
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  148 ( 1158),  selected  148 , name T0341_D1.pdb
# PARAMETERS: T0341TS393_3-D1.T0341_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L       7           -
LGA    L       7      K       8           #
LGA    K       8      A       9          2.331
LGA    A       9      V      10          4.045
LGA    V      10      L      11          2.885
LGA    L      11      V      12           #
LGA    V      12      -       -           -
LGA    D      13      -       -           -
LGA    L      14      -       -           -
LGA    N      15      -       -           -
LGA    G      16      D      13           #
LGA    T      17      L      14          2.290
LGA    L      18      N      15          3.141
LGA    -       -      G      16           -
LGA    -       -      T      17           -
LGA    -       -      L      18           -
LGA    H      19      H      19          4.137
LGA    I      20      I      20           #
LGA    E      21      E      21          1.908
LGA    D      22      D      22          4.379
LGA    A      23      A      23          1.387
LGA    A      24      -       -           -
LGA    V      25      A      24          1.403
LGA    P      26      V      25          2.113
LGA    G      27      P      26           #
LGA    A      28      G      27           -
LGA    Q      29      A      28          2.817
LGA    E      30      Q      29          5.171
LGA    -       -      E      30           -
LGA    A      31      A      31           #
LGA    L      32      L      32          2.665
LGA    K      33      K      33          3.446
LGA    R      34      R      34          4.988
LGA    L      35      L      35          3.348
LGA    R      36      R      36          1.617
LGA    A      37      A      37          3.515
LGA    T      38      T      38          1.037
LGA    S      39      S      39          3.854
LGA    V      40      V      40          2.754
LGA    M      41      M      41          2.586
LGA    V      42      V      42          2.689
LGA    R      43      R      43          4.073
LGA    F      44      F      44          3.962
LGA    V      45      V      45          3.271
LGA    T      46      T      46          1.647
LGA    N      47      N      47          1.647
LGA    T      48      T      48          0.872
LGA    T      49      T      49          3.123
LGA    K      50      K      50          1.500
LGA    E      51      E      51          1.930
LGA    T      52      T      52          1.373
LGA    K      53      K      53          4.562
LGA    K      54      K      54          4.684
LGA    D      55      D      55          3.157
LGA    L      56      L      56          2.223
LGA    L      57      L      57          3.267
LGA    E      58      E      58          2.385
LGA    R      59      R      59          2.334
LGA    L      60      L      60          3.498
LGA    K      61      K      61          2.401
LGA    K      62      K      62          2.393
LGA    L      63      L      63          2.368
LGA    E      64      E      64          2.306
LGA    F      65      F      65          3.336
LGA    E      66      E      66          3.618
LGA    I      67      I      67          2.747
LGA    S      68      S      68          3.441
LGA    E      69      E      69          2.413
LGA    D      70      D      70          1.442
LGA    E      71      E      71          2.644
LGA    I      72      I      72          2.027
LGA    F      73      F      73          3.677
LGA    T      74      T      74          2.062
LGA    K     179      K     179          2.452
LGA    P     180      P     180          1.011
LGA    E     181      E     181          4.556
LGA    K     182      K     182          1.709
LGA    T     183      T     183          1.063
LGA    F     184      F     184          2.299
LGA    F     185      F     185          2.450
LGA    L     186      L     186          1.297
LGA    E     187      E     187          1.478
LGA    A     188      A     188          3.038
