
#######################################################
#                                                     #
#                        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 (   79),  selected   10 , name T0318TS021_1_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS021_1_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     355           -
LGA    -       -      T     356           -
LGA    -       -      I     357           -
LGA    -       -      F     358           -
LGA    -       -      D     359           -
LGA    -       -      M     360           -
LGA    -       -      A     361           -
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    T     156      L     385          1.697
LGA    N     157      E     386          2.053
LGA    E     158      N     387          3.233
LGA    D     159      E     388          3.391
LGA    -       -      I     389           -
LGA    A     160      I     390          3.289
LGA    V     161      K     391          2.242
LGA    -       -      A     392           -
LGA    F     162      G     393          1.686
LGA    -       -      K     394           -
LGA    -       -      A     395           -
LGA    -       -      S     396           -
LGA    -       -      G     397           -
LGA    -       -      D     398           -
LGA    -       -      L     399           -
LGA    L     163      V     400          1.906
LGA    T     164      A     401          3.294
LGA    D     165      P     402          1.498
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    -       -      I     458           -
LGA    -       -      A     459           -
LGA    -       -      A     460           -
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    2.54     0.00      2.152     0.379

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.475481 * X  +   0.201778 * Y  +   0.856273 * Z  +  -8.929071
  Y_new =   0.671888 * X  +   0.711600 * Y  +   0.205408 * Z  +  17.550255
  Z_new =  -0.567876 * X  +   0.672987 * Y  +  -0.473925 * Z  +  20.487741 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.184343   -0.957250  [ DEG:   125.1536    -54.8464 ]
  Theta =   0.603924    2.537669  [ DEG:    34.6023    145.3977 ]
  Phi   =   2.186658   -0.954935  [ DEG:   125.2863    -54.7137 ]
 
# 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: T0318TS021_1_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS021_1_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   2.54    0.00   2.152
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS021_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1209  N   THR   156       0.590  32.920  23.044  1.00455.85       1SG1210
ATOM   1210  CA  THR   156      -0.544  33.757  22.809  1.00455.85       1SG1211
ATOM   1211  CB  THR   156      -1.568  33.720  23.900  1.00455.85       1SG1212
ATOM   1212  OG1 THR   156      -0.986  34.147  25.123  1.00455.85       1SG1213
ATOM   1213  CG2 THR   156      -2.112  32.284  24.022  1.00455.85       1SG1214
ATOM   1214  C   THR   156      -0.038  35.154  22.695  1.00455.85       1SG1215
ATOM   1215  O   THR   156       1.130  35.384  22.390  1.00455.85       1SG1216
ATOM   1216  N   ASN   157      -0.936  36.128  22.912  1.00424.17       1SG1217
ATOM   1217  CA  ASN   157      -0.581  37.506  22.759  1.00424.17       1SG1218
ATOM   1218  CB  ASN   157      -1.756  38.470  22.990  1.00424.17       1SG1219
ATOM   1219  CG  ASN   157      -1.237  39.889  22.777  1.00424.17       1SG1220
ATOM   1220  OD1 ASN   157      -1.431  40.759  23.624  1.00424.17       1SG1221
ATOM   1221  ND2 ASN   157      -0.565  40.132  21.619  1.00424.17       1SG1222
ATOM   1222  C   ASN   157       0.481  37.855  23.738  1.00424.17       1SG1223
ATOM   1223  O   ASN   157       1.408  38.591  23.411  1.00424.17       1SG1224
ATOM   1224  N   GLU   158       0.388  37.339  24.974  1.00302.10       1SG1225
ATOM   1225  CA  GLU   158       1.391  37.707  25.928  1.00302.10       1SG1226
ATOM   1226  CB  GLU   158       1.045  37.241  27.349  1.00302.10       1SG1227
ATOM   1227  CG  GLU   158      -0.371  37.608  27.808  1.00302.10       1SG1228
ATOM   1228  CD  GLU   158      -0.589  39.107  27.668  1.00302.10       1SG1229
ATOM   1229  OE1 GLU   158       0.380  39.835  27.327  1.00302.10       1SG1230
ATOM   1230  OE2 GLU   158      -1.746  39.542  27.904  1.00302.10       1SG1231
ATOM   1231  C   GLU   158       2.624  36.954  25.531  1.00302.10       1SG1232
ATOM   1232  O   GLU   158       2.657  35.733  25.663  1.00302.10       1SG1233
