
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0350AL381_3-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350AL381_3-D1.T0350_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    S      36      S      36          1.735
LGA    Y      37      Y      37          1.329
LGA    T      38      T      38          1.332
LGA    N      39      N      39          1.096
LGA    L      40      L      40          0.404
LGA    A      41      A      41          0.774
LGA    E      42      E      42          1.056
LGA    M      43      M      43          1.128
LGA    V      44      V      44          1.292
LGA    G      45      G      45          1.563
LGA    E      46      E      46          0.833
LGA    M      47      M      47          1.027
LGA    N      48      N      48          1.144
LGA    K      49      K      49          2.280
LGA    L      50      L      50          2.727
LGA    L      51      L      51          3.442
LGA    E      52      E      52          3.632
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    P      53      H      57          3.608
LGA    S      54      L      58          4.771
LGA    Q      55      K      59          2.332
LGA    V      56      F      60          1.874
LGA    H      57      E      61          2.019
LGA    L      58      L      62          0.993
LGA    F      60      H      63          1.884
LGA    E      61      D      64          1.527
LGA    L      62      K      65          1.436
LGA    H      63      L      66          0.920
LGA    D      64      -       -           -
LGA    K      65      -       -           -
LGA    L      66      -       -           -
LGA    N      67      -       -           -
LGA    E      68      -       -           -
LGA    Y      69      N      67          2.548
LGA    Y      70      E      68          2.279
LGA    V      71      Y      69          2.268
LGA    K      72      Y      70          1.874
LGA    V      73      V      71          0.846
LGA    I      74      K      72          1.768
LGA    E      75      V      73          2.057
LGA    D      76      I      74          1.699
LGA    S      77      E      75          0.265
LGA    T      78      D      76          2.790
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    N      79      N      79          0.782
LGA    E      80      E      80          1.605
LGA    V      81      V      81          1.218
LGA    I      82      I      82          3.254
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      I      85           -
LGA    -       -      P      86           -
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    -       -      W      90           -
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    -       -      Y      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      T      98           -
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   91    5.0     41    2.03    56.10     39.767     1.926

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.452939 * X  +  -0.489089 * Y  +   0.745411 * Z  +  33.766003
  Y_new =  -0.759186 * X  +   0.649939 * Y  +  -0.034862 * Z  +  -5.571432
  Z_new =  -0.467422 * X  +  -0.581696 * Y  +  -0.665693 * Z  +   1.221178 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.423431    0.718162  [ DEG:  -138.8523     41.1477 ]
  Theta =   0.486372    2.655221  [ DEG:    27.8671    152.1329 ]
  Phi   =  -2.108720    1.032872  [ DEG:  -120.8208     59.1792 ]
 
# 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: T0350AL381_3-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL381_3-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   91   5.0   41   2.03   56.10  39.767
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL381_3-D1
