
#######################################################
#                                                     #
#                        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 T0341TS168_1-D1
# Molecule2: number of CA atoms  148 ( 1158),  selected  148 , name T0341_D1.pdb
# PARAMETERS: T0341TS168_1-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          2.482
LGA    K       8      K       8          3.226
LGA    A       9      A       9          3.749
LGA    V      10      V      10           #
LGA    L      11      L      11           #
LGA    V      12      V      12           #
LGA    D      13      D      13          4.308
LGA    L      14      L      14          3.550
LGA    N      15      N      15          2.919
LGA    G      16      G      16          4.334
LGA    T      17      T      17          4.178
LGA    L      18      L      18          3.276
LGA    H      19      H      19          3.118
LGA    I      20      I      20           #
LGA    E      21      E      21          2.501
LGA    D      22      D      22          3.094
LGA    A      23      A      23          2.194
LGA    A      24      A      24          3.989
LGA    V      25      V      25          1.728
LGA    P      26      P      26          2.283
LGA    G      27      G      27          4.513
LGA    A      28      A      28          3.448
LGA    Q      29      Q      29          2.371
LGA    E      30      E      30          4.051
LGA    A      31      A      31          4.194
LGA    L      32      L      32          2.196
LGA    K      33      K      33          2.416
LGA    R      34      R      34          3.663
LGA    L      35      L      35          3.003
LGA    R      36      R      36          1.110
LGA    A      37      A      37          1.831
LGA    T      38      T      38          1.793
LGA    S      39      S      39          3.945
LGA    V      40      V      40          3.229
LGA    M      41      M      41          2.298
LGA    V      42      V      42          1.770
LGA    R      43      R      43          2.365
LGA    F      44      F      44          3.718
LGA    V      45      V      45          3.578
LGA    T      46      T      46          2.057
LGA    N      47      N      47          2.835
LGA    T      48      T      48          2.768
LGA    T      49      T      49          3.098
LGA    K      50      K      50          2.593
LGA    E      51      E      51          1.086
LGA    T      52      T      52          1.040
LGA    K      53      K      53          2.220
LGA    K      54      K      54          2.481
LGA    D      55      D      55          2.994
LGA    L      56      L      56          2.739
LGA    L      57      L      57          2.436
LGA    E      58      E      58          2.521
LGA    R      59      R      59          3.822
LGA    L      60      L      60          4.331
LGA    K      61      K      61          3.323
LGA    K      62      K      62          3.915
LGA    L      63      L      63          3.148
LGA    E      64      E      64          3.405
LGA    F      65      F      65          4.393
LGA    E      66      E      66          3.566
LGA    I      67      I      67          2.117
LGA    S      68      S      68          3.405
LGA    E      69      E      69          4.023
LGA    D      70      D      70          2.660
LGA    E      71      E      71          2.944
LGA    I      72      I      72          2.629
LGA    F      73      F      73          2.410
LGA    T      74      T      74          2.078
LGA    K     179      K     179          4.590
LGA    P     180      P     180          1.529
LGA    E     181      E     181          3.430
LGA    K     182      K     182          1.119
LGA    T     183      T     183          1.514
LGA    F     184      F     184          1.647
LGA    F     185      F     185          1.368
LGA    L     186      L     186          1.812
LGA    E     187      E     187          2.159
LGA    A     188      A     188          2.446
LGA    L     189      L     189          2.827
