
#######################################################
#                                                     #
#                        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  149 (  149),  selected  149 , name T0341TS393_5-D1
# Molecule2: number of CA atoms  148 ( 1158),  selected  148 , name T0341_D1.pdb
# PARAMETERS: T0341TS393_5-D1.T0341_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L       7      L       7          5.584
LGA    K       8      K       8          4.570
LGA    A       9      A       9          2.911
LGA    V      10      V      10          4.020
LGA    L      11      L      11          4.290
LGA    V      12      V      12          5.155
LGA    D      13      D      13          1.959
LGA    L      14      L      14          2.953
LGA    N      15      N      15          2.976
LGA    G      16      G      16          3.924
LGA    T      17      T      17          3.319
LGA    L      18      L      18          3.172
LGA    H      19      H      19          2.654
LGA    I      20      I      20           #
LGA    E      21      E      21          2.554
LGA    D      22      D      22          4.401
LGA    A      23      A      23          3.318
LGA    A      24      A      24          2.187
LGA    V      25      V      25          2.687
LGA    P      26      P      26          2.774
LGA    G      27      G      27           #
LGA    A      28      A      28           #
LGA    Q      29      Q      29          4.404
LGA    E      30      E      30          4.863
LGA    A      31      A      31          4.468
LGA    L      32      L      32          3.001
LGA    K      33      K      33          2.842
LGA    R      34      R      34          2.768
LGA    L      35      L      35          2.204
LGA    R      36      R      36          1.935
LGA    A      37      A      37          2.598
LGA    T      38      T      38          2.033
LGA    S      39      S      39          3.296
LGA    V      40      V      40          3.332
LGA    M      41      M      41          1.906
LGA    V      42      V      42          1.535
LGA    R      43      R      43          1.456
LGA    F      44      F      44          1.960
LGA    V      45      V      45          3.692
LGA    T      46      T      46          2.687
LGA    N      47      N      47          2.428
LGA    T      48      T      48          2.037
LGA    T      49      T      49          2.870
LGA    K      50      K      50          2.142
LGA    E      51      E      51          0.412
LGA    T      52      T      52          1.561
LGA    K      53      K      53          1.593
LGA    K      54      K      54          2.027
LGA    D      55      D      55          0.887
LGA    L      56      L      56          1.693
LGA    L      57      L      57          2.463
LGA    E      58      E      58          0.846
LGA    R      59      R      59          1.902
LGA    L      60      L      60          3.638
LGA    K      61      K      61          2.910
LGA    K      62      K      62          1.561
LGA    L      63      L      63          2.689
LGA    E      64      E      64          2.724
LGA    F      65      F      65          2.282
LGA    E      66      E      66          1.624
LGA    I      67      I      67          2.760
LGA    S      68      S      68          3.222
LGA    E      69      E      69          2.800
LGA    D      70      D      70          1.848
LGA    E      71      E      71          2.228
LGA    I      72      I      72          3.409
LGA    F      73      F      73          1.765
LGA    T      74      T      74          3.683
LGA    K     179      K     179           #
LGA    P     180      P     180           #
LGA    E     181      E     181           #
LGA    K     182      K     182          3.817
LGA    T     183      T     183          3.903
LGA    F     184      F     184           #
LGA    F     185      F     185          3.190
LGA    L     186      L     186          3.187
LGA    E     187      E     187          4.119
LGA    A     188      A     188          3.670