REMARK Aligment from pdb entry: 1ylxA
ATOM      5  N   SER    36       0.795   9.505 -34.893  1.00  0.00              
ATOM      6  CA  SER    36       1.192   8.366 -34.071  1.00  0.00              
ATOM      7  C   SER    36       2.246   8.781 -33.045  1.00  0.00              
ATOM      8  O   SER    36       2.136   8.451 -31.859  1.00  0.00              
ATOM      9  N   TYR    37       3.257   9.516 -33.499  1.00  0.00              
ATOM     10  CA  TYR    37       4.316   9.973 -32.605  1.00  0.00              
ATOM     11  C   TYR    37       3.742  10.819 -31.472  1.00  0.00              
ATOM     12  O   TYR    37       4.080  10.618 -30.312  1.00  0.00              
ATOM     13  N   THR    38       2.870  11.766 -31.805  1.00  0.00              
ATOM     14  CA  THR    38       2.276  12.609 -30.777  1.00  0.00              
ATOM     15  C   THR    38       1.491  11.811 -29.740  1.00  0.00              
ATOM     16  O   THR    38       1.457  12.181 -28.569  1.00  0.00              
ATOM     17  N   ASN    39       0.858  10.716 -30.152  1.00  0.00              
ATOM     18  CA  ASN    39       0.112   9.906 -29.201  1.00  0.00              
ATOM     19  C   ASN    39       1.086   9.232 -28.231  1.00  0.00              
ATOM     20  O   ASN    39       0.784   9.063 -27.048  1.00  0.00              
ATOM     21  N   LEU    40       2.256   8.844 -28.727  1.00  0.00              
ATOM     22  CA  LEU    40       3.243   8.227 -27.848  1.00  0.00              
ATOM     23  C   LEU    40       3.809   9.302 -26.928  1.00  0.00              
ATOM     24  O   LEU    40       4.096   9.045 -25.760  1.00  0.00              
ATOM     25  N   ALA    41       3.964  10.513 -27.454  1.00  0.00              
ATOM     26  CA  ALA    41       4.487  11.605 -26.644  1.00  0.00              
ATOM     27  C   ALA    41       3.518  11.948 -25.512  1.00  0.00              
ATOM     28  O   ALA    41       3.949  12.294 -24.409  1.00  0.00              
ATOM     29  N   GLU    42       2.217  11.828 -25.765  1.00  0.00              
ATOM     30  CA  GLU    42       1.225  12.136 -24.732  1.00  0.00              
ATOM     31  C   GLU    42       1.349  11.234 -23.509  1.00  0.00              
ATOM     32  O   GLU    42       1.062  11.650 -22.389  1.00  0.00              
ATOM     33  N   MET    43       1.769   9.994 -23.727  1.00  0.00              
ATOM     34  CA  MET    43       1.903   9.037 -22.638  1.00  0.00              
ATOM     35  C   MET    43       3.273   9.089 -21.961  1.00  0.00              
ATOM     36  O   MET    43       3.462   8.524 -20.884  1.00  0.00              
ATOM     37  N   VAL    44       4.213   9.800 -22.575  1.00  0.00              
ATOM     38  CA  VAL    44       5.571   9.906 -22.048  1.00  0.00              
ATOM     39  C   VAL    44       5.657  10.400 -20.599  1.00  0.00              
ATOM     40  O   VAL    44       6.156   9.687 -19.728  1.00  0.00              
ATOM     41  N   GLY    45       5.177  11.613 -20.341  1.00  0.00              
ATOM     42  CA  GLY    45       5.220  12.178 -18.991  1.00  0.00              
ATOM     43  C   GLY    45       4.442  11.333 -17.978  1.00  0.00              
ATOM     44  O   GLY    45       4.923  11.088 -16.870  1.00  0.00              
ATOM     45  N   GLU    46       3.227  10.888 -18.334  1.00  0.00              
ATOM     46  CA  GLU    46       2.456  10.070 -17.391  1.00  0.00              
ATOM     47  C   GLU    46       3.195   8.783 -17.021  1.00  0.00              
ATOM     48  O   GLU    46       3.193   8.358 -15.862  1.00  0.00              
ATOM     49  N   MET    47       3.830   8.170 -18.014  1.00  0.00              
ATOM     50  CA  MET    47       4.570   6.934 -17.798  1.00  0.00              
