
#######################################################
#                                                     #
#                        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   10 (   78),  selected   10 , name T0318TS268_5_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_5_1-D2.T0318_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T     156           -
LGA    -       -      N     157           -
LGA    -       -      E     158           -
LGA    -       -      D     159           -
LGA    -       -      A     160           -
LGA    -       -      V     161           -
LGA    -       -      F     162           -
LGA    -       -      L     163           -
LGA    -       -      T     164           -
LGA    -       -      D     165           -
LGA    -       -      L     166           -
LGA    -       -      S     167           -
LGA    -       -      E     168           -
LGA    -       -      S     169           -
LGA    -       -      V     170           -
LGA    -       -      R     171           -
LGA    -       -      E     172           -
LGA    -       -      T     173           -
LGA    -       -      A     174           -
LGA    -       -      R     175           -
LGA    -       -      L     176           -
LGA    -       -      I     177           -
LGA    -       -      D     178           -
LGA    -       -      T     179           -
LGA    -       -      P     180           -
LGA    -       -      A     181           -
LGA    -       -      N     182           -
LGA    -       -      I     183           -
LGA    -       -      L     184           -
LGA    -       -      T     185           -
LGA    -       -      T     186           -
LGA    -       -      D     187           -
LGA    -       -      A     188           -
LGA    -       -      L     189           -
LGA    -       -      V     190           -
LGA    -       -      D     191           -
LGA    -       -      E     192           -
LGA    -       -      A     193           -
LGA    -       -      V     194           -
LGA    -       -      K     195           -
LGA    -       -      V     196           -
LGA    -       -      G     197           -
LGA    -       -      N     198           -
LGA    -       -      A     199           -
LGA    -       -      T     200           -
LGA    -       -      G     201           -
LGA    -       -      S     202           -
LGA    -       -      K     203           -
LGA    -       -      I     204           -
LGA    -       -      T     205           -
LGA    -       -      V     206           -
LGA    -       -      I     207           -
LGA    -       -      R     208           -
LGA    -       -      G     209           -
LGA    -       -      E     210           -
LGA    -       -      E     211           -
LGA    -       -      L     212           -
LGA    -       -      L     213           -
LGA    -       -      K     214           -
LGA    -       -      A     215           -
LGA    -       -      G     216           -
LGA    -       -      F     217           -
LGA    -       -      G     218           -
LGA    -       -      G     219           -
LGA    -       -      I     220           -
LGA    -       -      Y     221           -
LGA    -       -      H     222           -
LGA    -       -      V     223           -
LGA    -       -      G     224           -
LGA    -       -      K     225           -
LGA    -       -      A     226           -
LGA    -       -      G     227           -
LGA    -       -      P     228           -
LGA    -       -      T     229           -
LGA    -       -      P     230           -
LGA    -       -      P     231           -
LGA    -       -      A     232           -
LGA    -       -      F     233           -
LGA    -       -      V     234           -
LGA    -       -      V     235           -
LGA    -       -      L     236           -
LGA    -       -      S     237           -
LGA    -       -      H     238           -
LGA    -       -      E     239           -
LGA    -       -      V     240           -
LGA    -       -      P     241           -
LGA    -       -      G     242           -
LGA    -       -      S     243           -
