
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS168_4-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          4.819
LGA    P       4      P       4          3.833
LGA    L       5      L       5          1.364
LGA    N       6      N       6          3.567
LGA    V       7      V       7          4.786
LGA    A       8      A       8          2.416
LGA    V       9      V       9          2.511
LGA    V      10      V      10          2.395
LGA    G      11      G      11          2.395
LGA    A      12      A      12          2.992
LGA    T      13      T      13          4.850
LGA    G      14      G      14          1.828
LGA    S      15      S      15          1.405
LGA    V      16      V      16          1.444
LGA    G      17      G      17          1.498
LGA    E      18      E      18          1.161
LGA    A      19      A      19          1.151
LGA    L      20      L      20          1.580
LGA    V      21      V      21          1.365
LGA    G      22      G      22          1.169
LGA    L      23      L      23          1.633
LGA    L      24      L      24          1.960
LGA    D      25      D      25          2.063
LGA    E      26      E      26          2.317
LGA    R      27      R      27          3.958
LGA    D      28      D      28          1.848
LGA    F      29      F      29          1.637
LGA    P      30      P      30          3.202
LGA    L      31      L      31          4.168
LGA    H      32      H      32          3.802
LGA    R      33      R      33          2.543
LGA    L      34      L      34          1.704
LGA    H      35      H      35          3.141
LGA    L      36      L      36          2.342
LGA    L      37      L      37          1.873
LGA    A      38      A      38          1.983
LGA    S      39      S      39          3.499
LGA    A      40      A      40          1.862
LGA    E      41      E      41          4.378
LGA    S      42      S      42           -
LGA    -       -      A      43           -
LGA    A      43      G      44          4.500
LGA    G      44      Q      45           -
LGA    Q      45      -       -           -
LGA    R      46      R      46           #
LGA    M      47      M      47           #
LGA    G      48      G      48           -
LGA    F      49      -       -           -
LGA    A      50      -       -           -
LGA    E      51      F      49           #
LGA    -       -      A      50           -
LGA    -       -      E      51           -
LGA    S      52      S      52          3.599
LGA    S      53      S      53          1.961
LGA    L      54      L      54          1.820
LGA    R      55      R      55          2.251
LGA    V      56      V      56          2.573
LGA    G      57      G      57          2.009
LGA    D      58      D      58           #
LGA    -       -      V      59           -
LGA    -       -      D      60           -
LGA    V      59      S      61           #
LGA    D      60      F      62           #
LGA    S      61      D      63          3.617
LGA    F      62      -       -           -
LGA    D      63      -       -           -
LGA    F      64      F      64          2.205
LGA    S      65      S      65          1.191
LGA    S      66      S      66          1.122
LGA    V      67      V      67          3.369
LGA    G      68      G      68           #
LGA    L      69      L      69          3.965
LGA    A      70      A      70          2.250
LGA    F      71      F      71          1.803
LGA    F      72      F      72          5.048
LGA    A      73      A      73          1.231
LGA    A      74      A      74          2.828
LGA    A      75      A      75          1.897
LGA    A      76      A      76          2.916
LGA    E      77      E      77          1.957
LGA    V      78      V      78          0.648
LGA    S      79      S      79          1.705
LGA    R      80      R      80          1.700
LGA    A      81      A      81          0.780
