
#######################################################
#                                                     #
#                        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  148 (  148),  selected  148 , name T0298TS168_1-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS168_1-D1.T0298_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    Q       3      Q       3          3.408
LGA    P       4      P       4          1.297
LGA    L       5      L       5          3.380
LGA    N       6      N       6          0.829
LGA    V       7      V       7          1.117
LGA    A       8      A       8          0.368
LGA    V       9      V       9          0.985
LGA    V      10      V      10          1.344
LGA    G      11      G      11          1.511
LGA    A      12      A      12          1.640
LGA    T      13      T      13          2.817
LGA    G      14      G      14          1.581
LGA    S      15      S      15          2.009
LGA    V      16      V      16          3.493
LGA    G      17      G      17          4.576
LGA    E      18      E      18          2.842
LGA    A      19      A      19          1.283
LGA    L      20      L      20          3.134
LGA    V      21      V      21          2.887
LGA    G      22      G      22          1.496
LGA    L      23      L      23          2.087
LGA    L      24      L      24          2.015
LGA    D      25      D      25          1.983
LGA    E      26      E      26          3.415
LGA    R      27      R      27           -
LGA    -       -      D      28           -
LGA    -       -      F      29           -
LGA    -       -      P      30           -
LGA    D      28      L      31           #
LGA    F      29      H      32           -
LGA    P      30      -       -           -
LGA    L      31      -       -           -
LGA    H      32      R      33          4.575
LGA    R      33      L      34          2.721
LGA    L      34      -       -           -
LGA    H      35      H      35          3.667
LGA    L      36      L      36          3.454
LGA    L      37      L      37          1.614
LGA    A      38      A      38          2.191
LGA    S      39      S      39          3.435
LGA    A      40      A      40          2.163
LGA    E      41      E      41          4.383
LGA    -       -      S      42           -
LGA    S      42      A      43          4.430
LGA    A      43      G      44          4.712
LGA    G      44      -       -           -
LGA    Q      45      Q      45          5.557
LGA    R      46      R      46           #
LGA    M      47      M      47           #
LGA    G      48      G      48           -
LGA    F      49      -       -           -
LGA    A      50      -       -           -
LGA    E      51      -       -           -
LGA    S      52      F      49          5.066
LGA    -       -      A      50           -
LGA    -       -      E      51           -
LGA    -       -      S      52           -
LGA    S      53      S      53           #
LGA    L      54      L      54          0.747
LGA    R      55      R      55          1.388
LGA    V      56      V      56          2.375
LGA    G      57      G      57          1.286
LGA    D      58      D      58          3.955
LGA    -       -      V      59           -
LGA    V      59      D      60           #
LGA    D      60      -       -           -
LGA    S      61      S      61           #
LGA    F      62      F      62           #
LGA    D      63      D      63          3.779
LGA    F      64      F      64          3.136
LGA    S      65      S      65          3.236
LGA    S      66      S      66          1.929
LGA    V      67      V      67          2.218
LGA    G      68      G      68          1.314
LGA    L      69      L      69          1.142
LGA    A      70      A      70          1.071
LGA    F      71      F      71          0.888
LGA    F      72      F      72          1.617
LGA    A      73      A      73          1.428
LGA    A      74      A      74          1.537
