
#######################################################
#                                                     #
#                        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  143 (  143),  selected  143 , name T0338TS393_1-D1
# Molecule2: number of CA atoms  143 ( 1129),  selected  143 , name T0338_D1.pdb
# PARAMETERS: T0338TS393_1-D1.T0338_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      A       1           -
LGA    S       2      S       2           -
LGA    S       3      S       3           -
LGA    R       4      R       4           -
LGA    W       5      W       5           -
LGA    F       6      F       6           -
LGA    F       7      F       7           -
LGA    T       8      T       8           -
LGA    R       9      R       9           -
LGA    E      10      E      10           -
LGA    Q      11      Q      11           -
LGA    L      12      L      12           -
LGA    E      13      E      13           -
LGA    N      14      N      14           -
LGA    T      15      T      15           -
LGA    P      16      P      16           -
LGA    S      17      S      17           -
LGA    R      18      R      18           -
LGA    R      19      R      19           -
LGA    C      20      C      20           -
LGA    G      21      G      21           -
LGA    V      22      V      22           -
LGA    -       -      E      23           -
LGA    E      23      A      24          5.195
LGA    A      24      D      25          2.420
LGA    D      25      -       -           -
LGA    K      26      K      26          1.112
LGA    E      27      E      27          0.884
LGA    L      28      L      28          1.861
LGA    S      29      S      29          1.940
LGA    C      30      C      30          0.879
LGA    R      31      R      31          0.980
LGA    Q      32      Q      32          2.227
LGA    Q      33      Q      33          2.246
LGA    A      34      A      34          0.852
LGA    A      35      A      35          1.442
LGA    N      36      N      36          2.805
LGA    L      37      L      37          2.412
LGA    I      38      I      38          0.342
LGA    Q      39      Q      39          2.298
LGA    E      40      E      40          3.512
LGA    M      41      M      41          2.270
LGA    G      42      G      42          0.866
LGA    Q      43      Q      43          3.427
LGA    R      44      R      44          3.528
LGA    L      45      L      45          0.744
LGA    N      46      N      46          1.276
LGA    V      47      V      47          2.220
LGA    S      48      S      48          2.228
LGA    Q      49      Q      49          3.998
LGA    L      50      L      50          3.662
LGA    T      51      -       -           -
LGA    I      52      T      51          2.770
LGA    N      53      I      52          3.697
LGA    T      54      N      53          3.449
LGA    A      55      T      54          1.771
LGA    I      56      A      55          1.824
LGA    V      57      I      56          2.371
LGA    Y      58      V      57          2.063
LGA    M      59      Y      58          1.279
LGA    H      60      M      59          1.255
LGA    R      61      H      60          1.720
LGA    F      62      R      61          2.578
LGA    Y      63      F      62          2.273
LGA    M      64      Y      63          1.500
LGA    H      65      M      64          2.375
LGA    H      66      H      65          2.726
LGA    S      67      H      66          2.543
LGA    F      68      S      67          2.306
LGA    T      69      F      68          3.961
LGA    K      70      T      69          1.143
LGA    F      71      K      70          4.052
LGA    N      72      F      71          4.496
LGA    K      73      N      72          2.714
LGA    N      74      K      73          4.223
LGA    -       -      N      74           -
LGA    -       -      I      75           -
LGA    I      75      I      76          3.433
LGA    I      76      S      77          2.133
