
#######################################################
#                                                     #
#                        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  141 (  141),  selected  141 , name T0360TS168_3
# Molecule2: number of CA atoms  116 (  917),  selected  116 , name T0360.pdb
# PARAMETERS: T0360TS168_3.T0360.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    T       2      T       2           -
LGA    Q       3      Q       3           -
LGA    E       4      E       4           -
LGA    T       5      T       5           -
LGA    A       6      A       6           -
LGA    L       7      L       7           -
LGA    G       8      G       8           -
LGA    A       9      A       9           -
LGA    A      10      A      10           -
LGA    L      11      L      11           -
LGA    K      12      K      12           -
LGA    -       -      S      13           -
LGA    -       -      A      14           -
LGA    -       -      V      15           -
LGA    -       -      Q      16           -
LGA    -       -      T      17           -
LGA    -       -      M      18           -
LGA    S      13      S      19          5.106
LGA    A      14      -       -           -
LGA    V      15      -       -           -
LGA    Q      16      K      20           #
LGA    T      17      K      21          3.244
LGA    M      18      -       -           -
LGA    S      19      K      22          5.025
LGA    K      20      Q      23           -
LGA    K      21      T      24           -
LGA    K      22      -       -           -
LGA    Q      23      E      25          4.801
LGA    T      24      M      26           #
LGA    E      25      I      27           -
LGA    -       -      A      28           -
LGA    M      26      D      29          4.883
LGA    I      27      H      30          3.059
LGA    -       -      I      31           -
LGA    A      28      Y      32           #
LGA    D      29      -       -           -
LGA    H      30      -       -           -
LGA    I      31      G      33          1.775
LGA    Y      32      K      34          3.570
LGA    G      33      -       -           -
LGA    K      34      -       -           -
LGA    Y      35      Y      35          3.074
LGA    D      36      D      36          2.364
LGA    V      37      -       -           -
LGA    F      38      -       -           -
LGA    K      39      V      37          1.027
LGA    R      40      F      38           -
LGA    F      41      K      39           -
LGA    -       -      R      40           -
LGA    -       -      F      41           -
LGA    -       -      K      42           -
LGA    -       -      P      43           -
LGA    K      42      L      44           #
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      G      47           -
LGA    P      43      I      48          3.255
LGA    L      44      D      49           -
LGA    A      45      -       -           -
LGA    L      46      -       -           -
LGA    G      47      Q      50          4.456
LGA    I      48      D      51          2.550
LGA    D      49      L      52           #
LGA    -       -      I      53           -
LGA    -       -      A      54           -
LGA    Q      50      A      55          0.448
LGA    D      51      L      56          4.683
LGA    L      52      -       -           -
LGA    I      53      -       -           -
LGA    A      54      -       -           -
LGA    A      55      -       -           -
LGA    L      56      -       -           -
LGA    P      57      -       -           -
LGA    Q      58      -       -           -
LGA    Y      59      -       -           -
LGA    D      60      -       -           -
LGA    A      61      P      57          4.213
LGA    A      62      -       -           -
LGA    L      63      Q      58           #
LGA    I      64      Y      59          2.727
LGA    A      65      -       -           -
