
#######################################################
#                                                     #
#                        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   44 (   44),  selected   44 , name T0321TS464_2_2
# Molecule2: number of CA atoms  244 ( 1840),  selected  244 , name T0321.pdb
# PARAMETERS: T0321TS464_2_2.T0321.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      W       2           -
LGA    -       -      E       3           -
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    -       -      M       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      G      11           -
LGA    -       -      I      12           -
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    -       -      D      19           -
LGA    -       -      E      20           -
LGA    -       -      L      21           -
LGA    -       -      V      22           -
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    -       -      V      29           -
LGA    -       -      I      30           -
LGA    -       -      R      31           -
LGA    -       -      S      32           -
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    -       -      G      37           -
LGA    -       -      L      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      N      41           -
LGA    -       -      R      42           -
LGA    -       -      P      43           -
LGA    -       -      F      44           -
LGA    -       -      E      45           -
LGA    -       -      T      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      P      49           -
LGA    -       -      M      50           -
LGA    -       -      L      51           -
LGA    -       -      T      52           -
LGA    -       -      Q      53           -
LGA    -       -      N      54           -
LGA    -       -      L      55           -
LGA    -       -      L      56           -
LGA    -       -      G      57           -
LGA    -       -      L      58           -
LGA    -       -      P      59           -
LGA    -       -      L      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    -       -      G      65           -
LGA    -       -      C      66           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    -       -      A      75           -
LGA    -       -      S      76           -
LGA    -       -      I      77           -
LGA    -       -      G      78           -
LGA    -       -      L      79           -
LGA    -       -      A      80           -
LGA    -       -      A      81           -
LGA    -       -      I      82           -
LGA    -       -      N      83           -
LGA    -       -      A      84           -
LGA    -       -      Y      85           -
LGA    -       -      Y      86           -
LGA    -       -      N      87           -
LGA    -       -      N      88           -
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      A      92           -
LGA    -       -      R      93           -
LGA    -       -      E      94           -
LGA    -       -      H      95           -
LGA    -       -      G      96           -
LGA    -       -      V      97           -
LGA    -       -      I      98           -
LGA    -       -      F      99           -
LGA    -       -      S     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    E       3      N     110          2.038
LGA    I       4      D     111          2.802
LGA    -       -      P     112           -
LGA    Y       5      F     113          3.652
LGA    D       6      I     114          3.519
LGA    A       7      M     115          2.038
LGA    -       -      S     116           -
LGA    -       -      Q     117           -
LGA    -       -      N     118           -
LGA    -       -      E     119           -
LGA    -       -      V     120           -
LGA    -       -      K     121           -
LGA    -       -      G     122           -
LGA    -       -      K     123           -
LGA    -       -      K     124           -
LGA    -       -      V     125           -
LGA    -       -      G     126           -
LGA    -       -      V     127           -
LGA    -       -      V     128           -
LGA    -       -      G     129           -
LGA    -       -      H     130           -
LGA    -       -      F     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      E     135           -
LGA    -       -      S     136           -