LGA    S      77      S      78           #
LGA    S      78      T      79          3.996
LGA    T      79      A      80          1.843
LGA    A      80      L      81           #
LGA    L      81      -       -           -
LGA    F      82      -       -           -
LGA    L      83      F      82          2.888
LGA    A      84      -       -           -
LGA    A      85      -       -           -
LGA    K      86      -       -           -
LGA    V      87      -       -           -
LGA    E      88      -       -           -
LGA    E      89      -       -           -
LGA    Q      90      -       -           -
LGA    A      91      -       -           -
LGA    R      92      -       -           -
LGA    K      93      -       -           -
LGA    L      94      -       -           -
LGA    E      95      -       -           -
LGA    H      96      -       -           -
LGA    V      97      L      83          2.010
LGA    I      98      A      84          3.701
LGA    K      99      A      85          2.097
LGA    V     100      K      86          5.854
LGA    A     101      V      87           #
LGA    -       -      E      88           -
LGA    -       -      E      89           -
LGA    H     102      Q      90          0.531
LGA    A     103      A      91           #
LGA    C     104      R      92          4.405
LGA    L     105      K      93           -
LGA    H     106      L      94           -
LGA    P     107      E      95           -
LGA    L     108      H      96           -
LGA    E     109      V      97           -
LGA    P     110      I      98           -
LGA    L     111      K      99           -
LGA    L     112      V     100           -
LGA    D     113      A     101           -
LGA    T     114      H     102           -
LGA    K     115      A     103           -
LGA    C     116      C     104           -
LGA    D     117      L     105           -
LGA    A     118      H     106           -
LGA    Y     119      P     107           -
LGA    L     120      L     108           -
LGA    Q     121      E     109           -
LGA    Q     122      P     110           -
LGA    T     123      L     111           -
LGA    R     124      L     112           -
LGA    E     125      D     113           -
LGA    L     126      T     114           -
LGA    V     127      K     115           -
LGA    I     128      C     116           -
LGA    -       -      D     117           -
LGA    -       -      A     118           -
LGA    -       -      Y     119           -
LGA    -       -      L     120           -
LGA    -       -      Q     121           -
LGA    -       -      Q     122           -
LGA    -       -      T     123           -
LGA    -       -      R     124           -
LGA    -       -      E     125           -
LGA    -       -      L     126           -
LGA    -       -      V     127           -
LGA    -       -      I     128           -
LGA    -       -      L     129           -
LGA    -       -      E     130           -
LGA    -       -      T     131           -
LGA    -       -      I     132           -
LGA    -       -      M     133           -
LGA    L     129      L     134           #
LGA    E     130      Q     135           -
LGA    T     131      T     136           -
LGA    -       -      L     137           -
LGA    -       -      G     138           -
LGA    I     132      F     139          1.393
LGA    M     133      E     140          4.136
LGA    L     134      I     141           -
LGA    Q     135      T     142           -
LGA    T     136      I     143           -
LGA    L     137      -       -           -
LGA    G     138      -       -           -
LGA    F     139      -       -           -
LGA    E     140      -       -           -
LGA    I     141      -       -           -
LGA    T     142      -       -           -
LGA    I     143      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  143  143    5.0     63    2.74    42.86     29.154     2.220

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.857508 * X  +  -0.455356 * Y  +  -0.239439 * Z  + -23.597879
