
#######################################################
#                                                     #
#                        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  145 (  145),  selected  145 , name T0380TS168_3
# Molecule2: number of CA atoms  142 ( 1146),  selected  142 , name T0380.pdb
# PARAMETERS: T0380TS168_3.T0380.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      I       2           -
LGA    I       2      D       3           #
LGA    D       3      E       4          4.535
LGA    E       4      K       5          3.602
LGA    K       5      F       6          3.820
LGA    F       6      -       -           -
LGA    L       7      L       7          2.977
LGA    I       8      I       8          3.463
LGA    E       9      E       9          3.059
LGA    S      10      S      10          1.532
LGA    N      11      N      11          1.348
LGA    E      12      E      12          1.590
LGA    L      13      L      13          1.514
LGA    V      14      V      14          1.976
LGA    E      15      E      15          2.337
LGA    S      16      S      16          1.725
LGA    S      17      S      17          2.615
LGA    K      18      K      18          3.313
LGA    I      19      I      19          4.177
LGA    V      20      V      20          2.224
LGA    M      21      M      21          1.837
LGA    V      22      V      22          2.689
LGA    G      23      G      23          2.238
LGA    T      24      T      24          0.866
LGA    N      25      N      25          2.146
LGA    G      26      G      26          2.392
LGA    E      27      E      27          3.196
LGA    N      28      N      28          4.414
LGA    G      29      G      29           -
LGA    Y      30      Y      30           #
LGA    P      31      P      31          5.251
LGA    N      32      N      32          4.945
LGA    I      33      I      33          2.775
LGA    K      34      K      34          0.436
LGA    A      35      A      35          0.641
LGA    M      36      M      36          2.935
LGA    M      37      M      37          4.058
LGA    R      38      R      38          2.675
LGA    L      39      L      39          4.410
LGA    K      40      K      40          1.779
LGA    H      41      H      41          4.098
LGA    D      42      -       -           -
LGA    G      43      D      42          4.445
LGA    L      44      G      43          4.534
LGA    K      45      L      44           #
LGA    -       -      K      45           -
LGA    K      46      K      46          1.896
LGA    F      47      F      47          2.725
LGA    W      48      W      48          3.965
LGA    L      49      L      49          3.624
LGA    S      50      S      50          2.955
LGA    T      51      T      51          3.100
LGA    N      52      N      52          4.262
LGA    T      53      T      53          1.060
LGA    S      54      S      54          3.350
LGA    T      55      T      55           #
LGA    R      56      -       -           -
LGA    M      57      -       -           -
LGA    V      58      -       -           -
LGA    E      59      R      56          3.146
LGA    R      60      M      57          1.782
LGA    L      61      V      58          3.102
LGA    K      62      E      59          2.438
LGA    K      63      R      60          2.897
LGA    N      64      L      61          4.192
LGA    N      65      K      62          3.928
LGA    -       -      K      63           -
LGA    -       -      N      64           -
LGA    K      66      N      65          3.664
LGA    -       -      K      66           -
LGA    I      67      I      67          4.948
LGA    C      68      C      68          4.279
LGA    L      69      L      69          2.934
LGA    Y      70      Y      70          3.869
LGA    F      71      F      71          2.552
LGA    V      72      V      72          2.550
LGA    D      73      D      73          2.007
LGA    D      74      D      74          4.937
LGA    N      75      N      75           #
LGA    K      76      K      76          3.889
LGA    F      77      F      77          3.737
LGA    A      78      A      78          2.127