LGA    R      66      -       -           -
LGA    V      67      D      60          0.472
LGA    L      68      A      61          2.047
LGA    A      69      A      62          3.620
LGA    N      70      L      63          4.653
LGA    H      71      I      64          3.886
LGA    C      72      A      65          1.825
LGA    R      73      -       -           -
LGA    R      74      -       -           -
LGA    P      75      R      66          3.509
LGA    R      76      V      67           -
LGA    Y      77      L      68           -
LGA    L      78      A      69           #
LGA    K      79      -       -           -
LGA    A      80      -       -           -
LGA    L      81      -       -           -
LGA    A      82      -       -           -
LGA    R      83      -       -           -
LGA    G      84      -       -           -
LGA    G      85      N      70           #
LGA    -       -      H      71           -
LGA    -       -      C      72           -
LGA    K      86      R      73          1.370
LGA    R      87      R      74          0.702
LGA    F      88      P      75          2.974
LGA    D      89      R      76          1.841
LGA    L      90      Y      77          3.745
LGA    -       -      L      78           -
LGA    N      91      K      79          2.496
LGA    -       -      A      80           -
LGA    -       -      L      81           -
LGA    N      92      A      82          3.158
LGA    R      93      R      83          4.298
LGA    F      94      G      84          3.854
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    K      95      P     100          2.700
LGA    G      96      E     101          1.010
LGA    E      97      E     102          2.922
LGA    V      98      Q     103           #
LGA    T      99      A     104           -
LGA    P     100      I     105           -
LGA    E     101      A     106           -
LGA    E     102      Q     107           -
LGA    Q     103      N     108           -
LGA    A     104      H     109           -
LGA    I     105      P     110           -
LGA    A     106      F     111           -
LGA    Q     107      V     112           -
LGA    N     108      Q     113           -
LGA    H     109      Q     114           -
LGA    P     110      A     115           -
LGA    F     111      L     116           -
LGA    V     112      -       -           -
LGA    Q     113      -       -           -
LGA    Q     114      -       -           -
LGA    A     115      -       -           -
LGA    L     116      -       -           -
LGA    Q     117      -       -           -
LGA    Q     118      -       -           -
LGA    Q     119      -       -           -
LGA    S     120      -       -           -
LGA    A     121      -       -           -
LGA    Q     122      -       -           -
LGA    A     123      -       -           -
LGA    A     124      -       -           -
LGA    A     125      -       -           -
LGA    E     126      -       -           -
LGA    T     127      -       -           -
LGA    L     128      -       -           -
LGA    S     129      -       -           -
LGA    V     130      -       -           -
LGA    E     131      -       -           -
LGA    A     132      -       -           -
LGA    E     133      -       -           -
LGA    A     134      -       -           -
LGA    A     135      -       -           -
LGA    E     136      -       -           -
LGA    S     137      -       -           -
LGA    S     138      -       -           -
LGA    A     139      -       -           -
LGA    A     140      -       -           -
LGA    E     141      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  141  116    5.0     37    3.29    18.92     17.621     1.093

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.164528 * X  +  -0.985086 * Y  +   0.050368 * Z  + -82.490013
  Y_new =  -0.410630 * X  +  -0.021975 * Y  +   0.911537 * Z  +   5.171048
