
#######################################################
#                                                     #
#                        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_5_2
# Molecule2: number of CA atoms  391 ( 2894),  selected  391 , name T0301.pdb
# PARAMETERS: T0301TS464_5_2.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    -       -      K     143           -
LGA    -       -      T     144           -
LGA    -       -      I     145           -
LGA    -       -      I     146           -
LGA    -       -      A     147           -
LGA    -       -      H     148           -
LGA    -       -      V     149           -
LGA    -       -      P     150           -
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    -       -      A     172           -
LGA    -       -      E     173           -
LGA    -       -      I     174           -
LGA    -       -      V     175           -
LGA    -       -      L     176           -
LGA    -       -      E     177           -
LGA    -       -      F     178           -
LGA    -       -      L     179           -
LGA    -       -      D     180           -
LGA    -       -      P     181           -
LGA    -       -      S     182           -
LGA    -       -      D     187           -
LGA    -       -      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    K      20      I     218          1.984
LGA    G      21      P     219          4.716
LGA    V      22      T     220          3.653
LGA    F      23      V     221          3.854
LGA    F      24      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    R      25      K     277          4.087
LGA    L      26      I     278          4.839
LGA    E      27      A     279           #
LGA    D      28      -       -           -
LGA    L      29      F     280          4.217
LGA    P      30      -       -           -
LGA    E      31      -       -           -
LGA    S      32      -       -           -
LGA    C      33      V     281           #
LGA    -       -      A     282           -
LGA    C      71      P     283          4.049
LGA    V      72      P     284          4.968
LGA    -       -      R     285           -
LGA    -       -      D     286           -
LGA    -       -      Y     287           -
LGA    -       -      R     288           -
LGA    -       -      T     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      G     292           -
LGA    -       -      K     293           -
LGA    -       -      L     294           -
LGA    -       -      V     295           -
LGA    -       -      A     296           -
LGA    -       -      A     297           -
LGA    -       -      G     298           -
LGA    -       -      D     299           -
LGA    -       -      I     300           -
LGA    -       -      D     301           -
LGA    -       -      L     302           -
LGA    I      73      L     303          3.098
LGA    L      74      V     304          4.742
LGA    S      75      -       -           -
LGA    K      76      -       -           -
LGA    S      77      -       -           -
LGA    G     110      -       -           -
LGA    A     111      -       -           -
LGA    G     112      -       -           -
LGA    A     113      -       -           -
LGA    F     114      -       -           -
LGA    A     115      -       -           -
LGA    I     141      -       -           -
LGA    G     142      -       -           -
LGA    K     143      -       -           -
LGA    T     144      -       -           -
LGA    I     145      -       -           -
LGA    E     227      -       -           -
LGA    I     228      -       -           -
LGA    G     229      -       -           -
LGA    Y     230      -       -           -
LGA    R     231      -       -           -
LGA    G     232      -       -           -
LGA    T     233      -       -           -
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    V     335      R     305          1.384
LGA    -       -      A     306           -
LGA    -       -      L     307           -
LGA    -       -      S     308           -
