
#######################################################
#                                                     #
#                        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  108 (  108),  selected  108 , name T0291TS393_2-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS393_2-D1.T0291_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       1      T       1           #
LGA    Y       2      Y       2          5.405
LGA    V       3      V       3          3.043
LGA    D       4      D       4          4.996
LGA    P       5      P       5          2.913
LGA    H       6      H       6          3.453
LGA    T       7      -       -           -
LGA    Y       8      -       -           -
LGA    E       9      -       -           -
LGA    D      10      -       -           -
LGA    P      11      -       -           -
LGA    T      12      -       -           -
LGA    Q      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      V      15          1.472
LGA    H      16      H      16          1.863
LGA    E      17      E      17          2.256
LGA    F      18      F      18          1.917
LGA    A      19      A      19          2.477
LGA    K      20      K      20          2.674
LGA    E      21      E      21          1.770
LGA    L      22      L      22          2.244
LGA    D      23      D      23          1.829
LGA    A      24      A      24          3.493
LGA    T      25      T      25          1.916
LGA    N      26      N      26          2.111
LGA    I      27      I      27          3.688
LGA    S      28      S      28          1.738
LGA    I      29      I      29          2.800
LGA    D      30      D      30          2.243
LGA    K      31      -       -           -
LGA    V      32      K      31          1.645
LGA    V      33      V      32          4.300
LGA    G      34      V      33          1.097
LGA    A      35      G      34          2.282
LGA    G      36      A      35          3.412
LGA    E      37      G      36          2.638
LGA    F      38      E      37          2.228
LGA    -       -      F      38           -
LGA    G      39      G      39          2.519
LGA    E      40      E      40          2.542
LGA    V      41      V      41          2.341
LGA    C      42      C      42          1.463
LGA    S      43      S      43          1.864
LGA    G      44      G      44          1.109
LGA    R      45      R      45          1.422
LGA    L      46      L      46          0.942
LGA    K      47      K      47          1.591
LGA    L      48      L      48          3.818
LGA    P      49      P      49          1.834
LGA    S      50      S      50          3.168
LGA    K      51      K      51          2.067
LGA    K      52      K      52          4.031
LGA    E      53      E      53          1.642
LGA    I      54      I      54          2.204
LGA    S      55      S      55          2.556
LGA    V      56      V      56          3.272
LGA    A      57      A      57          2.979
LGA    I      58      I      58          1.415
LGA    K      59      K      59          0.795
LGA    T      60      T      60          1.288
LGA    L      61      L      61          1.029
LGA    K      62      K      62          0.504
LGA    V      63      V      63          1.805
LGA    G      64      G      64          2.099
LGA    Y      65      Y      65          2.063
LGA    T      66      T      66          1.709
LGA    E      67      E      67          1.756
LGA    K      68      K      68          1.887
LGA    Q      69      Q      69          1.300
LGA    R      70      R      70          0.806
LGA    R      71      R      71          1.108
LGA    D      72      D      72          1.210