LGA    H      82      H      82          1.781
LGA    A      83      A      83          4.385
LGA    E      84      -       -           -
LGA    R      85      -       -           -
LGA    A      86      E      84          1.651
LGA    R      87      R      85           #
LGA    A      88      -       -           -
LGA    A      89      A      86           #
LGA    G      90      R      87          3.304
LGA    -       -      A      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    C      91      C      91          3.048
LGA    S      92      S      92          1.855
LGA    V      93      V      93          1.786
LGA    I      94      I      94          1.607
LGA    D      95      D      95          2.851
LGA    L      96      L      96          1.543
LGA    S      97      S      97          2.117
LGA    G      98      G      98          3.132
LGA    A      99      A      99          2.587
LGA    L     100      L     100          2.884
LGA    E     101      E     101          1.522
LGA    P     102      P     102          2.064
LGA    S     103      S     103          4.400
LGA    V     104      -       -           -
LGA    A     105      V     104          2.753
LGA    P     106      A     105          2.198
LGA    P     107      P     106          2.658
LGA    V     108      P     107          2.137
LGA    M     109      V     108          0.755
LGA    V     110      M     109          4.530
LGA    S     111      V     110          3.788
LGA    -       -      S     111           -
LGA    V     112      V     112          5.104
LGA    N     113      N     113          3.924
LGA    -       -      A     114           -
LGA    -       -      E     115           -
LGA    A     114      R     116          4.593
LGA    E     115      L     117          4.606
LGA    R     116      A     118          4.282
LGA    L     117      S     119          4.767
LGA    A     118      Q     120          3.340
LGA    S     119      -       -           -
LGA    Q     120      A     121          4.990
LGA    A     121      A     122          4.792
LGA    A     122      P     123          4.008
LGA    P     123      F     124          1.348
LGA    F     124      L     125          4.062
LGA    L     125      -       -           -
LGA    L     126      L     126          1.799
LGA    S     127      S     127          2.105
LGA    S     128      S     128          2.685
LGA    P     129      P     129          3.108
LGA    V     316      V     316           -
LGA    -       -      R     317           -
LGA    R     317      K     318           #
LGA    K     318      G     319           -
LGA    G     319      A     320           -
LGA    A     320      A     321           -
LGA    A     321      L     322           -
LGA    L     322      N     323           -
LGA    N     323      A     324           -
LGA    A     324      V     325           -
LGA    V     325      L     326           -
LGA    L     326      L     327           -
LGA    L     327      G     328           -
LGA    G     328      E     329           -
LGA    E     329      L     330           -
LGA    L     330      L     331           -
LGA    L     331      I     332           -
LGA    I     332      K     333           -
LGA    K     333      H     334           -
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    104    2.92    81.73     39.503     3.440

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.557326 * X  +   0.363321 * Y  +   0.746583 * Z  + -15.136775
  Y_new =  -0.702580 * X  +   0.685530 * Y  +   0.190868 * Z  +  72.751038
  Z_new =  -0.442458 * X  +  -0.630910 * Y  +   0.637325 * Z  +   1.993895 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.780339    2.361253  [ DEG:   -44.7102    135.2898 ]
  Theta =   0.458338    2.683255  [ DEG:    26.2608    153.7392 ]
  Phi   =  -0.900181    2.241412  [ DEG:   -51.5766    128.4234 ]
 