LGA    A      75      A      75          1.458
LGA    A      76      A      76          3.919
LGA    E      77      E      77          3.130
LGA    V      78      V      78          2.025
LGA    S      79      S      79          1.797
LGA    R      80      R      80          1.980
LGA    A      81      A      81          1.622
LGA    H      82      H      82          0.321
LGA    A      83      A      83          3.395
LGA    E      84      E      84           #
LGA    R      85      R      85          2.109
LGA    A      86      A      86          3.892
LGA    R      87      R      87           #
LGA    A      88      A      88           #
LGA    A      89      A      89          4.464
LGA    G      90      G      90          3.765
LGA    C      91      C      91          2.305
LGA    S      92      S      92          2.501
LGA    V      93      V      93          1.909
LGA    I      94      I      94          3.772
LGA    D      95      D      95          1.517
LGA    L      96      L      96          1.069
LGA    S      97      S      97          0.855
LGA    G      98      G      98          1.588
LGA    A      99      A      99          0.984
LGA    L     100      L     100          0.812
LGA    E     101      E     101          2.532
LGA    P     102      P     102          3.143
LGA    S     103      S     103          3.984
LGA    V     104      V     104          3.329
LGA    A     105      -       -           -
LGA    P     106      A     105          4.036
LGA    P     107      P     106          3.469
LGA    V     108      P     107          2.688
LGA    M     109      V     108          1.895
LGA    V     110      M     109          1.597
LGA    S     111      V     110          1.855
LGA    V     112      S     111          2.319
LGA    N     113      V     112          3.203
LGA    -       -      N     113           -
LGA    A     114      A     114          2.305
LGA    E     115      E     115          1.154
LGA    R     116      R     116          1.239
LGA    L     117      L     117          2.630
LGA    A     118      A     118          3.176
LGA    S     119      S     119          3.082
LGA    Q     120      Q     120          1.594
LGA    A     121      A     121          1.692
LGA    A     122      A     122          3.820
LGA    P     123      P     123          4.996
LGA    F     124      F     124          2.539
LGA    L     125      L     125           #
LGA    L     126      L     126          5.232
LGA    S     127      S     127           #
LGA    S     128      S     128          0.977
LGA    P     129      P     129          1.254
LGA    V     316      V     316          3.138
LGA    R     317      R     317          3.615
LGA    K     318      K     318          2.253
LGA    G     319      G     319          0.918
LGA    A     320      A     320          1.251
LGA    A     321      A     321          2.314
LGA    L     322      L     322          3.003
LGA    N     323      N     323          1.517
LGA    A     324      A     324          1.832
LGA    V     325      V     325          4.035
LGA    L     326      L     326          3.779
LGA    L     327      L     327          1.626
LGA    G     328      G     328          3.711
LGA    E     329      E     329           #
LGA    L     330      L     330          4.030
LGA    L     331      L     331          3.191
LGA    -       -      I     332           -
LGA    I     332      K     333          2.812
LGA    K     333      H     334          5.458
LGA    H     334      Y     335           #
LGA    Y     335      L     336           -
LGA    L     336      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  148  148    5.0    120    2.80    88.33     47.825     4.144

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.183806 * X  +  -0.891613 * Y  +   0.413814 * Z  + -12.342332
  Y_new =   0.140447 * X  +   0.392845 * Y  +   0.908817 * Z  +  73.094414
  Z_new =  -0.972877 * X  +   0.225165 * Y  +   0.053017 * Z  +   0.025647 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.339549   -1.802043  [ DEG:    76.7505   -103.2495 ]