LGA    F      73      F      73          0.734
LGA    L      74      L      74          0.918
LGA    G      75      G      75          0.665
LGA    E      76      E      76          1.947
LGA    A      77      A      77          2.052
LGA    S      78      S      78          1.893
LGA    I      79      I      79          2.588
LGA    M      80      M      80          3.119
LGA    G      81      G      81          2.983
LGA    Q      82      Q      82          3.742
LGA    F      83      F      83          3.845
LGA    D      84      D      84          3.815
LGA    H      85      H      85          4.584
LGA    P      86      P      86          3.292
LGA    N      87      N      87          2.106
LGA    I      88      I      88          1.835
LGA    I      89      I      89          1.274
LGA    R      90      R      90          1.269
LGA    L      91      L      91          1.847
LGA    E      92      E      92          1.166
LGA    G      93      G      93          1.263
LGA    V      94      V      94          0.785
LGA    V      95      V      95          1.004
LGA    T      96      T      96          1.231
LGA    K      97      K      97          2.241
LGA    S      98      S      98          2.942
LGA    K      99      K      99          1.246
LGA    P     100      P     100          1.172
LGA    V     101      V     101          0.741
LGA    M     102      M     102          0.680
LGA    I     103      I     103          0.353
LGA    V     104      V     104          1.397
LGA    T     105      T     105          1.877
LGA    E     106      E     106          2.735
LGA    Y     107      Y     107          1.823
LGA    M     108      M     108          2.832

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     98    2.36    93.88     70.805     3.985

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.054438 * X  +   0.790222 * Y  +   0.610398 * Z  +  -0.861845
  Y_new =  -0.678125 * X  +   0.477966 * Y  +  -0.558296 * Z  +   9.521629
  Z_new =  -0.732928 * X  +  -0.383534 * Y  +   0.561889 * Z  +  55.221924 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.598939    2.542654  [ DEG:   -34.3166    145.6833 ]
  Theta =   0.822616    2.318977  [ DEG:    47.1324    132.8676 ]
  Phi   =  -1.490690    1.650902  [ DEG:   -85.4103     94.5897 ]
 
# 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: T0291TS393_2-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS393_2-D1.T0291_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  108  100   5.0   98   2.36   93.88  70.805
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS393_2-D1
PFRMAT TS
TARGET T0291
MODEL 2
PARENT N/A
ATOM      1  CA  THR     1      -4.065  35.779  45.335  1.00 25.00           C
ATOM      2  CA  TYR     2      -4.554  32.917  47.753  1.00 25.00           C
ATOM      3  CA  VAL     3      -6.178  30.247  49.808  1.00 25.00           C
ATOM      4  CA  ASP     4      -9.342  28.759  51.176  1.00 25.00           C
ATOM      5  CA  PRO     5     -12.481  29.172  53.254  1.00 25.00           C
ATOM      6  CA  HIS     6     -12.576  30.004  56.961  1.00 25.00           C
ATOM      7  CA  THR     7     -12.062  33.740  56.382  1.00 25.00           C
ATOM      8  CA  TYR     8     -14.060  36.477  54.694  1.00 25.00           C
ATOM      9  CA  GLU     9     -17.370  36.480  56.566  1.00 25.00           C
ATOM     10  CA  ASP    10     -19.997  34.147  55.201  1.00 25.00           C
ATOM     11  CA  PRO    11     -17.942  31.048  54.485  1.00 25.00           C
ATOM     12  CA  THR    12     -21.062  29.317  53.093  1.00 25.00           C
ATOM     13  CA  GLN    13     -20.480  30.956  49.682  1.00 25.00           C
ATOM     14  CA  ALA    14     -16.832  29.793  49.717  1.00 25.00           C
