
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS393_3-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          4.067
LGA    P       4      P       4          2.117
LGA    L       5      L       5          3.426
LGA    N       6      N       6          1.243
LGA    V       7      V       7          1.335
LGA    A       8      A       8          1.464
LGA    V       9      V       9          1.151
LGA    V      10      V      10          1.760
LGA    G      11      G      11          0.487
LGA    A      12      A      12          2.490
LGA    -       -      T      13           -
LGA    T      13      G      14          0.760
LGA    G      14      S      15          2.164
LGA    S      15      V      16          2.131
LGA    V      16      -       -           -
LGA    G      17      G      17          1.648
LGA    E      18      E      18          2.758
LGA    A      19      A      19          3.140
LGA    L      20      L      20          1.947
LGA    V      21      V      21          1.321
LGA    G      22      G      22          2.412
LGA    L      23      L      23          2.335
LGA    L      24      L      24          1.218
LGA    D      25      D      25          0.661
LGA    E      26      E      26          2.212
LGA    R      27      R      27          4.624
LGA    D      28      D      28          2.672
LGA    F      29      F      29          3.330
LGA    P      30      P      30          2.530
LGA    L      31      L      31          4.740
LGA    H      32      H      32          2.121
LGA    R      33      R      33          3.735
LGA    L      34      L      34          3.846
LGA    H      35      H      35          3.551
LGA    L      36      L      36          1.393
LGA    L      37      L      37          2.817
LGA    A      38      A      38          2.571
LGA    S      39      S      39          2.199
LGA    -       -      A      40           -
LGA    A      40      E      41          2.739
LGA    E      41      S      42          3.512
LGA    S      42      A      43          5.175
LGA    A      43      -       -           -
LGA    G      44      -       -           -
LGA    Q      45      G      44          3.070
LGA    R      46      Q      45          3.140
LGA    M      47      R      46          1.624
LGA    G      48      M      47          2.042
LGA    F      49      G      48          1.333
LGA    A      50      F      49           #
LGA    E      51      A      50           -
LGA    -       -      E      51           -
LGA    S      52      S      52          4.512
LGA    S      53      S      53          2.861
LGA    L      54      L      54          2.375
LGA    R      55      R      55          1.837
LGA    V      56      V      56          2.118
LGA    G      57      G      57          1.977
LGA    D      58      D      58          3.740
LGA    V      59      V      59           #
LGA    D      60      D      60           -
LGA    S      61      S      61           #
LGA    F      62      F      62           #
LGA    D      63      D      63          2.775
LGA    F      64      F      64          2.571
LGA    S      65      S      65          2.133
LGA    S      66      S      66          2.288
LGA    V      67      V      67          3.110
LGA    G      68      G      68          1.227
LGA    L      69      L      69          1.554
LGA    A      70      A      70          1.917
LGA    F      71      F      71          2.318
LGA    F      72      F      72          3.783
LGA    A      73      A      73          1.209
LGA    A      74      A      74          2.893
LGA    A      75      A      75          2.490
LGA    A      76      A      76          0.537
LGA    E      77      E      77          1.731
LGA    V      78      V      78          1.609
LGA    S      79      S      79          3.048
LGA    R      80      R      80          2.840
LGA    A      81      A      81          1.016
LGA    H      82      H      82          0.865
LGA    A      83      A      83          0.872
LGA    E      84      E      84          3.465
LGA    R      85      R      85          2.809