LGA    G      79      G      79          1.911
LGA    L      80      L      80          2.024
LGA    M      81      M      81          2.206
LGA    L      82      L      82          1.157
LGA    V      83      V      83          5.558
LGA    G      84      G      84          3.734
LGA    T      85      T      85          3.162
LGA    I      86      I      86          2.439
LGA    E      87      E      87          2.901
LGA    I      88      I      88          2.886
LGA    L      89      L      89          2.589
LGA    H      90      H      90          2.867
LGA    D      91      D      91          2.239
LGA    R      92      R      92          2.030
LGA    A      93      A      93          1.862
LGA    S      94      S      94          2.218
LGA    K      95      K      95          2.119
LGA    E      96      E      96          2.039
LGA    M      97      M      97          3.057
LGA    L      98      L      98          3.556
LGA    W      99      W      99          2.675
LGA    T     100      T     100          3.045
LGA    D     101      D     101           #
LGA    G     102      G     102           -
LGA    -       -      C     103           -
LGA    -       -      E     104           -
LGA    -       -      I     105           -
LGA    -       -      Y     106           -
LGA    -       -      Y     107           -
LGA    -       -      P     108           -
LGA    -       -      L     109           -
LGA    -       -      G     110           -
LGA    -       -      I     111           -
LGA    -       -      D     112           -
LGA    -       -      D     113           -
LGA    -       -      P     114           -
LGA    -       -      D     115           -
LGA    -       -      Y     116           -
LGA    -       -      T     117           -
LGA    -       -      A     118           -
LGA    C     103      L     119           #
LGA    E     104      C     120          2.208
LGA    I     105      F     121          2.056
LGA    Y     106      T     122          1.856
LGA    Y     107      A     123          4.718
LGA    P     108      E     124           #
LGA    L     109      -       -           -
LGA    G     110      -       -           -
LGA    I     111      -       -           -
LGA    D     112      -       -           -
LGA    D     113      -       -           -
LGA    P     114      -       -           -
LGA    D     115      -       -           -
LGA    Y     116      -       -           -
LGA    T     117      -       -           -
LGA    A     118      -       -           -
LGA    L     119      -       -           -
LGA    C     120      -       -           -
LGA    F     121      -       -           -
LGA    T     122      -       -           -
LGA    A     123      -       -           -
LGA    E     124      -       -           -
LGA    W     125      -       -           -
LGA    G     126      -       -           -
LGA    N     127      -       -           -
LGA    Y     128      -       -           -
LGA    Y     129      -       -           -
LGA    R     130      -       -           -
LGA    H     131      -       -           -
LGA    L     132      -       -           -
LGA    K     133      -       -           -
LGA    N     134      -       -           -
LGA    I     135      W     125           #
LGA    T     136      G     126          4.180
LGA    -       -      N     127           -
LGA    -       -      Y     128           -
LGA    -       -      Y     129           -
LGA    -       -      R     130           -
LGA    -       -      H     131           -
LGA    -       -      L     132           -
LGA    -       -      K     133           -
LGA    -       -      N     134           -
LGA    -       -      I     135           -
LGA    -       -      T     136           -
LGA    -       -      F     137           -
LGA    F     137      K     138           #
LGA    K     138      I     139          3.239
LGA    I     139      -       -           -
LGA    D     140      D     140          1.957
LGA    E     141      E     141           #
LGA    I     142      I     142           -
LGA    Y     143      Y     143           -
LGA    N     144      -       -           -