LGA    L     189      L     189          2.583
LGA    R     190      R     190          3.653
LGA    D     191      D     191          1.707
LGA    A     192      -       -           -
LGA    D     193      -       -           -
LGA    C     194      A     192          3.274
LGA    A     195      D     193          3.014
LGA    P     196      C     194          1.111
LGA    E     197      A     195          2.875
LGA    E     198      P     196          2.365
LGA    A     199      E     198           #
LGA    V     200      A     199          5.159
LGA    -       -      V     200           -
LGA    M     201      M     201          1.760
LGA    I     202      I     202          5.307
LGA    G     203      G     203          1.585
LGA    D     204      D     204          2.739
LGA    D     205      D     205          2.310
LGA    C     206      C     206          3.599
LGA    R     207      R     207          3.719
LGA    D     208      D     208          4.279
LGA    D     209      D     209          2.764
LGA    V     210      V     210          1.953
LGA    D     211      D     211          1.455
LGA    G     212      G     212          0.790
LGA    A     213      A     213          1.535
LGA    Q     214      Q     214          1.594
LGA    N     215      N     215          0.780
LGA    I     216      I     216          2.073
LGA    G     217      G     217          0.853
LGA    M     218      M     218          3.202
LGA    L     219      L     219          2.919
LGA    G     220      G     220          1.195
LGA    I     221      I     221          3.284
LGA    L     222      L     222          0.793
LGA    V     223      V     223          2.246
LGA    K     224      K     224          3.446
LGA    T     225      T     225          3.097
LGA    G     226      G     226          2.763
LGA    K     227      K     227          3.935
LGA    Y     228      Y     228          2.883
LGA    K     229      K     229          2.905
LGA    A     230      A     230          3.189
LGA    A     231      -       -           -
LGA    D     232      A     231          1.766
LGA    E     233      D     232          3.888
LGA    E     234      E     233           #
LGA    K     235      E     234          4.280
LGA    I     236      K     235           #
LGA    -       -      I     236           -
LGA    N     237      N     237          4.592
LGA    P     238      P     238          2.459
LGA    P     239      P     239          4.387
LGA    P     240      P     240          2.903
LGA    Y     241      Y     241          1.514
LGA    L     242      L     242          1.508
LGA    T     243      T     243          4.035
LGA    C     244      C     244          1.338
LGA    E     245      E     245          2.828
LGA    S     246      S     246          1.985
LGA    F     247      F     247          3.005
LGA    P     248      P     248          1.808
LGA    H     249      H     249          2.765
LGA    A     250      A     250          3.345
LGA    V     251      V     251          3.043
LGA    D     252      D     252          2.069
LGA    H     253      H     253          2.126
LGA    I     254      I     254          3.478
LGA    L     255      L     255          3.701
LGA    Q     256      Q     256          1.899
LGA    H     257      H     257          1.925
LGA    L     258      L     258          2.767
LGA    L     259      L     259           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  148    5.0    135    2.94    93.33     51.510     4.442

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.768206 * X  +   0.324732 * Y  +   0.551732 * Z  +  28.985327
  Y_new =  -0.090630 * X  +  -0.797967 * Y  +   0.595848 * Z  +  33.850227
  Z_new =   0.633755 * X  +  -0.507737 * Y  +  -0.583573 * Z  +  91.395424 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.425574    0.716019  [ DEG:  -138.9751     41.0249 ]
  Theta =  -0.686398   -2.455195  [ DEG:   -39.3277   -140.6723 ]
  Phi   =  -0.117433    3.024160  [ DEG:    -6.7284    173.2716 ]
 
