
#######################################################
#                                                     #
#                        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   76 (   76),  selected   76 , name T0301TS464_3_1
# Molecule2: number of CA atoms  391 ( 2894),  selected  391 , name T0301.pdb
# PARAMETERS: T0301TS464_3_1.T0301.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      A       2           -
LGA    -       -      H       3           -
LGA    -       -      P       4           -
LGA    -       -      P       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      R       8           -
LGA    -       -      I       9           -
LGA    -       -      P      10           -
LGA    -       -      A      11           -
LGA    -       -      T      12           -
LGA    -       -      Y      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      G      16           -
LGA    -       -      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    -       -      F      24           -
LGA    -       -      R      25           -
LGA    -       -      L      26           -
LGA    -       -      E      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      P      30           -
LGA    -       -      E      31           -
LGA    -       -      S      32           -
LGA    -       -      C      33           -
LGA    -       -      R      34           -
LGA    -       -      V      35           -
LGA    -       -      P      36           -
LGA    -       -      G      37           -
LGA    -       -      E      38           -
LGA    -       -      A      39           -
LGA    -       -      R      40           -
LGA    -       -      D      41           -
LGA    -       -      R      42           -
LGA    -       -      L      43           -
LGA    -       -      F      44           -
LGA    -       -      M      45           -
LGA    -       -      R      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      G      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      D      52           -
LGA    -       -      P      53           -
LGA    -       -      Y      54           -
LGA    -       -      A      55           -
LGA    -       -      A      56           -
LGA    -       -      H      57           -
LGA    -       -      I      58           -
LGA    -       -      D      59           -
LGA    -       -      G      60           -
LGA    -       -      M      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      A      64           -
LGA    -       -      T      65           -
LGA    -       -      S      66           -
LGA    -       -      S      67           -
LGA    -       -      T      68           -
LGA    -       -      S      69           -
LGA    -       -      K      70           -
LGA    -       -      C      71           -
LGA    -       -      V      72           -
LGA    -       -      I      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      K      76           -
LGA    -       -      S      77           -
LGA    -       -      S      78           -
LGA    -       -      Q      79           -
LGA    -       -      P      80           -
LGA    -       -      G      81           -
LGA    -       -      H      82           -
LGA    -       -      D      83           -
LGA    -       -      V      84           -
LGA    -       -      D      85           -
LGA    -       -      Y      86           -
LGA    -       -      L      87           -
LGA    -       -      Y      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      D      94           -
LGA    -       -      K      95           -
LGA    -       -      P      96           -
LGA    -       -      F      97           -
LGA    -       -      V      98           -
LGA    -       -      D      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      G     102           -
LGA    -       -      N     103           -
LGA    -       -      C     104           -
LGA    -       -      G     105           -
LGA    -       -      N     106           -
LGA    -       -      L     107           -
LGA    -       -      S     108           -
LGA    -       -      T     109           -
LGA    -       -      G     110           -
LGA    -       -      A     111           -
LGA    -       -      G     112           -
LGA    -       -      A     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -
LGA    -       -      H     117           -
LGA    -       -      A     118           -
LGA    -       -      G     119           -