  Y_new =  -0.189451 * X  +   0.153216 * Y  +  -0.969863 * Z  +  21.042688
  Z_new =   0.478319 * X  +   0.877027 * Y  +   0.045116 * Z  +  58.681274 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.519400   -1.622193  [ DEG:    87.0552    -92.9448 ]
  Theta =  -0.498739   -2.642853  [ DEG:   -28.5757   -151.4243 ]
  Phi   =  -0.217439    2.924154  [ DEG:   -12.4583    167.5417 ]
 
# 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: T0338TS393_1-D1                               
REMARK     2: T0338_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS393_1-D1.T0338_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  143  143   5.0   63   2.74   42.86  29.154
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS393_1-D1
PFRMAT TS
TARGET T0338
MODEL 1
PARENT N/A
ATOM      1  CA  ALA     1     -35.394  37.347  79.099  1.00 25.00           C
ATOM      2  CA  SER     2     -32.496  39.639  78.102  1.00 25.00           C
ATOM      3  CA  SER     3     -31.872  39.582  74.322  1.00 25.00           C
ATOM      4  CA  ARG     4     -29.579  36.563  74.232  1.00 25.00           C
ATOM      5  CA  TRP     5     -28.328  34.007  71.722  1.00 25.00           C
ATOM      6  CA  PHE     6     -26.459  36.723  69.895  1.00 25.00           C
ATOM      7  CA  PHE     7     -22.740  37.442  69.728  1.00 25.00           C
ATOM      8  CA  THR     8     -20.805  34.238  68.800  1.00 25.00           C
ATOM      9  CA  ARG     9     -17.496  35.413  70.339  1.00 25.00           C
ATOM     10  CA  GLU    10     -17.538  34.647  74.090  1.00 25.00           C
ATOM     11  CA  GLN    11     -18.254  30.958  73.355  1.00 25.00           C
ATOM     12  CA  LEU    12     -15.351  30.867  70.859  1.00 25.00           C
ATOM     13  CA  GLU    13     -13.031  32.450  73.462  1.00 25.00           C
ATOM     14  CA  ASN    14     -13.272  29.819  76.149  1.00 25.00           C
ATOM     15  CA  THR    15     -15.354  26.873  74.911  1.00 25.00           C
ATOM     16  CA  PRO    16     -13.989  24.147  77.176  1.00 25.00           C
ATOM     17  CA  SER    17     -13.355  21.015  79.280  1.00 25.00           C
ATOM     18  CA  ARG    18     -12.597  17.514  78.202  1.00 25.00           C
ATOM     19  CA  ARG    19     -10.403  15.303  76.108  1.00 25.00           C
ATOM     20  CA  CYS    20      -7.657  15.451  73.503  1.00 25.00           C
ATOM     21  CA  GLY    21      -4.615  13.573  72.210  1.00 25.00           C
ATOM     22  CA  VAL    22      -2.653  15.334  69.453  1.00 25.00           C
ATOM     23  CA  GLU    23      -1.406  14.095  66.099  1.00 25.00           C
ATOM     24  CA  ALA    24      -1.039  16.709  63.360  1.00 25.00           C
ATOM     25  CA  ASP    25      -0.149  19.806  65.429  1.00 25.00           C
ATOM     26  CA  LYS    26      -0.144  21.954  62.258  1.00 25.00           C
ATOM     27  CA  GLU    27      -3.571  20.554  61.277  1.00 25.00           C
ATOM     28  CA  LEU    28      -4.920  21.336  64.775  1.00 25.00           C
ATOM     29  CA  SER    29      -3.560  24.907  64.528  1.00 25.00           C
ATOM     30  CA  CYS    30      -5.219  25.329  61.102  1.00 25.00           C
ATOM     31  CA  ARG    31      -8.538  24.055  62.525  1.00 25.00           C
ATOM     32  CA  GLN    32      -8.262  26.519  65.443  1.00 25.00           C
ATOM     33  CA  GLN    33      -7.573  29.382  62.993  1.00 25.00           C
ATOM     34  CA  ALA    34     -10.623  28.366  60.911  1.00 25.00           C
ATOM     35  CA  ALA    35     -12.787  28.300  64.071  1.00 25.00           C
ATOM     36  CA  ASN    36     -11.521  31.782  65.041  1.00 25.00           C
ATOM     37  CA  LEU    37     -12.332  33.082  61.531  1.00 25.00           C
ATOM     38  CA  ILE    38     -15.852  31.592  61.766  1.00 25.00           C
ATOM     39  CA  GLN    39     -16.353  33.253  65.181  1.00 25.00           C
ATOM     40  CA  GLU    40     -15.194  36.609  63.746  1.00 25.00           C
ATOM     41  CA  MET    41     -17.630  36.227  60.817  1.00 25.00           C
