
#######################################################
#                                                     #
#                        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  136 (  136),  selected  136 , name T0339TS393_5-D1
# Molecule2: number of CA atoms  136 ( 1077),  selected  136 , name T0339_D1.pdb
# PARAMETERS: T0339TS393_5-D1.T0339_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E       1      E       1           -
LGA    R       2      R       2           -
LGA    K       3      K       3           -
LGA    V       4      V       4           -
LGA    Y       5      Y       5           -
LGA    -       -      M       6           -
LGA    M       6      D       7           #
LGA    D       7      Y       8           -
LGA    Y       8      E     289           -
LGA    -       -      A     290           -
LGA    -       -      Y     291           -
LGA    -       -      E     292           -
LGA    -       -      A     293           -
LGA    E     289      H     294          3.807
LGA    A     290      M     295          3.330
LGA    Y     291      -       -           -
LGA    E     292      R     296          4.147
LGA    A     293      D     297          3.542
LGA    H     294      V     298          3.592
LGA    M     295      R     299          3.276
LGA    R     296      D     300          2.477
LGA    D     297      Y     301          2.511
LGA    V     298      L     302          2.901
LGA    R     299      E     303          2.325
LGA    D     300      E     304          1.968
LGA    Y     301      R     305          2.273
LGA    L     302      L     306          3.057
LGA    E     303      E     307          2.788
LGA    E     304      A     308          2.407
LGA    R     305      E     309          3.200
LGA    -       -      F     310           -
LGA    L     306      G     311          2.768
LGA    E     307      Q     312           -
LGA    A     308      -       -           -
LGA    E     309      -       -           -
LGA    F     310      -       -           -
LGA    G     311      -       -           -
LGA    Q     312      K     313           #
LGA    K     313      R     314          3.275
LGA    R     314      I     315          1.373
LGA    I     315      H     316          3.246
LGA    H     316      L     317          3.117
LGA    L     317      N     318          1.806
LGA    N     318      S     319          3.697
LGA    S     319      Q     320          1.572
LGA    Q     320      F     321           #
LGA    F     321      -       -           -
LGA    P     322      P     322          2.947
LGA    G     323      -       -           -
LGA    T     324      -       -           -
LGA    Q     325      G     323          4.796
LGA    R     326      T     324           #
LGA    -       -      Q     325           -
LGA    L     327      R     326          1.630
LGA    -       -      L     327           -
LGA    P     328      P     328          3.400
LGA    N     329      N     329          3.106
LGA    T     330      T     330          2.865
LGA    C     331      C     331          2.651
LGA    N     332      N     332          2.761
LGA    F     333      F     333           #
LGA    S     334      S     334          5.560
LGA    I     335      I     335          5.118
LGA    -       -      R     336           -
LGA    -       -      G     337           -
LGA    R     336      P     338          4.237
LGA    G     337      R     339          4.395
LGA    P     338      L     340          2.381
LGA    R     339      Q     341          2.472
LGA    L     340      G     342          1.827
LGA    Q     341      H     343          2.776
LGA    G     342      V     344          2.750
LGA    H     343      V     345          1.627
LGA    V     344      L     346          1.573
LGA    V     345      A     347          0.969
LGA    L     346      Q     348          2.453