LGA    -       -      L     120           -
LGA    -       -      V     121           -
LGA    -       -      D     122           -
LGA    -       -      P     123           -
LGA    -       -      A     124           -
LGA    -       -      R     125           -
LGA    -       -      I     126           -
LGA    -       -      P     127           -
LGA    -       -      E     128           -
LGA    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      I     131           -
LGA    -       -      C     132           -
LGA    -       -      E     133           -
LGA    -       -      V     134           -
LGA    -       -      R     135           -
LGA    -       -      I     136           -
LGA    -       -      W     137           -
LGA    -       -      Q     138           -
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    G      60      K     143          4.648
LGA    M      61      T     144           -
LGA    G      62      I     145           #
LGA    G      63      I     146           -
LGA    A      64      A     147           -
LGA    -       -      H     148           -
LGA    G     166      V     149          4.027
LGA    V     167      P     150          3.620
LGA    -       -      V     151           -
LGA    -       -      S     152           -
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    -       -      V     156           -
LGA    -       -      Q     157           -
LGA    -       -      E     158           -
LGA    -       -      T     159           -
LGA    -       -      G     160           -
LGA    -       -      D     161           -
LGA    -       -      F     162           -
LGA    -       -      E     163           -
LGA    -       -      L     164           -
LGA    -       -      D     165           -
LGA    -       -      G     166           -
LGA    -       -      V     167           -
LGA    -       -      T     168           -
LGA    -       -      F     169           -
LGA    -       -      P     170           -
LGA    -       -      A     171           -
LGA    T     168      A     172           #
LGA    F     169      E     173           #
LGA    P     170      I     174          4.273
LGA    A     171      V     175          3.130
LGA    A     172      L     176          0.672
LGA    E     173      E     177          4.383
LGA    I     174      -       -           -
LGA    V     175      -       -           -
LGA    L     176      F     178          2.403
LGA    E     177      L     179           -
LGA    F     178      D     180           -
LGA    L     179      -       -           -
LGA    D     180      P     181          3.209
LGA    P     181      S     182          3.666
LGA    S     182      D     187           -
LGA    G     207      G     188           -
LGA    -       -      G     189           -
LGA    -       -      A     190           -
LGA    -       -      I     191           -
LGA    -       -      F     192           -
LGA    -       -      P     193           -
LGA    -       -      T     194           -
LGA    -       -      G     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      V     198           -
LGA    -       -      D     199           -
LGA    -       -      D     200           -
LGA    -       -      L     201           -
LGA    -       -      E     202           -
LGA    -       -      V     203           -
LGA    -       -      P     204           -
LGA    -       -      G     205           -
LGA    -       -      V     206           -
LGA    -       -      G     207           -
LGA    -       -      T     208           -
LGA    -       -      F     209           -
LGA    -       -      K     210           -
LGA    -       -      A     211           -
LGA    -       -      T     212           -
LGA    -       -      M     213           -
LGA    -       -      I     214           -
LGA    -       -      N     215           -
LGA    -       -      A     216           -
LGA    -       -      G     217           -
LGA    -       -      I     218           -
LGA    -       -      P     219           -
LGA    -       -      T     220           -
LGA    -       -      V     221           -
LGA    -       -      F     222           -
LGA    -       -      V     223           -
LGA    -       -      N     224           -
LGA    -       -      A     225           -
LGA    -       -      E     226           -
LGA    -       -      E     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      Y     230           -
LGA    -       -      R     231           -
LGA    -       -      G     232           -
