
#######################################################
#                                                     #
#                        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 T0339TS168_4-D1
# Molecule2: number of CA atoms  136 ( 1077),  selected  136 , name T0339_D1.pdb
# PARAMETERS: T0339TS168_4-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      M       6           -
LGA    D       7      D       7           -
LGA    Y       8      Y       8           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    E     289      Y     291          3.261
LGA    A     290      E     292           #
LGA    -       -      A     293           -
LGA    -       -      H     294           -
LGA    Y     291      M     295          4.298
LGA    E     292      R     296          3.195
LGA    A     293      D     297          3.860
LGA    H     294      V     298          3.490
LGA    M     295      R     299          1.451
LGA    R     296      D     300          1.367
LGA    D     297      Y     301          1.736
LGA    V     298      L     302          1.646
LGA    R     299      E     303          1.936
LGA    D     300      E     304          1.660
LGA    Y     301      R     305          1.182
LGA    L     302      L     306          3.846
LGA    E     303      E     307          4.561
LGA    E     304      A     308          2.688
LGA    R     305      E     309          4.470
LGA    L     306      -       -           -
LGA    E     307      -       -           -
LGA    A     308      -       -           -
LGA    E     309      -       -           -
LGA    F     310      F     310           #
LGA    G     311      G     311          4.392
LGA    -       -      Q     312           -
LGA    Q     312      K     313          4.705
LGA    K     313      R     314          1.705
LGA    R     314      I     315          3.576
LGA    I     315      H     316          1.566
LGA    H     316      L     317          2.458
LGA    L     317      N     318          0.338
LGA    N     318      S     319          3.377
LGA    S     319      Q     320           #
LGA    Q     320      F     321          3.316
LGA    F     321      -       -           -
LGA    P     322      -       -           -
LGA    G     323      P     322          5.544
LGA    T     324      G     323          5.988
LGA    Q     325      T     324           #
LGA    R     326      Q     325           #
LGA    L     327      R     326          3.835
LGA    P     328      L     327          2.315
LGA    -       -      P     328           -
LGA    N     329      N     329          4.309
LGA    T     330      T     330          2.635
LGA    C     331      C     331          2.715
LGA    N     332      N     332          3.051
LGA    F     333      F     333           #
LGA    S     334      S     334          4.669
LGA    I     335      I     335          3.721
LGA    R     336      R     336          2.799
LGA    G     337      G     337          2.671
LGA    -       -      P     338           -
LGA    P     338      R     339          3.196
LGA    R     339      L     340          2.847
LGA    -       -      Q     341           -
LGA    L     340      G     342          2.766
LGA    Q     341      H     343          2.840
LGA    G     342      V     344          3.036
LGA    H     343      V     345          1.632
LGA    V     344      L     346          0.714
LGA    V     345      A     347          0.824
LGA    L     346      Q     348          2.662
LGA    A     347      C     349          3.268
LGA    Q     348      -       -           -
LGA    C     349      -       -           -
LGA    R     350      R     350          1.193
LGA    V     351      V     351          2.115
LGA    L     352      L     352          2.442