ATOM     51  C   MET    47       5.790   7.185 -16.920  1.00  0.00              
ATOM     52  O   MET    47       6.102   6.392 -16.030  1.00  0.00              
ATOM     53  N   ASN    48       6.483   8.291 -17.174  1.00  0.00              
ATOM     54  CA  ASN    48       7.666   8.625 -16.397  1.00  0.00              
ATOM     55  C   ASN    48       7.302   8.874 -14.938  1.00  0.00              
ATOM     56  O   ASN    48       8.010   8.439 -14.032  1.00  0.00              
ATOM     57  N   LYS    49       6.189   9.564 -14.712  1.00  0.00              
ATOM     58  CA  LYS    49       5.755   9.858 -13.351  1.00  0.00              
ATOM     59  C   LYS    49       5.313   8.586 -12.639  1.00  0.00              
ATOM     60  O   LYS    49       5.656   8.367 -11.482  1.00  0.00              
ATOM     61  N   LEU    50       4.558   7.744 -13.337  1.00  0.00              
ATOM     62  CA  LEU    50       4.061   6.505 -12.749  1.00  0.00              
ATOM     63  C   LEU    50       5.160   5.534 -12.330  1.00  0.00              
ATOM     64  O   LEU    50       5.027   4.841 -11.317  1.00  0.00              
ATOM     65  N   LEU    51       6.245   5.480 -13.096  1.00  0.00              
ATOM     66  CA  LEU    51       7.335   4.558 -12.784  1.00  0.00              
ATOM     67  C   LEU    51       8.596   5.226 -12.246  1.00  0.00              
ATOM     68  O   LEU    51       9.629   4.572 -12.076  1.00  0.00              
ATOM     69  N   GLU    52       8.508   6.523 -11.964  1.00  0.00              
ATOM     70  CA  GLU    52       9.648   7.253 -11.435  1.00  0.00              
ATOM     71  C   GLU    52      10.857   7.232 -12.349  1.00  0.00              
ATOM     72  O   GLU    52      11.993   7.101 -11.891  1.00  0.00              
ATOM     73  N   PRO    53      10.615   7.373 -13.648  1.00  0.00              
ATOM     74  CA  PRO    53      11.689   7.356 -14.633  1.00  0.00              
ATOM     75  C   PRO    53      12.222   8.762 -14.852  1.00  0.00              
ATOM     76  O   PRO    53      11.457   9.718 -14.984  1.00  0.00              
ATOM     77  N   SER    54      13.544   8.874 -14.898  1.00  0.00              
ATOM     78  CA  SER    54      14.212  10.157 -15.072  1.00  0.00              
ATOM     79  C   SER    54      14.490  10.552 -16.523  1.00  0.00              
ATOM     80  O   SER    54      14.401  11.726 -16.876  1.00  0.00              
ATOM     81  N   GLN    55      14.827   9.580 -17.362  1.00  0.00              
ATOM     82  CA  GLN    55      15.148   9.876 -18.753  1.00  0.00              
ATOM     83  C   GLN    55      14.540   8.865 -19.719  1.00  0.00              
ATOM     84  O   GLN    55      14.947   7.705 -19.763  1.00  0.00              
ATOM     85  N   VAL    56      13.564   9.322 -20.496  1.00  0.00              
ATOM     86  CA  VAL    56      12.884   8.467 -21.464  1.00  0.00              
ATOM     87  C   VAL    56      12.624   9.261 -22.732  1.00  0.00              
ATOM     88  O   VAL    56      12.332  10.458 -22.680  1.00  0.00              
ATOM     89  N   HIS    57      12.727   8.593 -23.875  1.00  0.00              
ATOM     90  CA  HIS    57      12.476   9.270 -25.132  1.00  0.00              
ATOM     91  C   HIS    57      11.704   8.369 -26.075  1.00  0.00              
ATOM     92  O   HIS    57      11.464   7.203 -25.759  1.00  0.00              
ATOM     93  N   LEU    58      11.304   8.912 -27.222  1.00  0.00              
ATOM     94  CA  LEU    58      10.567   8.141 -28.221  1.00  0.00              
ATOM     95  C   LEU    58      11.539   7.365 -29.099  1.00  0.00              
ATOM     96  O   LEU    58      12.582   7.877 -29.500  1.00  0.00              