LGA    A      86      A      86          3.055
LGA    R      87      -       -           -
LGA    A      88      -       -           -
LGA    A      89      -       -           -
LGA    G      90      -       -           -
LGA    C      91      R      87          0.873
LGA    S      92      A      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    -       -      C      91           -
LGA    -       -      S      92           -
LGA    V      93      V      93          1.399
LGA    I      94      I      94          3.826
LGA    D      95      D      95          1.502
LGA    L      96      L      96          1.355
LGA    S      97      S      97          2.024
LGA    G      98      G      98          2.710
LGA    -       -      A      99           -
LGA    A      99      L     100          1.960
LGA    -       -      E     101           -
LGA    -       -      P     102           -
LGA    -       -      S     103           -
LGA    -       -      V     104           -
LGA    L     100      A     105          0.411
LGA    E     101      P     106          0.547
LGA    P     102      P     107           #
LGA    S     103      -       -           -
LGA    V     104      -       -           -
LGA    A     105      -       -           -
LGA    P     106      -       -           -
LGA    P     107      -       -           -
LGA    V     108      V     108          3.970
LGA    M     109      M     109          2.935
LGA    V     110      V     110          5.473
LGA    S     111      -       -           -
LGA    V     112      S     111          4.423
LGA    N     113      V     112          4.196
LGA    A     114      N     113           -
LGA    E     115      -       -           -
LGA    R     116      A     114          3.699
LGA    L     117      -       -           -
LGA    A     118      -       -           -
LGA    S     119      -       -           -
LGA    Q     120      E     115           #
LGA    A     121      R     116           -
LGA    A     122      -       -           -
LGA    P     123      L     117          1.371
LGA    F     124      A     118           #
LGA    -       -      S     119           -
LGA    L     125      Q     120           #
LGA    -       -      A     121           -
LGA    -       -      A     122           -
LGA    -       -      P     123           -
LGA    -       -      F     124           -
LGA    L     126      L     125          4.600
LGA    S     127      L     126          3.558
LGA    -       -      S     127           -
LGA    S     128      S     128          2.199
LGA    P     129      P     129          2.823
LGA    V     316      -       -           -
LGA    R     317      -       -           -
LGA    K     318      -       -           -
LGA    G     319      -       -           -
LGA    A     320      -       -           -
LGA    A     321      V     316          5.101
LGA    L     322      R     317          5.164
LGA    -       -      K     318           -
LGA    N     323      G     319          3.685
LGA    A     324      A     320          3.504
LGA    V     325      A     321          1.881
LGA    L     326      L     322          4.030
LGA    L     327      N     323          3.884
LGA    G     328      A     324          1.475
LGA    E     329      V     325          2.549
LGA    L     330      L     326          3.603
LGA    L     331      L     327          1.700
LGA    I     332      G     328          2.036
LGA    K     333      E     329          3.659
LGA    H     334      L     330          2.412
LGA    Y     335      L     331          4.396
LGA    L     336      I     332          2.900
LGA    -       -      K     333           -
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    112    2.81    71.43     44.043     3.848

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.828260 * X  +  -0.047613 * Y  +  -0.558317 * Z  + -10.020689
  Y_new =  -0.163623 * X  +  -0.932407 * Y  +   0.322250 * Z  +  74.573982
  Z_new =  -0.535922 * X  +   0.358260 * Y  +   0.764485 * Z  +  -1.596346 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.438238   -2.703355  [ DEG:    25.1092   -154.8908 ]
