
#######################################################
#                                                     #
#                        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 T0318TS022_3_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS022_3_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    T     156      K     349          2.595
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    -       -      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    N     157      I     445          2.514
LGA    E     158      G     446          4.315
LGA    -       -      F     447           -
LGA    D     159      G     448          2.371
LGA    A     160      E     449          2.235
LGA    -       -      G     450           -
LGA    V     161      L     451          2.306
LGA    F     162      R     452          1.110
LGA    L     163      W     453          0.971
LGA    T     164      L     454          0.673
LGA    D     165      H     455          0.979
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    2.26     0.00      2.325     0.423

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.500892 * X  +   0.470274 * Y  +   0.726601 * Z  + -21.279165
  Y_new =   0.830284 * X  +   0.024018 * Y  +   0.556822 * Z  +  31.384939
  Z_new =   0.244407 * X  +   0.882193 * Y  +  -0.402492 * Z  +  -3.560254 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.998827   -1.142765  [ DEG:   114.5244    -65.4756 ]
  Theta =  -0.246908   -2.894684  [ DEG:   -14.1468   -165.8532 ]
  Phi   =   2.113622   -1.027970  [ DEG:   121.1016    -58.8984 ]
 
# 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: T0318TS022_3_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS022_3_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   2.26    0.00   2.325
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS022_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1olm_A
ATOM   1170  N   THR   156      -9.035  42.382   7.764  1.00  0.00
ATOM   1171  CA  THR   156      -9.355  41.321   8.669  1.00  0.00
ATOM   1172  C   THR   156      -9.954  42.009   9.840  1.00  0.00
ATOM   1173  O   THR   156      -9.690  43.188  10.068  1.00  0.00
ATOM   1174  CB  THR   156      -8.100  40.526   9.074  1.00  0.00
ATOM   1175  OG1 THR   156      -7.197  41.382   9.786  1.00  0.00
ATOM   1176  CG2 THR   156      -7.394  39.981   7.841  1.00  0.00
ATOM   1177  N   ASN   157     -10.796  41.311  10.616  1.00  0.00
ATOM   1178  CA  ASN   157     -11.386  41.991  11.725  1.00  0.00
ATOM   1179  C   ASN   157     -10.450  41.896  12.883  1.00  0.00
ATOM   1180  O   ASN   157      -9.675  40.948  12.999  1.00  0.00
ATOM   1181  CB  ASN   157     -12.726  41.351  12.095  1.00  0.00
ATOM   1182  CG  ASN   157     -13.791  41.579  11.042  1.00  0.00
ATOM   1183  OD1 ASN   157     -13.727  42.543  10.278  1.00  0.00
ATOM   1184  ND2 ASN   157     -14.777  40.690  10.997  1.00  0.00
ATOM   1185  N   GLU   158     -10.483  42.909  13.767  1.00  0.00
ATOM   1186  CA  GLU   158      -9.594  42.889  14.888  1.00  0.00
ATOM   1187  C   GLU   158      -9.942  41.700  15.716  1.00  0.00
ATOM   1188  O   GLU   158      -9.067  40.950  16.146  1.00  0.00
ATOM   1189  CB  GLU   158      -9.749  44.166  15.717  1.00  0.00
ATOM   1190  CG  GLU   158      -9.209  45.415  15.040  1.00  0.00
ATOM   1191  CD  GLU   158      -9.502  46.677  15.827  1.00  0.00
ATOM   1192  OE1 GLU   158     -10.197  46.585  16.861  1.00  0.00
ATOM   1193  OE2 GLU   158      -9.036  47.759  15.411  1.00  0.00
ATOM   1194  N   ASP   159     -11.247  41.501  15.959  1.00  0.00