LGA    -       -      T     233           -
LGA    -       -      E     234           -
LGA    -       -      L     235           -
LGA    -       -      R     236           -
LGA    -       -      E     237           -
LGA    -       -      E     238           -
LGA    -       -      I     239           -
LGA    -       -      N     240           -
LGA    -       -      G     241           -
LGA    -       -      D     242           -
LGA    -       -      P     243           -
LGA    -       -      Q     244           -
LGA    -       -      Q     245           -
LGA    -       -      L     246           -
LGA    -       -      A     247           -
LGA    -       -      R     248           -
LGA    -       -      F     249           -
LGA    -       -      E     250           -
LGA    -       -      R     251           -
LGA    -       -      I     252           -
LGA    -       -      R     253           -
LGA    -       -      V     254           -
LGA    -       -      A     255           -
LGA    -       -      G     256           -
LGA    -       -      A     257           -
LGA    -       -      L     258           -
LGA    -       -      R     259           -
LGA    -       -      M     260           -
LGA    -       -      G     261           -
LGA    -       -      L     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      P     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      A     269           -
LGA    -       -      A     270           -
LGA    -       -      T     271           -
LGA    -       -      R     272           -
LGA    -       -      Q     273           -
LGA    -       -      H     274           -
LGA    -       -      T     275           -
LGA    -       -      P     276           -
LGA    -       -      K     277           -
LGA    -       -      I     278           -
LGA    -       -      A     279           -
LGA    -       -      F     280           -
LGA    -       -      V     281           -
LGA    -       -      A     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      R     285           -
LGA    -       -      D     286           -
LGA    -       -      Y     287           -
LGA    -       -      R     288           -
LGA    T     208      T     289           #
LGA    F     209      A     290           -
LGA    K     210      S     291           -
LGA    -       -      G     292           -
LGA    -       -      K     293           -
LGA    -       -      L     294           -
LGA    A     211      V     295          3.926
LGA    -       -      A     296           -
LGA    -       -      A     297           -
LGA    -       -      G     298           -
LGA    T     212      D     299           #
LGA    M     213      -       -           -
LGA    I     214      -       -           -
LGA    N     215      I     300          1.863
LGA    A     216      D     301          2.530
LGA    G     217      L     302          1.855
LGA    I     218      L     303          3.728
LGA    P     219      V     304          1.647
LGA    T     220      R     305          1.069
LGA    V     221      -       -           -
LGA    F     222      -       -           -
LGA    P     276      -       -           -
LGA    K     277      A     306          3.581
LGA    I     278      L     307           #
LGA    A     279      S     308           #
LGA    -       -      M     309           -
LGA    -       -      G     310           -
LGA    -       -      K     311           -
LGA    -       -      L     312           -
LGA    F     280      H     313          4.091
LGA    V     281      H     314          0.995
LGA    A     282      A     315           #
LGA    D     299      -       -           -
LGA    I     300      -       -           -
LGA    D     301      -       -           -
LGA    L     302      -       -           -
LGA    L     303      M     316          3.271
LGA    V     304      M     317           #
LGA    A     327      G     318          2.701
LGA    -       -      T     319           -
LGA    -       -      A     320           -
LGA    A     328      A     321          2.439
LGA    A     329      V     322          5.326
LGA    -       -      A     323           -
LGA    I     330      I     324          1.634
LGA    -       -      G     325           -
LGA    -       -      T     326           -
LGA    -       -      A     327           -
LGA    -       -      A     328           -
LGA    -       -      A     329           -
LGA    -       -      I     330           -
LGA    -       -      P     331           -