  Theta =   0.565600    2.575993  [ DEG:    32.4065    147.5935 ]
  Phi   =  -2.946554    0.195039  [ DEG:  -168.8251     11.1749 ]
 
# 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_3-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS393_3-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  112   2.81   71.43  44.043
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS393_3-D1
PFRMAT TS
TARGET T0298
MODEL 3
PARENT N/A
ATOM      3  CA  GLN     3     -39.804  68.318 -16.240  1.00 25.00           C
ATOM      4  CA  PRO     4     -36.041  67.606 -16.407  1.00 25.00           C
ATOM      5  CA  LEU     5     -32.545  66.579 -15.444  1.00 25.00           C
ATOM      6  CA  ASN     6     -29.108  66.129 -13.856  1.00 25.00           C
ATOM      7  CA  VAL     7     -26.432  66.243 -11.165  1.00 25.00           C
ATOM      8  CA  ALA     8     -23.841  63.694 -12.361  1.00 25.00           C
ATOM      9  CA  VAL     9     -20.403  64.709 -11.289  1.00 25.00           C
ATOM     10  CA  VAL    10     -16.773  65.620 -11.575  1.00 25.00           C
ATOM     11  CA  GLY    11     -15.042  62.697  -9.900  1.00 25.00           C
ATOM     12  CA  ALA    12     -15.584  60.170  -7.112  1.00 25.00           C
ATOM     13  CA  THR    13     -12.333  59.356  -5.291  1.00 25.00           C
ATOM     14  CA  GLY    14     -12.002  61.638  -2.288  1.00 25.00           C
ATOM     15  CA  SER    15     -14.599  63.163   0.034  1.00 25.00           C
ATOM     16  CA  VAL    16     -16.400  66.039  -1.742  1.00 25.00           C
ATOM     17  CA  GLY    17     -18.041  63.557  -4.152  1.00 25.00           C
ATOM     18  CA  GLU    18     -19.172  61.398  -1.198  1.00 25.00           C
ATOM     19  CA  ALA    19     -20.639  64.487   0.528  1.00 25.00           C
ATOM     20  CA  LEU    20     -22.499  65.428  -2.684  1.00 25.00           C
ATOM     21  CA  VAL    21     -23.888  61.868  -2.953  1.00 25.00           C
ATOM     22  CA  GLY    22     -25.047  62.020   0.695  1.00 25.00           C
ATOM     23  CA  LEU    23     -26.758  65.382   0.038  1.00 25.00           C
ATOM     24  CA  LEU    24     -28.506  63.920  -3.039  1.00 25.00           C
ATOM     25  CA  ASP    25     -29.690  60.921  -0.973  1.00 25.00           C
ATOM     26  CA  GLU    26     -31.031  63.280   1.729  1.00 25.00           C
ATOM     27  CA  ARG    27     -34.255  63.538  -0.206  1.00 25.00           C
ATOM     28  CA  ASP    28     -33.969  66.539  -2.498  1.00 25.00           C
ATOM     29  CA  PHE    29     -32.961  64.125  -5.219  1.00 25.00           C
ATOM     30  CA  PRO    30     -35.878  65.541  -7.275  1.00 25.00           C
ATOM     31  CA  LEU    31     -35.537  61.983  -8.729  1.00 25.00           C
ATOM     32  CA  HIS    32     -32.683  63.585 -10.741  1.00 25.00           C
ATOM     33  CA  ARG    33     -30.570  60.449 -10.111  1.00 25.00           C
ATOM     34  CA  LEU    34     -27.356  60.715  -8.133  1.00 25.00           C
ATOM     35  CA  HIS    35     -25.927  58.755 -11.070  1.00 25.00           C
ATOM     36  CA  LEU    36     -22.102  58.891 -10.956  1.00 25.00           C
ATOM     37  CA  LEU    37     -18.340  59.158 -11.411  1.00 25.00           C
ATOM     38  CA  ALA    38     -16.799  60.832 -14.504  1.00 25.00           C
ATOM     39  CA  SER    39     -13.585  58.779 -14.674  1.00 25.00           C
ATOM     40  CA  ALA    40     -11.371  55.811 -13.813  1.00 25.00           C
ATOM     41  CA  GLU    41     -12.544  53.072 -16.102  1.00 25.00           C
ATOM     42  CA  SER    42     -12.942  51.520 -19.512  1.00 25.00           C
ATOM     43  CA  ALA    43     -14.252  47.989 -18.964  1.00 25.00           C
ATOM     44  CA  GLY    44     -17.643  46.264 -18.966  1.00 25.00           C
ATOM     45  CA  GLN    45     -19.291  48.696 -16.627  1.00 25.00           C
ATOM     46  CA  ARG    46     -20.391  49.871 -13.134  1.00 25.00           C
ATOM     47  CA  MET    47     -20.264  52.044  -9.983  1.00 25.00           C