LGA    R     190      -       -           -
LGA    D     191      R     190          1.205
LGA    A     192      D     191          1.090
LGA    D     193      -       -           -
LGA    C     194      A     192          0.966
LGA    A     195      D     193          3.494
LGA    P     196      C     194          2.411
LGA    E     197      A     195          1.634
LGA    E     198      P     196          3.182
LGA    -       -      E     198           -
LGA    A     199      A     199          3.324
LGA    V     200      V     200          3.289
LGA    M     201      M     201          2.547
LGA    I     202      I     202          1.769
LGA    G     203      G     203          0.941
LGA    D     204      D     204          4.504
LGA    D     205      D     205          1.136
LGA    C     206      C     206          1.504
LGA    R     207      R     207          1.934
LGA    D     208      D     208          2.000
LGA    D     209      D     209          1.733
LGA    V     210      V     210          2.272
LGA    D     211      D     211          1.845
LGA    G     212      G     212          2.230
LGA    A     213      A     213          2.821
LGA    Q     214      Q     214          2.251
LGA    N     215      N     215          2.256
LGA    I     216      I     216          2.344
LGA    G     217      G     217          2.183
LGA    M     218      M     218          1.887
LGA    L     219      L     219          1.890
LGA    G     220      G     220          2.018
LGA    I     221      I     221          3.121
LGA    L     222      L     222          1.447
LGA    V     223      V     223          2.270
LGA    K     224      K     224          4.776
LGA    T     225      T     225          3.210
LGA    G     226      G     226          2.595
LGA    K     227      K     227          3.400
LGA    Y     228      Y     228          2.492
LGA    K     229      K     229          2.477
LGA    A     230      A     230          2.759
LGA    A     231      A     231          4.858
LGA    D     232      D     232          4.877
LGA    E     233      E     233          4.563
LGA    E     234      E     234          4.320
LGA    K     235      K     235          5.433
LGA    I     236      I     236           #
LGA    N     237      -       -           -
LGA    P     238      N     237           #
LGA    P     239      P     238          5.646
LGA    P     240      P     239          2.196
LGA    Y     241      P     240          3.818
LGA    L     242      Y     241          2.928
LGA    T     243      L     242          2.139
LGA    C     244      T     243           #
LGA    E     245      C     244          4.935
LGA    S     246      E     245          3.689
LGA    F     247      S     246          4.492
LGA    P     248      F     247          4.830
LGA    H     249      P     248          4.165
LGA    A     250      H     249          2.019
LGA    V     251      A     250          2.455
LGA    D     252      V     251          3.894
LGA    H     253      D     252          2.405
LGA    I     254      H     253          2.662
LGA    L     255      I     254          4.799
LGA    Q     256      L     255          4.865
LGA    H     257      Q     256          4.600
LGA    -       -      H     257           -
LGA    L     258      L     258          5.349
LGA    L     259      L     259          3.224

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  148    5.0    139    3.11    83.45     50.406     4.337

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.849736 * X  +  -0.039622 * Y  +   0.525717 * Z  +  28.229338
  Y_new =  -0.527172 * X  +  -0.075598 * Y  +   0.846389 * Z  +  33.451248
  Z_new =   0.006208 * X  +  -0.996351 * Y  +  -0.085125 * Z  +  91.285774 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.656026    1.485566  [ DEG:   -94.8833     85.1167 ]
  Theta =  -0.006208   -3.135385  [ DEG:    -0.3557   -179.6443 ]
  Phi   =  -0.555281    2.586312  [ DEG:   -31.8152    148.1848 ]
 