LGA    -       -      T     244           -
LGA    -       -      E     245           -
LGA    -       -      H     246           -
LGA    -       -      I     247           -
LGA    -       -      A     248           -
LGA    -       -      L     249           -
LGA    -       -      V     250           -
LGA    -       -      G     251           -
LGA    -       -      K     252           -
LGA    -       -      G     253           -
LGA    -       -      V     254           -
LGA    -       -      V     255           -
LGA    -       -      Y     256           -
LGA    -       -      D     257           -
LGA    -       -      T     258           -
LGA    -       -      G     259           -
LGA    -       -      G     260           -
LGA    -       -      L     261           -
LGA    -       -      Q     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      K     266           -
LGA    -       -      T     267           -
LGA    -       -      G     268           -
LGA    -       -      M     269           -
LGA    -       -      P     270           -
LGA    -       -      N     271           -
LGA    -       -      M     272           -
LGA    -       -      K     273           -
LGA    -       -      R     274           -
LGA    -       -      D     275           -
LGA    -       -      M     276           -
LGA    -       -      G     277           -
LGA    -       -      G     278           -
LGA    -       -      A     279           -
LGA    -       -      A     280           -
LGA    -       -      G     281           -
LGA    -       -      M     282           -
LGA    -       -      L     283           -
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      Y     286           -
LGA    -       -      S     287           -
LGA    -       -      A     288           -
LGA    -       -      L     289           -
LGA    -       -      V     290           -
LGA    -       -      K     291           -
LGA    -       -      H     292           -
LGA    -       -      G     293           -
LGA    -       -      F     294           -
LGA    -       -      S     295           -
LGA    -       -      Q     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      H     299           -
LGA    -       -      A     300           -
LGA    -       -      C     301           -
LGA    -       -      L     302           -
LGA    -       -      C     303           -
LGA    -       -      I     304           -
LGA    -       -      V     305           -
LGA    -       -      E     306           -
LGA    -       -      N     307           -
LGA    -       -      N     308           -
LGA    -       -      V     309           -
LGA    -       -      S     310           -
LGA    -       -      P     311           -
LGA    -       -      I     312           -
LGA    -       -      A     313           -
LGA    -       -      N     314           -
LGA    -       -      K     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      D     318           -
LGA    -       -      I     319           -
LGA    -       -      I     320           -
LGA    -       -      K     321           -
LGA    -       -      M     322           -
LGA    -       -      L     323           -
LGA    -       -      S     324           -
LGA    -       -      G     325           -
LGA    -       -      K     326           -
LGA    -       -      T     327           -
LGA    -       -      V     328           -
LGA    -       -      E     329           -
LGA    -       -      I     330           -
LGA    -       -      N     331           -
LGA    -       -      N     332           -
LGA    -       -      T     333           -
LGA    -       -      D     334           -
LGA    -       -      A     335           -
LGA    -       -      E     336           -
LGA    -       -      G     337           -
LGA    -       -      R     338           -
LGA    -       -      L     339           -
LGA    -       -      I     340           -
LGA    -       -      L     341           -
LGA    -       -      A     342           -
LGA    -       -      D     343           -
LGA    -       -      G     344           -
