
#######################################################
#                                                     #
#                        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_4_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_4_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    T     156      E     158          1.691
LGA    N     157      D     159          1.973
LGA    -       -      A     160           -
LGA    -       -      V     161           -
LGA    E     158      F     162          1.189
LGA    D     159      L     163          2.480
LGA    -       -      T     164           -
LGA    -       -      D     165           -
LGA    -       -      L     166           -
LGA    A     160      S     167          1.931
LGA    V     161      E     168          1.658
LGA    -       -      S     169           -
LGA    -       -      V     170           -
LGA    F     162      R     171          0.863
LGA    L     163      E     172          1.082
LGA    -       -      T     173           -
LGA    -       -      A     174           -
LGA    T     164      R     175          0.599
LGA    D     165      L     176          1.611
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    -       -      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    -       -      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    1.60     0.00      2.780     0.588

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.872774 * X  +   0.285421 * Y  +   0.395981 * Z  + -54.310280
  Y_new =   0.313797 * X  +  -0.293311 * Y  +   0.903050 * Z  +  51.070061
  Z_new =   0.373895 * X  +   0.912416 * Y  +   0.166430 * Z  + -13.258392 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.390374   -1.751219  [ DEG:    79.6626   -100.3374 ]
  Theta =  -0.383205   -2.758387  [ DEG:   -21.9561   -158.0439 ]
  Phi   =   2.796445   -0.345148  [ DEG:   160.2245    -19.7755 ]
 
# 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_4_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_4_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   1.60    0.00   2.780
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_4_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1l5g_A
ATOM   1209  N   THR   156      24.181  27.881  12.546  1.00  0.00
ATOM   1210  CA  THR   156      24.551  28.780  11.501  1.00  0.00
ATOM   1211  C   THR   156      24.319  30.129  12.079  1.00  0.00
ATOM   1212  O   THR   156      23.573  30.277  13.044  1.00  0.00
ATOM   1213  CB  THR   156      23.694  28.562  10.240  1.00  0.00
ATOM   1214  OG1 THR   156      22.319  28.831  10.541  1.00  0.00
ATOM   1215  CG2 THR   156      23.819  27.126   9.752  1.00  0.00
ATOM   1216  N   ASN   157      24.953  31.168  11.520  1.00  0.00
ATOM   1217  CA  ASN   157      24.833  32.413  12.205  1.00  0.00
ATOM   1218  C   ASN   157      23.773  33.254  11.591  1.00  0.00
ATOM   1219  O   ASN   157      23.602  33.298  10.373  1.00  0.00
ATOM   1220  CB  ASN   157      26.152  33.186  12.148  1.00  0.00
ATOM   1221  CG  ASN   157      27.253  32.520  12.948  1.00  0.00
ATOM   1222  OD1 ASN   157      26.986  31.799  13.910  1.00  0.00
ATOM   1223  ND2 ASN   157      28.499  32.760  12.553  1.00  0.00
ATOM   1224  N   GLU   158      23.000  33.919  12.467  1.00  0.00
ATOM   1225  CA  GLU   158      22.031  34.874  12.040  1.00  0.00
ATOM   1226  C   GLU   158      22.710  36.183  12.248  1.00  0.00
ATOM   1227  O   GLU   158      23.522  36.322  13.160  1.00  0.00
ATOM   1228  CB  GLU   158      20.757  34.754  12.878  1.00  0.00
ATOM   1229  CG  GLU   158      20.034  33.425  12.724  1.00  0.00
ATOM   1230  CD  GLU   158      18.754  33.361  13.533  1.00  0.00
ATOM   1231  OE1 GLU   158      18.461  34.334  14.259  1.00  0.00