ATOM     15  CA  VAL    15     -17.951  26.232  50.575  1.00 25.00           C
ATOM     16  CA  HIS    16     -20.480  26.308  47.701  1.00 25.00           C
ATOM     17  CA  GLU    17     -17.753  27.517  45.299  1.00 25.00           C
ATOM     18  CA  PHE    18     -15.441  24.697  46.466  1.00 25.00           C
ATOM     19  CA  ALA    19     -18.241  22.142  45.921  1.00 25.00           C
ATOM     20  CA  LYS    20     -18.851  23.525  42.402  1.00 25.00           C
ATOM     21  CA  GLU    21     -20.843  20.360  41.880  1.00 25.00           C
ATOM     22  CA  LEU    22     -21.357  17.149  39.841  1.00 25.00           C
ATOM     23  CA  ASP    23     -25.096  17.061  40.795  1.00 25.00           C
ATOM     24  CA  ALA    24     -27.819  14.775  42.255  1.00 25.00           C
ATOM     25  CA  THR    25     -28.242  11.569  40.203  1.00 25.00           C
ATOM     26  CA  ASN    26     -24.439  11.206  39.941  1.00 25.00           C
ATOM     27  CA  ILE    27     -24.008   7.775  38.286  1.00 25.00           C
ATOM     28  CA  SER    28     -23.822   5.003  40.853  1.00 25.00           C
ATOM     29  CA  ILE    29     -24.055   3.418  44.309  1.00 25.00           C
ATOM     30  CA  ASP    30     -21.369   0.706  44.020  1.00 25.00           C
ATOM     31  CA  LYS    31     -19.647  -2.005  46.049  1.00 25.00           C
ATOM     32  CA  VAL    32     -17.951  -1.652  49.476  1.00 25.00           C
ATOM     33  CA  VAL    33     -14.358  -0.702  50.350  1.00 25.00           C
ATOM     34  CA  GLY    34     -14.975  -0.906  54.095  1.00 25.00           C
ATOM     35  CA  ALA    35     -14.145   0.125  57.611  1.00 25.00           C
ATOM     36  CA  GLY    36     -13.656   3.695  58.709  1.00 25.00           C
ATOM     37  CA  GLU    37     -15.014   5.591  61.716  1.00 25.00           C
ATOM     38  CA  PHE    38     -17.148   8.642  60.933  1.00 25.00           C
ATOM     39  CA  GLY    39     -18.519   6.433  58.222  1.00 25.00           C
ATOM     40  CA  GLU    40     -17.523   4.069  55.358  1.00 25.00           C
ATOM     41  CA  VAL    41     -15.299   3.835  52.248  1.00 25.00           C
ATOM     42  CA  CYS    42     -18.447   3.680  50.040  1.00 25.00           C
ATOM     43  CA  SER    43     -17.594   3.266  46.385  1.00 25.00           C
ATOM     44  CA  GLY    44     -17.711   3.853  42.572  1.00 25.00           C
ATOM     45  CA  ARG    45     -18.139   4.974  38.929  1.00 25.00           C
ATOM     46  CA  LEU    46     -19.070   8.589  39.259  1.00 25.00           C
ATOM     47  CA  LYS    47     -19.160  11.085  36.333  1.00 25.00           C
ATOM     48  CA  LEU    48     -21.401  13.750  34.802  1.00 25.00           C
ATOM     49  CA  PRO    49     -18.689  13.972  32.143  1.00 25.00           C
ATOM     50  CA  SER    50     -19.677  12.356  28.911  1.00 25.00           C
ATOM     51  CA  LYS    51     -17.578   9.417  30.042  1.00 25.00           C
ATOM     52  CA  LYS    52     -16.606   5.711  30.079  1.00 25.00           C
ATOM     53  CA  GLU    53     -15.061   5.996  33.563  1.00 25.00           C
ATOM     54  CA  ILE    54     -14.593   8.705  36.275  1.00 25.00           C
ATOM     55  CA  SER    55     -13.511   7.503  39.727  1.00 25.00           C
ATOM     56  CA  VAL    56     -13.866  10.238  42.349  1.00 25.00           C
ATOM     57  CA  ALA    57     -15.332   8.007  45.029  1.00 25.00           C
ATOM     58  CA  ILE    58     -15.433   8.020  48.846  1.00 25.00           C
ATOM     59  CA  LYS    59     -17.314   8.461  52.106  1.00 25.00           C
ATOM     60  CA  THR    60     -20.033   9.688  54.494  1.00 25.00           C
ATOM     61  CA  LEU    61     -21.270  12.264  57.075  1.00 25.00           C