# 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_4-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS168_4-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  104   2.92   81.73  39.503
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS168_4-D1
PFRMAT TS
TARGET T0298
MODEL 4
PARENT N/A
ATOM      3  CA  GLN     3     -38.756  72.547 -10.905  1.00 25.00           C
ATOM      4  CA  PRO     4     -35.365  71.520 -12.405  1.00 25.00           C
ATOM      5  CA  LEU     5     -32.029  69.887 -13.220  1.00 25.00           C
ATOM      6  CA  ASN     6     -29.251  69.507 -15.791  1.00 25.00           C
ATOM      7  CA  VAL     7     -25.618  68.677 -16.176  1.00 25.00           C
ATOM      8  CA  ALA     8     -22.968  66.202 -15.092  1.00 25.00           C
ATOM      9  CA  VAL     9     -20.199  64.985 -12.740  1.00 25.00           C
ATOM     10  CA  VAL    10     -17.102  66.095 -10.798  1.00 25.00           C
ATOM     11  CA  GLY    11     -14.530  63.467 -11.976  1.00 25.00           C
ATOM     12  CA  ALA    12     -14.957  60.993  -9.106  1.00 25.00           C
ATOM     13  CA  THR    13     -11.514  60.243  -7.667  1.00 25.00           C
ATOM     14  CA  GLY    14     -12.401  58.090  -4.686  1.00 25.00           C
ATOM     15  CA  SER    15     -14.623  60.223  -2.429  1.00 25.00           C
ATOM     16  CA  VAL    16     -16.353  63.640  -2.471  1.00 25.00           C
ATOM     17  CA  GLY    17     -18.538  62.524  -5.413  1.00 25.00           C
ATOM     18  CA  GLU    18     -19.469  59.318  -3.536  1.00 25.00           C
ATOM     19  CA  ALA    19     -20.382  61.370  -0.434  1.00 25.00           C
ATOM     20  CA  LEU    20     -22.555  63.685  -2.576  1.00 25.00           C
ATOM     21  CA  VAL    21     -24.308  60.651  -4.121  1.00 25.00           C
ATOM     22  CA  GLY    22     -24.948  59.212  -0.631  1.00 25.00           C
ATOM     23  CA  LEU    23     -26.394  62.569   0.515  1.00 25.00           C
ATOM     24  CA  LEU    24     -28.673  62.665  -2.561  1.00 25.00           C
ATOM     25  CA  ASP    25     -29.858  59.098  -1.826  1.00 25.00           C
ATOM     26  CA  GLU    26     -30.588  60.063   1.808  1.00 25.00           C
ATOM     27  CA  ARG    27     -32.750  62.750   3.377  1.00 25.00           C
ATOM     28  CA  ASP    28     -32.236  65.231   0.517  1.00 25.00           C
ATOM     29  CA  PHE    29     -32.946  67.012  -2.824  1.00 25.00           C
ATOM     30  CA  PRO    30     -36.432  65.970  -4.049  1.00 25.00           C
ATOM     31  CA  LEU    31     -34.440  63.499  -6.164  1.00 25.00           C
ATOM     32  CA  HIS    32     -31.967  63.970  -9.068  1.00 25.00           C
ATOM     33  CA  ARG    33     -31.369  60.829 -11.129  1.00 25.00           C
ATOM     34  CA  LEU    34     -27.697  61.243 -10.196  1.00 25.00           C
ATOM     35  CA  HIS    35     -24.727  59.127 -11.174  1.00 25.00           C
ATOM     36  CA  LEU    36     -22.713  60.672 -13.951  1.00 25.00           C
ATOM     37  CA  LEU    37     -19.394  59.585 -12.479  1.00 25.00           C
ATOM     38  CA  ALA    38     -16.448  59.278 -14.813  1.00 25.00           C
ATOM     39  CA  SER    39     -13.473  57.553 -13.097  1.00 25.00           C
ATOM     40  CA  ALA    40     -12.231  56.979 -16.681  1.00 25.00           C
ATOM     41  CA  GLU    41     -12.442  53.489 -18.182  1.00 25.00           C
ATOM     42  CA  SER    42     -15.149  53.078 -20.862  1.00 25.00           C
ATOM     43  CA  ALA    43     -15.956  49.564 -19.627  1.00 25.00           C
ATOM     44  CA  GLY    44     -19.135  47.929 -20.843  1.00 25.00           C
ATOM     45  CA  GLN    45     -22.215  48.325 -18.561  1.00 25.00           C
ATOM     46  CA  ARG    46     -23.129  50.214 -15.395  1.00 25.00           C
ATOM     47  CA  MET    47     -26.025  52.685 -15.480  1.00 25.00           C
ATOM     48  CA  GLY    48     -28.492  53.410 -12.609  1.00 25.00           C
ATOM     49  CA  PHE    49     -31.713  53.172 -10.587  1.00 25.00           C
ATOM     50  CA  ALA    50     -34.013  50.475  -9.255  1.00 25.00           C