LGA    M     353      M     353          0.658
LGA    A     354      A     354          1.191
LGA    S     355      S     355          1.317
LGA    V     356      V     356          4.412
LGA    G     357      G     357          5.159
LGA    A     358      A     358          5.203
LGA    A     359      A     359          5.602
LGA    C     360      -       -           -
LGA    H     361      -       -           -
LGA    S     362      -       -           -
LGA    D     363      -       -           -
LGA    H     364      C     360          4.642
LGA    G     365      H     361          3.665
LGA    D     366      S     362           #
LGA    -       -      D     363           -
LGA    -       -      H     364           -
LGA    -       -      G     365           -
LGA    -       -      D     366           -
LGA    -       -      Q     367           -
LGA    Q     367      P     368           #
LGA    P     368      S     369          2.829
LGA    S     369      P     370          1.347
LGA    P     370      V     371          3.943
LGA    V     371      L     372          2.462
LGA    L     372      L     373          1.920
LGA    L     373      S     374          3.980
LGA    S     374      Y     375          2.061
LGA    Y     375      G     376          2.971
LGA    G     376      V     377          3.289
LGA    V     377      P     378          1.248
LGA    P     378      F     379          3.131
LGA    F     379      -       -           -
LGA    D     380      D     380          3.178
LGA    V     381      V     381          2.909
LGA    A     382      -       -           -
LGA    R     383      A     382          1.507
LGA    N     384      R     383           #
LGA    A     385      N     384           #
LGA    L     386      A     385          4.899
LGA    R     387      L     386          2.755
LGA    L     388      R     387          3.248
LGA    S     389      L     388          2.993
LGA    -       -      S     389           -
LGA    V     390      V     390          2.714
LGA    G     391      G     391          3.834
LGA    R     392      R     392          4.630
LGA    S     393      S     393          2.309
LGA    T     394      T     394          1.708
LGA    T     395      T     395          1.977
LGA    R     396      R     396          2.062
LGA    A     397      A     397          1.635
LGA    E     398      E     398          1.513
LGA    V     399      V     399          1.293
LGA    D     400      D     400          1.202
LGA    L     401      L     401          1.363
LGA    V     402      V     402          1.143
LGA    V     403      V     403          1.277
LGA    Q     404      Q     404          1.186
LGA    D     405      D     405          1.177
LGA    L     406      L     406          1.297
LGA    K     407      K     407          1.307
LGA    Q     408      Q     408          1.405
LGA    A     409      A     409          1.432
LGA    V     410      V     410          2.021
LGA    A     411      A     411          1.746
LGA    Q     412      Q     412          1.709
LGA    L     413      L     413          2.154
LGA    E     414      E     414          2.122
LGA    D     415      D     415          1.333
LGA    Q     416      Q     416           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  136  136    5.0    103    2.95    48.54     44.268     3.377

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.530831 * X  +  -0.800200 * Y  +   0.279104 * Z  + -10.687108
  Y_new =  -0.600294 * X  +   0.122556 * Y  +  -0.790333 * Z  + -13.463425
  Z_new =   0.598219 * X  +  -0.587078 * Y  +  -0.545412 * Z  +  12.157359 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.319419    0.822173  [ DEG:  -132.8929     47.1071 ]