LGA    -       -      V     345           -
LGA    -       -      F     346           -
LGA    -       -      Y     347           -
LGA    -       -      A     348           -
LGA    -       -      K     349           -
LGA    -       -      E     350           -
LGA    -       -      T     351           -
LGA    -       -      L     352           -
LGA    -       -      K     353           -
LGA    -       -      A     354           -
LGA    T     156      T     355          0.862
LGA    N     157      T     356          0.684
LGA    E     158      I     357          1.371
LGA    D     159      F     358          1.348
LGA    A     160      D     359          0.815
LGA    V     161      M     360          2.081
LGA    F     162      A     361          1.445
LGA    -       -      T     362           -
LGA    -       -      L     363           -
LGA    -       -      T     364           -
LGA    -       -      G     365           -
LGA    -       -      A     366           -
LGA    -       -      Q     367           -
LGA    -       -      A     368           -
LGA    -       -      W     369           -
LGA    -       -      L     370           -
LGA    -       -      S     371           -
LGA    -       -      G     372           -
LGA    -       -      R     373           -
LGA    -       -      L     374           -
LGA    -       -      H     375           -
LGA    -       -      G     376           -
LGA    -       -      A     377           -
LGA    -       -      A     378           -
LGA    -       -      M     379           -
LGA    -       -      T     380           -
LGA    -       -      N     381           -
LGA    -       -      D     382           -
LGA    -       -      E     383           -
LGA    -       -      Q     384           -
LGA    -       -      L     385           -
LGA    -       -      E     386           -
LGA    -       -      N     387           -
LGA    -       -      E     388           -
LGA    -       -      I     389           -
LGA    -       -      I     390           -
LGA    -       -      K     391           -
LGA    -       -      A     392           -
LGA    -       -      G     393           -
LGA    -       -      K     394           -
LGA    -       -      A     395           -
LGA    -       -      S     396           -
LGA    -       -      G     397           -
LGA    -       -      D     398           -
LGA    -       -      L     399           -
LGA    -       -      V     400           -
LGA    -       -      A     401           -
LGA    -       -      P     402           -
LGA    -       -      M     403           -
LGA    -       -      L     404           -
LGA    -       -      F     405           -
LGA    -       -      A     406           -
LGA    -       -      P     407           -
LGA    -       -      D     408           -
LGA    -       -      L     409           -
LGA    -       -      F     410           -
LGA    -       -      F     411           -
LGA    -       -      G     412           -
LGA    -       -      D     413           -
LGA    -       -      L     414           -
LGA    -       -      K     415           -
LGA    -       -      S     416           -
LGA    -       -      S     417           -
LGA    -       -      I     418           -
LGA    -       -      A     419           -
LGA    -       -      D     420           -
LGA    -       -      M     421           -
LGA    -       -      K     422           -
LGA    -       -      N     423           -
LGA    -       -      S     424           -
LGA    -       -      N     425           -
LGA    -       -      L     426           -
LGA    -       -      G     427           -
LGA    -       -      K     428           -
LGA    -       -      M     429           -
LGA    -       -      D     430           -
LGA    -       -      G     431           -
LGA    -       -      P     432           -
LGA    -       -      P     433           -
LGA    -       -      S     434           -
LGA    -       -      A     435           -
LGA    -       -      V     436           -
LGA    -       -      A     437           -
LGA    -       -      G     438           -
LGA    -       -      L     439           -