ATOM     51  CA  GLU    51     -31.644  50.408  -6.297  1.00 25.00           C
ATOM     52  CA  SER    52     -28.567  48.277  -5.693  1.00 25.00           C
ATOM     53  CA  SER    53     -25.520  50.056  -7.049  1.00 25.00           C
ATOM     54  CA  LEU    54     -24.262  52.644  -9.552  1.00 25.00           C
ATOM     55  CA  ARG    55     -21.407  53.418 -11.900  1.00 25.00           C
ATOM     56  CA  VAL    56     -21.764  55.570 -15.075  1.00 25.00           C
ATOM     57  CA  GLY    57     -20.602  56.831 -18.456  1.00 25.00           C
ATOM     58  CA  ASP    58     -22.426  59.345 -20.717  1.00 25.00           C
ATOM     59  CA  VAL    59     -24.028  62.432 -22.355  1.00 25.00           C
ATOM     60  CA  ASP    60     -25.854  63.480 -25.485  1.00 25.00           C
ATOM     61  CA  SER    61     -22.413  64.516 -26.814  1.00 25.00           C
ATOM     62  CA  PHE    62     -20.509  67.837 -26.919  1.00 25.00           C
ATOM     63  CA  ASP    63     -20.822  68.166 -23.116  1.00 25.00           C
ATOM     64  CA  PHE    64     -23.773  69.603 -21.258  1.00 25.00           C
ATOM     65  CA  SER    65     -26.931  68.507 -23.038  1.00 25.00           C
ATOM     66  CA  SER    66     -27.990  66.559 -19.928  1.00 25.00           C
ATOM     67  CA  VAL    67     -28.499  64.584 -16.679  1.00 25.00           C
ATOM     68  CA  GLY    68     -27.889  65.427 -12.994  1.00 25.00           C
ATOM     69  CA  LEU    69     -26.545  67.978 -10.506  1.00 25.00           C
ATOM     70  CA  ALA    70     -23.101  69.629 -10.439  1.00 25.00           C
ATOM     71  CA  PHE    71     -20.675  68.076  -7.868  1.00 25.00           C
ATOM     72  CA  PHE    72     -17.650  67.651  -5.574  1.00 25.00           C
ATOM     73  CA  ALA    73     -14.409  65.993  -6.742  1.00 25.00           C
ATOM     74  CA  ALA    74     -10.675  65.660  -7.387  1.00 25.00           C
ATOM     75  CA  ALA    75      -8.659  67.828  -9.774  1.00 25.00           C
ATOM     76  CA  ALA    76      -5.594  67.895 -11.975  1.00 25.00           C
ATOM     77  CA  GLU    77      -6.248  66.598 -15.443  1.00 25.00           C
ATOM     78  CA  VAL    78     -10.044  66.386 -14.985  1.00 25.00           C
ATOM     79  CA  SER    79     -10.157  70.085 -14.003  1.00 25.00           C
ATOM     80  CA  ARG    80      -8.101  70.996 -17.103  1.00 25.00           C
ATOM     81  CA  ALA    81     -10.482  68.963 -19.309  1.00 25.00           C
ATOM     82  CA  HIS    82     -13.491  70.742 -17.744  1.00 25.00           C
ATOM     83  CA  ALA    83     -11.844  74.141 -18.383  1.00 25.00           C
ATOM     84  CA  GLU    84     -11.186  73.166 -22.028  1.00 25.00           C
ATOM     85  CA  ARG    85     -14.840  72.090 -22.424  1.00 25.00           C
ATOM     86  CA  ALA    86     -16.008  75.423 -20.943  1.00 25.00           C
ATOM     87  CA  ARG    87     -13.728  77.325 -23.361  1.00 25.00           C
ATOM     88  CA  ALA    88     -15.132  75.315 -26.304  1.00 25.00           C
ATOM     89  CA  ALA    89     -18.888  75.624 -25.513  1.00 25.00           C
ATOM     90  CA  GLY    90     -20.830  75.974 -22.309  1.00 25.00           C
ATOM     91  CA  CYS    91     -22.520  74.406 -19.289  1.00 25.00           C
ATOM     92  CA  SER    92     -22.749  73.989 -15.500  1.00 25.00           C
ATOM     93  CA  VAL    93     -19.743  72.638 -13.740  1.00 25.00           C
ATOM     94  CA  ILE    94     -18.995  72.396 -10.043  1.00 25.00           C
ATOM     95  CA  ASP    95     -17.059  72.317  -6.796  1.00 25.00           C
ATOM     96  CA  LEU    96     -13.445  71.106  -7.218  1.00 25.00           C
ATOM     97  CA  SER    97     -10.240  72.231  -5.531  1.00 25.00           C
ATOM     98  CA  GLY    98      -8.199  75.436  -5.368  1.00 25.00           C
ATOM     99  CA  ALA    99      -7.271  74.616  -8.908  1.00 25.00           C
ATOM    100  CA  LEU   100      -9.407  77.530  -9.935  1.00 25.00           C