LGA    A     347      C     349          3.375
LGA    Q     348      -       -           -
LGA    C     349      -       -           -
LGA    R     350      R     350          1.574
LGA    V     351      V     351          3.029
LGA    L     352      L     352          2.708
LGA    M     353      M     353          1.722
LGA    A     354      A     354          1.835
LGA    S     355      S     355          1.731
LGA    V     356      V     356          5.023
LGA    G     357      G     357           #
LGA    A     358      A     358          4.347
LGA    A     359      A     359          5.943
LGA    C     360      -       -           -
LGA    H     361      -       -           -
LGA    S     362      -       -           -
LGA    D     363      -       -           -
LGA    H     364      -       -           -
LGA    G     365      C     360          5.219
LGA    -       -      H     361           -
LGA    -       -      S     362           -
LGA    -       -      D     363           -
LGA    -       -      H     364           -
LGA    -       -      G     365           -
LGA    -       -      D     366           -
LGA    -       -      Q     367           -
LGA    D     366      P     368          6.072
LGA    Q     367      S     369          1.614
LGA    P     368      P     370          2.850
LGA    -       -      V     371           -
LGA    S     369      L     372           #
LGA    P     370      L     373          4.649
LGA    V     371      S     374          2.025
LGA    L     372      Y     375          4.208
LGA    L     373      G     376          2.911
LGA    S     374      -       -           -
LGA    Y     375      -       -           -
LGA    G     376      V     377          4.163
LGA    V     377      P     378          1.479
LGA    P     378      F     379          2.083
LGA    F     379      -       -           -
LGA    D     380      -       -           -
LGA    V     381      D     380          3.073
LGA    A     382      V     381           #
LGA    R     383      A     382          2.053
LGA    -       -      R     383           -
LGA    N     384      N     384          4.860
LGA    A     385      A     385          3.042
LGA    L     386      L     386          2.371
LGA    R     387      R     387          2.132
LGA    L     388      L     388          1.137
LGA    S     389      S     389          1.214
LGA    V     390      V     390          3.244
LGA    G     391      G     391          3.867
LGA    R     392      R     392           #
LGA    S     393      S     393          1.303
LGA    T     394      T     394          1.504
LGA    T     395      T     395          0.311
LGA    R     396      R     396          1.844
LGA    A     397      A     397          2.228
LGA    E     398      E     398          3.050
LGA    V     399      V     399          2.085
LGA    D     400      D     400          1.483
LGA    L     401      L     401          2.635
LGA    V     402      V     402          2.338
LGA    V     403      V     403          1.502
LGA    Q     404      Q     404          2.027
LGA    D     405      D     405          2.428
LGA    L     406      L     406          1.660
LGA    K     407      K     407          1.728
LGA    Q     408      Q     408          2.563
LGA    A     409      A     409          2.008
LGA    V     410      V     410          1.622
LGA    A     411      A     411          2.463
LGA    Q     412      Q     412          2.749
LGA    L     413      L     413          1.841
LGA    E     414      E     414          1.970
LGA    D     415      D     415          2.444
LGA    Q     416      Q     416          2.737

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  136  136    5.0    100    2.97    52.00     43.311     3.255

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.592790 * X  +  -0.526118 * Y  +   0.609754 * Z  +  -9.384529