ATOM     97  N   PHE    60      11.169   6.126 -29.404  1.00  0.00              
ATOM     98  CA  PHE    60      11.974   5.226 -30.220  1.00  0.00              
ATOM     99  C   PHE    60      11.226   4.845 -31.496  1.00  0.00              
ATOM    100  O   PHE    60      10.027   4.568 -31.457  1.00  0.00              
ATOM    101  N   GLU    61      11.940   4.836 -32.619  1.00  0.00              
ATOM    102  CA  GLU    61      11.357   4.445 -33.902  1.00  0.00              
ATOM    103  C   GLU    61      12.367   3.620 -34.684  1.00  0.00              
ATOM    104  O   GLU    61      13.560   3.905 -34.671  1.00  0.00              
ATOM    105  N   LEU    62      11.888   2.592 -35.365  1.00  0.00              
ATOM    106  CA  LEU    62      12.769   1.787 -36.189  1.00  0.00              
ATOM    107  C   LEU    62      12.020   1.414 -37.454  1.00  0.00              
ATOM    108  O   LEU    62      10.845   1.049 -37.400  1.00  0.00              
ATOM    109  N   HIS    63      12.696   1.548 -38.591  1.00  0.00              
ATOM    110  CA  HIS    63      12.103   1.218 -39.883  1.00  0.00              
ATOM    111  C   HIS    63      12.517  -0.210 -40.187  1.00  0.00              
ATOM    112  O   HIS    63      13.695  -0.480 -40.419  1.00  0.00              
ATOM    113  N   ASP    64      11.550  -1.121 -40.172  1.00  0.00              
ATOM    114  CA  ASP    64      11.847  -2.519 -40.432  1.00  0.00              
ATOM    115  C   ASP    64      11.843  -2.867 -41.906  1.00  0.00              
ATOM    116  O   ASP    64      11.725  -1.990 -42.762  1.00  0.00              
ATOM    117  N   LYS    65      11.979  -4.154 -42.204  1.00  0.00              
ATOM    118  CA  LYS    65      11.980  -4.613 -43.588  1.00  0.00              
ATOM    119  C   LYS    65      10.546  -4.686 -44.091  1.00  0.00              
ATOM    120  O   LYS    65       9.616  -4.899 -43.308  1.00  0.00              
ATOM    121  N   LEU    66      10.366  -4.510 -45.394  1.00  0.00              
ATOM    122  CA  LEU    66       9.032  -4.559 -45.958  1.00  0.00              
ATOM    123  C   LEU    66       8.180  -3.424 -45.423  1.00  0.00              
ATOM    124  O   LEU    66       8.598  -2.268 -45.437  1.00  0.00              
ATOM    125  N   ASN    67       6.989  -3.749 -44.937  1.00  0.00              
ATOM    126  CA  ASN    67       6.097  -2.725 -44.405  1.00  0.00              
ATOM    127  C   ASN    67       6.170  -2.605 -42.883  1.00  0.00              
ATOM    128  O   ASN    67       5.320  -1.963 -42.266  1.00  0.00              
ATOM    129  N   GLU    68       7.191  -3.207 -42.278  1.00  0.00              
ATOM    130  CA  GLU    68       7.327  -3.172 -40.825  1.00  0.00              
ATOM    131  C   GLU    68       7.896  -1.858 -40.278  1.00  0.00              
ATOM    132  O   GLU    68       8.828  -1.277 -40.837  1.00  0.00              
ATOM    133  N   TYR    69       7.318  -1.399 -39.173  1.00  0.00              
ATOM    134  CA  TYR    69       7.757  -0.167 -38.521  1.00  0.00              
ATOM    135  C   TYR    69       7.546  -0.377 -37.030  1.00  0.00              
ATOM    136  O   TYR    69       6.573  -1.008 -36.618  1.00  0.00              
ATOM    137  N   TYR    70       8.449   0.147 -36.213  1.00  0.00              
ATOM    138  CA  TYR    70       8.329  -0.040 -34.779  1.00  0.00              
ATOM    139  C   TYR    70       8.379   1.288 -34.049  1.00  0.00              
ATOM    140  O   TYR    70       9.208   2.147 -34.355  1.00  0.00              
ATOM    141  N   VAL    71       7.471   1.459 -33.096  1.00  0.00              
ATOM    142  CA  VAL    71       7.423   2.685 -32.311  1.00  0.00              
