.054  13.345  1.00  0.00              
ATOM    138  CA  MET    90      17.718  10.658  13.659  1.00  0.00              
ATOM    139  C   MET    90      16.756  10.471  14.827  1.00  0.00              
ATOM    140  O   MET    90      15.866   9.619  14.759  1.00  0.00              
ATOM    141  N   ALA    91      16.933  11.251  15.891  1.00  0.00              
ATOM    142  CA  ALA    91      16.067  11.146  17.063  1.00  0.00              
ATOM    143  C   ALA    91      14.629  11.556  16.764  1.00  0.00              
ATOM    144  O   ALA    91      13.689  10.972  17.310  1.00  0.00              
ATOM    145  N   ILE    92      14.455  12.566  15.915  1.00  0.00              
ATOM    146  CA  ILE    92      13.110  12.999  15.563  1.00  0.00              
ATOM    147  C   ILE    92      12.413  11.833  14.853  1.00  0.00              
ATOM    148  O   ILE    92      11.307  11.452  15.221  1.00  0.00              
ATOM    149  N   LEU    93      13.069  11.247  13.855  1.00  0.00              
ATOM    150  CA  LEU    93      12.471  10.119  13.139  1.00  0.00              
ATOM    151  C   LEU    93      12.196   8.955  14.077  1.00  0.00              
ATOM    152  O   LEU    93      11.171   8.285  13.958  1.00  0.00              
ATOM    153  N   ASN    94      13.121   8.718  15.002  1.00  0.00              
ATOM    154  CA  ASN    94      12.988   7.629  15.960  1.00  0.00              
ATOM    155  C   ASN    94      11.676   7.740  16.733  1.00  0.00              
ATOM    156  O   ASN    94      10.992   6.738  16.943  1.00  0.00              
ATOM    157  N   ASP    95      11.324   8.952  17.154  1.00  0.00              
ATOM    158  CA  ASP    95      10.083   9.146  17.900  1.00  0.00              
ATOM    159  C   ASP    95       8.830   9.229  17.022  1.00  0.00              
ATOM    160  O   ASP    95       7.753   9.584  17.505  1.00  0.00              
ATOM    161  N   LEU    96       8.980   8.899  15.739  1.00  0.00              
ATOM    162  CA  LEU    96       7.848   8.896  14.828  1.00  0.00              
ATOM    163  C   LEU    96       7.508  10.156  14.049  1.00  0.00              
ATOM    164  O   LEU    96       6.503  10.181  13.333  1.00  0.00              
END