  Y_new =  -0.601844 * X  +  -0.213702 * Y  +  -0.769490 * Z  + -13.869004
  Z_new =   0.535148 * X  +  -0.823123 * Y  +  -0.189961 * Z  +  12.470945 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.797606    1.343987  [ DEG:  -102.9952     77.0048 ]
  Theta =  -0.564683   -2.576909  [ DEG:   -32.3540   -147.6460 ]
  Phi   =  -2.348616    0.792977  [ DEG:  -134.5658     45.4342 ]
 
# 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: T0339TS393_5-D1                               
REMARK     2: T0339_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0339TS393_5-D1.T0339_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  136  136   5.0  100   2.97   52.00  43.311
REMARK  ---------------------------------------------------------- 
MOLECULE T0339TS393_5-D1
PFRMAT TS
TARGET T0339
MODEL 5
PARENT N/A
ATOM      1  CA  GLU     1     -26.460 -37.540  23.762  1.00 25.00           C
ATOM      2  CA  ARG     2     -27.600 -35.196  21.015  1.00 25.00           C
ATOM      3  CA  LYS     3     -24.169 -34.952  19.431  1.00 25.00           C
ATOM      4  CA  VAL     4     -23.026 -31.647  18.008  1.00 25.00           C
ATOM      5  CA  TYR     5     -22.013 -29.890  14.749  1.00 25.00           C
ATOM      6  CA  MET     6     -18.667 -27.982  14.503  1.00 25.00           C
ATOM      7  CA  ASP     7     -19.425 -24.468  13.146  1.00 25.00           C
ATOM      8  CA  TYR     8     -21.663 -22.481  15.540  1.00 25.00           C
ATOM    289  CA  GLU   289      -0.489 -26.995   8.724  1.00 25.00           C
ATOM    290  CA  ALA   290      -1.003 -30.713   9.482  1.00 25.00           C
ATOM    291  CA  TYR   291      -4.734 -30.386   8.685  1.00 25.00           C
ATOM    292  CA  GLU   292      -3.900 -28.643   5.379  1.00 25.00           C
ATOM    293  CA  ALA   293      -1.434 -31.437   4.499  1.00 25.00           C
ATOM    294  CA  HIS   294      -4.100 -34.072   5.286  1.00 25.00           C
ATOM    295  CA  MET   295      -6.616 -32.223   3.067  1.00 25.00           C
ATOM    296  CA  ARG   296      -4.051 -32.092   0.226  1.00 25.00           C
ATOM    297  CA  ASP   297      -3.401 -35.848   0.607  1.00 25.00           C
ATOM    298  CA  VAL   298      -7.167 -36.536   0.491  1.00 25.00           C
ATOM    299  CA  ARG   299      -7.484 -34.404  -2.675  1.00 25.00           C
ATOM    300  CA  ASP   300      -4.583 -36.318  -4.284  1.00 25.00           C
ATOM    301  CA  TYR   301      -6.248 -39.647  -3.385  1.00 25.00           C
ATOM    302  CA  LEU   302      -9.546 -38.439  -4.912  1.00 25.00           C
ATOM    303  CA  GLU   303      -7.710 -37.390  -8.106  1.00 25.00           C
ATOM    304  CA  GLU   304      -6.026 -40.825  -8.294  1.00 25.00           C
ATOM    305  CA  ARG   305      -9.421 -42.542  -7.860  1.00 25.00           C
ATOM    306  CA  LEU   306     -10.902 -40.373 -10.648  1.00 25.00           C
ATOM    307  CA  GLU   307      -7.968 -41.271 -12.938  1.00 25.00           C
ATOM    308  CA  ALA   308      -8.481 -44.989 -12.180  1.00 25.00           C
ATOM    309  CA  GLU   309     -12.213 -44.661 -12.978  1.00 25.00           C
ATOM    310  CA  PHE   310     -14.281 -44.734  -9.823  1.00 25.00           C
ATOM    311  CA  GLY   311     -16.345 -42.383  -7.630  1.00 25.00           C
ATOM    312  CA  GLN   312     -18.071 -38.984  -7.455  1.00 25.00           C
ATOM    313  CA  LYS   313     -17.663 -36.239  -4.833  1.00 25.00           C
ATOM    314  CA  ARG   314     -15.839 -32.877  -4.748  1.00 25.00           C
ATOM    315  CA  ILE   315     -14.084 -30.126  -2.769  1.00 25.00           C
ATOM    316  CA  HIS   316     -16.292 -27.719  -4.764  1.00 25.00           C
ATOM    317  CA  LEU   317     -16.312 -24.339  -2.935  1.00 25.00           C
ATOM    318  CA  ASN   318     -13.922 -21.383  -2.684  1.00 25.00           C
