
#######################################################
#                                                     #
#                        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 T0298TS393_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS393_2-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          4.788
LGA    P       4      P       4          3.440
LGA    L       5      L       5          1.730
LGA    N       6      N       6          2.539
LGA    V       7      V       7          2.293
LGA    A       8      A       8          1.700
LGA    V       9      V       9          1.516
LGA    V      10      V      10          2.112
LGA    G      11      G      11          2.140
LGA    A      12      A      12          3.706
LGA    T      13      T      13          3.435
LGA    G      14      G      14          1.691
LGA    S      15      S      15          1.177
LGA    V      16      V      16          1.065
LGA    G      17      G      17          1.065
LGA    E      18      E      18          1.259
LGA    A      19      A      19          1.174
LGA    L      20      L      20          0.921
LGA    V      21      V      21          1.174
LGA    G      22      G      22          1.356
LGA    L      23      L      23          1.073
LGA    L      24      L      24          1.069
LGA    D      25      D      25          1.256
LGA    E      26      E      26          0.700
LGA    R      27      R      27          3.691
LGA    D      28      D      28          0.973
LGA    F      29      F      29          3.879
LGA    P      30      P      30          2.935
LGA    L      31      L      31          2.910
LGA    H      32      H      32           #
LGA    R      33      R      33           #
LGA    L      34      L      34          4.219
LGA    H      35      H      35          1.981
LGA    L      36      L      36          0.983
LGA    L      37      L      37          0.345
LGA    A      38      A      38          0.493
LGA    S      39      S      39          3.165
LGA    A      40      A      40          2.556
LGA    E      41      E      41          2.461
LGA    S      42      S      42           #
LGA    A      43      -       -           -
LGA    G      44      -       -           -
LGA    Q      45      A      43          4.966
LGA    R      46      G      44          3.245
LGA    -       -      Q      45           -
LGA    M      47      R      46          2.870
LGA    G      48      M      47          3.186
LGA    F      49      G      48          2.637
LGA    A      50      F      49           -
LGA    -       -      A      50           -
LGA    E      51      E      51          5.276
LGA    S      52      S      52          4.154
LGA    S      53      S      53          5.090
LGA    L      54      L      54          4.036
LGA    R      55      R      55          4.412
LGA    -       -      V      56           -
LGA    V      56      G      57          1.402
LGA    G      57      D      58          3.170
LGA    -       -      V      59           -
LGA    D      58      D      60          4.134
LGA    V      59      S      61          4.273
LGA    D      60      F      62          5.510
LGA    S      61      -       -           -
LGA    F      62      -       -           -
LGA    D      63      D      63          3.027
LGA    F      64      F      64          2.298
LGA    S      65      S      65          2.599
LGA    S      66      S      66          2.582
LGA    V      67      V      67          1.531
LGA    G      68      G      68          0.963
LGA    L      69      L      69          0.977
LGA    A      70      A      70          1.991
LGA    F      71      F      71          2.351
LGA    F      72      F      72          2.888
LGA    A      73      A      73          3.615
LGA    A      74      A      74           #
LGA    A      75      -       -           -
LGA    A      76      A      75           #
LGA    E      77      A      76          2.056
LGA    V      78      E      77          2.602
LGA    S      79      V      78          2.279