# 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: T0341TS168_1-D1                               
REMARK     2: T0341_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS168_1-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  139   3.11   83.45  50.406
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS168_1-D1
PFRMAT TS
TARGET T0341
MODEL 1
PARENT N/A
ATOM      7  CA  LEU     7      24.943  44.612 103.729  1.00 25.00           C
ATOM      8  CA  LYS     8      23.174  41.292 103.123  1.00 25.00           C
ATOM      9  CA  ALA     9      22.291  38.505 100.651  1.00 25.00           C
ATOM     10  CA  VAL    10      23.675  36.547  97.706  1.00 25.00           C
ATOM     11  CA  LEU    11      24.002  33.835  95.006  1.00 25.00           C
ATOM     12  CA  VAL    12      25.187  30.286  95.765  1.00 25.00           C
ATOM     13  CA  ASP    13      28.683  28.837  96.119  1.00 25.00           C
ATOM     14  CA  LEU    14      30.601  26.148  94.330  1.00 25.00           C
ATOM     15  CA  ASN    15      33.387  26.380  91.807  1.00 25.00           C
ATOM     16  CA  GLY    16      35.721  29.383  91.956  1.00 25.00           C
ATOM     17  CA  THR    17      34.134  30.867  95.079  1.00 25.00           C
ATOM     18  CA  LEU    18      33.617  28.297  97.770  1.00 25.00           C
ATOM     19  CA  HIS    19      33.252  24.632  98.877  1.00 25.00           C
ATOM     20  CA  ILE    20      32.917  21.077 100.262  1.00 25.00           C
ATOM     21  CA  GLU    21      35.895  20.027  98.065  1.00 25.00           C
ATOM     22  CA  ASP    22      39.325  18.654  98.845  1.00 25.00           C
ATOM     23  CA  ALA    23      40.459  20.771 101.866  1.00 25.00           C
ATOM     24  CA  ALA    24      39.825  24.174 100.214  1.00 25.00           C
ATOM     25  CA  VAL    25      37.753  25.273 103.137  1.00 25.00           C
ATOM     26  CA  PRO    26      38.884  26.548 106.585  1.00 25.00           C
ATOM     27  CA  GLY    27      38.098  30.170 105.738  1.00 25.00           C
ATOM     28  CA  ALA    28      34.763  29.626 103.935  1.00 25.00           C
ATOM     29  CA  GLN    29      33.293  28.024 107.087  1.00 25.00           C
ATOM     30  CA  GLU    30      34.498  30.991 109.188  1.00 25.00           C
ATOM     31  CA  ALA    31      32.908  33.429 106.699  1.00 25.00           C
ATOM     32  CA  LEU    32      29.615  31.481 106.856  1.00 25.00           C
ATOM     33  CA  LYS    33      29.707  31.585 110.683  1.00 25.00           C
ATOM     34  CA  ARG    34      30.328  35.363 110.590  1.00 25.00           C
ATOM     35  CA  LEU    35      27.379  35.813 108.188  1.00 25.00           C
ATOM     36  CA  ARG    36      25.142  33.745 110.508  1.00 25.00           C
ATOM     37  CA  ALA    37      26.227  35.880 113.498  1.00 25.00           C
ATOM     38  CA  THR    38      23.332  38.249 112.803  1.00 25.00           C
ATOM     39  CA  SER    39      20.102  36.753 111.633  1.00 25.00           C
ATOM     40  CA  VAL    40      21.610  36.872 108.163  1.00 25.00           C
ATOM     41  CA  MET    41      22.244  35.490 104.647  1.00 25.00           C
ATOM     42  CA  VAL    42      25.681  34.162 103.631  1.00 25.00           C
ATOM     43  CA  ARG    43      25.991  32.765 100.045  1.00 25.00           C
ATOM     44  CA  PHE    44      28.547  34.046  97.523  1.00 25.00           C
ATOM     45  CA  VAL    45      29.598  34.056  93.865  1.00 25.00           C
ATOM     46  CA  THR    46      29.858  30.992  91.662  1.00 25.00           C
ATOM     47  CA  ASN    47      26.823  29.077  90.354  1.00 25.00           C
ATOM     48  CA  THR    48      28.683  25.793  90.021  1.00 25.00           C
ATOM     49  CA  THR    49      25.768  24.919  87.710  1.00 25.00           C
ATOM     50  CA  LYS    50      27.091  21.302  87.703  1.00 25.00           C
ATOM     51  CA  GLU    51      24.658  20.180  90.453  1.00 25.00           C
ATOM     52  CA  THR    52      21.905  22.319  92.000  1.00 25.00           C
ATOM     53  CA  LYS    53      21.399  21.548  95.730  1.00 25.00           C