ATOM     42  CA  GLY    42     -20.478  35.446  63.255  1.00 25.00           C
ATOM     43  CA  GLN    43     -19.587  38.544  65.324  1.00 25.00           C
ATOM     44  CA  ARG    44     -19.584  40.691  62.153  1.00 25.00           C
ATOM     45  CA  LEU    45     -23.253  39.880  61.869  1.00 25.00           C
ATOM     46  CA  ASN    46     -24.772  37.456  64.351  1.00 25.00           C
ATOM     47  CA  VAL    47     -25.168  33.747  63.771  1.00 25.00           C
ATOM     48  CA  SER    48     -26.654  30.575  65.342  1.00 25.00           C
ATOM     49  CA  GLN    49     -29.450  28.000  64.680  1.00 25.00           C
ATOM     50  CA  LEU    50     -28.037  24.460  65.047  1.00 25.00           C
ATOM     51  CA  THR    51     -28.733  23.771  61.346  1.00 25.00           C
ATOM     52  CA  ILE    52     -26.974  27.033  60.382  1.00 25.00           C
ATOM     53  CA  ASN    53     -23.958  26.072  62.538  1.00 25.00           C
ATOM     54  CA  THR    54     -23.834  22.626  60.871  1.00 25.00           C
ATOM     55  CA  ALA    55     -23.962  24.267  57.412  1.00 25.00           C
ATOM     56  CA  ILE    56     -21.110  26.624  58.399  1.00 25.00           C
ATOM     57  CA  VAL    57     -19.041  23.647  59.633  1.00 25.00           C
ATOM     58  CA  TYR    58     -19.681  21.806  56.337  1.00 25.00           C
ATOM     59  CA  MET    59     -18.596  24.906  54.366  1.00 25.00           C
ATOM     60  CA  HIS    60     -15.403  25.154  56.465  1.00 25.00           C
ATOM     61  CA  ARG    61     -14.666  21.451  55.826  1.00 25.00           C
ATOM     62  CA  PHE    62     -15.184  21.971  52.067  1.00 25.00           C
ATOM     63  CA  TYR    63     -12.811  24.976  52.131  1.00 25.00           C
ATOM     64  CA  MET    64     -10.186  22.894  53.985  1.00 25.00           C
ATOM     65  CA  HIS    65     -10.540  20.095  51.396  1.00 25.00           C
ATOM     66  CA  HIS    66      -8.303  22.011  48.927  1.00 25.00           C
ATOM     67  CA  SER    67      -5.818  24.567  50.335  1.00 25.00           C
ATOM     68  CA  PHE    68      -5.046  22.829  53.605  1.00 25.00           C
ATOM     69  CA  THR    69      -1.270  22.562  54.034  1.00 25.00           C
ATOM     70  CA  LYS    70      -0.034  26.184  53.971  1.00 25.00           C
ATOM     71  CA  PHE    71      -3.504  27.684  53.596  1.00 25.00           C
ATOM     72  CA  ASN    72      -3.684  31.364  54.683  1.00 25.00           C
ATOM     73  CA  LYS    73      -7.179  30.419  55.894  1.00 25.00           C
ATOM     74  CA  ASN    74      -8.688  27.987  53.349  1.00 25.00           C
ATOM     75  CA  ILE    75     -11.951  27.878  55.352  1.00 25.00           C
ATOM     76  CA  ILE    76     -12.047  31.705  55.453  1.00 25.00           C
ATOM     77  CA  SER    77     -11.489  31.842  51.666  1.00 25.00           C
ATOM     78  CA  SER    78     -14.324  29.324  51.132  1.00 25.00           C
ATOM     79  CA  THR    79     -16.636  31.418  53.355  1.00 25.00           C
ATOM     80  CA  ALA    80     -15.736  34.566  51.368  1.00 25.00           C
ATOM     81  CA  LEU    81     -16.475  32.736  48.086  1.00 25.00           C
ATOM     82  CA  PHE    82     -19.856  31.581  49.464  1.00 25.00           C
ATOM     83  CA  LEU    83     -20.681  35.169  50.519  1.00 25.00           C
ATOM     84  CA  ALA    84     -19.750  36.435  47.026  1.00 25.00           C
ATOM     85  CA  ALA    85     -21.988  33.764  45.436  1.00 25.00           C
ATOM     86  CA  LYS    86     -24.879  34.782  47.731  1.00 25.00           C
ATOM     87  CA  VAL    87     -24.376  38.457  46.776  1.00 25.00           C
ATOM     88  CA  GLU    88     -24.398  37.519  43.063  1.00 25.00           C
ATOM     89  CA  GLU    89     -21.948  38.346  40.276  1.00 25.00           C
ATOM     90  CA  GLN    90     -20.977  34.722  40.099  1.00 25.00           C
ATOM     91  CA  ALA    91     -23.754  32.250  40.703  1.00 25.00           C
ATOM     92  CA  ARG    92     -24.907  29.913  43.478  1.00 25.00           C