  Theta =   1.337359    1.804233  [ DEG:    76.6250    103.3750 ]
  Phi   =   2.489126   -0.652467  [ DEG:   142.6164    -37.3836 ]
 
# 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: T0298TS168_1-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS168_1-D1.T0298_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  148  148   5.0  120   2.80   88.33  47.825
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS168_1-D1
PFRMAT TS
TARGET T0298
MODEL 1
PARENT N/A
ATOM      3  CA  GLN     3     -39.513  69.447 -13.809  1.00 25.00           C
ATOM      4  CA  PRO     4     -36.561  67.902 -15.663  1.00 25.00           C
ATOM      5  CA  LEU     5     -32.968  66.684 -15.508  1.00 25.00           C
ATOM      6  CA  ASN     6     -29.505  66.700 -13.880  1.00 25.00           C
ATOM      7  CA  VAL     7     -26.940  65.993 -11.249  1.00 25.00           C
ATOM      8  CA  ALA     8     -23.775  64.774 -12.857  1.00 25.00           C
ATOM      9  CA  VAL     9     -20.871  63.230 -10.979  1.00 25.00           C
ATOM     10  CA  VAL    10     -18.073  64.322 -13.310  1.00 25.00           C
ATOM     11  CA  GLY    11     -15.153  63.208 -11.123  1.00 25.00           C
ATOM     12  CA  ALA    12     -16.504  61.230  -8.190  1.00 25.00           C
ATOM     13  CA  THR    13     -15.985  59.047  -5.119  1.00 25.00           C
ATOM     14  CA  GLY    14     -12.664  60.513  -4.106  1.00 25.00           C
ATOM     15  CA  SER    15     -14.488  61.714  -1.012  1.00 25.00           C
ATOM     16  CA  VAL    16     -16.267  64.313   1.166  1.00 25.00           C
ATOM     17  CA  GLY    17     -17.954  65.795  -1.936  1.00 25.00           C
ATOM     18  CA  GLU    18     -19.090  62.301  -3.018  1.00 25.00           C
ATOM     19  CA  ALA    19     -20.508  61.653   0.481  1.00 25.00           C
ATOM     20  CA  LEU    20     -22.380  64.993   0.367  1.00 25.00           C
ATOM     21  CA  VAL    21     -23.813  64.101  -3.071  1.00 25.00           C
ATOM     22  CA  GLY    22     -24.943  60.692  -1.742  1.00 25.00           C
ATOM     23  CA  LEU    23     -26.619  62.388   1.254  1.00 25.00           C
ATOM     24  CA  LEU    24     -28.406  64.828  -1.094  1.00 25.00           C
ATOM     25  CA  ASP    25     -29.610  61.906  -3.255  1.00 25.00           C
ATOM     26  CA  GLU    26     -30.905  60.101  -0.136  1.00 25.00           C
ATOM     27  CA  ARG    27     -31.495  56.608  -1.441  1.00 25.00           C
ATOM     28  CA  ASP    28     -33.846  56.952  -4.457  1.00 25.00           C
ATOM     29  CA  PHE    29     -32.846  53.720  -6.313  1.00 25.00           C
ATOM     30  CA  PRO    30     -31.347  53.370  -9.834  1.00 25.00           C
ATOM     31  CA  LEU    31     -29.647  54.951 -12.884  1.00 25.00           C
ATOM     32  CA  HIS    32     -29.704  57.963 -15.172  1.00 25.00           C
ATOM     33  CA  ARG    33     -30.546  60.818 -12.794  1.00 25.00           C
ATOM     34  CA  LEU    34     -26.951  60.341 -11.565  1.00 25.00           C
ATOM     35  CA  HIS    35     -23.545  58.721 -11.124  1.00 25.00           C
ATOM     36  CA  LEU    36     -20.122  57.793  -9.649  1.00 25.00           C
ATOM     37  CA  LEU    37     -18.612  58.847 -12.993  1.00 25.00           C
ATOM     38  CA  ALA    38     -15.048  57.953 -12.020  1.00 25.00           C
ATOM     39  CA  SER    39     -11.321  57.925 -12.484  1.00 25.00           C
ATOM     40  CA  ALA    40     -11.766  56.483 -15.934  1.00 25.00           C
ATOM     41  CA  GLU    41     -12.257  53.616 -18.391  1.00 25.00           C
ATOM     42  CA  SER    42     -14.610  50.626 -18.405  1.00 25.00           C
ATOM     43  CA  ALA    43     -13.986  47.553 -16.338  1.00 25.00           C
ATOM     44  CA  GLY    44     -17.365  46.048 -17.388  1.00 25.00           C
ATOM     45  CA  GLN    45     -20.121  48.515 -16.396  1.00 25.00           C
ATOM     46  CA  ARG    46     -23.928  48.585 -15.841  1.00 25.00           C
ATOM     47  CA  MET    47     -26.199  51.398 -14.751  1.00 25.00           C