ATOM   1233  N   ASP   159       3.669  37.655  25.036  1.00219.23       1SG1234
ATOM   1234  CA  ASP   159       4.854  36.956  24.611  1.00219.23       1SG1235
ATOM   1235  CB  ASP   159       5.740  37.754  23.632  1.00219.23       1SG1236
ATOM   1236  CG  ASP   159       6.832  36.892  23.015  1.00219.23       1SG1237
ATOM   1237  OD1 ASP   159       7.332  35.949  23.682  1.00219.23       1SG1238
ATOM   1238  OD2 ASP   159       7.189  37.191  21.845  1.00219.23       1SG1239
ATOM   1239  C   ASP   159       5.643  36.618  25.827  1.00219.23       1SG1240
ATOM   1240  O   ASP   159       5.901  37.462  26.683  1.00219.23       1SG1241
ATOM   1241  N   ALA   160       6.079  35.352  25.898  1.00129.94       1SG1242
ATOM   1242  CA  ALA   160       6.806  34.877  27.028  1.00129.94       1SG1243
ATOM   1243  CB  ALA   160       7.253  33.417  26.883  1.00129.94       1SG1244
ATOM   1244  C   ALA   160       8.040  35.710  27.149  1.00129.94       1SG1245
ATOM   1245  O   ALA   160       8.442  36.041  28.260  1.00129.94       1SG1246
ATOM   1246  N   VAL   161       8.650  36.089  26.008  1.00236.05       1SG1247
ATOM   1247  CA  VAL   161       9.875  36.843  25.990  1.00236.05       1SG1248
ATOM   1248  CB  VAL   161      10.736  36.506  24.809  1.00236.05       1SG1249
ATOM   1249  CG1 VAL   161      10.030  37.052  23.561  1.00236.05       1SG1250
ATOM   1250  CG2 VAL   161      12.167  37.036  25.023  1.00236.05       1SG1251
ATOM   1251  C   VAL   161       9.508  38.290  25.915  1.00236.05       1SG1252
ATOM   1252  O   VAL   161       8.330  38.629  26.003  1.00236.05       1SG1253
ATOM   1253  N   PHE   162      10.521  39.181  25.806  1.00310.55       1SG1254
ATOM   1254  CA  PHE   162      10.297  40.596  25.789  1.00310.55       1SG1255
ATOM   1255  CB  PHE   162      11.559  41.403  25.435  1.00310.55       1SG1256
ATOM   1256  CG  PHE   162      11.228  42.855  25.441  1.00310.55       1SG1257
ATOM   1257  CD1 PHE   162      11.273  43.585  26.605  1.00310.55       1SG1258
ATOM   1258  CD2 PHE   162      10.873  43.493  24.274  1.00310.55       1SG1259
ATOM   1259  CE1 PHE   162      10.971  44.925  26.609  1.00310.55       1SG1260
ATOM   1260  CE2 PHE   162      10.569  44.833  24.273  1.00310.55       1SG1261
ATOM   1261  CZ  PHE   162      10.614  45.554  25.440  1.00310.55       1SG1262
ATOM   1262  C   PHE   162       9.252  40.882  24.770  1.00310.55       1SG1263
ATOM   1263  O   PHE   162       9.379  40.537  23.596  1.00310.55       1SG1264
ATOM   1264  N   LEU   163       8.173  41.508  25.265  1.00466.95       1SG1265
ATOM   1265  CA  LEU   163       6.975  41.895  24.587  1.00466.95       1SG1266
ATOM   1266  CB  LEU   163       6.922  41.614  23.075  1.00466.95       1SG1267
ATOM   1267  CG  LEU   163       5.584  42.040  22.437  1.00466.95       1SG1268
ATOM   1268  CD1 LEU   163       5.329  43.546  22.604  1.00466.95       1SG1269
ATOM   1269  CD2 LEU   163       5.494  41.583  20.972  1.00466.95       1SG1270
ATOM   1270  C   LEU   163       5.903  41.102  25.237  1.00466.95       1SG1271
ATOM   1271  O   LEU   163       5.288  40.242  24.611  1.00466.95       1SG1272
ATOM   1272  N   THR   164       5.639  41.412  26.517  1.00279.18       1SG1273
ATOM   1273  CA  THR   164       4.675  40.698  27.294  1.00279.18       1SG1274
ATOM   1274  CB  THR   164       5.281  39.930  28.433  1.00279.18       1SG1275
ATOM   1275  OG1 THR   164       4.314  39.081  29.034  1.00279.18       1SG1276
ATOM   1276  CG2 THR   164       5.806  40.937  29.472  1.00279.18       1SG1277
ATOM   1277  C   THR   164       3.787  41.723  27.899  1.00279.18       1SG1278
ATOM   1278  O   THR   164       3.960  42.920  27.667  1.00279.18       1SG1279
ATOM   1279  N   ASP   165       2.784  41.280  28.675  1.00 94.17       1SG1280
ATOM   1280  CA  ASP   165       1.919  42.250  29.260  1.00 94.17       1SG1281
ATOM   1281  CB  ASP   165       0.635  41.665  29.866  1.00 94.17       1SG1282
ATOM   1282  CG  ASP   165      -0.318  42.831  30.080  1.00 94.17       1SG1283
ATOM   1283  OD1 ASP   165       0.085  43.987  29.782  1.00 94.17       1SG1284
ATOM   1284  OD2 ASP   165      -1.464  42.581  30.541  1.00 94.17       1SG1285
ATOM   1285  C   ASP   165       2.704  42.931  30.376  1.00 94.17       1SG1286
ATOM   1286  O   ASP   165       2.660  42.429  31.531  1.00 94.17       1SG1287
ATOM   1287  OXT ASP   165       3.365  43.965  30.085  1.00 94.17       1SG1288
TER
END