  Z_new =  -0.896835 * X  +  -0.170656 * Y  +  -0.408121 * Z  + -20.155479 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.745539    0.396054  [ DEG:  -157.3078     22.6922 ]
  Theta =   1.112563    2.029030  [ DEG:    63.7452    116.2548 ]
  Phi   =  -1.189711    1.951881  [ DEG:   -68.1654    111.8346 ]
 
# 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: T0360TS168_3                                  
REMARK     2: T0360.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0360TS168_3.T0360.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  141  116   5.0   37   3.29   18.92  17.621
REMARK  ---------------------------------------------------------- 
MOLECULE T0360TS168_3
PFRMAT TS
TARGET T0360
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1    -105.017  15.959 -15.409  1.00 25.00           C
ATOM      2  CA  THR     2    -102.022  17.999 -14.187  1.00 25.00           C
ATOM      3  CA  GLN     3    -103.353  17.482 -10.619  1.00 25.00           C
ATOM      4  CA  GLU     4    -101.560  19.301  -7.765  1.00 25.00           C
ATOM      5  CA  THR     5    -102.391  16.426  -5.377  1.00 25.00           C
ATOM      6  CA  ALA     6    -101.041  13.896  -7.913  1.00 25.00           C
ATOM      7  CA  LEU     7     -97.822  15.939  -8.275  1.00 25.00           C
ATOM      8  CA  GLY     8     -97.435  16.049  -4.466  1.00 25.00           C
ATOM      9  CA  ALA     9     -97.931  12.256  -4.282  1.00 25.00           C
ATOM     10  CA  ALA    10     -95.290  11.753  -7.008  1.00 25.00           C
ATOM     11  CA  LEU    11     -92.854  14.010  -5.100  1.00 25.00           C
ATOM     12  CA  LYS    12     -93.486  12.019  -1.890  1.00 25.00           C
ATOM     13  CA  SER    13     -92.846   8.743  -3.767  1.00 25.00           C
ATOM     14  CA  ALA    14     -89.580  10.161  -5.179  1.00 25.00           C
ATOM     15  CA  VAL    15     -88.498  11.234  -1.665  1.00 25.00           C
ATOM     16  CA  GLN    16     -89.283   7.733  -0.328  1.00 25.00           C
ATOM     17  CA  THR    17     -87.237   6.166  -3.159  1.00 25.00           C
ATOM     18  CA  MET    18     -85.204   4.732  -0.242  1.00 25.00           C
ATOM     19  CA  SER    19     -87.273   1.586  -0.610  1.00 25.00           C
ATOM     20  CA  LYS    20     -83.939  -0.248  -0.430  1.00 25.00           C
ATOM     21  CA  LYS    21     -82.683  -3.742   0.512  1.00 25.00           C
ATOM     22  CA  LYS    22     -85.305  -5.330  -1.783  1.00 25.00           C
ATOM     23  CA  GLN    23     -84.235  -3.020  -4.645  1.00 25.00           C
ATOM     24  CA  THR    24     -80.569  -3.970  -4.073  1.00 25.00           C
ATOM     25  CA  GLU    25     -81.497  -7.684  -4.127  1.00 25.00           C
ATOM     26  CA  MET    26     -83.425  -7.181  -7.397  1.00 25.00           C
ATOM     27  CA  ILE    27     -80.412  -5.376  -8.924  1.00 25.00           C
ATOM     28  CA  ALA    28     -78.115  -8.243  -7.840  1.00 25.00           C
ATOM     29  CA  ASP    29     -80.510 -10.788  -9.407  1.00 25.00           C
ATOM     30  CA  HIS    30     -80.560  -8.773 -12.663  1.00 25.00           C
ATOM     31  CA  ILE    31     -76.731  -8.663 -12.682  1.00 25.00           C
ATOM     32  CA  TYR    32     -76.596 -12.451 -12.136  1.00 25.00           C
ATOM     33  CA  GLY    33     -73.166 -14.147 -12.263  1.00 25.00           C
ATOM     34  CA  LYS    34     -73.518 -12.976 -15.859  1.00 25.00           C
ATOM     35  CA  TYR    35     -71.962  -9.727 -14.558  1.00 25.00           C
ATOM     36  CA  ASP    36     -68.668 -10.569 -16.322  1.00 25.00           C
ATOM     37  CA  VAL    37     -70.559 -11.258 -19.580  1.00 25.00           C
ATOM     38  CA  PHE    38     -72.389  -7.909 -19.254  1.00 25.00           C
ATOM     39  CA  LYS    39     -69.053  -6.116 -18.680  1.00 25.00           C
ATOM     40  CA  ARG    40     -67.575  -7.821 -21.774  1.00 25.00           C
ATOM     41  CA  PHE    41     -70.615  -6.755 -23.844  1.00 25.00           C