LGA    -       -      M     309           -
LGA    -       -      G     310           -
LGA    -       -      K     311           -
LGA    -       -      L     312           -
LGA    -       -      H     313           -
LGA    -       -      H     314           -
LGA    N     336      A     315          4.867
LGA    L     337      M     316          2.995
LGA    A     338      M     317          1.255
LGA    A     339      G     318          1.681
LGA    S     353      T     319          1.867
LGA    G     354      A     320          1.765
LGA    T     355      A     321          2.008
LGA    L     356      V     322          1.218
LGA    R     357      A     323          0.614
LGA    V     358      I     324          1.090
LGA    G     359      G     325          1.670
LGA    A     360      T     326          1.394
LGA    E     361      A     327          0.646
LGA    A     362      A     328          1.011
LGA    S     363      A     329          1.017
LGA    Q     364      I     330          1.011
LGA    A     365      P     331          1.884
LGA    -       -      G     332           -
LGA    -       -      T     333           -
LGA    -       -      L     334           -
LGA    -       -      V     335           -
LGA    -       -      N     336           -
LGA    -       -      L     337           -
LGA    -       -      A     338           -
LGA    -       -      A     339           -
LGA    -       -      G     340           -
LGA    -       -      G     341           -
LGA    N     366      G     342          3.403
LGA    G     367      E     343          2.983
LGA    E     368      R     344          2.626
LGA    W     369      S     345          3.137
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    -       -      G     354           -
LGA    -       -      T     355           -
LGA    -       -      L     356           -
LGA    -       -      R     357           -
LGA    -       -      V     358           -
LGA    -       -      G     359           -
LGA    -       -      A     360           -
LGA    -       -      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    -       -      A     374           -
LGA    -       -      I     375           -
LGA    -       -      M     376           -
LGA    -       -      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    2.95     6.06      5.630     1.082

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.266961 * X  +   0.392511 * Y  +  -0.880152 * Z  +  96.996536
  Y_new =  -0.620764 * X  +   0.768625 * Y  +   0.154489 * Z  + -27.809015
  Z_new =   0.737145 * X  +   0.505124 * Y  +   0.448850 * Z  +  -0.674538 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.844320   -2.297273  [ DEG:    48.3760   -131.6240 ]
  Theta =  -0.828836   -2.312757  [ DEG:   -47.4888   -132.5112 ]
  Phi   =  -1.164654    1.976938  [ DEG:   -66.7298    113.2702 ]
 
# 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_5_2                                
REMARK     2: T0301.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_5_2.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   2.95    6.06   5.630
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_5_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  LYS    20      95.987  11.301   6.140  1.00  0.00
ATOM      2  CA  GLY    21      98.449  12.771   8.595  1.00  0.00
ATOM      3  CA  VAL    22      97.460  10.468  11.432  1.00  0.00
ATOM      4  CA  PHE    23      97.708   7.489   9.107  1.00  0.00
ATOM      5  CA  PHE    24     101.415   8.196   8.538  1.00  0.00
ATOM      6  CA  ARG    25     101.804   8.643  12.273  1.00  0.00
ATOM      7  CA  LEU    26     100.186   5.265  13.003  1.00  0.00
ATOM      8  CA  GLU    27     102.328   3.549  10.396  1.00  0.00
ATOM      9  CA  ASP    28     105.391   4.904  12.202  1.00  0.00
ATOM     10  CA  LEU    29     104.221   3.495  15.504  1.00  0.00
ATOM     11  CA  PRO    30     103.158   0.131  14.061  1.00  0.00
ATOM     12  CA  GLU    31     106.489  -0.289  12.244  1.00  0.00
ATOM     13  CA  SER    32     108.524   0.654  15.304  1.00  0.00
ATOM     14  CA  CYS    33     106.136  -1.367  17.472  1.00  0.00