# 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: T0341TS393_5-D1                               
REMARK     2: T0341_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS393_5-D1.T0341_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  149  148   5.0  135   2.94   93.33  51.510
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS393_5-D1
PFRMAT TS
TARGET T0341
MODEL 5
PARENT N/A
ATOM      7  CA  LEU     7      28.953  45.067 101.548  1.00 25.00           C
ATOM      8  CA  LYS     8      26.098  42.699 102.613  1.00 25.00           C
ATOM      9  CA  ALA     9      24.965  39.630 100.595  1.00 25.00           C
ATOM     10  CA  VAL    10      26.843  36.714  98.963  1.00 25.00           C
ATOM     11  CA  LEU    11      25.115  35.459  95.841  1.00 25.00           C
ATOM     12  CA  VAL    12      28.087  33.696  94.238  1.00 25.00           C
ATOM     13  CA  ASP    13      30.065  30.846  95.855  1.00 25.00           C
ATOM     14  CA  LEU    14      31.153  27.671  94.074  1.00 25.00           C
ATOM     15  CA  ASN    15      33.719  26.016  91.744  1.00 25.00           C
ATOM     16  CA  GLY    16      35.753  29.185  92.364  1.00 25.00           C
ATOM     17  CA  THR    17      34.521  30.252  95.797  1.00 25.00           C
ATOM     18  CA  LEU    18      34.478  27.059  97.777  1.00 25.00           C
ATOM     19  CA  HIS    19      34.286  23.354  98.423  1.00 25.00           C
ATOM     20  CA  ILE    20      34.196  20.066 100.340  1.00 25.00           C
ATOM     21  CA  GLU    21      37.040  19.071  98.015  1.00 25.00           C
ATOM     22  CA  ASP    22      40.447  19.122  99.594  1.00 25.00           C
ATOM     23  CA  ALA    23      41.094  20.685 103.048  1.00 25.00           C
ATOM     24  CA  ALA    24      38.922  23.541 101.708  1.00 25.00           C
ATOM     25  CA  VAL    25      37.549  25.035 104.976  1.00 25.00           C
ATOM     26  CA  PRO    26      39.508  27.975 106.309  1.00 25.00           C
ATOM     27  CA  GLY    27      38.266  30.659 103.828  1.00 25.00           C
ATOM     28  CA  ALA    28      34.828  30.813 102.149  1.00 25.00           C
ATOM     29  CA  GLN    29      33.507  28.142 104.555  1.00 25.00           C
ATOM     30  CA  GLU    30      34.877  30.115 107.538  1.00 25.00           C
ATOM     31  CA  ALA    31      33.196  33.300 106.235  1.00 25.00           C
ATOM     32  CA  LEU    32      29.883  31.419 105.844  1.00 25.00           C
ATOM     33  CA  LYS    33      30.189  30.087 109.422  1.00 25.00           C
ATOM     34  CA  ARG    34      30.870  33.629 110.709  1.00 25.00           C
ATOM     35  CA  LEU    35      27.800  34.931 108.824  1.00 25.00           C
ATOM     36  CA  ARG    36      25.659  32.136 110.330  1.00 25.00           C
ATOM     37  CA  ALA    37      26.946  33.003 113.831  1.00 25.00           C
ATOM     38  CA  THR    38      26.107  36.741 114.014  1.00 25.00           C
ATOM     39  CA  SER    39      22.536  37.082 112.931  1.00 25.00           C
ATOM     40  CA  VAL    40      22.997  36.546 109.150  1.00 25.00           C
ATOM     41  CA  MET    41      23.355  36.671 105.365  1.00 25.00           C
ATOM     42  CA  VAL    42      24.790  33.832 103.278  1.00 25.00           C
ATOM     43  CA  ARG    43      24.202  32.532  99.814  1.00 25.00           C
ATOM     44  CA  PHE    44      25.433  30.338  96.985  1.00 25.00           C
ATOM     45  CA  VAL    45      25.426  28.744  93.501  1.00 25.00           C
ATOM     46  CA  THR    46      26.382  31.231  90.762  1.00 25.00           C
ATOM     47  CA  ASN    47      29.818  29.668  89.953  1.00 25.00           C
ATOM     48  CA  THR    48      29.050  26.127  88.770  1.00 25.00           C
ATOM     49  CA  THR    49      25.724  26.253  86.925  1.00 25.00           C
ATOM     50  CA  LYS    50      26.406  22.542  86.656  1.00 25.00           C
ATOM     51  CA  GLU    51      24.523  20.857  89.519  1.00 25.00           C
ATOM     52  CA  THR    52      21.533  22.808  90.789  1.00 25.00           C
ATOM     53  CA  LYS    53      20.365  22.279  94.388  1.00 25.00           C