LGA    Y     145      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  145  142    5.0     95    3.11    80.00     36.335     2.958

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.401102 * X  +  -0.266157 * Y  +  -0.876515 * Z  + -10.289411
  Y_new =   0.737545 * X  +   0.661318 * Y  +   0.136696 * Z  +  -6.436870
  Z_new =   0.543273 * X  +  -0.701298 * Y  +   0.461558 * Z  +  13.500930 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.988714    2.152879  [ DEG:   -56.6491    123.3509 ]
  Theta =  -0.574330   -2.567262  [ DEG:   -32.9067   -147.0933 ]
  Phi   =   1.072700   -2.068893  [ DEG:    61.4612   -118.5388 ]
 
# 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: T0380TS168_3                                  
REMARK     2: T0380.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0380TS168_3.T0380.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  145  142   5.0   95   3.11   80.00  36.335
REMARK  ---------------------------------------------------------- 
MOLECULE T0380TS168_3
PFRMAT TS
TARGET T0380
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1     -19.863   6.243  -1.793  1.00 25.00           C
ATOM      2  CA  ILE     2     -21.173   6.995   1.719  1.00 25.00           C
ATOM      3  CA  ASP     3     -24.445   8.115   3.357  1.00 25.00           C
ATOM      4  CA  GLU     4     -24.062   5.037   5.605  1.00 25.00           C
ATOM      5  CA  LYS     5     -22.639   7.710   7.949  1.00 25.00           C
ATOM      6  CA  PHE     6     -20.989   4.992  10.085  1.00 25.00           C
ATOM      7  CA  LEU     7     -19.467   3.414   6.945  1.00 25.00           C
ATOM      8  CA  ILE     8     -18.130   6.830   5.845  1.00 25.00           C
ATOM      9  CA  GLU     9     -16.597   7.373   9.313  1.00 25.00           C
ATOM     10  CA  SER    10     -14.951   3.919   9.154  1.00 25.00           C
ATOM     11  CA  ASN    11     -13.537   4.726   5.688  1.00 25.00           C
ATOM     12  CA  GLU    12     -12.158   8.050   6.997  1.00 25.00           C
ATOM     13  CA  LEU    13     -10.533   6.240   9.955  1.00 25.00           C
ATOM     14  CA  VAL    14      -8.960   3.694   7.564  1.00 25.00           C
ATOM     15  CA  GLU    15      -7.613   6.540   5.383  1.00 25.00           C
ATOM     16  CA  SER    16      -5.370   7.622   8.242  1.00 25.00           C
ATOM     17  CA  SER    17      -6.031   7.384  11.970  1.00 25.00           C
ATOM     18  CA  LYS    18      -5.245   3.740  11.414  1.00 25.00           C
ATOM     19  CA  ILE    19      -7.079   0.881  13.099  1.00 25.00           C
ATOM     20  CA  VAL    20      -7.824  -0.385  16.666  1.00 25.00           C
ATOM     21  CA  MET    21      -7.848  -3.565  18.806  1.00 25.00           C
ATOM     22  CA  VAL    22      -8.791  -6.072  21.455  1.00 25.00           C
ATOM     23  CA  GLY    23     -12.156  -7.626  22.356  1.00 25.00           C
ATOM     24  CA  THR    24     -10.314 -10.913  22.818  1.00 25.00           C
ATOM     25  CA  ASN    25     -12.465 -13.819  24.072  1.00 25.00           C
ATOM     26  CA  GLY    26      -9.661 -14.270  26.506  1.00 25.00           C
ATOM     27  CA  GLU    27      -9.151 -17.099  28.921  1.00 25.00           C
ATOM     28  CA  ASN    28      -7.654 -19.179  31.710  1.00 25.00           C
ATOM     29  CA  GLY    29      -4.480 -17.090  31.612  1.00 25.00           C
ATOM     30  CA  TYR    30      -6.111 -13.694  31.011  1.00 25.00           C
ATOM     31  CA  PRO    31      -6.528 -10.811  28.592  1.00 25.00           C
ATOM     32  CA  ASN    32      -3.450  -9.402  26.856  1.00 25.00           C
ATOM     33  CA  ILE    33      -5.255  -6.316  25.663  1.00 25.00           C
ATOM     34  CA  LYS    34      -4.225  -4.206  22.692  1.00 25.00           C
ATOM     35  CA  ALA    35      -2.891  -2.696  19.500  1.00 25.00           C
ATOM     36  CA  MET    36      -3.621  -5.942  17.586  1.00 25.00           C
ATOM     37  CA  MET    37      -4.348  -3.450  14.732  1.00 25.00           C
ATOM     38  CA  ARG    38      -1.971  -1.587  12.355  1.00 25.00           C
ATOM     39  CA  LEU    39      -3.589  -1.177   8.905  1.00 25.00           C