LGA    L     189      L     189          2.974
LGA    R     190      R     190          1.661
LGA    D     191      D     191          1.659
LGA    A     192      A     192          3.657
LGA    D     193      -       -           -
LGA    C     194      D     193          2.857
LGA    A     195      C     194          1.503
LGA    P     196      A     195          2.435
LGA    E     197      P     196          3.217
LGA    E     198      E     198          2.488
LGA    A     199      A     199          3.091
LGA    V     200      V     200          4.994
LGA    M     201      M     201          4.576
LGA    I     202      I     202          3.439
LGA    G     203      G     203          2.432
LGA    D     204      D     204          2.823
LGA    D     205      D     205          1.624
LGA    C     206      C     206          0.686
LGA    R     207      R     207          2.077
LGA    D     208      D     208          4.617
LGA    D     209      D     209          3.023
LGA    V     210      V     210          2.054
LGA    D     211      D     211          1.875
LGA    G     212      G     212          3.194
LGA    A     213      A     213          3.387
LGA    Q     214      Q     214          3.229
LGA    N     215      N     215          3.534
LGA    I     216      I     216          1.614
LGA    G     217      G     217          1.611
LGA    M     218      M     218          0.993
LGA    L     219      L     219          3.028
LGA    G     220      G     220          2.492
LGA    I     221      I     221          3.311
LGA    L     222      L     222          1.885
LGA    V     223      V     223          3.651
LGA    K     224      K     224          3.644
LGA    T     225      T     225          1.188
LGA    G     226      G     226          1.169
LGA    K     227      K     227          3.023
LGA    Y     228      Y     228          1.172
LGA    K     229      K     229          1.681
LGA    A     230      A     230          4.134
LGA    A     231      -       -           -
LGA    D     232      A     231          4.197
LGA    E     233      D     232          2.580
LGA    E     234      -       -           -
LGA    K     235      E     233           #
LGA    I     236      E     234          2.808
LGA    N     237      K     235           #
LGA    P     238      I     236           #
LGA    P     239      N     237           #
LGA    -       -      P     238           -
LGA    -       -      P     239           -
LGA    P     240      P     240          1.768
LGA    Y     241      Y     241          2.967
LGA    L     242      L     242          1.673
LGA    T     243      T     243          1.941
LGA    C     244      C     244          2.395
LGA    E     245      E     245          3.555
LGA    S     246      S     246          1.589
LGA    F     247      F     247          0.973
LGA    P     248      P     248          2.314
LGA    H     249      H     249          2.814
LGA    A     250      A     250          1.897
LGA    V     251      V     251          1.832
LGA    D     252      D     252          1.772
LGA    H     253      H     253          1.522
LGA    I     254      I     254          2.654
LGA    L     255      L     255          2.923
LGA    Q     256      Q     256          1.077
LGA    H     257      H     257          1.963
LGA    L     258      L     258          2.731
LGA    L     259      L     259          3.710

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  148    5.0    130    2.80    87.69     50.145     4.479

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.940793 * X  +  -0.080793 * Y  +   0.329214 * Z  +  28.449041
  Y_new =  -0.334765 * X  +  -0.374174 * Y  +   0.864827 * Z  +  33.452511
  Z_new =   0.053312 * X  +  -0.923832 * Y  +  -0.379067 * Z  +  91.217400 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.960167    1.181426  [ DEG:  -112.3093     67.6907 ]
  Theta =  -0.053337   -3.088256  [ DEG:    -3.0560   -176.9440 ]
  Phi   =  -0.341861    2.799731  [ DEG:   -19.5872    160.4128 ]
 