ATOM     54  CA  LYS    54      20.506  18.588  95.400  1.00 25.00           C
ATOM     55  CA  ASP    55      24.330  18.655  95.203  1.00 25.00           C
ATOM     56  CA  LEU    56      24.411  21.806  97.378  1.00 25.00           C
ATOM     57  CA  LEU    57      22.109  20.129  99.938  1.00 25.00           C
ATOM     58  CA  GLU    58      24.379  17.044  99.993  1.00 25.00           C
ATOM     59  CA  ARG    59      27.442  19.277 100.532  1.00 25.00           C
ATOM     60  CA  LEU    60      25.660  21.069 103.409  1.00 25.00           C
ATOM     61  CA  LYS    61      24.765  17.697 104.989  1.00 25.00           C
ATOM     62  CA  LYS    62      28.409  16.559 104.683  1.00 25.00           C
ATOM     63  CA  LEU    63      30.583  19.249 106.378  1.00 25.00           C
ATOM     64  CA  GLU    64      29.358  19.861 109.964  1.00 25.00           C
ATOM     65  CA  PHE    65      29.379  23.505 108.838  1.00 25.00           C
ATOM     66  CA  GLU    66      25.574  23.013 109.053  1.00 25.00           C
ATOM     67  CA  ILE    67      22.631  24.158 106.932  1.00 25.00           C
ATOM     68  CA  SER    68      18.913  24.121 106.093  1.00 25.00           C
ATOM     69  CA  GLU    69      17.598  24.034 102.557  1.00 25.00           C
ATOM     70  CA  ASP    70      16.677  27.582 101.446  1.00 25.00           C
ATOM     71  CA  GLU    71      20.348  28.643 101.703  1.00 25.00           C
ATOM     72  CA  ILE    72      19.588  30.896  98.787  1.00 25.00           C
ATOM     73  CA  PHE    73      20.678  30.150  95.235  1.00 25.00           C
ATOM     74  CA  THR    74      20.515  27.647  92.418  1.00 25.00           C
ATOM    179  CA  LYS   179      25.916  37.285  91.005  1.00 25.00           C
ATOM    180  CA  PRO   180      27.329  40.795  91.399  1.00 25.00           C
ATOM    181  CA  GLU   181      26.212  42.604  88.257  1.00 25.00           C
ATOM    182  CA  LYS   182      22.838  41.059  88.733  1.00 25.00           C
ATOM    183  CA  THR   183      19.105  40.295  89.110  1.00 25.00           C
ATOM    184  CA  PHE   184      19.928  37.132  91.106  1.00 25.00           C
ATOM    185  CA  PHE   185      22.267  39.144  93.375  1.00 25.00           C
ATOM    186  CA  LEU   186      19.523  41.757  93.929  1.00 25.00           C
ATOM    187  CA  GLU   187      17.028  38.986  94.806  1.00 25.00           C
ATOM    188  CA  ALA   188      19.530  37.484  97.286  1.00 25.00           C
ATOM    189  CA  LEU   189      20.047  40.924  98.887  1.00 25.00           C
ATOM    190  CA  ARG   190      16.257  41.381  99.190  1.00 25.00           C
ATOM    191  CA  ASP   191      15.947  37.931 100.821  1.00 25.00           C
ATOM    192  CA  ALA   192      19.207  36.608 102.232  1.00 25.00           C
ATOM    193  CA  ASP   193      18.584  39.090 104.995  1.00 25.00           C
ATOM    194  CA  CYS   194      19.301  42.685 103.766  1.00 25.00           C
ATOM    195  CA  ALA   195      17.488  45.525 102.071  1.00 25.00           C
ATOM    196  CA  PRO   196      19.984  46.161  99.348  1.00 25.00           C
ATOM    197  CA  GLU   197      22.492  48.993  99.943  1.00 25.00           C
ATOM    198  CA  GLU   198      25.245  46.945  98.241  1.00 25.00           C
ATOM    199  CA  ALA   199      24.046  43.497  97.023  1.00 25.00           C
ATOM    200  CA  VAL   200      27.119  41.318  96.395  1.00 25.00           C
ATOM    201  CA  MET   201      30.314  39.181  96.297  1.00 25.00           C
ATOM    202  CA  ILE   202      31.818  36.825  93.780  1.00 25.00           C
ATOM    203  CA  GLY   203      33.884  34.719  96.108  1.00 25.00           C
ATOM    204  CA  ASP   204      36.641  35.435  93.526  1.00 25.00           C
ATOM    205  CA  ASP   205      38.930  33.151  91.507  1.00 25.00           C
ATOM    206  CA  CYS   206      41.228  36.172  91.247  1.00 25.00           C
ATOM    207  CA  ARG   207      40.511  39.139  89.002  1.00 25.00           C
ATOM    208  CA  ASP   208      37.590  38.921  86.535  1.00 25.00           C