ATOM    101  CA  GLU   101     -11.009  80.899  -9.203  1.00 25.00           C
ATOM    102  CA  PRO   102      -8.820  83.452 -10.975  1.00 25.00           C
ATOM    103  CA  SER   103      -9.804  81.355 -14.005  1.00 25.00           C
ATOM    104  CA  VAL   104     -10.290  84.554 -15.898  1.00 25.00           C
ATOM    105  CA  ALA   105     -14.041  84.637 -15.333  1.00 25.00           C
ATOM    106  CA  PRO   106     -15.184  82.046 -12.737  1.00 25.00           C
ATOM    107  CA  PRO   107     -16.595  84.001  -9.740  1.00 25.00           C
ATOM    108  CA  VAL   108     -15.667  81.699  -6.859  1.00 25.00           C
ATOM    109  CA  MET   109     -17.943  80.920  -3.917  1.00 25.00           C
ATOM    110  CA  VAL   110     -21.498  79.756  -4.417  1.00 25.00           C
ATOM    111  CA  SER   111     -24.601  80.855  -2.528  1.00 25.00           C
ATOM    112  CA  VAL   112     -23.582  83.593  -0.095  1.00 25.00           C
ATOM    113  CA  ASN   113     -22.842  86.111  -2.831  1.00 25.00           C
ATOM    114  CA  ALA   114     -26.076  85.766  -4.784  1.00 25.00           C
ATOM    115  CA  GLU   115     -25.656  88.959  -6.857  1.00 25.00           C
ATOM    116  CA  ARG   116     -22.112  87.888  -7.834  1.00 25.00           C
ATOM    117  CA  LEU   117     -23.413  84.438  -8.869  1.00 25.00           C
ATOM    118  CA  ALA   118     -26.156  86.078 -10.979  1.00 25.00           C
ATOM    119  CA  SER   119     -23.553  88.330 -12.658  1.00 25.00           C
ATOM    120  CA  GLN   120     -20.989  86.710 -15.026  1.00 25.00           C
ATOM    121  CA  ALA   121     -23.723  84.744 -16.793  1.00 25.00           C
ATOM    122  CA  ALA   122     -25.659  82.266 -14.635  1.00 25.00           C
ATOM    123  CA  PRO   123     -22.429  80.312 -14.379  1.00 25.00           C
ATOM    124  CA  PHE   124     -21.745  80.192 -10.612  1.00 25.00           C
ATOM    125  CA  LEU   125     -21.432  76.577 -11.755  1.00 25.00           C
ATOM    126  CA  LEU   126     -17.846  77.046 -10.605  1.00 25.00           C
ATOM    127  CA  SER   127     -14.872  75.669  -8.804  1.00 25.00           C
ATOM    128  CA  SER   128     -14.003  76.306  -5.170  1.00 25.00           C
ATOM    129  CA  PRO   129     -14.639  73.575  -2.655  1.00 25.00           C
ATOM    316  CA  VAL   316     -12.981  66.161  14.523  1.00 25.00           C
ATOM    317  CA  ARG   317     -12.624  68.945  11.917  1.00 25.00           C
ATOM    318  CA  LYS   318     -13.768  71.537  14.494  1.00 25.00           C
ATOM    319  CA  GLY   319     -11.220  70.189  17.016  1.00 25.00           C
ATOM    320  CA  ALA   320      -8.456  70.401  14.375  1.00 25.00           C
ATOM    321  CA  ALA   321      -9.456  74.011  13.581  1.00 25.00           C
ATOM    322  CA  LEU   322      -9.367  74.882  17.309  1.00 25.00           C
ATOM    323  CA  ASN   323      -5.891  73.305  17.620  1.00 25.00           C
ATOM    324  CA  ALA   324      -4.681  75.319  14.595  1.00 25.00           C
ATOM    325  CA  VAL   325      -6.071  78.532  16.146  1.00 25.00           C
ATOM    326  CA  LEU   326      -4.292  77.739  19.444  1.00 25.00           C
ATOM    327  CA  LEU   327      -1.013  77.136  17.558  1.00 25.00           C
ATOM    328  CA  GLY   328      -1.425  80.475  15.727  1.00 25.00           C
ATOM    329  CA  GLU   329      -2.054  82.253  19.060  1.00 25.00           C
ATOM    330  CA  LEU   330       1.082  80.633  20.545  1.00 25.00           C
ATOM    331  CA  LEU   331       3.129  81.753  17.507  1.00 25.00           C
ATOM    332  CA  ILE   332       1.788  85.321  17.888  1.00 25.00           C
ATOM    333  CA  LYS   333       2.714  85.297  21.604  1.00 25.00           C
ATOM    334  CA  HIS   334       6.239  84.074  20.744  1.00 25.00           C
ATOM    335  CA  TYR   335       8.088  87.423  21.115  1.00 25.00           C
ATOM    336  CA  LEU   336       5.076  89.478  19.923  1.00 25.00           C
TER
END