LGA    -       -      L     137           -
LGA    -       -      L     138           -
LGA    -       -      E     139           -
LGA    -       -      P     140           -
LGA    -       -      I     141           -
LGA    -       -      C     142           -
LGA    -       -      D     143           -
LGA    -       -      L     144           -
LGA    -       -      S     145           -
LGA    -       -      I     146           -
LGA    -       -      L     147           -
LGA    -       -      E     148           -
LGA    -       -      W     149           -
LGA    -       -      S     150           -
LGA    -       -      P     151           -
LGA    -       -      E     152           -
LGA    -       -      E     153           -
LGA    -       -      G     154           -
LGA    -       -      D     155           -
LGA    -       -      Y     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      P     159           -
LGA    -       -      A     160           -
LGA    -       -      S     161           -
LGA    -       -      E     162           -
LGA    -       -      F     163           -
LGA    -       -      I     164           -
LGA    -       -      L     165           -
LGA    -       -      P     166           -
LGA    -       -      E     167           -
LGA    V      18      C     168          1.555
LGA    D      19      D     169          0.508
LGA    E      20      Y     170          1.351
LGA    L      21      V     171          1.005
LGA    V      22      Y     172          0.646
LGA    C      23      I     173          0.799
LGA    G      24      T     174          0.772
LGA    N      87      C     175           -
LGA    N      88      A     176           -
LGA    P      89      S     177           -
LGA    Q      90      V     178           -
LGA    V      91      V     179           -
LGA    A      92      D     180           -
LGA    R      93      K     181           -
LGA    E      94      T     182           -
LGA    H      95      L     183           -
LGA    -       -      P     184           -
LGA    -       -      R     185           -
LGA    -       -      L     186           -
LGA    -       -      L     187           -
LGA    -       -      E     188           -
LGA    -       -      L     189           -
LGA    -       -      S     190           -
LGA    -       -      R     191           -
LGA    N     110      N     192          1.596
LGA    D     111      A     193          0.955
LGA    P     112      R     194          3.160
LGA    -       -      R     195           -
LGA    F     113      I     196          0.562
LGA    I     114      T     197          0.769
LGA    M     115      L     198          0.648
LGA    S     116      V     199          1.912
LGA    T     203      G     200           -
LGA    P     204      P     201           -
LGA    L     205      G     202           -
LGA    A     206      T     203           -
LGA    P     207      P     204           -
LGA    V     208      L     205           -
LGA    L     209      A     206           -
LGA    F     210      P     207           -
LGA    E     211      V     208           -
LGA    H     212      L     209           -
LGA    G     213      F     210           -
LGA    L     214      E     211           -
LGA    Q     215      H     212           -
LGA    E     216      G     213           -
LGA    L     217      L     214           -
LGA    S     218      Q     215           -
LGA    -       -      E     216           -
LGA    -       -      L     217           -
LGA    -       -      S     218           -
LGA    -       -      G     219           -
LGA    -       -      F     220           -
LGA    -       -      M     221           -
LGA    -       -      V     222           -
LGA    -       -      K     223           -
LGA    -       -      D     224           -
LGA    -       -      N     225           -
LGA    -       -      A     226           -
LGA    -       -      R     227           -
LGA    -       -      A     228           -
LGA    -       -      F     229           -
LGA    -       -      R     230           -
LGA    -       -      I     231           -
LGA    -       -      V     232           -
LGA    -       -      A     233           -
LGA    -       -      G     234           -
LGA    -       -      A     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      V     238           -
LGA    -       -      K     239           -