ATOM    209  CA  ASP   209      35.228  37.927  89.381  1.00 25.00           C
ATOM    210  CA  VAL   210      36.464  40.887  91.473  1.00 25.00           C
ATOM    211  CA  ASP   211      35.892  43.249  88.513  1.00 25.00           C
ATOM    212  CA  GLY   212      32.349  41.865  88.062  1.00 25.00           C
ATOM    213  CA  ALA   213      31.646  42.381  91.791  1.00 25.00           C
ATOM    214  CA  GLN   214      32.927  45.983  91.560  1.00 25.00           C
ATOM    215  CA  ASN   215      30.679  46.614  88.524  1.00 25.00           C
ATOM    216  CA  ILE   216      27.723  48.816  89.483  1.00 25.00           C
ATOM    217  CA  GLY   217      27.229  49.223  93.189  1.00 25.00           C
ATOM    218  CA  MET   218      27.054  45.486  93.406  1.00 25.00           C
ATOM    219  CA  LEU   219      30.074  45.405  95.706  1.00 25.00           C
ATOM    220  CA  GLY   220      33.384  43.569  96.392  1.00 25.00           C
ATOM    221  CA  ILE   221      35.023  40.155  96.320  1.00 25.00           C
ATOM    222  CA  LEU   222      38.696  39.152  96.531  1.00 25.00           C
ATOM    223  CA  VAL   223      38.257  35.863  98.383  1.00 25.00           C
ATOM    224  CA  LYS   224      41.135  34.795  96.136  1.00 25.00           C
ATOM    225  CA  THR   225      39.955  31.263  96.571  1.00 25.00           C
ATOM    226  CA  GLY   226      43.506  29.923  96.237  1.00 25.00           C
ATOM    227  CA  LYS   227      45.549  31.236  93.250  1.00 25.00           C
ATOM    228  CA  TYR   228      45.926  34.823  94.316  1.00 25.00           C
ATOM    229  CA  LYS   229      49.485  35.624  93.305  1.00 25.00           C
ATOM    230  CA  ALA   230      51.322  37.918  95.714  1.00 25.00           C
ATOM    231  CA  ALA   231      53.316  40.003  93.197  1.00 25.00           C
ATOM    232  CA  ASP   232      50.370  39.912  90.750  1.00 25.00           C
ATOM    233  CA  GLU   233      47.993  41.033  93.536  1.00 25.00           C
ATOM    234  CA  GLU   234      50.357  43.909  94.432  1.00 25.00           C
ATOM    235  CA  LYS   235      48.631  47.007  93.124  1.00 25.00           C
ATOM    236  CA  ILE   236      45.371  48.006  91.601  1.00 25.00           C
ATOM    237  CA  ASN   237      43.407  51.086  90.652  1.00 25.00           C
ATOM    238  CA  PRO   238      40.445  50.203  92.867  1.00 25.00           C
ATOM    239  CA  PRO   239      42.894  49.960  95.798  1.00 25.00           C
ATOM    240  CA  PRO   240      41.301  46.590  96.740  1.00 25.00           C
ATOM    241  CA  TYR   241      38.810  46.224  99.591  1.00 25.00           C
ATOM    242  CA  LEU   242      40.243  42.770 100.305  1.00 25.00           C
ATOM    243  CA  THR   243      39.872  39.313 101.832  1.00 25.00           C
ATOM    244  CA  CYS   244      43.280  37.733 102.554  1.00 25.00           C
ATOM    245  CA  GLU   245      44.598  35.786 105.506  1.00 25.00           C
ATOM    246  CA  SER   246      42.622  32.872 104.095  1.00 25.00           C
ATOM    247  CA  PHE   247      39.655  35.139 104.849  1.00 25.00           C
ATOM    248  CA  PRO   248      36.907  34.727 107.484  1.00 25.00           C
ATOM    249  CA  HIS   249      38.962  36.774 109.984  1.00 25.00           C
ATOM    250  CA  ALA   250      39.463  39.520 107.361  1.00 25.00           C
ATOM    251  CA  VAL   251      35.701  39.564 106.652  1.00 25.00           C
ATOM    252  CA  ASP   252      34.973  39.847 110.402  1.00 25.00           C
ATOM    253  CA  HIS   253      37.455  42.749 110.690  1.00 25.00           C
ATOM    254  CA  ILE   254      35.788  44.503 107.722  1.00 25.00           C
ATOM    255  CA  LEU   255      32.351  44.036 109.345  1.00 25.00           C
ATOM    256  CA  GLN   256      33.679  45.490 112.631  1.00 25.00           C
ATOM    257  CA  HIS   257      35.121  48.495 110.746  1.00 25.00           C
ATOM    258  CA  LEU   258      31.758  49.043 108.997  1.00 25.00           C
ATOM    259  CA  LEU   259      28.693  50.264 110.928  1.00 25.00           C
TER
END