LGA    R      80      S      79          0.983
LGA    A      81      R      80          0.936
LGA    H      82      A      81          0.735
LGA    A      83      H      82          0.862
LGA    E      84      A      83          1.575
LGA    R      85      E      84          3.629
LGA    A      86      R      85          2.958
LGA    R      87      A      86          1.508
LGA    A      88      R      87          4.225
LGA    A      89      A      88          2.426
LGA    G      90      A      89          2.756
LGA    -       -      G      90           -
LGA    C      91      C      91          2.689
LGA    S      92      S      92          3.870
LGA    V      93      V      93          3.628
LGA    I      94      I      94           #
LGA    D      95      D      95           #
LGA    L      96      L      96          4.833
LGA    S      97      S      97          2.034
LGA    G      98      G      98          2.819
LGA    A      99      A      99          3.813
LGA    L     100      L     100          3.525
LGA    E     101      E     101          3.081
LGA    P     102      P     102          2.400
LGA    S     103      S     103          2.248
LGA    V     104      V     104          3.378
LGA    A     105      A     105           #
LGA    P     106      P     106           #
LGA    P     107      P     107           -
LGA    V     108      V     108          4.803
LGA    M     109      M     109          5.093
LGA    V     110      V     110          3.516
LGA    S     111      S     111          4.606
LGA    V     112      V     112          3.139
LGA    N     113      N     113          2.792
LGA    A     114      A     114          3.773
LGA    E     115      E     115          2.745
LGA    R     116      R     116          1.039
LGA    L     117      L     117          0.948
LGA    A     118      A     118          0.740
LGA    S     119      S     119          0.490
LGA    Q     120      Q     120          2.995
LGA    A     121      A     121           -
LGA    A     122      A     122           -
LGA    P     123      P     123           -
LGA    F     124      F     124           #
LGA    L     125      L     125          0.606
LGA    L     126      L     126          2.686
LGA    S     127      S     127           #
LGA    S     128      S     128          1.640
LGA    P     129      P     129          2.478
LGA    -       -      V     316           -
LGA    -       -      R     317           -
LGA    -       -      K     318           -
LGA    -       -      G     319           -
LGA    V     316      A     320          2.629
LGA    R     317      A     321          1.741
LGA    K     318      L     322          1.310
LGA    G     319      N     323          2.124
LGA    A     320      A     324          0.635
LGA    A     321      V     325          2.911
LGA    L     322      L     326          4.014
LGA    N     323      L     327          3.064
LGA    A     324      G     328          3.842
LGA    V     325      E     329           #
LGA    L     326      -       -           -
LGA    L     327      -       -           -
LGA    G     328      L     330          3.401
LGA    E     329      L     331           -
LGA    L     330      I     332           -
LGA    -       -      K     333           -
LGA    L     331      H     334           #
LGA    I     332      Y     335           #
LGA    K     333      L     336           -
LGA    H     334      -       -           -
LGA    Y     335      -       -           -
LGA    L     336      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  148  148    5.0    116    2.85    74.14     45.632     3.934

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.902598 * X  +   0.086991 * Y  +   0.421604 * Z  + -14.964855
  Y_new =   0.156806 * X  +  -0.845650 * Y  +   0.510185 * Z  +  72.405556
  Z_new =   0.400911 * X  +   0.526602 * Y  +   0.749641 * Z  +   1.633691 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.612383   -2.529209  [ DEG:    35.0870   -144.9130 ]