ATOM     62  CA  LYS    62     -23.773   9.955  58.849  1.00 25.00           C
ATOM     63  CA  VAL    63     -27.059   8.978  60.520  1.00 25.00           C
ATOM     64  CA  GLY    64     -28.423  10.869  63.575  1.00 25.00           C
ATOM     65  CA  TYR    65     -26.340  14.022  64.013  1.00 25.00           C
ATOM     66  CA  THR    66     -26.689  17.794  63.583  1.00 25.00           C
ATOM     67  CA  GLU    67     -25.931  20.957  61.668  1.00 25.00           C
ATOM     68  CA  LYS    68     -22.648  21.349  63.600  1.00 25.00           C
ATOM     69  CA  GLN    69     -21.576  17.828  62.540  1.00 25.00           C
ATOM     70  CA  ARG    70     -22.395  18.650  58.890  1.00 25.00           C
ATOM     71  CA  ARG    71     -20.346  21.877  59.132  1.00 25.00           C
ATOM     72  CA  ASP    72     -17.402  19.925  60.612  1.00 25.00           C
ATOM     73  CA  PHE    73     -17.637  17.368  57.771  1.00 25.00           C
ATOM     74  CA  LEU    74     -17.663  20.200  55.191  1.00 25.00           C
ATOM     75  CA  GLY    75     -14.583  21.765  56.842  1.00 25.00           C
ATOM     76  CA  GLU    76     -12.789  18.381  56.762  1.00 25.00           C
ATOM     77  CA  ALA    77     -13.657  17.982  53.053  1.00 25.00           C
ATOM     78  CA  SER    78     -12.311  21.496  52.336  1.00 25.00           C
ATOM     79  CA  ILE    79      -9.075  20.666  54.208  1.00 25.00           C
ATOM     80  CA  MET    80      -8.707  17.432  52.190  1.00 25.00           C
ATOM     81  CA  GLY    81      -9.234  19.376  48.933  1.00 25.00           C
ATOM     82  CA  GLN    82      -6.582  21.926  49.996  1.00 25.00           C
ATOM     83  CA  PHE    83      -3.011  21.001  49.256  1.00 25.00           C
ATOM     84  CA  ASP    84      -2.273  19.933  45.695  1.00 25.00           C
ATOM     85  CA  HIS    85       1.192  18.647  46.444  1.00 25.00           C
ATOM     86  CA  PRO    86       1.861  16.174  43.579  1.00 25.00           C
ATOM     87  CA  ASN    87       2.398  13.269  46.028  1.00 25.00           C
ATOM     88  CA  ILE    88      -1.068  14.197  47.291  1.00 25.00           C
ATOM     89  CA  ILE    89      -4.779  13.746  48.131  1.00 25.00           C
ATOM     90  CA  ARG    90      -6.891  15.099  45.263  1.00 25.00           C
ATOM     91  CA  LEU    91     -10.486  15.369  44.142  1.00 25.00           C
ATOM     92  CA  GLU    92     -13.470  15.557  41.710  1.00 25.00           C
ATOM     93  CA  GLY    93     -15.550  16.444  44.761  1.00 25.00           C
ATOM     94  CA  VAL    94     -18.863  17.165  46.493  1.00 25.00           C
ATOM     95  CA  VAL    95     -22.705  17.019  46.775  1.00 25.00           C
ATOM     96  CA  THR    96     -23.727  19.218  49.715  1.00 25.00           C
ATOM     97  CA  LYS    97     -27.435  18.467  49.881  1.00 25.00           C
ATOM     98  CA  SER    98     -30.289  16.596  51.532  1.00 25.00           C
ATOM     99  CA  LYS    99     -28.800  13.221  50.655  1.00 25.00           C
ATOM    100  CA  PRO   100     -26.422  12.649  53.539  1.00 25.00           C
ATOM    101  CA  VAL   101     -23.388  14.513  52.178  1.00 25.00           C
ATOM    102  CA  MET   102     -20.919  12.344  50.319  1.00 25.00           C
ATOM    103  CA  ILE   103     -17.380  13.855  50.133  1.00 25.00           C
ATOM    104  CA  VAL   104     -14.988  12.334  47.618  1.00 25.00           C
ATOM    105  CA  THR   105     -11.186  11.819  47.832  1.00 25.00           C
ATOM    106  CA  GLU   106      -8.355   9.664  46.376  1.00 25.00           C
ATOM    107  CA  TYR   107      -9.352   7.689  43.321  1.00 25.00           C
ATOM    108  CA  MET   108      -7.674   4.247  43.453  1.00 25.00           C
TER
END