LGA    -       -      L     440           -
LGA    -       -      I     441           -
LGA    -       -      G     442           -
LGA    -       -      A     443           -
LGA    -       -      H     444           -
LGA    -       -      I     445           -
LGA    -       -      G     446           -
LGA    -       -      F     447           -
LGA    -       -      G     448           -
LGA    -       -      E     449           -
LGA    -       -      G     450           -
LGA    -       -      L     451           -
LGA    -       -      R     452           -
LGA    -       -      W     453           -
LGA    -       -      L     454           -
LGA    -       -      H     455           -
LGA    -       -      L     456           -
LGA    -       -      D     457           -
LGA    L     163      I     458          0.879
LGA    T     164      A     459          1.361
LGA    D     165      A     460          1.473
LGA    -       -      P     461           -
LGA    -       -      A     462           -
LGA    -       -      E     463           -
LGA    -       -      V     464           -
LGA    -       -      G     465           -
LGA    -       -      D     466           -
LGA    -       -      R     467           -
LGA    -       -      G     468           -
LGA    -       -      T     469           -
LGA    -       -      G     470           -
LGA    -       -      Y     471           -
LGA    -       -      G     472           -
LGA    -       -      P     473           -
LGA    -       -      A     474           -
LGA    -       -      L     475           -
LGA    -       -      F     476           -
LGA    -       -      S     477           -
LGA    -       -      T     478           -
LGA    -       -      L     479           -
LGA    -       -      L     480           -
LGA    -       -      G     481           -
LGA    -       -      K     482           -
LGA    -       -      Y     483           -
LGA    -       -      T     484           -
LGA    -       -      S     485           -
LGA    -       -      V     486           -
LGA    -       -      P     487           -
LGA    -       -      M     488           -
LGA    -       -      L     489           -
LGA    -       -      K     490           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  335    5.0     10    1.30    10.00      2.869     0.717

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.922173 * X  +  -0.338980 * Y  +  -0.186251 * Z  +  78.761520
  Y_new =   0.298147 * X  +   0.316255 * Y  +   0.900606 * Z  +  25.028379
  Z_new =  -0.246385 * X  +  -0.886045 * Y  +   0.392707 * Z  +  32.281746 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.153600    1.987993  [ DEG:   -66.0964    113.9036 ]
  Theta =   0.248948    2.892644  [ DEG:    14.2637    165.7363 ]
  Phi   =   0.312702   -2.828891  [ DEG:    17.9165   -162.0835 ]
 
# 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: T0318TS268_5_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_5_1-D2.T0318_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  335   5.0   10   1.30   10.00   2.869
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1jv2_A
ATOM   1209  N   THR   156      -4.333  35.957   8.416  1.00  0.00
ATOM   1210  CA  THR   156      -5.062  36.115   9.636  1.00  0.00
ATOM   1211  C   THR   156      -4.098  36.411  10.735  1.00  0.00
ATOM   1212  O   THR   156      -4.358  37.270  11.575  1.00  0.00
ATOM   1213  CB  THR   156      -5.848  34.840   9.994  1.00  0.00
ATOM   1214  OG1 THR   156      -6.805  34.561   8.964  1.00  0.00
ATOM   1215  CG2 THR   156      -6.583  35.020  11.313  1.00  0.00
ATOM   1216  N   ASN   157      -2.945  35.722  10.773  1.00  0.00
ATOM   1217  CA  ASN   157      -2.064  36.030  11.857  1.00  0.00
ATOM   1218  C   ASN   157      -1.260  37.231  11.490  1.00  0.00
ATOM   1219  O   ASN   157      -0.253  37.129  10.792  1.00  0.00
ATOM   1220  CB  ASN   157      -1.124  34.854  12.134  1.00  0.00
ATOM   1221  CG  ASN   157      -0.293  35.057  13.386  1.00  0.00
ATOM   1222  OD1 ASN   157       0.445  36.036  13.500  1.00  0.00
ATOM   1223  ND2 ASN   157      -0.410  34.129  14.328  1.00  0.00
ATOM   1224  N   GLU   158      -1.707  38.415  11.958  1.00  0.00