ATOM     48  CA  GLY    48     -23.385  51.575  -7.782  1.00 25.00           C
ATOM     49  CA  PHE    49     -25.957  52.090  -5.067  1.00 25.00           C
ATOM     50  CA  ALA    50     -25.582  48.723  -3.217  1.00 25.00           C
ATOM     51  CA  GLU    51     -26.788  46.084  -5.725  1.00 25.00           C
ATOM     52  CA  SER    52     -29.474  47.286  -8.047  1.00 25.00           C
ATOM     53  CA  SER    53     -26.906  48.847 -10.448  1.00 25.00           C
ATOM     54  CA  LEU    54     -25.158  51.481 -12.560  1.00 25.00           C
ATOM     55  CA  ARG    55     -23.032  54.251 -14.072  1.00 25.00           C
ATOM     56  CA  VAL    56     -20.046  56.236 -15.160  1.00 25.00           C
ATOM     57  CA  GLY    57     -19.628  56.373 -18.919  1.00 25.00           C
ATOM     58  CA  ASP    58     -19.103  60.138 -19.393  1.00 25.00           C
ATOM     59  CA  VAL    59     -21.720  59.871 -22.164  1.00 25.00           C
ATOM     60  CA  ASP    60     -24.126  61.387 -24.775  1.00 25.00           C
ATOM     61  CA  SER    61     -21.710  61.914 -27.676  1.00 25.00           C
ATOM     62  CA  PHE    62     -19.869  65.227 -27.118  1.00 25.00           C
ATOM     63  CA  ASP    63     -19.950  64.661 -23.331  1.00 25.00           C
ATOM     64  CA  PHE    64     -23.372  65.286 -21.788  1.00 25.00           C
ATOM     65  CA  SER    65     -25.380  67.559 -24.047  1.00 25.00           C
ATOM     66  CA  SER    66     -27.341  68.415 -20.883  1.00 25.00           C
ATOM     67  CA  VAL    67     -24.772  69.032 -18.168  1.00 25.00           C
ATOM     68  CA  GLY    68     -27.319  70.567 -15.769  1.00 25.00           C
ATOM     69  CA  LEU    69     -24.398  71.059 -13.307  1.00 25.00           C
ATOM     70  CA  ALA    70     -21.366  70.044 -11.181  1.00 25.00           C
ATOM     71  CA  PHE    71     -21.381  69.262  -7.449  1.00 25.00           C
ATOM     72  CA  PHE    72     -17.898  67.713  -6.962  1.00 25.00           C
ATOM     73  CA  ALA    73     -14.335  66.422  -6.638  1.00 25.00           C
ATOM     74  CA  ALA    74     -11.111  64.447  -7.118  1.00 25.00           C
ATOM     75  CA  ALA    75     -10.003  67.540  -8.978  1.00 25.00           C
ATOM     76  CA  ALA    76      -7.567  69.674 -10.896  1.00 25.00           C
ATOM     77  CA  GLU    77      -7.520  67.173 -13.743  1.00 25.00           C
ATOM     78  CA  VAL    78     -10.156  65.386 -15.870  1.00 25.00           C
ATOM     79  CA  SER    79     -12.919  67.496 -14.263  1.00 25.00           C
ATOM     80  CA  ARG    80     -10.931  70.689 -14.981  1.00 25.00           C
ATOM     81  CA  ALA    81     -10.468  69.610 -18.626  1.00 25.00           C
ATOM     82  CA  HIS    82     -14.224  68.930 -18.929  1.00 25.00           C
ATOM     83  CA  ALA    83     -14.992  72.385 -17.466  1.00 25.00           C
ATOM     84  CA  GLU    84     -12.577  74.004 -19.960  1.00 25.00           C
ATOM     85  CA  ARG    85     -14.257  72.126 -22.844  1.00 25.00           C
ATOM     86  CA  ALA    86     -17.696  73.300 -21.637  1.00 25.00           C
ATOM     87  CA  ARG    87     -16.431  76.909 -21.459  1.00 25.00           C
ATOM     88  CA  ALA    88     -15.039  76.622 -25.016  1.00 25.00           C
ATOM     89  CA  ALA    89     -18.742  77.158 -25.485  1.00 25.00           C
ATOM     90  CA  GLY    90     -21.319  77.250 -22.636  1.00 25.00           C
ATOM     91  CA  CYS    91     -21.405  75.877 -19.054  1.00 25.00           C
ATOM     92  CA  SER    92     -22.039  75.009 -15.404  1.00 25.00           C
ATOM     93  CA  VAL    93     -20.154  74.869 -12.071  1.00 25.00           C
ATOM     94  CA  ILE    94     -16.914  72.869 -11.911  1.00 25.00           C
ATOM     95  CA  ASP    95     -15.749  71.560  -8.567  1.00 25.00           C
ATOM     96  CA  LEU    96     -13.061  71.250  -5.823  1.00 25.00           C
ATOM     97  CA  SER    97     -10.954  73.273  -8.249  1.00 25.00           C
ATOM     98  CA  GLY    98     -10.102  76.489 -10.102  1.00 25.00           C
ATOM     99  CA  ALA    99     -12.018  78.494 -12.781  1.00 25.00           C