ATOM     48  CA  GLY    48     -29.867  51.169 -15.924  1.00 25.00           C
ATOM     49  CA  PHE    49     -33.419  52.287 -14.998  1.00 25.00           C
ATOM     50  CA  ALA    50     -35.104  54.886 -12.888  1.00 25.00           C
ATOM     51  CA  GLU    51     -33.503  57.391 -10.448  1.00 25.00           C
ATOM     52  CA  SER    52     -30.529  57.811  -8.116  1.00 25.00           C
ATOM     53  CA  SER    53     -27.575  55.418  -8.265  1.00 25.00           C
ATOM     54  CA  LEU    54     -25.116  53.467 -10.311  1.00 25.00           C
ATOM     55  CA  ARG    55     -21.992  52.891 -12.368  1.00 25.00           C
ATOM     56  CA  VAL    56     -20.907  54.787 -15.516  1.00 25.00           C
ATOM     57  CA  GLY    57     -19.106  56.956 -18.096  1.00 25.00           C
ATOM     58  CA  ASP    58     -18.649  58.039 -21.774  1.00 25.00           C
ATOM     59  CA  VAL    59     -22.258  57.965 -23.001  1.00 25.00           C
ATOM     60  CA  ASP    60     -23.290  60.094 -25.981  1.00 25.00           C
ATOM     61  CA  SER    61     -21.984  62.418 -28.666  1.00 25.00           C
ATOM     62  CA  PHE    62     -18.365  62.165 -27.439  1.00 25.00           C
ATOM     63  CA  ASP    63     -19.515  62.789 -23.841  1.00 25.00           C
ATOM     64  CA  PHE    64     -21.787  65.729 -22.959  1.00 25.00           C
ATOM     65  CA  SER    65     -24.198  67.780 -25.043  1.00 25.00           C
ATOM     66  CA  SER    66     -26.611  66.946 -22.200  1.00 25.00           C
ATOM     67  CA  VAL    67     -25.582  67.917 -18.618  1.00 25.00           C
ATOM     68  CA  GLY    68     -27.294  70.536 -16.393  1.00 25.00           C
ATOM     69  CA  LEU    69     -24.934  70.519 -13.396  1.00 25.00           C
ATOM     70  CA  ALA    70     -21.492  69.393 -12.114  1.00 25.00           C
ATOM     71  CA  PHE    71     -19.806  68.684  -8.778  1.00 25.00           C
ATOM     72  CA  PHE    72     -16.423  67.154  -9.639  1.00 25.00           C
ATOM     73  CA  ALA    73     -13.803  66.065  -7.149  1.00 25.00           C
ATOM     74  CA  ALA    74     -10.803  64.926  -9.114  1.00 25.00           C
ATOM     75  CA  ALA    75      -8.430  67.293 -10.884  1.00 25.00           C
ATOM     76  CA  ALA    76      -5.652  67.143 -13.430  1.00 25.00           C
ATOM     77  CA  GLU    77      -6.577  66.211 -17.042  1.00 25.00           C
ATOM     78  CA  VAL    78     -10.318  65.452 -16.739  1.00 25.00           C
ATOM     79  CA  SER    79     -10.917  68.902 -15.188  1.00 25.00           C
ATOM     80  CA  ARG    80      -8.966  70.551 -18.042  1.00 25.00           C
ATOM     81  CA  ALA    81     -11.043  68.615 -20.612  1.00 25.00           C
ATOM     82  CA  HIS    82     -14.272  69.727 -18.877  1.00 25.00           C
ATOM     83  CA  ALA    83     -13.072  73.363 -18.920  1.00 25.00           C
ATOM     84  CA  GLU    84     -12.259  73.076 -22.652  1.00 25.00           C
ATOM     85  CA  ARG    85     -15.739  71.627 -23.325  1.00 25.00           C
ATOM     86  CA  ALA    86     -17.342  74.505 -21.371  1.00 25.00           C
ATOM     87  CA  ARG    87     -15.303  77.043 -23.389  1.00 25.00           C
ATOM     88  CA  ALA    88     -16.407  75.370 -26.653  1.00 25.00           C
ATOM     89  CA  ALA    89     -20.118  74.876 -25.809  1.00 25.00           C
ATOM     90  CA  GLY    90     -22.681  74.488 -23.025  1.00 25.00           C
ATOM     91  CA  CYS    91     -23.731  72.775 -19.761  1.00 25.00           C
ATOM     92  CA  SER    92     -22.611  73.887 -16.293  1.00 25.00           C
ATOM     93  CA  VAL    93     -19.459  74.249 -14.246  1.00 25.00           C
ATOM     94  CA  ILE    94     -17.365  72.055 -11.870  1.00 25.00           C
ATOM     95  CA  ASP    95     -14.600  73.569  -9.752  1.00 25.00           C
ATOM     96  CA  LEU    96     -14.622  71.024  -6.919  1.00 25.00           C
ATOM     97  CA  SER    97     -10.789  70.654  -7.082  1.00 25.00           C
ATOM     98  CA  GLY    98      -9.694  73.996  -8.550  1.00 25.00           C
ATOM     99  CA  ALA    99      -8.092  75.153 -11.780  1.00 25.00           C