  Theta =  -0.412511   -2.729082  [ DEG:   -23.6351   -156.3649 ]
  Phi   =   2.969582   -0.172011  [ DEG:   170.1445     -9.8555 ]
 
# 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: T0298TS393_2-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS393_2-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  116   2.85   74.14  45.632
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS393_2-D1
PFRMAT TS
TARGET T0298
MODEL 2
PARENT N/A
ATOM      3  CA  GLN     3     -38.699  71.307 -10.914  1.00 25.00           C
ATOM      4  CA  PRO     4     -35.394  69.595 -11.422  1.00 25.00           C
ATOM      5  CA  LEU     5     -31.948  68.116 -11.776  1.00 25.00           C
ATOM      6  CA  ASN     6     -28.770  66.055 -12.155  1.00 25.00           C
ATOM      7  CA  VAL     7     -25.051  65.441 -11.647  1.00 25.00           C
ATOM      8  CA  ALA     8     -22.196  64.952 -14.039  1.00 25.00           C
ATOM      9  CA  VAL     9     -19.738  63.851 -11.293  1.00 25.00           C
ATOM     10  CA  VAL    10     -15.945  63.780 -10.761  1.00 25.00           C
ATOM     11  CA  GLY    11     -15.357  60.724  -8.499  1.00 25.00           C
ATOM     12  CA  ALA    12     -15.874  57.600  -6.443  1.00 25.00           C
ATOM     13  CA  THR    13     -12.022  57.404  -6.601  1.00 25.00           C
ATOM     14  CA  GLY    14     -12.121  60.331  -4.125  1.00 25.00           C
ATOM     15  CA  SER    15     -13.464  60.699  -0.646  1.00 25.00           C
ATOM     16  CA  VAL    16     -15.029  64.165  -1.093  1.00 25.00           C
ATOM     17  CA  GLY    17     -17.135  62.865  -4.017  1.00 25.00           C
ATOM     18  CA  GLU    18     -18.296  59.897  -1.892  1.00 25.00           C
ATOM     19  CA  ALA    19     -19.245  62.276   0.955  1.00 25.00           C
ATOM     20  CA  LEU    20     -21.211  64.465  -1.496  1.00 25.00           C
ATOM     21  CA  VAL    21     -23.037  61.374  -2.831  1.00 25.00           C
ATOM     22  CA  GLY    22     -23.895  60.306   0.746  1.00 25.00           C
ATOM     23  CA  LEU    23     -25.229  63.816   1.500  1.00 25.00           C
ATOM     24  CA  LEU    24     -27.366  63.712  -1.678  1.00 25.00           C
ATOM     25  CA  ASP    25     -28.748  60.286  -0.666  1.00 25.00           C
ATOM     26  CA  GLU    26     -29.589  61.627   2.822  1.00 25.00           C
ATOM     27  CA  ARG    27     -32.903  62.744   1.219  1.00 25.00           C
ATOM     28  CA  ASP    28     -33.157  65.247  -1.632  1.00 25.00           C
ATOM     29  CA  PHE    29     -32.215  62.988  -4.546  1.00 25.00           C
ATOM     30  CA  PRO    30     -35.235  64.432  -6.230  1.00 25.00           C
ATOM     31  CA  LEU    31     -33.766  63.042  -9.431  1.00 25.00           C
ATOM     32  CA  HIS    32     -30.616  60.972 -10.108  1.00 25.00           C
ATOM     33  CA  ARG    33     -28.519  58.434  -8.167  1.00 25.00           C
ATOM     34  CA  LEU    34     -25.571  60.909  -8.477  1.00 25.00           C
ATOM     35  CA  HIS    35     -25.265  59.856 -12.129  1.00 25.00           C
ATOM     36  CA  LEU    36     -21.699  58.828 -12.974  1.00 25.00           C
ATOM     37  CA  LEU    37     -18.378  59.970 -14.380  1.00 25.00           C
ATOM     38  CA  ALA    38     -14.598  59.759 -13.884  1.00 25.00           C
ATOM     39  CA  SER    39     -11.591  57.705 -12.839  1.00 25.00           C
ATOM     40  CA  ALA    40     -10.487  57.692 -16.497  1.00 25.00           C
ATOM     41  CA  GLU    41     -11.018  53.905 -16.949  1.00 25.00           C
ATOM     42  CA  SER    42     -12.593  51.649 -19.627  1.00 25.00           C
ATOM     43  CA  ALA    43     -13.704  48.009 -19.383  1.00 25.00           C
ATOM     44  CA  GLY    44     -17.380  46.940 -19.050  1.00 25.00           C
ATOM     45  CA  GLN    45     -17.313  49.517 -16.255  1.00 25.00           C
ATOM     46  CA  ARG    46     -20.199  50.612 -14.018  1.00 25.00           C
ATOM     47  CA  MET    47     -21.522  52.917 -11.336  1.00 25.00           C
ATOM     48  CA  GLY    48     -24.118  51.601  -8.951  1.00 25.00           C