LGA    -       -      G     332           -
LGA    -       -      T     333           -
LGA    -       -      L     334           -
LGA    P     331      V     335          2.307
LGA    L     356      N     336           -
LGA    R     357      L     337           -
LGA    V     358      A     338           -
LGA    G     359      A     339           -
LGA    A     360      G     340           -
LGA    -       -      G     341           -
LGA    -       -      G     342           -
LGA    -       -      E     343           -
LGA    -       -      R     344           -
LGA    -       -      S     345           -
LGA    -       -      A     346           -
LGA    -       -      V     347           -
LGA    -       -      R     348           -
LGA    -       -      F     349           -
LGA    -       -      G     350           -
LGA    -       -      H     351           -
LGA    -       -      P     352           -
LGA    -       -      S     353           -
LGA    M     376      G     354           #
LGA    S     377      T     355          4.308
LGA    R     378      L     356          4.531
LGA    S     379      -       -           -
LGA    A     380      -       -           -
LGA    R     381      R     357          1.021
LGA    I     382      V     358          1.204
LGA    L     383      -       -           -
LGA    M     384      G     359          5.177
LGA    E     385      A     360          5.237
LGA    G     386      E     361           #
LGA    -       -      A     362           -
LGA    -       -      S     363           -
LGA    -       -      Q     364           -
LGA    -       -      A     365           -
LGA    -       -      N     366           -
LGA    -       -      G     367           -
LGA    -       -      E     368           -
LGA    -       -      W     369           -
LGA    -       -      T     370           -
LGA    -       -      V     371           -
LGA    -       -      T     372           -
LGA    -       -      K     373           -
LGA    W     387      A     374          3.335
LGA    V     388      I     375           #
LGA    R     389      M     376           -
LGA    V     390      S     377           -
LGA    -       -      R     378           -
LGA    -       -      S     379           -
LGA    -       -      A     380           -
LGA    -       -      R     381           -
LGA    -       -      I     382           -
LGA    -       -      L     383           -
LGA    -       -      M     384           -
LGA    -       -      E     385           -
LGA    -       -      G     386           -
LGA    -       -      W     387           -
LGA    -       -      V     388           -
LGA    -       -      R     389           -
LGA    -       -      V     390           -
LGA    -       -      P     391           -
LGA    -       -      G     392           -
LGA    -       -      D     393           -
LGA    -       -      A     394           -
LGA    -       -      F     395           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   76  391    5.0     33    3.36    12.12      4.908     0.954

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.842753 * X  +  -0.538236 * Y  +   0.008333 * Z  +  77.456268
  Y_new =  -0.531027 * X  +  -0.833802 * Y  +  -0.150949 * Z  +  33.209709
  Z_new =   0.088194 * X  +   0.122788 * Y  +  -0.988506 * Z  +  40.960018 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.018010   -0.123583  [ DEG:   172.9192     -7.0808 ]
  Theta =  -0.088309   -3.053284  [ DEG:    -5.0597   -174.9403 ]
  Phi   =  -0.562265    2.579327  [ DEG:   -32.2154    147.7846 ]
 
# 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: T0301TS464_3_1                                
REMARK     2: T0301.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_3_1.T0301.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   76  391   5.0   33   3.36   12.12   4.908
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_3_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  GLY    60      79.697   9.871   0.060  1.00  0.00
ATOM      2  CA  MET    61      80.537   6.355   1.356  1.00  0.00
ATOM      3  CA  GLY    62      79.326   6.894   5.022  1.00  0.00
ATOM      4  CA  GLY    63      82.877   6.506   6.339  1.00  0.00
ATOM      5  CA  ALA    64      84.867   9.561   7.495  1.00  0.00
ATOM      6  CA  GLY   166      68.911  11.049  19.423  1.00  0.00
ATOM      7  CA  VAL   167      71.291  14.016  19.737  1.00  0.00
ATOM      8  CA  THR   168      74.405  11.838  19.516  1.00  0.00