ATOM     42  CA  LYS    42     -74.337  -5.837 -23.602  1.00 25.00           C
ATOM     43  CA  PRO    43     -73.835  -2.301 -24.952  1.00 25.00           C
ATOM     44  CA  LEU    44     -71.464  -3.569 -27.638  1.00 25.00           C
ATOM     45  CA  ALA    45     -72.336  -1.445 -30.612  1.00 25.00           C
ATOM     46  CA  LEU    46     -75.463  -3.542 -30.736  1.00 25.00           C
ATOM     47  CA  GLY    47     -78.093  -1.588 -28.802  1.00 25.00           C
ATOM     48  CA  ILE    48     -81.086  -1.710 -26.454  1.00 25.00           C
ATOM     49  CA  ASP    49     -80.499  -5.486 -26.701  1.00 25.00           C
ATOM     50  CA  GLN    50     -82.450  -6.027 -23.450  1.00 25.00           C
ATOM     51  CA  ASP    51     -85.331  -3.892 -24.796  1.00 25.00           C
ATOM     52  CA  LEU    52     -85.352  -5.923 -28.042  1.00 25.00           C
ATOM     53  CA  ILE    53     -85.437  -9.182 -26.033  1.00 25.00           C
ATOM     54  CA  ALA    54     -88.358  -7.848 -23.947  1.00 25.00           C
ATOM     55  CA  ALA    55     -90.232  -6.883 -27.145  1.00 25.00           C
ATOM     56  CA  LEU    56     -92.035 -10.156 -26.774  1.00 25.00           C
ATOM     57  CA  PRO    57     -95.520 -10.391 -28.384  1.00 25.00           C
ATOM     58  CA  GLN    58     -98.328  -8.945 -26.218  1.00 25.00           C
ATOM     59  CA  TYR    59     -95.809  -6.110 -25.577  1.00 25.00           C
ATOM     60  CA  ASP    60     -96.290  -5.074 -21.978  1.00 25.00           C
ATOM     61  CA  ALA    61     -92.451  -4.681 -22.050  1.00 25.00           C
ATOM     62  CA  ALA    62     -93.324  -1.241 -23.490  1.00 25.00           C
ATOM     63  CA  LEU    63     -93.638   0.188 -19.951  1.00 25.00           C
ATOM     64  CA  ILE    64     -90.232  -1.298 -19.022  1.00 25.00           C
ATOM     65  CA  ALA    65     -88.677   0.241 -22.166  1.00 25.00           C
ATOM     66  CA  ARG    66     -90.199   3.642 -21.285  1.00 25.00           C
ATOM     67  CA  VAL    67     -88.802   3.374 -17.730  1.00 25.00           C
ATOM     68  CA  LEU    68     -85.341   2.516 -19.127  1.00 25.00           C
ATOM     69  CA  ALA    69     -85.516   5.533 -21.480  1.00 25.00           C
ATOM     70  CA  ASN    70     -86.492   7.794 -18.546  1.00 25.00           C
ATOM     71  CA  HIS    71     -83.554   6.443 -16.495  1.00 25.00           C
ATOM     72  CA  CYS    72     -81.175   7.102 -19.424  1.00 25.00           C
ATOM     73  CA  ARG    73     -82.515  10.676 -19.739  1.00 25.00           C
ATOM     74  CA  ARG    74     -82.005  11.226 -15.984  1.00 25.00           C
ATOM     75  CA  PRO    75     -78.418   9.912 -16.254  1.00 25.00           C
ATOM     76  CA  ARG    76     -77.750  12.269 -19.197  1.00 25.00           C
ATOM     77  CA  TYR    77     -79.145  15.215 -17.188  1.00 25.00           C
ATOM     78  CA  LEU    78     -76.905  14.286 -14.224  1.00 25.00           C
ATOM     79  CA  LYS    79     -73.864  14.114 -16.546  1.00 25.00           C
ATOM     80  CA  ALA    80     -74.737  17.554 -17.985  1.00 25.00           C
ATOM     81  CA  LEU    81     -75.051  18.982 -14.446  1.00 25.00           C
ATOM     82  CA  ALA    82     -71.645  17.497 -13.518  1.00 25.00           C
ATOM     83  CA  ARG    83     -68.517  16.610 -11.481  1.00 25.00           C
ATOM     84  CA  GLY    84     -70.597  14.590  -9.107  1.00 25.00           C
ATOM     85  CA  GLY    85     -70.494  11.328 -11.142  1.00 25.00           C
ATOM     86  CA  LYS    86     -68.416   8.702 -12.944  1.00 25.00           C
ATOM     87  CA  ARG    87     -68.797   6.601  -9.796  1.00 25.00           C
ATOM     88  CA  PHE    88     -66.290   3.841  -9.426  1.00 25.00           C
ATOM     89  CA  ASP    89     -62.859   2.320  -8.930  1.00 25.00           C
ATOM     90  CA  LEU    90     -61.996   3.416 -12.498  1.00 25.00           C
ATOM     91  CA  ASN    91     -58.361   3.182 -13.653  1.00 25.00           C