# 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_3-D1                               
REMARK     2: T0341_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS393_3-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  130   2.80   87.69  50.145
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS393_3-D1
PFRMAT TS
TARGET T0341
MODEL 3
PARENT N/A
ATOM      7  CA  LEU     7      27.859  44.363 102.514  1.00 25.00           C
ATOM      8  CA  LYS     8      26.103  41.075 102.134  1.00 25.00           C
ATOM      9  CA  ALA     9      23.500  38.858 100.510  1.00 25.00           C
ATOM     10  CA  VAL    10      25.078  37.003  97.553  1.00 25.00           C
ATOM     11  CA  LEU    11      25.233  35.123  94.228  1.00 25.00           C
ATOM     12  CA  VAL    12      25.017  31.386  95.173  1.00 25.00           C
ATOM     13  CA  ASP    13      27.679  28.660  95.310  1.00 25.00           C
ATOM     14  CA  LEU    14      29.219  26.383  92.676  1.00 25.00           C
ATOM     15  CA  ASN    15      32.206  25.985  90.389  1.00 25.00           C
ATOM     16  CA  GLY    16      33.524  29.310  91.727  1.00 25.00           C
ATOM     17  CA  THR    17      32.640  29.775  95.382  1.00 25.00           C
ATOM     18  CA  LEU    18      32.221  26.279  96.865  1.00 25.00           C
ATOM     19  CA  HIS    19      33.518  22.669  97.217  1.00 25.00           C
ATOM     20  CA  ILE    20      33.876  19.255  98.935  1.00 25.00           C
ATOM     21  CA  GLU    21      36.256  18.591  96.030  1.00 25.00           C
ATOM     22  CA  ASP    22      40.045  18.950  96.563  1.00 25.00           C
ATOM     23  CA  ALA    23      39.905  19.386 100.340  1.00 25.00           C
ATOM     24  CA  ALA    24      39.764  23.192 100.215  1.00 25.00           C
ATOM     25  CA  VAL    25      37.349  24.162 102.952  1.00 25.00           C
ATOM     26  CA  PRO    26      38.690  27.158 104.790  1.00 25.00           C
ATOM     27  CA  GLY    27      37.170  29.133 101.934  1.00 25.00           C
ATOM     28  CA  ALA    28      33.529  27.950 101.837  1.00 25.00           C
ATOM     29  CA  GLN    29      33.728  26.952 105.528  1.00 25.00           C
ATOM     30  CA  GLU    30      35.174  30.387 106.405  1.00 25.00           C
ATOM     31  CA  ALA    31      32.347  32.098 104.470  1.00 25.00           C
ATOM     32  CA  LEU    32      29.757  29.974 106.326  1.00 25.00           C
ATOM     33  CA  LYS    33      31.359  30.906 109.677  1.00 25.00           C
ATOM     34  CA  ARG    34      31.267  34.612 108.719  1.00 25.00           C
ATOM     35  CA  LEU    35      27.572  34.298 107.761  1.00 25.00           C
ATOM     36  CA  ARG    36      26.822  32.606 111.114  1.00 25.00           C
ATOM     37  CA  ALA    37      28.652  35.414 112.968  1.00 25.00           C
ATOM     38  CA  THR    38      25.618  37.545 113.658  1.00 25.00           C
ATOM     39  CA  SER    39      22.700  36.330 111.470  1.00 25.00           C
ATOM     40  CA  VAL    40      22.718  36.995 107.689  1.00 25.00           C
ATOM     41  CA  MET    41      22.402  35.348 104.275  1.00 25.00           C
ATOM     42  CA  VAL    42      24.694  33.926 101.554  1.00 25.00           C
ATOM     43  CA  ARG    43      27.357  31.723  99.948  1.00 25.00           C
ATOM     44  CA  PHE    44      29.125  33.675  97.243  1.00 25.00           C
ATOM     45  CA  VAL    45      29.550  33.262  93.435  1.00 25.00           C
ATOM     46  CA  THR    46      28.082  30.926  90.825  1.00 25.00           C
ATOM     47  CA  ASN    47      29.917  29.681  87.729  1.00 25.00           C
ATOM     48  CA  THR    48      27.228  26.921  87.818  1.00 25.00           C
ATOM     49  CA  THR    49      24.194  24.640  87.489  1.00 25.00           C
ATOM     50  CA  LYS    50      26.258  21.533  86.836  1.00 25.00           C
ATOM     51  CA  GLU    51      25.078  19.257  89.627  1.00 25.00           C
ATOM     52  CA  THR    52      22.006  20.466  91.491  1.00 25.00           C
ATOM     53  CA  LYS    53      21.048  19.048  94.864  1.00 25.00           C