  Theta =  -0.641276   -2.500316  [ DEG:   -36.7424   -143.2576 ]
  Phi   =  -2.294860    0.846732  [ DEG:  -131.4858     48.5142 ]
 
# 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: T0339TS168_4-D1                               
REMARK     2: T0339_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0339TS168_4-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  103   2.95   48.54  44.268
REMARK  ---------------------------------------------------------- 
MOLECULE T0339TS168_4-D1
PFRMAT TS
TARGET T0339
MODEL 4
PARENT N/A
ATOM      1  CA  GLU     1     -38.769 -19.385   8.629  1.00 25.00           C
ATOM      2  CA  ARG     2     -36.765 -18.620  11.728  1.00 25.00           C
ATOM      3  CA  LYS     3     -37.074 -20.021  15.293  1.00 25.00           C
ATOM      4  CA  VAL     4     -33.598 -21.621  15.061  1.00 25.00           C
ATOM      5  CA  TYR     5     -31.731 -21.354  11.782  1.00 25.00           C
ATOM      6  CA  MET     6     -28.324 -19.725  11.283  1.00 25.00           C
ATOM      7  CA  ASP     7     -24.662 -20.405  10.401  1.00 25.00           C
ATOM      8  CA  TYR     8     -24.098 -20.421  14.157  1.00 25.00           C
ATOM    289  CA  GLU   289       0.251 -26.459  10.929  1.00 25.00           C
ATOM    290  CA  ALA   290      -1.537 -29.823  11.317  1.00 25.00           C
ATOM    291  CA  TYR   291      -4.668 -28.379   9.648  1.00 25.00           C
ATOM    292  CA  GLU   292      -2.540 -27.044   6.757  1.00 25.00           C
ATOM    293  CA  ALA   293      -0.897 -30.478   6.347  1.00 25.00           C
ATOM    294  CA  HIS   294      -4.343 -32.148   6.297  1.00 25.00           C
ATOM    295  CA  MET   295      -5.538 -29.661   3.642  1.00 25.00           C
ATOM    296  CA  ARG   296      -2.425 -30.382   1.531  1.00 25.00           C
ATOM    297  CA  ASP   297      -3.060 -34.147   1.836  1.00 25.00           C
ATOM    298  CA  VAL   298      -6.700 -33.645   0.758  1.00 25.00           C
ATOM    299  CA  ARG   299      -5.549 -31.582  -2.256  1.00 25.00           C
ATOM    300  CA  ASP   300      -3.057 -34.327  -3.215  1.00 25.00           C
ATOM    301  CA  TYR   301      -5.822 -36.964  -2.950  1.00 25.00           C
ATOM    302  CA  LEU   302      -8.102 -34.830  -5.167  1.00 25.00           C
ATOM    303  CA  GLU   303      -5.294 -34.461  -7.745  1.00 25.00           C
ATOM    304  CA  GLU   304      -4.737 -38.250  -7.716  1.00 25.00           C
ATOM    305  CA  ARG   305      -8.487 -38.830  -8.232  1.00 25.00           C
ATOM    306  CA  LEU   306      -8.489 -36.367 -11.164  1.00 25.00           C
ATOM    307  CA  GLU   307      -5.486 -38.169 -12.713  1.00 25.00           C
ATOM    308  CA  ALA   308      -7.275 -41.534 -12.326  1.00 25.00           C
ATOM    309  CA  GLU   309     -10.405 -40.090 -13.995  1.00 25.00           C
ATOM    310  CA  PHE   310     -12.767 -39.852 -10.993  1.00 25.00           C
ATOM    311  CA  GLY   311     -15.271 -41.122  -8.407  1.00 25.00           C
ATOM    312  CA  GLN   312     -17.778 -38.645  -9.900  1.00 25.00           C
ATOM    313  CA  LYS   313     -17.569 -36.709  -6.588  1.00 25.00           C
ATOM    314  CA  ARG   314     -18.497 -33.017  -6.740  1.00 25.00           C
ATOM    315  CA  ILE   315     -15.500 -31.324  -5.138  1.00 25.00           C
ATOM    316  CA  HIS   316     -15.327 -27.508  -4.948  1.00 25.00           C
ATOM    317  CA  LEU   317     -15.544 -25.685  -1.644  1.00 25.00           C
ATOM    318  CA  ASN   318     -14.459 -22.128  -2.426  1.00 25.00           C
ATOM    319  CA  SER   319     -14.799 -22.566  -6.195  1.00 25.00           C
ATOM    320  CA  GLN   320     -11.144 -22.211  -7.238  1.00 25.00           C
ATOM    321  CA  PHE   321      -9.567 -23.533  -4.069  1.00 25.00           C