ATOM      9  CA  PHE   169      73.069  10.432  16.260  1.00  0.00
ATOM     10  CA  PRO   170      72.375  13.922  14.912  1.00  0.00
ATOM     11  CA  ALA   171      76.103  14.266  15.668  1.00  0.00
ATOM     12  CA  ALA   172      77.163  11.594  13.119  1.00  0.00
ATOM     13  CA  GLU   173      74.828  13.190  10.575  1.00  0.00
ATOM     14  CA  ILE   174      76.499  16.594  10.928  1.00  0.00
ATOM     15  CA  VAL   175      79.999  15.102  10.822  1.00  0.00
ATOM     16  CA  LEU   176      79.238  12.771   7.873  1.00  0.00
ATOM     17  CA  GLU   177      77.618  15.640   5.920  1.00  0.00
ATOM     18  CA  PHE   178      80.706  17.847   6.297  1.00  0.00
ATOM     19  CA  LEU   179      83.663  15.524   6.022  1.00  0.00
ATOM     20  CA  ASP   180      82.493  12.638   3.890  1.00  0.00
ATOM     21  CA  PRO   181      83.600  14.022   0.550  1.00  0.00
ATOM     22  CA  SER   182      83.001  10.857  -1.579  1.00  0.00
ATOM     23  CA  GLY   207      94.540  13.099  31.429  1.00  0.00
ATOM     24  CA  THR   208      90.922  12.008  31.042  1.00  0.00
ATOM     25  CA  PHE   209      90.903  11.889  27.191  1.00  0.00
ATOM     26  CA  LYS   210      94.295  10.109  27.090  1.00  0.00
ATOM     27  CA  ALA   211      92.968   7.207  29.174  1.00  0.00
ATOM     28  CA  THR   212      89.921   7.610  26.943  1.00  0.00
ATOM     29  CA  MET   213      91.903   6.744  23.805  1.00  0.00
ATOM     30  CA  ILE   214      93.642   3.819  25.586  1.00  0.00
ATOM     31  CA  ASN   215      90.274   2.197  26.451  1.00  0.00
ATOM     32  CA  ALA   216      89.476   2.478  22.745  1.00  0.00
ATOM     33  CA  GLY   217      92.707   0.892  21.491  1.00  0.00
ATOM     34  CA  ILE   218      93.920   4.260  20.161  1.00  0.00
ATOM     35  CA  PRO   219      97.524   5.413  20.456  1.00  0.00
ATOM     36  CA  THR   220      97.996   9.128  21.103  1.00  0.00
ATOM     37  CA  VAL   221     100.488  10.605  23.259  1.00  0.00
ATOM     38  CA  PHE   222     100.313  13.552  25.713  1.00  0.00
ATOM     39  CA  PRO   276      99.106   5.437  13.778  1.00  0.00
ATOM     40  CA  LYS   277     100.062   7.977  16.437  1.00  0.00
ATOM     41  CA  ILE   278      97.446  10.409  17.779  1.00  0.00
ATOM     42  CA  ALA   279      98.652  13.538  19.581  1.00  0.00
ATOM     43  CA  PHE   280      96.560  14.745  22.574  1.00  0.00
ATOM     44  CA  VAL   281      97.267  18.463  23.092  1.00  0.00
ATOM     45  CA  ALA   282      96.839  19.503  26.736  1.00  0.00
ATOM     46  CA  ASP   299     103.689  12.202  13.513  1.00  0.00
ATOM     47  CA  ILE   300     100.148  12.494  14.687  1.00  0.00
ATOM     48  CA  ASP   301      96.692  12.800  13.105  1.00  0.00
ATOM     49  CA  LEU   302      94.772  15.019  15.509  1.00  0.00
ATOM     50  CA  LEU   303      95.205  16.961  18.690  1.00  0.00
ATOM     51  CA  VAL   304      92.941  17.270  21.632  1.00  0.00
ATOM     52  CA  ALA   327      88.572  13.357  13.546  1.00  0.00
ATOM     53  CA  ALA   328      88.075   9.632  14.136  1.00  0.00
ATOM     54  CA  ALA   329      91.132   8.181  15.920  1.00  0.00
ATOM     55  CA  ILE   330      91.835   4.519  14.956  1.00  0.00
ATOM     56  CA  PRO   331      93.602   1.621  16.772  1.00  0.00
ATOM     57  CA  LEU   356      92.133  16.383  13.134  1.00  0.00
ATOM     58  CA  ARG   357      90.897  18.783  15.747  1.00  0.00
ATOM     59  CA  VAL   358      88.732  16.989  18.336  1.00  0.00
ATOM     60  CA  GLY   359      86.085  19.673  18.560  1.00  0.00
ATOM     61  CA  ALA   360      83.832  21.695  16.230  1.00  0.00
ATOM     62  CA  MET   376      87.602  15.147  21.420  1.00  0.00
ATOM     63  CA  SER   377      85.903  12.205  23.171  1.00  0.00
ATOM     64  CA  ARG   378      83.396  12.240  20.344  1.00  0.00
ATOM     65  CA  SER   379      86.077  11.897  17.659  1.00  0.00
ATOM     66  CA  ALA   380      87.639   9.122  19.730  1.00  0.00
ATOM     67  CA  ARG   381      84.462   7.057  20.002  1.00  0.00
ATOM     68  CA  ILE   382      83.604   7.309  16.318  1.00  0.00
ATOM     69  CA  LEU   383      87.203   6.426  15.571  1.00  0.00
ATOM     70  CA  MET   384      87.041   3.407  17.870  1.00  0.00
ATOM     71  CA  GLU   385      83.761   2.354  16.215  1.00  0.00
ATOM     72  CA  GLY   386      85.586   2.417  12.868  1.00  0.00
ATOM     73  CA  TRP   387      83.715   5.433  11.480  1.00  0.00
ATOM     74  CA  VAL   388      86.584   7.894  11.121  1.00  0.00
ATOM     75  CA  ARG   389      90.264   7.959  10.205  1.00  0.00
ATOM     76  CA  VAL   390      92.107  10.218  12.669  1.00  0.00
TER
END