ATOM     54  CA  LYS    54      21.449  18.198  97.586  1.00 25.00           C
ATOM     55  CA  ASP    55      25.279  18.190  97.518  1.00 25.00           C
ATOM     56  CA  LEU    56      25.335  21.763  98.893  1.00 25.00           C
ATOM     57  CA  LEU    57      22.923  20.752 101.690  1.00 25.00           C
ATOM     58  CA  GLU    58      25.140  17.750 102.550  1.00 25.00           C
ATOM     59  CA  ARG    59      28.219  20.026 102.662  1.00 25.00           C
ATOM     60  CA  LEU    60      26.368  22.458 104.970  1.00 25.00           C
ATOM     61  CA  LYS    61      25.369  19.559 107.264  1.00 25.00           C
ATOM     62  CA  LYS    62      29.004  18.355 107.366  1.00 25.00           C
ATOM     63  CA  LEU    63      31.294  21.282 106.555  1.00 25.00           C
ATOM     64  CA  GLU    64      29.762  22.857 109.669  1.00 25.00           C
ATOM     65  CA  PHE    65      26.196  24.094 109.762  1.00 25.00           C
ATOM     66  CA  GLU    66      22.560  23.278 109.245  1.00 25.00           C
ATOM     67  CA  ILE    67      22.118  25.219 106.020  1.00 25.00           C
ATOM     68  CA  SER    68      18.510  24.124 106.057  1.00 25.00           C
ATOM     69  CA  GLU    69      16.106  24.099 103.057  1.00 25.00           C
ATOM     70  CA  ASP    70      15.346  27.268 101.045  1.00 25.00           C
ATOM     71  CA  GLU    71      19.066  28.178 101.025  1.00 25.00           C
ATOM     72  CA  ILE    72      20.505  27.011  97.663  1.00 25.00           C
ATOM     73  CA  PHE    73      20.125  30.294  95.781  1.00 25.00           C
ATOM     74  CA  THR    74      21.854  29.303  92.507  1.00 25.00           C
ATOM    179  CA  LYS   179      28.257  37.660  90.642  1.00 25.00           C
ATOM    180  CA  PRO   180      29.781  38.444  87.288  1.00 25.00           C
ATOM    181  CA  GLU   181      29.380  41.801  85.413  1.00 25.00           C
ATOM    182  CA  LYS   182      26.160  42.893  87.047  1.00 25.00           C
ATOM    183  CA  THR   183      22.488  42.106  86.288  1.00 25.00           C
ATOM    184  CA  PHE   184      22.676  38.983  88.495  1.00 25.00           C
ATOM    185  CA  PHE   185      24.214  41.048  91.331  1.00 25.00           C
ATOM    186  CA  LEU   186      21.425  43.650  90.981  1.00 25.00           C
ATOM    187  CA  GLU   187      18.788  40.876  91.111  1.00 25.00           C
ATOM    188  CA  ALA   188      20.425  39.433  94.259  1.00 25.00           C
ATOM    189  CA  LEU   189      20.426  42.903  95.878  1.00 25.00           C
ATOM    190  CA  ARG   190      16.721  43.336  95.011  1.00 25.00           C
ATOM    191  CA  ASP   191      15.938  39.911  96.536  1.00 25.00           C
ATOM    192  CA  ALA   192      15.967  37.491  99.398  1.00 25.00           C
ATOM    193  CA  ASP   193      14.453  40.405 101.405  1.00 25.00           C
ATOM    194  CA  CYS   194      18.011  41.709 101.882  1.00 25.00           C
ATOM    195  CA  ALA   195      18.764  45.410 101.160  1.00 25.00           C
ATOM    196  CA  PRO   196      18.639  47.314  97.920  1.00 25.00           C
ATOM    197  CA  GLU   197      21.967  49.126  98.474  1.00 25.00           C
ATOM    198  CA  GLU   198      23.744  45.768  98.952  1.00 25.00           C
ATOM    199  CA  ALA   199      24.752  42.195  98.373  1.00 25.00           C
ATOM    200  CA  VAL   200      28.182  40.487  98.056  1.00 25.00           C
ATOM    201  CA  MET   201      30.498  38.780  95.555  1.00 25.00           C
ATOM    202  CA  ILE   202      32.928  36.452  97.328  1.00 25.00           C
ATOM    203  CA  GLY   203      35.724  35.238  95.079  1.00 25.00           C
ATOM    204  CA  ASP   204      35.603  34.523  91.339  1.00 25.00           C
ATOM    205  CA  ASP   205      39.324  35.061  91.217  1.00 25.00           C
ATOM    206  CA  CYS   206      40.234  38.665  91.699  1.00 25.00           C
ATOM    207  CA  ARG   207      38.675  39.949  88.484  1.00 25.00           C
ATOM    208  CA  ASP   208      35.047  38.816  88.015  1.00 25.00           C