ATOM     49  CA  PHE    49     -26.388  51.071  -5.962  1.00 25.00           C
ATOM     50  CA  ALA    50     -27.157  47.643  -7.333  1.00 25.00           C
ATOM     51  CA  GLU    51     -30.811  48.739  -6.863  1.00 25.00           C
ATOM     52  CA  SER    52     -30.296  50.254 -10.352  1.00 25.00           C
ATOM     53  CA  SER    53     -28.625  52.935 -12.470  1.00 25.00           C
ATOM     54  CA  LEU    54     -25.920  54.785 -14.458  1.00 25.00           C
ATOM     55  CA  ARG    55     -23.785  53.978 -17.509  1.00 25.00           C
ATOM     56  CA  VAL    56     -20.334  55.410 -16.964  1.00 25.00           C
ATOM     57  CA  GLY    57     -19.317  58.415 -19.152  1.00 25.00           C
ATOM     58  CA  ASP    58     -18.349  60.571 -22.124  1.00 25.00           C
ATOM     59  CA  VAL    59     -19.400  64.067 -23.204  1.00 25.00           C
ATOM     60  CA  ASP    60     -19.847  63.599 -27.004  1.00 25.00           C
ATOM     61  CA  SER    61     -23.572  64.402 -26.939  1.00 25.00           C
ATOM     62  CA  PHE    62     -24.799  61.095 -25.446  1.00 25.00           C
ATOM     63  CA  ASP    63     -24.361  62.501 -21.910  1.00 25.00           C
ATOM     64  CA  PHE    64     -24.010  66.252 -22.299  1.00 25.00           C
ATOM     65  CA  SER    65     -27.532  67.134 -23.385  1.00 25.00           C
ATOM     66  CA  SER    66     -27.865  68.531 -19.876  1.00 25.00           C
ATOM     67  CA  VAL    67     -26.505  67.932 -16.399  1.00 25.00           C
ATOM     68  CA  GLY    68     -28.121  71.119 -15.066  1.00 25.00           C
ATOM     69  CA  LEU    69     -25.730  71.296 -12.149  1.00 25.00           C
ATOM     70  CA  ALA    70     -22.548  69.742 -10.631  1.00 25.00           C
ATOM     71  CA  PHE    71     -21.194  68.541  -7.301  1.00 25.00           C
ATOM     72  CA  PHE    72     -17.680  67.199  -8.088  1.00 25.00           C
ATOM     73  CA  ALA    73     -16.177  68.720  -4.893  1.00 25.00           C
ATOM     74  CA  ALA    74     -14.922  71.320  -7.319  1.00 25.00           C
ATOM     75  CA  ALA    75     -12.912  73.444  -9.795  1.00 25.00           C
ATOM     76  CA  ALA    76      -9.295  72.831 -10.668  1.00 25.00           C
ATOM     77  CA  GLU    77      -6.534  70.826 -12.310  1.00 25.00           C
ATOM     78  CA  VAL    78      -5.719  70.371 -16.024  1.00 25.00           C
ATOM     79  CA  SER    79      -8.329  67.579 -16.279  1.00 25.00           C
ATOM     80  CA  ARG    80     -10.931  69.825 -14.590  1.00 25.00           C
ATOM     81  CA  ALA    81     -10.111  72.656 -17.035  1.00 25.00           C
ATOM     82  CA  HIS    82     -10.488  70.247 -19.989  1.00 25.00           C
ATOM     83  CA  ALA    83     -13.870  69.072 -18.631  1.00 25.00           C
ATOM     84  CA  GLU    84     -15.014  72.709 -18.263  1.00 25.00           C
ATOM     85  CA  ARG    85     -13.928  73.441 -21.862  1.00 25.00           C
ATOM     86  CA  ALA    86     -15.857  70.369 -23.094  1.00 25.00           C
ATOM     87  CA  ARG    87     -18.966  71.524 -21.180  1.00 25.00           C
ATOM     88  CA  ALA    88     -18.652  75.014 -22.726  1.00 25.00           C
ATOM     89  CA  ALA    89     -22.121  74.699 -24.297  1.00 25.00           C
ATOM     90  CA  GLY    90     -23.490  74.448 -20.723  1.00 25.00           C
ATOM     91  CA  CYS    91     -22.017  73.419 -17.339  1.00 25.00           C
ATOM     92  CA  SER    92     -20.555  73.219 -13.830  1.00 25.00           C
ATOM     93  CA  VAL    93     -17.934  72.138 -11.270  1.00 25.00           C
ATOM     94  CA  ILE    94     -15.411  69.385 -12.252  1.00 25.00           C
ATOM     95  CA  ASP    95     -12.581  67.804 -10.233  1.00 25.00           C
ATOM     96  CA  LEU    96     -11.392  67.821  -6.598  1.00 25.00           C
ATOM     97  CA  SER    97     -10.162  71.244  -5.487  1.00 25.00           C
ATOM     98  CA  GLY    98      -8.610  74.717  -5.486  1.00 25.00           C
ATOM     99  CA  ALA    99      -8.259  77.200  -8.306  1.00 25.00           C