ATOM   1232  OE2 GLU   158      18.043  32.338  13.439  1.00  0.00
ATOM   1233  N   ASP   159      22.441  37.169  11.373  1.00  0.00
ATOM   1234  CA  ASP   159      23.110  38.429  11.503  1.00  0.00
ATOM   1235  C   ASP   159      22.333  39.339  12.406  1.00  0.00
ATOM   1236  O   ASP   159      21.273  38.978  12.914  1.00  0.00
ATOM   1237  CB  ASP   159      23.252  39.103  10.137  1.00  0.00
ATOM   1238  CG  ASP   159      21.917  39.517   9.551  1.00  0.00
ATOM   1239  OD1 ASP   159      20.917  39.531  10.300  1.00  0.00
ATOM   1240  OD2 ASP   159      21.870  39.829   8.342  1.00  0.00
ATOM   1241  N   ALA   160      22.890  40.544  12.650  1.00  0.00
ATOM   1242  CA  ALA   160      22.242  41.568  13.418  1.00  0.00
ATOM   1243  C   ALA   160      22.416  42.812  12.613  1.00  0.00
ATOM   1244  O   ALA   160      23.452  42.991  11.975  1.00  0.00
ATOM   1245  CB  ALA   160      22.893  41.696  14.787  1.00  0.00
ATOM   1246  N   VAL   161      21.414  43.714  12.601  1.00  0.00
ATOM   1247  CA  VAL   161      21.620  44.852  11.756  1.00  0.00
ATOM   1248  C   VAL   161      21.037  46.067  12.401  1.00  0.00
ATOM   1249  O   VAL   161      20.050  45.994  13.131  1.00  0.00
ATOM   1250  CB  VAL   161      20.950  44.663  10.382  1.00  0.00
ATOM   1251  CG1 VAL   161      21.100  45.921   9.539  1.00  0.00
ATOM   1252  CG2 VAL   161      21.589  43.504   9.633  1.00  0.00
ATOM   1253  N   PHE   162      21.665  47.227  12.124  1.00  0.00
ATOM   1254  CA  PHE   162      21.251  48.495  12.652  1.00  0.00
ATOM   1255  C   PHE   162      20.904  49.363  11.486  1.00  0.00
ATOM   1256  O   PHE   162      21.664  49.462  10.523  1.00  0.00
ATOM   1257  CB  PHE   162      22.379  49.132  13.466  1.00  0.00
ATOM   1258  CG  PHE   162      22.755  48.352  14.694  1.00  0.00
ATOM   1259  CD1 PHE   162      23.758  47.400  14.647  1.00  0.00
ATOM   1260  CD2 PHE   162      22.104  48.571  15.896  1.00  0.00
ATOM   1261  CE1 PHE   162      24.104  46.683  15.777  1.00  0.00
ATOM   1262  CE2 PHE   162      22.449  47.854  17.026  1.00  0.00
ATOM   1263  CZ  PHE   162      23.445  46.914  16.970  1.00  0.00
ATOM   1264  N   LEU   163      19.724  50.010  11.537  1.00  0.00
ATOM   1265  CA  LEU   163      19.317  50.861  10.459  1.00  0.00
ATOM   1266  C   LEU   163      18.925  52.172  11.055  1.00  0.00
ATOM   1267  O   LEU   163      18.386  52.223  12.160  1.00  0.00
ATOM   1268  CB  LEU   163      18.133  50.248   9.709  1.00  0.00
ATOM   1269  CG  LEU   163      18.389  48.907   9.017  1.00  0.00
ATOM   1270  CD1 LEU   163      17.093  48.327   8.473  1.00  0.00
ATOM   1271  CD2 LEU   163      19.357  49.078   7.857  1.00  0.00
ATOM   1272  N   THR   164      19.202  53.276  10.337  1.00  0.00
ATOM   1273  CA  THR   164      18.847  54.569  10.841  1.00  0.00
ATOM   1274  C   THR   164      17.999  55.229   9.808  1.00  0.00
ATOM   1275  O   THR   164      18.105  54.937   8.617  1.00  0.00
ATOM   1276  CB  THR   164      20.094  55.430  11.114  1.00  0.00
ATOM   1277  OG1 THR   164      20.816  55.630   9.892  1.00  0.00
ATOM   1278  CG2 THR   164      21.005  54.744  12.119  1.00  0.00
ATOM   1279  N   ASP   165      17.111  56.136  10.248  1.00  0.00
ATOM   1280  CA  ASP   165      16.266  56.809   9.313  1.00  0.00
ATOM   1281  C   ASP   165      17.141  57.746   8.492  1.00  0.00
ATOM   1282  O   ASP   165      18.369  57.807   8.768  1.00  0.00
ATOM   1283  CB  ASP   165      15.189  57.612  10.045  1.00  0.00
ATOM   1284  CG  ASP   165      14.099  58.109   9.115  1.00  0.00
ATOM   1285  OD1 ASP   165      14.067  57.666   7.948  1.00  0.00
ATOM   1286  OD2 ASP   165      13.278  58.941   9.554  1.00  0.00
TER
END