ATOM     54  CA  LYS    54      21.966  15.804  96.679  1.00 25.00           C
ATOM     55  CA  ASP    55      25.685  16.681  96.421  1.00 25.00           C
ATOM     56  CA  LEU    56      24.982  20.174  97.829  1.00 25.00           C
ATOM     57  CA  LEU    57      23.015  18.635 100.731  1.00 25.00           C
ATOM     58  CA  GLU    58      25.906  16.230 101.451  1.00 25.00           C
ATOM     59  CA  ARG    59      28.377  19.156 101.431  1.00 25.00           C
ATOM     60  CA  LEU    60      26.134  21.098 103.854  1.00 25.00           C
ATOM     61  CA  LYS    61      25.950  18.049 106.164  1.00 25.00           C
ATOM     62  CA  LYS    62      29.764  17.719 106.074  1.00 25.00           C
ATOM     63  CA  LEU    63      31.281  21.129 105.292  1.00 25.00           C
ATOM     64  CA  GLU    64      30.030  22.208 108.688  1.00 25.00           C
ATOM     65  CA  PHE    65      26.425  23.553 108.489  1.00 25.00           C
ATOM     66  CA  GLU    66      22.907  22.149 108.623  1.00 25.00           C
ATOM     67  CA  ILE    67      21.637  24.495 105.858  1.00 25.00           C
ATOM     68  CA  SER    68      17.799  24.714 105.792  1.00 25.00           C
ATOM     69  CA  GLU    69      18.098  26.553 102.513  1.00 25.00           C
ATOM     70  CA  ASP    70      15.929  28.575 100.090  1.00 25.00           C
ATOM     71  CA  GLU    71      19.054  30.274  98.670  1.00 25.00           C
ATOM     72  CA  ILE    72      21.664  27.470  98.721  1.00 25.00           C
ATOM     73  CA  PHE    73      21.845  27.439  94.954  1.00 25.00           C
ATOM     74  CA  THR    74      23.957  27.728  91.825  1.00 25.00           C
ATOM    179  CA  LYS   179      28.859  35.860  88.966  1.00 25.00           C
ATOM    180  CA  PRO   180      30.558  38.492  86.806  1.00 25.00           C
ATOM    181  CA  GLU   181      28.434  40.987  88.627  1.00 25.00           C
ATOM    182  CA  LYS   182      25.648  43.422  87.719  1.00 25.00           C
ATOM    183  CA  THR   183      22.681  41.019  87.416  1.00 25.00           C
ATOM    184  CA  PHE   184      24.102  38.868  90.247  1.00 25.00           C
ATOM    185  CA  PHE   185      24.530  41.983  92.433  1.00 25.00           C
ATOM    186  CA  LEU   186      20.915  43.018  91.707  1.00 25.00           C
ATOM    187  CA  GLU   187      19.697  39.508  92.640  1.00 25.00           C
ATOM    188  CA  ALA   188      21.689  39.658  95.907  1.00 25.00           C
ATOM    189  CA  LEU   189      20.170  43.081  96.706  1.00 25.00           C
ATOM    190  CA  ARG   190      16.660  41.709  96.027  1.00 25.00           C
ATOM    191  CA  ASP   191      17.353  38.728  98.328  1.00 25.00           C
ATOM    192  CA  ALA   192      18.112  37.465 101.886  1.00 25.00           C
ATOM    193  CA  ASP   193      16.105  40.153 103.585  1.00 25.00           C
ATOM    194  CA  CYS   194      17.967  42.675 101.463  1.00 25.00           C
ATOM    195  CA  ALA   195      18.510  46.404 100.970  1.00 25.00           C
ATOM    196  CA  PRO   196      18.940  48.651  97.962  1.00 25.00           C
ATOM    197  CA  GLU   197      22.647  49.072  97.095  1.00 25.00           C
ATOM    198  CA  GLU   198      23.581  46.424  99.700  1.00 25.00           C
ATOM    199  CA  ALA   199      24.934  43.479  97.844  1.00 25.00           C
ATOM    200  CA  VAL   200      27.383  41.392  95.875  1.00 25.00           C
ATOM    201  CA  MET   201      29.667  39.508  93.486  1.00 25.00           C
ATOM    202  CA  ILE   202      31.435  37.368  96.119  1.00 25.00           C
ATOM    203  CA  GLY   203      34.059  35.616  93.921  1.00 25.00           C
ATOM    204  CA  ASP   204      36.712  33.199  92.661  1.00 25.00           C
ATOM    205  CA  ASP   205      39.705  34.677  90.835  1.00 25.00           C
ATOM    206  CA  CYS   206      39.485  38.469  90.811  1.00 25.00           C
ATOM    207  CA  ARG   207      38.814  40.508  87.646  1.00 25.00           C
ATOM    208  CA  ASP   208      35.273  41.261  86.394  1.00 25.00           C