ATOM    319  CA  SER   319     -11.360 -24.183  -2.548  1.00 25.00           C
ATOM    320  CA  GLN   320     -10.522 -25.890  -5.866  1.00 25.00           C
ATOM    321  CA  PHE   321     -13.026 -23.730  -7.693  1.00 25.00           C
ATOM    322  CA  PRO   322     -10.013 -21.469  -8.196  1.00 25.00           C
ATOM    323  CA  GLY   323      -6.307 -22.178  -7.680  1.00 25.00           C
ATOM    324  CA  THR   324      -3.479 -22.334  -5.119  1.00 25.00           C
ATOM    325  CA  GLN   325      -5.111 -19.657  -3.011  1.00 25.00           C
ATOM    326  CA  ARG   326      -7.054 -21.029  -0.102  1.00 25.00           C
ATOM    327  CA  LEU   327      -6.837 -20.575   3.632  1.00 25.00           C
ATOM    328  CA  PRO   328      -6.345 -24.298   4.076  1.00 25.00           C
ATOM    329  CA  ASN   329      -8.027 -24.783   7.429  1.00 25.00           C
ATOM    330  CA  THR   330     -11.449 -24.916   5.710  1.00 25.00           C
ATOM    331  CA  CYS   331     -12.996 -27.134   3.092  1.00 25.00           C
ATOM    332  CA  ASN   332     -16.667 -26.652   3.760  1.00 25.00           C
ATOM    333  CA  PHE   333     -19.791 -28.628   4.485  1.00 25.00           C
ATOM    334  CA  SER   334     -22.178 -31.017   2.723  1.00 25.00           C
ATOM    335  CA  ILE   335     -22.467 -33.612  -0.047  1.00 25.00           C
ATOM    336  CA  ARG   336     -24.943 -35.417  -2.242  1.00 25.00           C
ATOM    337  CA  GLY   337     -23.214 -38.724  -2.564  1.00 25.00           C
ATOM    338  CA  PRO   338     -21.648 -38.872   0.865  1.00 25.00           C
ATOM    339  CA  ARG   339     -25.062 -37.852   2.239  1.00 25.00           C
ATOM    340  CA  LEU   340     -23.224 -35.822   4.801  1.00 25.00           C
ATOM    341  CA  GLN   341     -25.110 -37.744   7.523  1.00 25.00           C
ATOM    342  CA  GLY   342     -23.517 -41.022   6.346  1.00 25.00           C
ATOM    343  CA  HIS   343     -20.050 -39.399   6.436  1.00 25.00           C
ATOM    344  CA  VAL   344     -20.713 -38.122   9.985  1.00 25.00           C
ATOM    345  CA  VAL   345     -21.817 -41.626  11.066  1.00 25.00           C
ATOM    346  CA  LEU   346     -18.637 -43.124   9.545  1.00 25.00           C
ATOM    347  CA  ALA   347     -16.505 -40.538  11.396  1.00 25.00           C
ATOM    348  CA  GLN   348     -18.291 -41.377  14.678  1.00 25.00           C
ATOM    349  CA  CYS   349     -17.670 -45.109  14.091  1.00 25.00           C
ATOM    350  CA  ARG   350     -14.126 -44.790  12.724  1.00 25.00           C
ATOM    351  CA  VAL   351     -12.596 -41.839  14.500  1.00 25.00           C
ATOM    352  CA  LEU   352     -12.224 -38.334  13.193  1.00 25.00           C
ATOM    353  CA  MET   353     -14.415 -35.280  12.710  1.00 25.00           C
ATOM    354  CA  ALA   354     -15.943 -32.106  11.228  1.00 25.00           C
ATOM    355  CA  SER   355     -19.474 -30.824  10.396  1.00 25.00           C
ATOM    356  CA  VAL   356     -19.249 -28.002  12.893  1.00 25.00           C
ATOM    357  CA  GLY   357     -18.946 -25.379  15.591  1.00 25.00           C
ATOM    358  CA  ALA   358     -16.253 -22.744  15.019  1.00 25.00           C
ATOM    359  CA  ALA   359     -19.018 -20.163  15.240  1.00 25.00           C
ATOM    360  CA  CYS   360     -17.995 -18.395  12.059  1.00 25.00           C
ATOM    361  CA  HIS   361     -17.389 -21.711  10.232  1.00 25.00           C
ATOM    362  CA  SER   362     -16.922 -25.328   9.236  1.00 25.00           C
ATOM    363  CA  ASP   363     -20.672 -25.515   8.730  1.00 25.00           C
ATOM    364  CA  HIS   364     -23.018 -24.083  11.310  1.00 25.00           C
ATOM    365  CA  GLY   365     -24.950 -20.812  11.295  1.00 25.00           C
ATOM    366  CA  ASP   366     -26.978 -22.292   8.479  1.00 25.00           C
ATOM    367  CA  GLN   367     -24.056 -22.727   6.139  1.00 25.00           C