ATOM    322  CA  PRO   322      -6.415 -24.335  -5.951  1.00 25.00           C
ATOM    323  CA  GLY   323      -4.500 -22.421  -8.572  1.00 25.00           C
ATOM    324  CA  THR   324      -2.157 -20.970  -5.983  1.00 25.00           C
ATOM    325  CA  GLN   325      -3.318 -21.704  -2.459  1.00 25.00           C
ATOM    326  CA  ARG   326      -5.059 -23.377   0.517  1.00 25.00           C
ATOM    327  CA  LEU   327      -4.841 -22.069   4.040  1.00 25.00           C
ATOM    328  CA  PRO   328      -7.650 -22.380   6.525  1.00 25.00           C
ATOM    329  CA  ASN   329      -9.005 -24.845   9.029  1.00 25.00           C
ATOM    330  CA  THR   330     -11.442 -25.845   6.276  1.00 25.00           C
ATOM    331  CA  CYS   331     -13.075 -27.161   3.099  1.00 25.00           C
ATOM    332  CA  ASN   332     -16.518 -26.326   4.383  1.00 25.00           C
ATOM    333  CA  PHE   333     -19.086 -28.996   3.829  1.00 25.00           C
ATOM    334  CA  SER   334     -20.837 -32.158   2.746  1.00 25.00           C
ATOM    335  CA  ILE   335     -21.128 -34.378  -0.349  1.00 25.00           C
ATOM    336  CA  ARG   336     -22.726 -34.261  -3.739  1.00 25.00           C
ATOM    337  CA  GLY   337     -25.830 -36.468  -3.860  1.00 25.00           C
ATOM    338  CA  PRO   338     -24.225 -38.592  -1.192  1.00 25.00           C
ATOM    339  CA  ARG   339     -26.061 -36.762   1.531  1.00 25.00           C
ATOM    340  CA  LEU   340     -22.971 -36.675   3.723  1.00 25.00           C
ATOM    341  CA  GLN   341     -24.743 -37.761   6.940  1.00 25.00           C
ATOM    342  CA  GLY   342     -23.482 -41.345   6.454  1.00 25.00           C
ATOM    343  CA  HIS   343     -19.918 -40.045   5.928  1.00 25.00           C
ATOM    344  CA  VAL   344     -20.187 -37.945   9.119  1.00 25.00           C
ATOM    345  CA  VAL   345     -21.427 -41.005  11.058  1.00 25.00           C
ATOM    346  CA  LEU   346     -18.497 -43.074   9.716  1.00 25.00           C
ATOM    347  CA  ALA   347     -16.045 -40.326  10.764  1.00 25.00           C
ATOM    348  CA  GLN   348     -17.595 -40.243  14.265  1.00 25.00           C
ATOM    349  CA  CYS   349     -17.280 -44.051  14.523  1.00 25.00           C
ATOM    350  CA  ARG   350     -14.367 -45.348  12.416  1.00 25.00           C
ATOM    351  CA  VAL   351     -11.817 -42.858  13.865  1.00 25.00           C
ATOM    352  CA  LEU   352     -11.530 -39.226  12.876  1.00 25.00           C
ATOM    353  CA  MET   353     -13.931 -36.313  12.889  1.00 25.00           C
ATOM    354  CA  ALA   354     -15.082 -32.745  12.196  1.00 25.00           C
ATOM    355  CA  SER   355     -17.475 -31.119   9.752  1.00 25.00           C
ATOM    356  CA  VAL   356     -18.851 -28.776  12.379  1.00 25.00           C
ATOM    357  CA  GLY   357     -18.441 -25.691  14.617  1.00 25.00           C
ATOM    358  CA  ALA   358     -16.130 -23.540  16.697  1.00 25.00           C
ATOM    359  CA  ALA   359     -18.518 -20.714  15.886  1.00 25.00           C
ATOM    360  CA  CYS   360     -17.595 -19.098  12.606  1.00 25.00           C
ATOM    361  CA  HIS   361     -15.166 -21.875  11.703  1.00 25.00           C
ATOM    362  CA  SER   362     -15.954 -25.260  10.236  1.00 25.00           C
ATOM    363  CA  ASP   363     -19.612 -24.473   9.794  1.00 25.00           C
ATOM    364  CA  HIS   364     -21.899 -22.224  11.902  1.00 25.00           C
ATOM    365  CA  GLY   365     -23.369 -25.214  13.806  1.00 25.00           C
ATOM    366  CA  ASP   366     -24.553 -26.710  10.544  1.00 25.00           C
ATOM    367  CA  GLN   367     -26.635 -23.846   9.292  1.00 25.00           C
ATOM    368  CA  PRO   368     -24.176 -21.729   7.331  1.00 25.00           C
ATOM    369  CA  SER   369     -27.106 -21.027   4.968  1.00 25.00           C