LGA    -       -      I     240           -
LGA    -       -      Y     241           -
LGA    -       -      S     242           -
LGA    -       -      A     243           -
LGA    -       -      G     244           -
LGA    -       -      Q     245           -
LGA    -       -      K     246           -
LGA    -       -      V     247           -
LGA    -       -      T     248           -
LGA    -       -      I     249           -
LGA    -       -      K     250           -
LGA    -       -      K     251           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44  244    5.0     19    1.88    10.53      7.127     0.957

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.972091 * X  +   0.064938 * Y  +   0.225438 * Z  + -48.439316
  Y_new =  -0.233282 * X  +   0.165686 * Y  +   0.958190 * Z  +  -5.123215
  Z_new =   0.024871 * X  +  -0.984038 * Y  +   0.176211 * Z  +  84.474129 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.393605    1.747987  [ DEG:   -79.8477    100.1523 ]
  Theta =  -0.024873   -3.116719  [ DEG:    -1.4251   -178.5749 ]
  Phi   =  -0.235526    2.906067  [ DEG:   -13.4946    166.5054 ]
 
# 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: T0321TS464_2_2                                
REMARK     2: T0321.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_2_2.T0321.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44  244   5.0   19   1.88   10.53   7.127
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  GLU     3       9.927  47.584  79.226  1.00  0.00
ATOM      2  CA  ILE     4      11.818  45.527  76.631  1.00  0.00
ATOM      3  CA  TYR     5      15.270  47.018  77.289  1.00  0.00
ATOM      4  CA  ASP     6      14.599  47.313  81.038  1.00  0.00
ATOM      5  CA  ALA     7      13.214  43.816  81.272  1.00  0.00
ATOM      6  CA  VAL    18      18.451  33.248  64.346  1.00  0.00
ATOM      7  CA  ASP    19      16.642  32.618  67.644  1.00  0.00
ATOM      8  CA  GLU    20      13.849  35.183  67.667  1.00  0.00
ATOM      9  CA  LEU    21      12.345  37.898  65.562  1.00  0.00
ATOM     10  CA  VAL    22      11.129  41.283  66.533  1.00  0.00
ATOM     11  CA  CYS    23       8.592  42.537  64.003  1.00  0.00
ATOM     12  CA  GLY    24       7.349  46.019  64.835  1.00  0.00
ATOM     13  CA  ASN    87      10.054  40.651  73.325  1.00  0.00
ATOM     14  CA  ASN    88      13.056  38.392  72.598  1.00  0.00
ATOM     15  CA  PRO    89      15.304  41.061  74.139  1.00  0.00
ATOM     16  CA  GLN    90      13.355  41.230  77.410  1.00  0.00
ATOM     17  CA  VAL    91      13.258  37.435  77.484  1.00  0.00
ATOM     18  CA  ALA    92      17.051  37.182  76.988  1.00  0.00
ATOM     19  CA  ARG    93      17.934  39.899  79.498  1.00  0.00
ATOM     20  CA  GLU    94      15.706  38.440  82.217  1.00  0.00
ATOM     21  CA  HIS    95      16.614  34.783  81.588  1.00  0.00
ATOM     22  CA  ASN   110      10.131  27.457  65.477  1.00  0.00
ATOM     23  CA  ASP   111      11.541  30.941  66.140  1.00  0.00
ATOM     24  CA  PRO   112      10.511  33.082  69.116  1.00  0.00
ATOM     25  CA  PHE   113       8.408  35.991  67.859  1.00  0.00
ATOM     26  CA  ILE   114       7.970  39.482  69.343  1.00  0.00
ATOM     27  CA  MET   115       5.506  41.989  67.931  1.00  0.00
ATOM     28  CA  SER   116       4.691  45.639  68.583  1.00  0.00
ATOM     29  CA  THR   203      15.908  48.801  64.108  1.00  0.00
ATOM     30  CA  PRO   204      15.824  51.435  66.839  1.00  0.00
ATOM     31  CA  LEU   205      15.008  48.639  69.355  1.00  0.00
ATOM     32  CA  ALA   206      18.068  46.596  68.359  1.00  0.00
ATOM     33  CA  PRO   207      20.321  49.617  68.593  1.00  0.00
ATOM     34  CA  VAL   208      19.098  49.053  72.171  1.00  0.00
ATOM     35  CA  LEU   209      20.283  45.418  72.130  1.00  0.00
ATOM     36  CA  PHE   210      23.782  46.514  71.133  1.00  0.00
ATOM     37  CA  GLU   211      24.027  48.907  74.116  1.00  0.00
ATOM     38  CA  HIS   212      22.607  46.367  76.572  1.00  0.00
ATOM     39  CA  GLY   213      24.922  43.530  75.478  1.00  0.00
ATOM     40  CA  LEU   214      21.836  41.401  74.772  1.00  0.00
ATOM     41  CA  GLN   215      22.642  37.918  73.459  1.00  0.00
ATOM     42  CA  GLU   216      20.310  37.847  70.454  1.00  0.00
ATOM     43  CA  LEU   217      20.508  35.429  67.536  1.00  0.00
ATOM     44  CA  SER   218      18.732  37.109  64.637  1.00  0.00
TER
END