ATOM    209  CA  ASP   209      34.370  39.353  91.746  1.00 25.00           C
ATOM    210  CA  VAL   210      35.897  42.858  91.544  1.00 25.00           C
ATOM    211  CA  ASP   211      33.707  43.663  88.507  1.00 25.00           C
ATOM    212  CA  GLY   212      30.604  42.436  90.387  1.00 25.00           C
ATOM    213  CA  ALA   213      31.535  44.617  93.394  1.00 25.00           C
ATOM    214  CA  GLN   214      31.978  47.646  91.092  1.00 25.00           C
ATOM    215  CA  ASN   215      28.558  46.972  89.508  1.00 25.00           C
ATOM    216  CA  ILE   216      25.036  47.714  90.869  1.00 25.00           C
ATOM    217  CA  GLY   217      26.066  48.316  94.462  1.00 25.00           C
ATOM    218  CA  MET   218      27.612  44.911  95.209  1.00 25.00           C
ATOM    219  CA  LEU   219      30.236  45.122  97.951  1.00 25.00           C
ATOM    220  CA  GLY   220      34.017  44.709  97.850  1.00 25.00           C
ATOM    221  CA  ILE   221      34.794  41.275  96.561  1.00 25.00           C
ATOM    222  CA  LEU   222      38.164  39.523  96.276  1.00 25.00           C
ATOM    223  CA  VAL   223      40.390  36.408  96.679  1.00 25.00           C
ATOM    224  CA  LYS   224      40.058  32.770  95.788  1.00 25.00           C
ATOM    225  CA  THR   225      40.245  29.095  96.669  1.00 25.00           C
ATOM    226  CA  GLY   226      43.784  29.446  95.329  1.00 25.00           C
ATOM    227  CA  LYS   227      45.253  31.290  92.375  1.00 25.00           C
ATOM    228  CA  TYR   228      45.669  34.985  92.725  1.00 25.00           C
ATOM    229  CA  LYS   229      49.407  35.461  92.521  1.00 25.00           C
ATOM    230  CA  ALA   230      52.460  37.726  92.389  1.00 25.00           C
ATOM    231  CA  ALA   231      53.199  39.798  89.253  1.00 25.00           C
ATOM    232  CA  ASP   232      49.681  39.080  87.920  1.00 25.00           C
ATOM    233  CA  GLU   233      48.166  40.145  91.272  1.00 25.00           C
ATOM    234  CA  GLU   234      50.212  43.383  91.196  1.00 25.00           C
ATOM    235  CA  LYS   235      49.173  45.841  88.453  1.00 25.00           C
ATOM    236  CA  ILE   236      46.154  48.205  88.749  1.00 25.00           C
ATOM    237  CA  ASN   237      47.477  49.270  92.151  1.00 25.00           C
ATOM    238  CA  PRO   238      45.537  46.336  93.605  1.00 25.00           C
ATOM    239  CA  PRO   239      42.649  48.450  94.875  1.00 25.00           C
ATOM    240  CA  PRO   240      38.956  47.752  94.164  1.00 25.00           C
ATOM    241  CA  TYR   241      38.615  48.045  97.911  1.00 25.00           C
ATOM    242  CA  LEU   242      39.369  44.354  98.345  1.00 25.00           C
ATOM    243  CA  THR   243      41.392  42.822 101.186  1.00 25.00           C
ATOM    244  CA  CYS   244      40.554  41.564 104.717  1.00 25.00           C
ATOM    245  CA  GLU   245      44.007  41.851 106.194  1.00 25.00           C
ATOM    246  CA  SER   246      44.802  38.935 103.894  1.00 25.00           C
ATOM    247  CA  PHE   247      45.031  35.115 104.216  1.00 25.00           C
ATOM    248  CA  PRO   248      42.165  32.575 104.256  1.00 25.00           C
ATOM    249  CA  HIS   249      41.940  32.852 108.069  1.00 25.00           C
ATOM    250  CA  ALA   250      41.838  36.671 107.810  1.00 25.00           C
ATOM    251  CA  VAL   251      39.052  36.444 105.192  1.00 25.00           C
ATOM    252  CA  ASP   252      37.075  34.080 107.467  1.00 25.00           C
ATOM    253  CA  HIS   253      37.503  36.504 110.400  1.00 25.00           C
ATOM    254  CA  ILE   254      36.284  39.403 108.213  1.00 25.00           C
ATOM    255  CA  LEU   255      33.234  37.347 107.146  1.00 25.00           C
ATOM    256  CA  GLN   256      32.465  36.539 110.809  1.00 25.00           C
ATOM    257  CA  HIS   257      32.736  40.252 111.711  1.00 25.00           C
ATOM    258  CA  LEU   258      30.364  41.146 108.840  1.00 25.00           C
ATOM    259  CA  LEU   259      27.662  41.852 111.482  1.00 25.00           C
TER
END