ATOM   1195  CA  ASP   159     -11.677  40.386  16.745  1.00  0.00
ATOM   1196  C   ASP   159     -11.401  39.131  15.986  1.00  0.00
ATOM   1197  O   ASP   159     -10.901  38.153  16.540  1.00  0.00
ATOM   1198  CB  ASP   159     -13.176  40.484  17.037  1.00  0.00
ATOM   1199  CG  ASP   159     -13.504  41.560  18.052  1.00  0.00
ATOM   1200  OD1 ASP   159     -12.567  42.062  18.710  1.00  0.00
ATOM   1201  OD2 ASP   159     -14.697  41.904  18.190  1.00  0.00
ATOM   1202  N   ALA   160     -11.696  39.147  14.672  1.00  0.00
ATOM   1203  CA  ALA   160     -11.621  37.949  13.888  1.00  0.00
ATOM   1204  C   ALA   160     -10.240  37.412  13.877  1.00  0.00
ATOM   1205  O   ALA   160     -10.030  36.228  14.126  1.00  0.00
ATOM   1206  CB  ALA   160     -12.037  38.230  12.452  1.00  0.00
ATOM   1207  N   VAL   161      -9.246  38.273  13.624  1.00  0.00
ATOM   1208  CA  VAL   161      -7.905  37.783  13.589  1.00  0.00
ATOM   1209  C   VAL   161      -7.433  37.834  14.991  1.00  0.00
ATOM   1210  O   VAL   161      -8.079  38.448  15.837  1.00  0.00
ATOM   1211  CB  VAL   161      -7.011  38.652  12.685  1.00  0.00
ATOM   1212  CG1 VAL   161      -7.530  38.642  11.255  1.00  0.00
ATOM   1213  CG2 VAL   161      -6.990  40.089  13.179  1.00  0.00
ATOM   1214  N   PHE   162      -6.323  37.134  15.288  1.00  0.00
ATOM   1215  CA  PHE   162      -5.802  37.238  16.605  1.00  0.00
ATOM   1216  C   PHE   162      -5.069  38.523  16.509  1.00  0.00
ATOM   1217  O   PHE   162      -3.841  38.564  16.455  1.00  0.00
ATOM   1218  CB  PHE   162      -4.896  36.046  16.919  1.00  0.00
ATOM   1219  CG  PHE   162      -4.578  35.893  18.379  1.00  0.00
ATOM   1220  CD1 PHE   162      -5.534  35.430  19.265  1.00  0.00
ATOM   1221  CD2 PHE   162      -3.322  36.212  18.865  1.00  0.00
ATOM   1222  CE1 PHE   162      -5.241  35.290  20.609  1.00  0.00
ATOM   1223  CE2 PHE   162      -3.029  36.073  20.208  1.00  0.00
ATOM   1224  CZ  PHE   162      -3.983  35.613  21.079  1.00  0.00
ATOM   1225  N   LEU   163      -5.843  39.618  16.492  1.00  0.00
ATOM   1226  CA  LEU   163      -5.284  40.905  16.270  1.00  0.00
ATOM   1227  C   LEU   163      -4.455  41.207  17.462  1.00  0.00
ATOM   1228  O   LEU   163      -4.863  40.961  18.597  1.00  0.00
ATOM   1229  CB  LEU   163      -6.390  41.949  16.104  1.00  0.00
ATOM   1230  CG  LEU   163      -5.938  43.362  15.728  1.00  0.00
ATOM   1231  CD1 LEU   163      -5.316  43.376  14.339  1.00  0.00
ATOM   1232  CD2 LEU   163      -7.118  44.322  15.731  1.00  0.00
ATOM   1233  N   THR   164      -3.246  41.740  17.230  1.00  0.00
ATOM   1234  CA  THR   164      -2.402  42.057  18.338  1.00  0.00
ATOM   1235  C   THR   164      -1.812  43.398  18.068  1.00  0.00
ATOM   1236  O   THR   164      -2.132  44.044  17.071  1.00  0.00
ATOM   1237  CB  THR   164      -1.276  41.018  18.505  1.00  0.00
ATOM   1238  OG1 THR   164      -0.392  41.082  17.379  1.00  0.00
ATOM   1239  CG2 THR   164      -1.856  39.615  18.597  1.00  0.00
ATOM   1240  N   ASP   165      -0.945  43.853  18.989  1.00  0.00
ATOM   1241  CA  ASP   165      -0.287  45.118  18.843  1.00  0.00
ATOM   1242  C   ASP   165       0.352  45.125  17.459  1.00  0.00
ATOM   1243  O   ASP   165       1.061  44.135  17.133  1.00  0.00
ATOM   1244  CB  ASP   165       0.781  45.294  19.924  1.00  0.00
ATOM   1245  CG  ASP   165       1.370  46.691  19.939  1.00  0.00
ATOM   1246  OD1 ASP   165       0.935  47.528  19.122  1.00  0.00
ATOM   1247  OD2 ASP   165       2.267  46.948  20.770  1.00  0.00
TER
END