ATOM    368  CA  PRO   368     -23.859 -18.894   6.183  1.00 25.00           C
ATOM    369  CA  SER   369     -26.780 -19.041   3.711  1.00 25.00           C
ATOM    370  CA  PRO   370     -25.372 -16.017   1.830  1.00 25.00           C
ATOM    371  CA  VAL   371     -21.929 -17.688   1.672  1.00 25.00           C
ATOM    372  CA  LEU   372     -23.522 -20.899   0.324  1.00 25.00           C
ATOM    373  CA  LEU   373     -25.401 -18.880  -2.334  1.00 25.00           C
ATOM    374  CA  SER   374     -22.145 -17.137  -3.347  1.00 25.00           C
ATOM    375  CA  TYR   375     -20.386 -20.528  -3.622  1.00 25.00           C
ATOM    376  CA  GLY   376     -22.444 -20.863  -6.844  1.00 25.00           C
ATOM    377  CA  VAL   377     -25.143 -23.317  -5.858  1.00 25.00           C
ATOM    378  CA  PRO   378     -28.218 -25.143  -4.708  1.00 25.00           C
ATOM    379  CA  PHE   379     -28.648 -24.377  -1.020  1.00 25.00           C
ATOM    380  CA  ASP   380     -30.495 -27.667  -0.362  1.00 25.00           C
ATOM    381  CA  VAL   381     -27.227 -29.617  -0.792  1.00 25.00           C
ATOM    382  CA  ALA   382     -25.466 -27.253   1.653  1.00 25.00           C
ATOM    383  CA  ARG   383     -21.976 -26.418   0.473  1.00 25.00           C
ATOM    384  CA  ASN   384     -21.397 -29.107  -2.144  1.00 25.00           C
ATOM    385  CA  ALA   385     -18.424 -30.313  -0.067  1.00 25.00           C
ATOM    386  CA  LEU   386     -17.418 -32.697   2.756  1.00 25.00           C
ATOM    387  CA  ARG   387     -15.331 -31.177   5.621  1.00 25.00           C
ATOM    388  CA  LEU   388     -11.645 -31.597   6.472  1.00 25.00           C
ATOM    389  CA  SER   389     -10.657 -29.108   9.213  1.00 25.00           C
ATOM    390  CA  VAL   390      -8.593 -30.361  12.150  1.00 25.00           C
ATOM    391  CA  GLY   391      -6.855 -29.025  15.251  1.00 25.00           C
ATOM    392  CA  ARG   392      -4.603 -32.106  15.617  1.00 25.00           C
ATOM    393  CA  SER   393      -1.331 -33.615  14.562  1.00 25.00           C
ATOM    394  CA  THR   394      -2.903 -35.587  11.750  1.00 25.00           C
ATOM    395  CA  THR   395      -0.002 -36.378   9.379  1.00 25.00           C
ATOM    396  CA  ARG   396       1.513 -38.387   6.498  1.00 25.00           C
ATOM    397  CA  ALA   397       1.098 -42.148   5.905  1.00 25.00           C
ATOM    398  CA  GLU   398      -1.550 -42.317   8.667  1.00 25.00           C
ATOM    399  CA  VAL   399      -3.410 -39.359   7.098  1.00 25.00           C
ATOM    400  CA  ASP   400      -3.311 -41.081   3.677  1.00 25.00           C
ATOM    401  CA  LEU   401      -4.680 -44.302   5.232  1.00 25.00           C
ATOM    402  CA  VAL   402      -7.498 -42.325   6.909  1.00 25.00           C
ATOM    403  CA  VAL   403      -8.346 -40.652   3.570  1.00 25.00           C
ATOM    404  CA  GLN   404      -8.428 -44.073   1.850  1.00 25.00           C
ATOM    405  CA  ASP   405     -10.747 -45.420   4.583  1.00 25.00           C
ATOM    406  CA  LEU   406     -13.054 -42.393   4.151  1.00 25.00           C
ATOM    407  CA  LYS   407     -13.128 -42.960   0.364  1.00 25.00           C
ATOM    408  CA  GLN   408     -13.990 -46.651   0.908  1.00 25.00           C
ATOM    409  CA  ALA   409     -16.812 -45.666   3.303  1.00 25.00           C
ATOM    410  CA  VAL   410     -18.164 -43.179   0.724  1.00 25.00           C
ATOM    411  CA  ALA   411     -18.068 -45.891  -1.978  1.00 25.00           C
ATOM    412  CA  GLN   412     -19.943 -48.298   0.336  1.00 25.00           C
ATOM    413  CA  LEU   413     -22.583 -45.612   1.031  1.00 25.00           C
ATOM    414  CA  GLU   414     -22.986 -45.000  -2.728  1.00 25.00           C
ATOM    415  CA  ASP   415     -23.400 -48.761  -3.321  1.00 25.00           C
ATOM    416  CA  GLN   416     -25.249 -50.263  -0.327  1.00 25.00           C
TER
END