ATOM     40  CA  LYS    40      -4.627  -3.336   5.978  1.00 25.00           C
ATOM     41  CA  HIS    41      -4.839  -1.686   2.550  1.00 25.00           C
ATOM     42  CA  ASP    42      -5.985  -2.070  -1.082  1.00 25.00           C
ATOM     43  CA  GLY    43      -6.835  -5.766  -0.864  1.00 25.00           C
ATOM     44  CA  LEU    44     -10.499  -4.682  -0.464  1.00 25.00           C
ATOM     45  CA  LYS    45     -11.698  -6.788   2.487  1.00 25.00           C
ATOM     46  CA  LYS    46     -10.935  -6.502   6.199  1.00 25.00           C
ATOM     47  CA  PHE    47      -9.034  -4.855   8.989  1.00 25.00           C
ATOM     48  CA  TRP    48      -5.636  -5.541  10.462  1.00 25.00           C
ATOM     49  CA  LEU    49      -5.226  -8.075  13.271  1.00 25.00           C
ATOM     50  CA  SER    50      -1.689  -8.584  11.962  1.00 25.00           C
ATOM     51  CA  THR    51      -0.392  -9.699  15.307  1.00 25.00           C
ATOM     52  CA  ASN    52       3.114 -11.244  14.963  1.00 25.00           C
ATOM     53  CA  THR    53       5.317 -12.920  17.610  1.00 25.00           C
ATOM     54  CA  SER    54       6.412 -11.471  21.001  1.00 25.00           C
ATOM     55  CA  THR    55       4.192  -8.457  21.498  1.00 25.00           C
ATOM     56  CA  ARG    56       1.186  -9.091  23.836  1.00 25.00           C
ATOM     57  CA  MET    57      -1.516  -9.710  21.193  1.00 25.00           C
ATOM     58  CA  VAL    58       0.650 -12.424  19.578  1.00 25.00           C
ATOM     59  CA  GLU    59       1.173 -14.074  22.994  1.00 25.00           C
ATOM     60  CA  ARG    60      -2.602 -13.998  23.636  1.00 25.00           C
ATOM     61  CA  LEU    61      -3.241 -15.586  20.210  1.00 25.00           C
ATOM     62  CA  LYS    62      -0.671 -18.323  20.971  1.00 25.00           C
ATOM     63  CA  LYS    63      -2.351 -18.996  24.346  1.00 25.00           C
ATOM     64  CA  ASN    64      -6.074 -18.291  23.747  1.00 25.00           C
ATOM     65  CA  ASN    65      -7.711 -18.149  20.378  1.00 25.00           C
ATOM     66  CA  LYS    66      -8.127 -14.356  19.891  1.00 25.00           C
ATOM     67  CA  ILE    67      -7.122 -10.905  18.648  1.00 25.00           C
ATOM     68  CA  CYS    68      -8.929  -8.078  16.854  1.00 25.00           C
ATOM     69  CA  LEU    69      -9.570  -5.664  14.062  1.00 25.00           C
ATOM     70  CA  TYR    70     -11.084  -2.234  13.536  1.00 25.00           C
ATOM     71  CA  PHE    71     -12.120   1.416  13.005  1.00 25.00           C
ATOM     72  CA  VAL    72     -10.444   4.029  15.234  1.00 25.00           C
ATOM     73  CA  ASP    73     -11.053   7.831  14.962  1.00 25.00           C
ATOM     74  CA  ASP    74     -10.380  11.581  15.099  1.00 25.00           C
ATOM     75  CA  ASN    75     -11.200  13.701  12.047  1.00 25.00           C
ATOM     76  CA  LYS    76     -14.932  13.420  12.600  1.00 25.00           C
ATOM     77  CA  PHE    77     -16.410  11.598  15.613  1.00 25.00           C
ATOM     78  CA  ALA    78     -17.009   8.056  14.409  1.00 25.00           C
ATOM     79  CA  GLY    79     -16.425   4.287  14.640  1.00 25.00           C
ATOM     80  CA  LEU    80     -17.274   1.032  12.763  1.00 25.00           C
ATOM     81  CA  MET    81     -17.613  -2.506  14.212  1.00 25.00           C
ATOM     82  CA  LEU    82     -15.635  -5.407  12.722  1.00 25.00           C
ATOM     83  CA  VAL    83     -13.994  -7.859  10.259  1.00 25.00           C
ATOM     84  CA  GLY    84     -11.961  -9.982  12.673  1.00 25.00           C
ATOM     85  CA  THR    85      -9.635 -12.965  13.137  1.00 25.00           C
ATOM     86  CA  ILE    86      -7.579 -15.531  14.992  1.00 25.00           C
ATOM     87  CA  GLU    87      -4.140 -16.821  14.174  1.00 25.00           C
ATOM     88  CA  ILE    88      -3.388 -13.865  11.924  1.00 25.00           C
ATOM     89  CA  LEU    89      -2.841 -15.618   8.631  1.00 25.00           C
ATOM     90  CA  HIS    90       0.111 -17.525  10.190  1.00 25.00           C
ATOM     91  CA  ASP    91       2.833 -19.037   7.946  1.00 25.00           C
ATOM     92  CA  ARG    92       5.118 -18.153   5.036  1.00 25.00           C