ATOM     93  CA  LYS    93     -23.513  29.156  46.937  1.00 25.00           C
ATOM     94  CA  LEU    94     -21.935  28.345  50.246  1.00 25.00           C
ATOM     95  CA  GLU    95     -23.610  27.263  53.517  1.00 25.00           C
ATOM     96  CA  HIS    96     -21.637  29.926  55.436  1.00 25.00           C
ATOM     97  CA  VAL    97     -22.700  32.583  52.891  1.00 25.00           C
ATOM     98  CA  ILE    98     -26.356  31.497  53.246  1.00 25.00           C
ATOM     99  CA  LYS    99     -26.076  31.717  57.059  1.00 25.00           C
ATOM    100  CA  VAL   100     -24.569  35.227  56.771  1.00 25.00           C
ATOM    101  CA  ALA   101     -27.425  36.288  54.449  1.00 25.00           C
ATOM    102  CA  HIS   102     -29.991  34.910  56.936  1.00 25.00           C
ATOM    103  CA  ALA   103     -28.297  36.827  59.785  1.00 25.00           C
ATOM    104  CA  CYS   104     -28.371  40.039  57.701  1.00 25.00           C
ATOM    105  CA  LEU   105     -32.100  40.493  56.879  1.00 25.00           C
ATOM    106  CA  HIS   106     -34.008  43.688  57.789  1.00 25.00           C
ATOM    107  CA  PRO   107     -35.560  46.913  56.379  1.00 25.00           C
ATOM    108  CA  LEU   108     -38.829  45.025  56.277  1.00 25.00           C
ATOM    109  CA  GLU   109     -39.949  43.836  59.774  1.00 25.00           C
ATOM    110  CA  PRO   110     -43.011  41.738  60.738  1.00 25.00           C
ATOM    111  CA  LEU   111     -42.146  38.224  61.714  1.00 25.00           C
ATOM    112  CA  LEU   112     -43.006  34.500  61.479  1.00 25.00           C
ATOM    113  CA  ASP   113     -43.339  34.790  57.675  1.00 25.00           C
ATOM    114  CA  THR   114     -39.940  36.547  57.487  1.00 25.00           C
ATOM    115  CA  LYS   115     -38.364  33.778  59.614  1.00 25.00           C
ATOM    116  CA  CYS   116     -39.887  31.117  57.319  1.00 25.00           C
ATOM    117  CA  ASP   117     -38.510  32.943  54.247  1.00 25.00           C
ATOM    118  CA  ALA   118     -35.043  33.104  55.866  1.00 25.00           C
ATOM    119  CA  TYR   119     -35.200  29.355  56.632  1.00 25.00           C
ATOM    120  CA  LEU   120     -36.190  28.628  53.005  1.00 25.00           C
ATOM    121  CA  GLN   121     -33.265  30.762  51.755  1.00 25.00           C
ATOM    122  CA  GLN   122     -30.868  28.880  54.073  1.00 25.00           C
ATOM    123  CA  THR   123     -32.201  25.533  52.775  1.00 25.00           C
ATOM    124  CA  ARG   124     -31.712  26.710  49.165  1.00 25.00           C
ATOM    125  CA  GLU   125     -28.125  27.782  49.973  1.00 25.00           C
ATOM    126  CA  LEU   126     -27.437  24.365  51.561  1.00 25.00           C
ATOM    127  CA  VAL   127     -28.840  22.613  48.457  1.00 25.00           C
ATOM    128  CA  ILE   128     -26.617  24.771  46.205  1.00 25.00           C
ATOM    129  CA  LEU   129     -23.564  23.907  48.347  1.00 25.00           C
ATOM    130  CA  GLU   130     -24.423  20.181  48.113  1.00 25.00           C
ATOM    131  CA  THR   131     -24.755  20.473  44.308  1.00 25.00           C
ATOM    132  CA  ILE   132     -21.357  22.229  44.122  1.00 25.00           C
ATOM    133  CA  MET   133     -19.782  19.460  46.247  1.00 25.00           C
ATOM    134  CA  LEU   134     -21.303  16.799  43.953  1.00 25.00           C
ATOM    135  CA  GLN   135     -19.926  18.625  40.881  1.00 25.00           C
ATOM    136  CA  THR   136     -16.459  18.785  42.500  1.00 25.00           C
ATOM    137  CA  LEU   137     -16.617  15.037  43.267  1.00 25.00           C
ATOM    138  CA  GLY   138     -13.992  14.830  40.462  1.00 25.00           C
ATOM    139  CA  PHE   139     -11.605  17.283  42.119  1.00 25.00           C
ATOM    140  CA  GLU   140     -11.917  16.906  45.892  1.00 25.00           C
ATOM    141  CA  ILE   141     -15.068  17.049  47.914  1.00 25.00           C
ATOM    142  CA  THR   142     -14.874  13.273  47.741  1.00 25.00           C
ATOM    143  CA  ILE   143     -18.656  12.707  47.516  1.00 25.00           C
TER
END