ATOM    100  CA  LEU   100     -10.498  77.568 -13.435  1.00 25.00           C
ATOM    101  CA  GLU   101     -11.797  78.644 -10.039  1.00 25.00           C
ATOM    102  CA  PRO   102     -11.972  82.189 -11.347  1.00 25.00           C
ATOM    103  CA  SER   103     -11.376  82.291 -15.112  1.00 25.00           C
ATOM    104  CA  VAL   104     -13.713  85.174 -15.814  1.00 25.00           C
ATOM    105  CA  ALA   105     -17.340  85.296 -14.520  1.00 25.00           C
ATOM    106  CA  PRO   106     -18.105  82.317 -12.305  1.00 25.00           C
ATOM    107  CA  PRO   107     -18.192  81.463  -8.561  1.00 25.00           C
ATOM    108  CA  VAL   108     -17.485  81.877  -4.805  1.00 25.00           C
ATOM    109  CA  MET   109     -20.089  80.451  -2.479  1.00 25.00           C
ATOM    110  CA  VAL   110     -19.020  79.033   0.916  1.00 25.00           C
ATOM    111  CA  SER   111     -22.460  79.449   2.404  1.00 25.00           C
ATOM    112  CA  VAL   112     -20.907  82.435   4.137  1.00 25.00           C
ATOM    113  CA  ASN   113     -21.595  84.249   0.846  1.00 25.00           C
ATOM    114  CA  ALA   114     -25.297  84.843   0.035  1.00 25.00           C
ATOM    115  CA  GLU   115     -25.327  88.075  -2.020  1.00 25.00           C
ATOM    116  CA  ARG   116     -22.598  86.672  -4.312  1.00 25.00           C
ATOM    117  CA  LEU   117     -24.610  83.446  -4.773  1.00 25.00           C
ATOM    118  CA  ALA   118     -27.734  85.488  -5.633  1.00 25.00           C
ATOM    119  CA  SER   119     -25.731  87.523  -8.185  1.00 25.00           C
ATOM    120  CA  GLN   120     -23.416  86.356 -11.003  1.00 25.00           C
ATOM    121  CA  ALA   121     -25.733  86.016 -14.006  1.00 25.00           C
ATOM    122  CA  ALA   122     -28.437  83.516 -12.990  1.00 25.00           C
ATOM    123  CA  PRO   123     -25.175  81.524 -12.450  1.00 25.00           C
ATOM    124  CA  PHE   124     -23.278  78.423 -11.276  1.00 25.00           C
ATOM    125  CA  LEU   125     -23.913  75.039  -9.615  1.00 25.00           C
ATOM    126  CA  LEU   126     -21.605  75.820  -6.694  1.00 25.00           C
ATOM    127  CA  SER   127     -19.487  72.869  -5.570  1.00 25.00           C
ATOM    128  CA  SER   128     -17.267  75.414  -3.885  1.00 25.00           C
ATOM    129  CA  PRO   129     -13.768  76.378  -2.906  1.00 25.00           C
ATOM    316  CA  VAL   316     -11.993  67.403   3.255  1.00 25.00           C
ATOM    317  CA  ARG   317     -15.060  65.594   1.844  1.00 25.00           C
ATOM    318  CA  LYS   318     -17.204  66.932   4.722  1.00 25.00           C
ATOM    319  CA  GLY   319     -15.921  70.480   4.061  1.00 25.00           C
ATOM    320  CA  ALA   320     -16.751  70.112   0.340  1.00 25.00           C
ATOM    321  CA  ALA   321     -20.274  68.895   1.220  1.00 25.00           C
ATOM    322  CA  LEU   322     -20.749  71.889   3.562  1.00 25.00           C
ATOM    323  CA  ASN   323     -19.589  74.269   0.795  1.00 25.00           C
ATOM    324  CA  ALA   324     -22.046  72.653  -1.659  1.00 25.00           C
ATOM    325  CA  VAL   325     -24.880  73.037   0.888  1.00 25.00           C
ATOM    326  CA  LEU   326     -23.968  76.723   1.385  1.00 25.00           C
ATOM    327  CA  LEU   327     -23.978  77.262  -2.407  1.00 25.00           C
ATOM    328  CA  GLY   328     -27.416  75.591  -2.660  1.00 25.00           C
ATOM    329  CA  GLU   329     -28.740  77.836   0.147  1.00 25.00           C
ATOM    330  CA  LEU   330     -27.371  80.930  -1.648  1.00 25.00           C
ATOM    331  CA  LEU   331     -29.051  79.814  -4.904  1.00 25.00           C
ATOM    332  CA  ILE   332     -32.364  79.311  -3.051  1.00 25.00           C
ATOM    333  CA  LYS   333     -32.061  82.804  -1.512  1.00 25.00           C
ATOM    334  CA  HIS   334     -31.382  84.297  -4.972  1.00 25.00           C
ATOM    335  CA  TYR   335     -32.560  87.644  -3.640  1.00 25.00           C
ATOM    336  CA  LEU   336     -33.569  88.569  -0.062  1.00 25.00           C
TER
END