ATOM    143  C   VAL    71       7.290   2.351 -30.840  1.00  0.00              
ATOM    144  O   VAL    71       6.539   1.454 -30.451  1.00  0.00              
ATOM    145  N   LYS    72       8.023   3.084 -30.014  1.00  0.00              
ATOM    146  CA  LYS    72       7.957   2.837 -28.592  1.00  0.00              
ATOM    147  C   LYS    72       8.757   3.849 -27.805  1.00  0.00              
ATOM    148  O   LYS    72       8.848   5.017 -28.177  1.00  0.00              
ATOM    149  N   VAL    73       9.357   3.378 -26.721  1.00  0.00              
ATOM    150  CA  VAL    73      10.141   4.232 -25.844  1.00  0.00              
ATOM    151  C   VAL    73      11.483   3.608 -25.521  1.00  0.00              
ATOM    152  O   VAL    73      11.622   2.393 -25.518  1.00  0.00              
ATOM    153  N   ILE    74      12.472   4.455 -25.261  1.00  0.00              
ATOM    154  CA  ILE    74      13.770   3.962 -24.835  1.00  0.00              
ATOM    155  C   ILE    74      13.997   4.638 -23.504  1.00  0.00              
ATOM    156  O   ILE    74      13.909   5.860 -23.385  1.00  0.00              
ATOM    157  N   GLU    75      14.243   3.813 -22.496  1.00  0.00              
ATOM    158  CA  GLU    75      14.464   4.270 -21.139  1.00  0.00              
ATOM    159  C   GLU    75      15.936   4.159 -20.799  1.00  0.00              
ATOM    160  O   GLU    75      16.576   3.154 -21.108  1.00  0.00              
ATOM    161  N   ASP    76      16.470   5.202 -20.178  1.00  0.00              
ATOM    162  CA  ASP    76      17.858   5.193 -19.753  1.00  0.00              
ATOM    163  C   ASP    76      17.789   4.951 -18.256  1.00  0.00              
ATOM    164  O   ASP    76      17.525   5.873 -17.486  1.00  0.00              
ATOM    165  N   SER    77      17.991   3.704 -17.854  1.00  0.00              
ATOM    166  CA  SER    77      17.963   3.350 -16.444  1.00  0.00              
ATOM    167  C   SER    77      19.404   3.182 -15.980  1.00  0.00              
ATOM    168  O   SER    77      20.016   2.131 -16.180  1.00  0.00              
ATOM    169  N   THR    78      19.940   4.236 -15.378  1.00  0.00              
ATOM    170  CA  THR    78      21.310   4.239 -14.882  1.00  0.00              
ATOM    171  C   THR    78      22.291   3.794 -15.964  1.00  0.00              
ATOM    172  O   THR    78      23.029   2.824 -15.793  1.00  0.00              
ATOM    173  N   ASN    79      22.279   4.515 -17.081  1.00  0.00              
ATOM    174  CA  ASN    79      23.160   4.242 -18.211  1.00  0.00              
ATOM    175  C   ASN    79      22.775   3.025 -19.044  1.00  0.00              
ATOM    176  O   ASN    79      23.288   2.847 -20.149  1.00  0.00              
ATOM    177  N   GLU    80      21.889   2.182 -18.525  1.00  0.00              
ATOM    178  CA  GLU    80      21.454   1.021 -19.294  1.00  0.00              
ATOM    179  C   GLU    80      20.280   1.449 -20.168  1.00  0.00              
ATOM    180  O   GLU    80      19.308   2.021 -19.674  1.00  0.00              
ATOM    181  N   VAL    81      20.372   1.171 -21.463  1.00  0.00              
ATOM    182  CA  VAL    81      19.315   1.543 -22.397  1.00  0.00              
ATOM    183  C   VAL    81      18.366   0.370 -22.604  1.00  0.00              
ATOM    184  O   VAL    81      18.778  -0.703 -23.043  1.00  0.00              
ATOM    185  N   ILE    82      17.095   0.575 -22.276  1.00  0.00              
ATOM    186  CA  ILE    82      16.090  -0.466 -22.444  1.00  0.00              
ATOM    187  C   ILE    82      15.002   0.103 -23.339  1.00  0.00              
ATOM    188  O   ILE    82      14.493   1.197 -23.091  1.00  0.00              
END