ATOM    100  CA  LEU   100     -15.115  80.280 -11.462  1.00 25.00           C
ATOM    101  CA  GLU   101     -14.874  82.023  -8.108  1.00 25.00           C
ATOM    102  CA  PRO   102     -17.348  84.610  -9.350  1.00 25.00           C
ATOM    103  CA  SER   103     -19.108  86.320 -12.242  1.00 25.00           C
ATOM    104  CA  VAL   104     -22.765  85.446 -12.643  1.00 25.00           C
ATOM    105  CA  ALA   105     -26.000  83.506 -12.084  1.00 25.00           C
ATOM    106  CA  PRO   106     -25.928  80.637  -9.631  1.00 25.00           C
ATOM    107  CA  PRO   107     -25.061  79.935  -5.943  1.00 25.00           C
ATOM    108  CA  VAL   108     -22.317  79.628  -3.345  1.00 25.00           C
ATOM    109  CA  MET   109     -20.824  77.070  -0.898  1.00 25.00           C
ATOM    110  CA  VAL   110     -18.630  77.896   2.149  1.00 25.00           C
ATOM    111  CA  SER   111     -19.611  76.433   5.485  1.00 25.00           C
ATOM    112  CA  VAL   112     -19.673  79.490   7.794  1.00 25.00           C
ATOM    113  CA  ASN   113     -22.445  81.534   6.257  1.00 25.00           C
ATOM    114  CA  ALA   114     -25.276  79.908   4.340  1.00 25.00           C
ATOM    115  CA  GLU   115     -27.629  82.920   4.581  1.00 25.00           C
ATOM    116  CA  ARG   116     -26.269  84.278   1.270  1.00 25.00           C
ATOM    117  CA  LEU   117     -26.806  80.864  -0.381  1.00 25.00           C
ATOM    118  CA  ALA   118     -30.397  80.761   0.946  1.00 25.00           C
ATOM    119  CA  SER   119     -31.031  84.281  -0.423  1.00 25.00           C
ATOM    120  CA  GLN   120     -29.356  83.621  -3.794  1.00 25.00           C
ATOM    121  CA  ALA   121     -31.332  84.085  -7.048  1.00 25.00           C
ATOM    122  CA  ALA   122     -28.542  86.299  -8.455  1.00 25.00           C
ATOM    123  CA  PRO   123     -25.323  84.680  -7.224  1.00 25.00           C
ATOM    124  CA  PHE   124     -21.800  83.210  -7.072  1.00 25.00           C
ATOM    125  CA  LEU   125     -21.345  81.048 -10.237  1.00 25.00           C
ATOM    126  CA  LEU   126     -19.336  78.201  -8.672  1.00 25.00           C
ATOM    127  CA  SER   127     -16.215  76.103  -7.983  1.00 25.00           C
ATOM    128  CA  SER   128     -14.964  77.160  -4.550  1.00 25.00           C
ATOM    129  CA  PRO   129     -11.629  75.431  -3.953  1.00 25.00           C
ATOM    316  CA  VAL   316      -4.642  67.302   2.117  1.00 25.00           C
ATOM    317  CA  ARG   317      -6.593  65.680  -0.751  1.00 25.00           C
ATOM    318  CA  LYS   318      -9.400  64.719   1.669  1.00 25.00           C
ATOM    319  CA  GLY   319      -9.515  68.308   3.001  1.00 25.00           C
ATOM    320  CA  ALA   320      -9.707  69.656  -0.579  1.00 25.00           C
ATOM    321  CA  ALA   321     -12.567  67.232  -1.364  1.00 25.00           C
ATOM    322  CA  LEU   322     -14.422  68.359   1.791  1.00 25.00           C
ATOM    323  CA  ASN   323     -13.958  72.025   0.783  1.00 25.00           C
ATOM    324  CA  ALA   324     -15.305  71.258  -2.719  1.00 25.00           C
ATOM    325  CA  VAL   325     -18.341  69.493  -1.192  1.00 25.00           C
ATOM    326  CA  LEU   326     -18.980  72.506   1.084  1.00 25.00           C
ATOM    327  CA  LEU   327     -18.763  74.859  -1.931  1.00 25.00           C
ATOM    328  CA  GLY   328     -21.240  72.661  -3.856  1.00 25.00           C
ATOM    329  CA  GLU   329     -23.637  72.705  -0.870  1.00 25.00           C
ATOM    330  CA  LEU   330     -23.368  76.521  -0.679  1.00 25.00           C
ATOM    331  CA  LEU   331     -24.104  76.785  -4.427  1.00 25.00           C
ATOM    332  CA  ILE   332     -27.158  74.510  -4.014  1.00 25.00           C
ATOM    333  CA  LYS   333     -28.401  76.670  -1.105  1.00 25.00           C
ATOM    334  CA  HIS   334     -27.956  79.827  -3.226  1.00 25.00           C
ATOM    335  CA  TYR   335     -31.522  79.193  -4.270  1.00 25.00           C
ATOM    336  CA  LEU   336     -33.745  76.290  -5.378  1.00 25.00           C
TER
END