ATOM     92  CA  ASN    92     -56.286   3.775 -16.854  1.00 25.00           C
ATOM     93  CA  ARG    93     -55.118   6.214 -19.542  1.00 25.00           C
ATOM     94  CA  PHE    94     -57.794   6.416 -22.241  1.00 25.00           C
ATOM     95  CA  LYS    95     -56.798   9.635 -23.960  1.00 25.00           C
ATOM     96  CA  GLY    96     -58.367  12.462 -25.993  1.00 25.00           C
ATOM     97  CA  GLU    97     -61.988  12.807 -24.929  1.00 25.00           C
ATOM     98  CA  VAL    98     -65.561  13.290 -23.662  1.00 25.00           C
ATOM     99  CA  THR    99     -66.232  16.749 -22.107  1.00 25.00           C
ATOM    100  CA  PRO   100     -68.301  19.072 -24.356  1.00 25.00           C
ATOM    101  CA  GLU   101     -69.666  15.930 -26.070  1.00 25.00           C
ATOM    102  CA  GLU   102     -71.772  15.127 -22.974  1.00 25.00           C
ATOM    103  CA  GLN   103     -73.140  18.703 -22.946  1.00 25.00           C
ATOM    104  CA  ALA   104     -74.023  18.421 -26.662  1.00 25.00           C
ATOM    105  CA  ILE   105     -75.813  15.099 -26.009  1.00 25.00           C
ATOM    106  CA  ALA   106     -77.772  16.692 -23.130  1.00 25.00           C
ATOM    107  CA  GLN   107     -78.766  19.617 -25.392  1.00 25.00           C
ATOM    108  CA  ASN   108     -79.132  22.444 -22.858  1.00 25.00           C
ATOM    109  CA  HIS   109     -80.855  21.379 -19.592  1.00 25.00           C
ATOM    110  CA  PRO   110     -83.475  23.709 -18.115  1.00 25.00           C
ATOM    111  CA  PHE   111     -87.209  22.858 -18.072  1.00 25.00           C
ATOM    112  CA  VAL   112     -87.601  24.283 -21.604  1.00 25.00           C
ATOM    113  CA  GLN   113     -84.617  22.202 -22.802  1.00 25.00           C
ATOM    114  CA  GLN   114     -86.148  19.060 -21.233  1.00 25.00           C
ATOM    115  CA  ALA   115     -89.486  19.794 -22.961  1.00 25.00           C
ATOM    116  CA  LEU   116     -87.682  20.242 -26.309  1.00 25.00           C
ATOM    117  CA  GLN   117     -85.857  16.914 -25.799  1.00 25.00           C
ATOM    118  CA  GLN   118     -89.181  15.185 -25.008  1.00 25.00           C
ATOM    119  CA  GLN   119     -90.739  16.674 -28.173  1.00 25.00           C
ATOM    120  CA  SER   120     -87.760  15.449 -30.246  1.00 25.00           C
ATOM    121  CA  ALA   121     -88.124  11.945 -28.741  1.00 25.00           C
ATOM    122  CA  GLN   122     -91.863  11.950 -29.572  1.00 25.00           C
ATOM    123  CA  ALA   123     -91.087  13.013 -33.168  1.00 25.00           C
ATOM    124  CA  ALA   124     -88.504  10.201 -33.468  1.00 25.00           C
ATOM    125  CA  ALA   125     -91.063   7.676 -32.148  1.00 25.00           C
ATOM    126  CA  GLU   126     -93.644   8.927 -34.686  1.00 25.00           C
ATOM    127  CA  THR   127     -91.075   8.579 -37.505  1.00 25.00           C
ATOM    128  CA  LEU   128     -90.274   5.011 -36.368  1.00 25.00           C
ATOM    129  CA  SER   129     -94.007   4.159 -36.324  1.00 25.00           C
ATOM    130  CA  VAL   130     -94.399   5.585 -39.857  1.00 25.00           C
ATOM    131  CA  GLU   131     -91.416   3.503 -41.054  1.00 25.00           C
ATOM    132  CA  ALA   132     -92.947   0.362 -39.485  1.00 25.00           C
ATOM    133  CA  GLU   133     -96.285   1.096 -41.213  1.00 25.00           C
ATOM    134  CA  ALA   134     -94.481   1.543 -44.562  1.00 25.00           C
ATOM    135  CA  ALA   135     -92.656  -1.785 -44.051  1.00 25.00           C
ATOM    136  CA  GLU   136     -95.980  -3.514 -43.260  1.00 25.00           C
ATOM    137  CA  SER   137     -93.815  -6.128 -41.527  1.00 25.00           C
ATOM    138  CA  SER   138     -90.214  -7.220 -41.826  1.00 25.00           C
ATOM    139  CA  ALA   139     -86.657  -8.379 -41.415  1.00 25.00           C
ATOM    140  CA  ALA   140     -83.154  -8.195 -39.981  1.00 25.00           C
ATOM    141  CA  GLU   141     -79.919  -6.937 -38.557  1.00 25.00           C
TER
END