ATOM     93  CA  ALA    93       3.347 -16.151   2.292  1.00 25.00           C
ATOM     94  CA  SER    94       0.836 -14.813   4.855  1.00 25.00           C
ATOM     95  CA  LYS    95       3.708 -13.797   7.177  1.00 25.00           C
ATOM     96  CA  GLU    96       5.452 -12.006   4.275  1.00 25.00           C
ATOM     97  CA  MET    97       2.203 -10.162   3.429  1.00 25.00           C
ATOM     98  CA  LEU    98       1.818  -9.111   7.092  1.00 25.00           C
ATOM     99  CA  TRP    99       5.430  -7.838   7.133  1.00 25.00           C
ATOM    100  CA  THR   100       4.790  -5.849   3.923  1.00 25.00           C
ATOM    101  CA  ASP   101       1.630  -4.330   5.465  1.00 25.00           C
ATOM    102  CA  GLY   102      -1.176  -6.140   3.584  1.00 25.00           C
ATOM    103  CA  CYS   103      -3.697  -8.736   4.778  1.00 25.00           C
ATOM    104  CA  GLU   104      -4.782 -11.000   7.599  1.00 25.00           C
ATOM    105  CA  ILE   105      -8.034  -9.779   9.268  1.00 25.00           C
ATOM    106  CA  TYR   106     -10.754 -12.216   8.231  1.00 25.00           C
ATOM    107  CA  TYR   107     -13.863 -13.906   9.639  1.00 25.00           C
ATOM    108  CA  PRO   108     -16.636 -16.339   8.522  1.00 25.00           C
ATOM    109  CA  LEU   109     -17.774 -19.766   7.304  1.00 25.00           C
ATOM    110  CA  GLY   110     -20.946 -19.866   9.369  1.00 25.00           C
ATOM    111  CA  ILE   111     -20.437 -21.844  12.562  1.00 25.00           C
ATOM    112  CA  ASP   112     -17.037 -23.423  11.992  1.00 25.00           C
ATOM    113  CA  ASP   113     -14.307 -20.818  12.218  1.00 25.00           C
ATOM    114  CA  PRO   114     -11.410 -18.394  12.745  1.00 25.00           C
ATOM    115  CA  ASP   115     -13.443 -17.388  15.764  1.00 25.00           C
ATOM    116  CA  TYR   116     -14.402 -13.732  15.018  1.00 25.00           C
ATOM    117  CA  THR   117     -12.459 -11.579  17.458  1.00 25.00           C
ATOM    118  CA  ALA   118     -14.121  -8.153  16.946  1.00 25.00           C
ATOM    119  CA  LEU   119     -12.941  -4.642  17.977  1.00 25.00           C
ATOM    120  CA  CYS   120     -12.263  -2.415  20.944  1.00 25.00           C
ATOM    121  CA  PHE   121      -9.516   0.109  21.815  1.00 25.00           C
ATOM    122  CA  THR   122     -10.607   0.518  25.401  1.00 25.00           C
ATOM    123  CA  ALA   123     -14.044  -0.448  26.664  1.00 25.00           C
ATOM    124  CA  GLU   124     -16.520  -1.465  29.389  1.00 25.00           C
ATOM    125  CA  TRP   125     -18.841  -4.415  28.596  1.00 25.00           C
ATOM    126  CA  GLY   126     -18.552  -5.428  24.913  1.00 25.00           C
ATOM    127  CA  ASN   127     -19.132  -1.714  24.305  1.00 25.00           C
ATOM    128  CA  TYR   128     -17.131  -1.235  21.075  1.00 25.00           C
ATOM    129  CA  TYR   129     -18.551  -4.507  19.681  1.00 25.00           C
ATOM    130  CA  ARG   130     -22.101  -3.373  20.567  1.00 25.00           C
ATOM    131  CA  HIS   131     -23.737  -5.234  23.473  1.00 25.00           C
ATOM    132  CA  LEU   132     -24.010  -8.409  21.293  1.00 25.00           C
ATOM    133  CA  LYS   133     -27.492  -7.164  20.336  1.00 25.00           C
ATOM    134  CA  ASN   134     -27.098  -4.462  17.660  1.00 25.00           C
ATOM    135  CA  ILE   135     -24.282  -4.990  15.158  1.00 25.00           C
ATOM    136  CA  THR   136     -21.999  -7.779  13.942  1.00 25.00           C
ATOM    137  CA  PHE   137     -19.010  -9.344  12.251  1.00 25.00           C
ATOM    138  CA  LYS   138     -19.011  -7.212   9.155  1.00 25.00           C
ATOM    139  CA  ILE   139     -19.439  -8.830   5.685  1.00 25.00           C
ATOM    140  CA  ASP   140     -21.377  -9.534   2.539  1.00 25.00           C
ATOM    141  CA  GLU   141     -22.801 -10.594  -0.820  1.00 25.00           C
ATOM    142  CA  ILE   142     -23.369 -10.580  -4.597  1.00 25.00           C
ATOM    143  CA  TYR   143     -26.773  -9.991  -6.019  1.00 25.00           C
ATOM    144  CA  ASN   144     -30.107  -8.395  -6.806  1.00 25.00           C
ATOM    145  CA  TYR   145     -33.156  -6.757  -5.193  1.00 25.00           C
TER
END