ATOM     15  CA  CYS    71      97.178   1.727  26.354  1.00  0.00
ATOM     16  CA  VAL    72      95.010   4.191  24.429  1.00  0.00
ATOM     17  CA  ILE    73      94.516   5.810  21.029  1.00  0.00
ATOM     18  CA  LEU    74      92.208   8.796  21.254  1.00  0.00
ATOM     19  CA  SER    75      90.888  11.034  18.498  1.00  0.00
ATOM     20  CA  LYS    76      88.351  13.681  17.506  1.00  0.00
ATOM     21  CA  SER    77      86.892  14.909  14.201  1.00  0.00
ATOM     22  CA  GLY   110     100.557  -0.836   4.200  1.00  0.00
ATOM     23  CA  ALA   111     100.156   1.137   7.430  1.00  0.00
ATOM     24  CA  GLY   112     101.534  -1.654   9.615  1.00  0.00
ATOM     25  CA  ALA   113      98.274  -3.034  10.971  1.00  0.00
ATOM     26  CA  PHE   114      98.957  -6.544  12.282  1.00  0.00
ATOM     27  CA  ALA   115      95.668  -7.155  14.036  1.00  0.00
ATOM     28  CA  ILE   141      98.053 -12.654   5.160  1.00  0.00
ATOM     29  CA  GLY   142      99.547 -13.934   8.407  1.00  0.00
ATOM     30  CA  LYS   143      97.667 -11.386  10.524  1.00  0.00
ATOM     31  CA  THR   144      95.477 -11.685  13.607  1.00  0.00
ATOM     32  CA  ILE   145      91.712 -11.325  13.728  1.00  0.00
ATOM     33  CA  GLU   227      69.862  14.413  15.110  1.00  0.00
ATOM     34  CA  ILE   228      73.640  14.164  14.708  1.00  0.00
ATOM     35  CA  GLY   229      73.231  10.518  13.685  1.00  0.00
ATOM     36  CA  TYR   230      74.682   8.711  16.701  1.00  0.00
ATOM     37  CA  ARG   231      73.400   5.176  17.303  1.00  0.00
ATOM     38  CA  GLY   232      73.560   5.442  21.110  1.00  0.00
ATOM     39  CA  THR   233      74.666   7.813  23.874  1.00  0.00
ATOM     40  CA  ALA   247      79.678  14.220   8.957  1.00  0.00
ATOM     41  CA  ARG   248      81.611  12.045  11.413  1.00  0.00
ATOM     42  CA  PHE   249      78.771   9.615  12.148  1.00  0.00
ATOM     43  CA  GLU   250      78.012   9.459   8.406  1.00  0.00
ATOM     44  CA  ARG   251      81.606   8.390   7.784  1.00  0.00
ATOM     45  CA  ILE   252      81.386   5.589  10.340  1.00  0.00
ATOM     46  CA  ARG   253      78.064   4.446   8.878  1.00  0.00
ATOM     47  CA  VAL   254      80.477   3.432   6.156  1.00  0.00
ATOM     48  CA  ALA   255      82.261   0.761   8.205  1.00  0.00
ATOM     49  CA  GLY   256      79.392  -0.581  10.313  1.00  0.00
ATOM     50  CA  ALA   257      81.315   0.357  13.441  1.00  0.00
ATOM     51  CA  LEU   258      79.174   1.049  16.507  1.00  0.00
ATOM     52  CA  ARG   259      79.043   4.885  17.081  1.00  0.00
ATOM     53  CA  MET   260      77.895   6.146  20.480  1.00  0.00
ATOM     54  CA  GLY   261      78.660   9.624  21.798  1.00  0.00
ATOM     55  CA  VAL   335      98.339   8.434  21.555  1.00  0.00
ATOM     56  CA  ASN   336      96.394  11.569  20.493  1.00  0.00
ATOM     57  CA  LEU   337      95.247  12.523  17.022  1.00  0.00
ATOM     58  CA  ALA   338      93.777  15.972  16.430  1.00  0.00
ATOM     59  CA  ALA   339      90.759  16.928  14.351  1.00  0.00
ATOM     60  CA  SER   353      89.385  13.886  11.497  1.00  0.00
ATOM     61  CA  GLY   354      91.694  11.477  13.391  1.00  0.00
ATOM     62  CA  THR   355      88.548   9.613  14.310  1.00  0.00
ATOM     63  CA  LEU   356      87.887   8.759  10.686  1.00  0.00
ATOM     64  CA  ARG   357      91.229   7.040  10.424  1.00  0.00
ATOM     65  CA  VAL   358      90.770   5.147  13.679  1.00  0.00
ATOM     66  CA  GLY   359      87.369   3.890  12.493  1.00  0.00
ATOM     67  CA  ALA   360      88.860   2.760   9.193  1.00  0.00
ATOM     68  CA  GLU   361      91.879   1.109  10.804  1.00  0.00
ATOM     69  CA  ALA   362      90.156  -0.611  13.728  1.00  0.00
ATOM     70  CA  SER   363      87.239  -1.813  11.611  1.00  0.00
ATOM     71  CA  GLN   364      89.739  -3.501   9.186  1.00  0.00
ATOM     72  CA  ALA   365      91.281  -5.183  12.235  1.00  0.00
ATOM     73  CA  ASN   366      87.878  -6.735  13.086  1.00  0.00
ATOM     74  CA  GLY   367      86.640  -4.431  15.829  1.00  0.00
ATOM     75  CA  GLU   368      82.890  -4.030  16.650  1.00  0.00
ATOM     76  CA  TRP   369      83.041  -0.351  17.633  1.00  0.00
TER
END