ATOM   1225  CA  GLU   158      -0.983  39.622  11.702  1.00  0.00
ATOM   1226  C   GLU   158      -1.377  40.614  12.749  1.00  0.00
ATOM   1227  O   GLU   158      -2.518  40.627  13.206  1.00  0.00
ATOM   1228  CB  GLU   158      -1.323  40.166  10.313  1.00  0.00
ATOM   1229  CG  GLU   158      -0.540  41.410   9.924  1.00  0.00
ATOM   1230  CD  GLU   158      -0.895  41.913   8.539  1.00  0.00
ATOM   1231  OE1 GLU   158      -1.766  41.297   7.889  1.00  0.00
ATOM   1232  OE2 GLU   158      -0.302  42.921   8.102  1.00  0.00
ATOM   1233  N   ASP   159      -0.416  41.453  13.183  1.00  0.00
ATOM   1234  CA  ASP   159      -0.696  42.492  14.134  1.00  0.00
ATOM   1235  C   ASP   159       0.466  43.433  14.095  1.00  0.00
ATOM   1236  O   ASP   159       1.604  42.996  13.947  1.00  0.00
ATOM   1237  CB  ASP   159      -0.859  41.904  15.537  1.00  0.00
ATOM   1238  CG  ASP   159      -1.488  42.882  16.510  1.00  0.00
ATOM   1239  OD1 ASP   159      -0.871  43.935  16.776  1.00  0.00
ATOM   1240  OD2 ASP   159      -2.598  42.596  17.005  1.00  0.00
ATOM   1241  N   ALA   160       0.221  44.756  14.191  1.00  0.00
ATOM   1242  CA  ALA   160       1.342  45.654  14.202  1.00  0.00
ATOM   1243  C   ALA   160       1.070  46.743  15.191  1.00  0.00
ATOM   1244  O   ALA   160      -0.045  47.256  15.276  1.00  0.00
ATOM   1245  CB  ALA   160       1.549  46.261  12.822  1.00  0.00
ATOM   1246  N   VAL   161       2.095  47.122  15.983  1.00  0.00
ATOM   1247  CA  VAL   161       1.915  48.202  16.910  1.00  0.00
ATOM   1248  C   VAL   161       3.236  48.881  17.104  1.00  0.00
ATOM   1249  O   VAL   161       4.295  48.264  16.995  1.00  0.00
ATOM   1250  CB  VAL   161       1.405  47.697  18.273  1.00  0.00
ATOM   1251  CG1 VAL   161       2.438  46.792  18.926  1.00  0.00
ATOM   1252  CG2 VAL   161       1.132  48.866  19.205  1.00  0.00
ATOM   1253  N   PHE   162       3.182  50.199  17.382  1.00  0.00
ATOM   1254  CA  PHE   162       4.350  51.010  17.565  1.00  0.00
ATOM   1255  C   PHE   162       4.757  50.957  19.001  1.00  0.00
ATOM   1256  O   PHE   162       3.929  50.778  19.892  1.00  0.00
ATOM   1257  CB  PHE   162       4.061  52.462  17.177  1.00  0.00
ATOM   1258  CG  PHE   162       3.844  52.664  15.705  1.00  0.00
ATOM   1259  CD1 PHE   162       2.565  52.740  15.183  1.00  0.00
ATOM   1260  CD2 PHE   162       4.919  52.776  14.841  1.00  0.00
ATOM   1261  CE1 PHE   162       2.365  52.926  13.829  1.00  0.00
ATOM   1262  CE2 PHE   162       4.720  52.963  13.486  1.00  0.00
ATOM   1263  CZ  PHE   162       3.449  53.037  12.980  1.00  0.00
ATOM   1264  N   LEU   163       6.072  51.090  19.254  1.00  0.00
ATOM   1265  CA  LEU   163       6.553  51.163  20.601  1.00  0.00
ATOM   1266  C   LEU   163       7.458  52.352  20.637  1.00  0.00
ATOM   1267  O   LEU   163       8.301  52.519  19.759  1.00  0.00
ATOM   1268  CB  LEU   163       7.311  49.886  20.969  1.00  0.00
ATOM   1269  CG  LEU   163       7.939  49.849  22.363  1.00  0.00
ATOM   1270  CD1 LEU   163       6.862  49.836  23.438  1.00  0.00
ATOM   1271  CD2 LEU   163       8.796  48.603  22.535  1.00  0.00
ATOM   1272  N   THR   164       7.306  53.228  21.645  1.00  0.00
ATOM   1273  CA  THR   164       8.157  54.381  21.686  1.00  0.00
ATOM   1274  C   THR   164       8.513  54.615  23.116  1.00  0.00
ATOM   1275  O   THR   164       8.305  53.752  23.965  1.00  0.00
ATOM   1276  CB  THR   164       7.450  55.625  21.117  1.00  0.00
ATOM   1277  OG1 THR   164       8.396  56.693  20.975  1.00  0.00
ATOM   1278  CG2 THR   164       6.335  56.075  22.049  1.00  0.00
ATOM   1279  N   ASP   165       9.089  55.792  23.418  1.00  0.00
ATOM   1280  CA  ASP   165       9.449  56.079  24.774  1.00  0.00
ATOM   1281  C   ASP   165       8.197  55.974  25.640  1.00  0.00
ATOM   1282  O   ASP   165       8.353  55.987  26.890  1.00  0.00
ATOM   1283  CB  ASP   165      10.029  57.490  24.887  1.00  0.00
ATOM   1284  CG  ASP   165      11.407  57.605  24.267  1.00  0.00
ATOM   1285  OD1 ASP   165      12.036  56.555  24.019  1.00  0.00
ATOM   1286  OD2 ASP   165      11.858  58.745  24.027  1.00  0.00
TER
END