ATOM    370  CA  PRO   370     -25.459 -17.753   3.858  1.00 25.00           C
ATOM    371  CA  VAL   371     -22.166 -19.599   3.212  1.00 25.00           C
ATOM    372  CA  LEU   372     -24.022 -22.240   1.152  1.00 25.00           C
ATOM    373  CA  LEU   373     -25.735 -19.483  -0.883  1.00 25.00           C
ATOM    374  CA  SER   374     -22.349 -17.807  -1.509  1.00 25.00           C
ATOM    375  CA  TYR   375     -20.877 -21.152  -2.652  1.00 25.00           C
ATOM    376  CA  GLY   376     -22.446 -21.312  -6.086  1.00 25.00           C
ATOM    377  CA  VAL   377     -25.395 -23.508  -5.141  1.00 25.00           C
ATOM    378  CA  PRO   378     -29.065 -24.568  -5.254  1.00 25.00           C
ATOM    379  CA  PHE   379     -30.709 -27.734  -3.865  1.00 25.00           C
ATOM    380  CA  ASP   380     -29.447 -31.157  -2.699  1.00 25.00           C
ATOM    381  CA  VAL   381     -25.859 -29.820  -2.579  1.00 25.00           C
ATOM    382  CA  ALA   382     -27.027 -26.803  -0.530  1.00 25.00           C
ATOM    383  CA  ARG   383     -23.839 -27.585   1.493  1.00 25.00           C
ATOM    384  CA  ASN   384     -21.374 -26.978  -1.342  1.00 25.00           C
ATOM    385  CA  ALA   385     -18.701 -29.724  -1.238  1.00 25.00           C
ATOM    386  CA  LEU   386     -15.923 -31.556   0.603  1.00 25.00           C
ATOM    387  CA  ARG   387     -15.140 -32.139   4.272  1.00 25.00           C
ATOM    388  CA  LEU   388     -12.525 -31.005   6.835  1.00 25.00           C
ATOM    389  CA  SER   389     -10.004 -30.064   9.452  1.00 25.00           C
ATOM    390  CA  VAL   390      -7.564 -32.155  11.437  1.00 25.00           C
ATOM    391  CA  GLY   391      -7.303 -29.696  14.361  1.00 25.00           C
ATOM    392  CA  ARG   392      -4.190 -31.778  15.141  1.00 25.00           C
ATOM    393  CA  SER   393      -1.829 -34.466  13.880  1.00 25.00           C
ATOM    394  CA  THR   394      -2.180 -34.861  10.158  1.00 25.00           C
ATOM    395  CA  THR   395       0.456 -36.107   7.654  1.00 25.00           C
ATOM    396  CA  ARG   396       1.405 -39.054   5.401  1.00 25.00           C
ATOM    397  CA  ALA   397       0.307 -42.556   6.497  1.00 25.00           C
ATOM    398  CA  GLU   398      -2.540 -41.042   8.564  1.00 25.00           C
ATOM    399  CA  VAL   399      -3.645 -38.948   5.554  1.00 25.00           C
ATOM    400  CA  ASP   400      -3.606 -42.070   3.337  1.00 25.00           C
ATOM    401  CA  LEU   401      -5.706 -43.961   5.921  1.00 25.00           C
ATOM    402  CA  VAL   402      -8.208 -41.065   6.045  1.00 25.00           C
ATOM    403  CA  VAL   403      -8.431 -41.061   2.221  1.00 25.00           C
ATOM    404  CA  GLN   404      -9.044 -44.841   2.230  1.00 25.00           C
ATOM    405  CA  ASP   405     -11.801 -44.413   4.854  1.00 25.00           C
ATOM    406  CA  LEU   406     -13.422 -41.663   2.738  1.00 25.00           C
ATOM    407  CA  LYS   407     -13.294 -43.928  -0.348  1.00 25.00           C
ATOM    408  CA  GLN   408     -14.910 -46.774   1.644  1.00 25.00           C
ATOM    409  CA  ALA   409     -17.668 -44.402   2.842  1.00 25.00           C
ATOM    410  CA  VAL   410     -18.287 -43.262  -0.762  1.00 25.00           C
ATOM    411  CA  ALA   411     -18.505 -46.911  -1.904  1.00 25.00           C
ATOM    412  CA  GLN   412     -21.002 -47.665   0.899  1.00 25.00           C
ATOM    413  CA  LEU   413     -23.109 -44.636  -0.127  1.00 25.00           C
ATOM    414  CA  GLU   414     -23.073 -45.816  -3.771  1.00 25.00           C
ATOM    415  CA  ASP   415     -24.171 -49.317  -2.674  1.00 25.00           C
ATOM    416  CA  GLN   416     -22.362 -52.681  -2.396  1.00 25.00           C
TER
END