ATOM    209  CA  ASP   209      33.816  40.082  89.734  1.00 25.00           C
ATOM    210  CA  VAL   210      36.283  42.317  91.628  1.00 25.00           C
ATOM    211  CA  ASP   211      35.303  45.299  89.433  1.00 25.00           C
ATOM    212  CA  GLY   212      31.596  44.607  90.104  1.00 25.00           C
ATOM    213  CA  ALA   213      32.283  44.445  93.867  1.00 25.00           C
ATOM    214  CA  GLN   214      34.171  47.772  93.691  1.00 25.00           C
ATOM    215  CA  ASN   215      31.248  49.357  91.791  1.00 25.00           C
ATOM    216  CA  ILE   216      28.007  48.411  90.105  1.00 25.00           C
ATOM    217  CA  GLY   217      26.821  47.897  93.672  1.00 25.00           C
ATOM    218  CA  MET   218      28.889  46.911  96.715  1.00 25.00           C
ATOM    219  CA  LEU   219      29.851  44.192  99.251  1.00 25.00           C
ATOM    220  CA  GLY   220      32.526  41.634  98.551  1.00 25.00           C
ATOM    221  CA  ILE   221      35.231  40.664  96.068  1.00 25.00           C
ATOM    222  CA  LEU   222      37.947  37.951  96.208  1.00 25.00           C
ATOM    223  CA  VAL   223      37.375  34.449  97.574  1.00 25.00           C
ATOM    224  CA  LYS   224      40.899  34.484  96.080  1.00 25.00           C
ATOM    225  CA  THR   225      41.573  31.236  97.941  1.00 25.00           C
ATOM    226  CA  GLY   226      41.201  29.749  94.446  1.00 25.00           C
ATOM    227  CA  LYS   227      44.717  29.810  93.111  1.00 25.00           C
ATOM    228  CA  TYR   228      44.976  33.583  93.079  1.00 25.00           C
ATOM    229  CA  LYS   229      48.750  34.246  92.961  1.00 25.00           C
ATOM    230  CA  ALA   230      49.810  34.804  89.419  1.00 25.00           C
ATOM    231  CA  ALA   231      53.027  36.766  90.105  1.00 25.00           C
ATOM    232  CA  ASP   232      51.485  39.895  88.523  1.00 25.00           C
ATOM    233  CA  GLU   233      48.353  39.475  90.687  1.00 25.00           C
ATOM    234  CA  GLU   234      50.531  39.120  93.816  1.00 25.00           C
ATOM    235  CA  LYS   235      51.406  42.744  93.099  1.00 25.00           C
ATOM    236  CA  ILE   236      48.055  44.407  92.482  1.00 25.00           C
ATOM    237  CA  ASN   237      47.928  48.100  91.531  1.00 25.00           C
ATOM    238  CA  PRO   238      44.182  47.847  92.053  1.00 25.00           C
ATOM    239  CA  PRO   239      44.499  46.250  95.485  1.00 25.00           C
ATOM    240  CA  PRO   240      40.852  45.329  95.823  1.00 25.00           C
ATOM    241  CA  TYR   241      40.491  46.036  99.517  1.00 25.00           C
ATOM    242  CA  LEU   242      39.723  42.591 100.849  1.00 25.00           C
ATOM    243  CA  THR   243      42.568  40.041 100.784  1.00 25.00           C
ATOM    244  CA  CYS   244      41.590  36.974 102.833  1.00 25.00           C
ATOM    245  CA  GLU   245      42.555  34.670 105.721  1.00 25.00           C
ATOM    246  CA  SER   246      40.812  31.976 103.637  1.00 25.00           C
ATOM    247  CA  PHE   247      37.585  33.673 104.761  1.00 25.00           C
ATOM    248  CA  PRO   248      35.588  33.758 108.029  1.00 25.00           C
ATOM    249  CA  HIS   249      38.398  35.735 109.722  1.00 25.00           C
ATOM    250  CA  ALA   250      38.445  38.214 106.803  1.00 25.00           C
ATOM    251  CA  VAL   251      34.646  38.628 107.061  1.00 25.00           C
ATOM    252  CA  ASP   252      34.945  39.257 110.826  1.00 25.00           C
ATOM    253  CA  HIS   253      37.667  41.877 110.198  1.00 25.00           C
ATOM    254  CA  ILE   254      35.449  43.590 107.588  1.00 25.00           C
ATOM    255  CA  LEU   255      32.525  43.626 110.059  1.00 25.00           C
ATOM    256  CA  GLN   256      34.785  45.152 112.749  1.00 25.00           C
ATOM    257  CA  HIS   257      35.951  47.837 110.280  1.00 25.00           C
ATOM    258  CA  LEU   258      32.313  48.630 109.385  1.00 25.00           C
ATOM    259  CA  LEU   259      30.346  47.619 112.420  1.00 25.00           C
TER
END