ATOM    100  CA  LEU   100     -11.220  79.113  -9.610  1.00 25.00           C
ATOM    101  CA  GLU   101     -10.723  82.681  -8.247  1.00 25.00           C
ATOM    102  CA  PRO   102      -7.975  83.458 -10.696  1.00 25.00           C
ATOM    103  CA  SER   103     -10.476  83.702 -13.546  1.00 25.00           C
ATOM    104  CA  VAL   104     -13.429  85.474 -15.194  1.00 25.00           C
ATOM    105  CA  ALA   105     -16.948  84.219 -15.228  1.00 25.00           C
ATOM    106  CA  PRO   106     -20.347  83.096 -14.013  1.00 25.00           C
ATOM    107  CA  PRO   107     -21.890  84.030 -10.689  1.00 25.00           C
ATOM    108  CA  VAL   108     -20.624  81.933  -7.738  1.00 25.00           C
ATOM    109  CA  MET   109     -22.314  81.289  -4.405  1.00 25.00           C
ATOM    110  CA  VAL   110     -20.814  79.885  -1.203  1.00 25.00           C
ATOM    111  CA  SER   111     -24.160  80.501   0.371  1.00 25.00           C
ATOM    112  CA  VAL   112     -22.627  83.601   1.836  1.00 25.00           C
ATOM    113  CA  ASN   113     -22.778  86.838  -0.150  1.00 25.00           C
ATOM    114  CA  ALA   114     -26.105  86.752  -1.987  1.00 25.00           C
ATOM    115  CA  GLU   115     -24.879  89.877  -3.831  1.00 25.00           C
ATOM    116  CA  ARG   116     -22.088  87.838  -5.482  1.00 25.00           C
ATOM    117  CA  LEU   117     -24.632  85.185  -6.560  1.00 25.00           C
ATOM    118  CA  ALA   118     -26.886  87.909  -8.031  1.00 25.00           C
ATOM    119  CA  SER   119     -23.907  89.380  -9.937  1.00 25.00           C
ATOM    120  CA  GLN   120     -21.759  88.560 -12.981  1.00 25.00           C
ATOM    121  CA  ALA   121     -18.026  88.886 -12.961  1.00 25.00           C
ATOM    122  CA  ALA   122     -17.516  86.624  -9.956  1.00 25.00           C
ATOM    123  CA  PRO   123     -16.045  83.105 -10.405  1.00 25.00           C
ATOM    124  CA  PHE   124     -16.187  79.793 -12.359  1.00 25.00           C
ATOM    125  CA  LEU   125     -19.633  78.238 -12.773  1.00 25.00           C
ATOM    126  CA  LEU   126     -20.039  76.547  -9.394  1.00 25.00           C
ATOM    127  CA  SER   127     -20.895  74.979  -6.068  1.00 25.00           C
ATOM    128  CA  SER   128     -17.612  76.277  -4.676  1.00 25.00           C
ATOM    129  CA  PRO   129     -13.884  75.766  -4.129  1.00 25.00           C
ATOM    316  CA  VAL   316     -16.512  67.697  -0.474  1.00 25.00           C
ATOM    317  CA  ARG   317     -20.299  67.170  -0.250  1.00 25.00           C
ATOM    318  CA  LYS   318     -20.471  69.515   2.773  1.00 25.00           C
ATOM    319  CA  GLY   319     -18.465  72.162   0.865  1.00 25.00           C
ATOM    320  CA  ALA   320     -20.830  71.831  -2.129  1.00 25.00           C
ATOM    321  CA  ALA   321     -23.855  72.233   0.186  1.00 25.00           C
ATOM    322  CA  LEU   322     -22.280  75.358   1.742  1.00 25.00           C
ATOM    323  CA  ASN   323     -21.643  76.805  -1.747  1.00 25.00           C
ATOM    324  CA  ALA   324     -25.280  76.112  -2.726  1.00 25.00           C
ATOM    325  CA  VAL   325     -26.495  77.839   0.469  1.00 25.00           C
ATOM    326  CA  LEU   326     -24.276  80.866  -0.295  1.00 25.00           C
ATOM    327  CA  LEU   327     -25.672  81.021  -3.857  1.00 25.00           C
ATOM    328  CA  GLY   328     -29.247  80.874  -2.490  1.00 25.00           C
ATOM    329  CA  GLU   329     -28.450  83.705  -0.035  1.00 25.00           C
ATOM    330  CA  LEU   330     -26.993  85.802  -2.889  1.00 25.00           C
ATOM    331  CA  LEU   331     -30.137  85.177  -4.986  1.00 25.00           C
ATOM    332  CA  ILE   332     -32.342  86.231  -2.037  1.00 25.00           C
ATOM    333  CA  LYS   333     -30.274  89.423  -1.598  1.00 25.00           C
ATOM    334  CA  HIS   334     -30.627  90.195  -5.333  1.00 25.00           C
ATOM    335  CA  TYR   335     -33.345  92.838  -4.626  1.00 25.00           C
ATOM    336  CA  LEU   336     -33.076  93.809  -0.927  1.00 25.00           C
TER
END
