***************** FILE 3D_ALI - sequence alignment based on 3D superposition ****************
FT   file: ctf.3D_ALI
DT    created at EMBL Sat Aug  3 23:43:54 1991      
NS    1  
FN    1ctf  chain: -; Range(PDB):   53 -  120         resolution: 1.7 angstroms. 
NA    15 
NL    68   
DB    RELEASE 17.0 OF EMBL/SWISS-PROT WITH  20024 SEQUENCES                 
TH    threshold_1 - % identity       0.35
TH    threshold_2 - % alignment      0.35
AU    This file was generated by the program CHARON
AU    Stefano Pascarella and Patrick Argos, EMBL, Postfach 10 22 09, 6900 Heidelberg, Germany
AU    
NT    The sequence alignments and part of the notation included in this file has been taken from the HSSP files: 
NT    Sander C. and Schneider R. : Database of homology-derived protein structures. Protins, in press.
NT    Notation:    seq_id = sequence identifyer eithr from PDB or from SWISSPROT.
NT                 %ide = percentage of identical residues.
NT                 ifir, ilast = first and last residue of the alignment in the test sequence.
NT			jfir, jlast = first and last residue of the alignment in the aligned protein.
NT                 lali = length of the alignment excluding insertions and deletions.
NT                 ngap, lgap = number and total length of all insertions and deletions.
NT                 lseq2 = length of the entire sequence of the aligned protein.
NT                 HSP = numeration in the HSSP file.
NT                 PDB = numeration in the PDB file.
NT                 A = aminoacid sequence.
NT                 STRUCT = secondary structure assignment as found in DSSP file.
NT                 PHI, PSI, CHIx = dihedral angles phi, psi and chi1, chi2....
NT                 ACC = accessibility as found in DSSPfiles.
NT     Symbols:    '-'  indicates a gap in the structural alignments.
NT                 '?'  indicates a structural gap: the sequence is known but the structure is unresolved.
NT                 ' ' indictes a gap in the sequence alignments.
NT                 pairs of lower case letters in the alignment bracket an insertion in the sequence.
EN

     ..............................................................................................................................
          seq_id          %ide  ifir  ilas  jfir  jlas  lali  ngap  lgap  lseq
->   1. 1ctf
  2. RL7$SALTY             0.99     1    68    53   120    68     0     0   120 50S RIBOSOMAL PROTEIN L7/L12 (L8) (GENE NAME: RPLL).
  3. RLA$DESVM             0.75     1    68    59   126    68     0     0   126 50S RIBOSOMAL PROTEIN ('A' TYPE).
  4. RLA$RHOSH             0.72     1    68    58   124    67     1     1   124 RIBOSOMAL PROTEIN RA ('A' TYPE).
  5. RLA$MICLY             0.69     1    68    51   118    68     0     0   118 70S RIBOSOMAL PROTEIN MA ('A' TYPE).
  6. RLA$BACST             0.66     1    68    55   122    68     0     0   122 50S RIBOSOMAL PROTEIN 'A' (L12) (BL13).
  7. RLA$HALEU             0.63     1    68    55   122    68     0     0   122 RIBOSOMAL PROTEIN 'A'.
  8. RLA$HALPR             0.63     1    68    55   122    68     0     0   122 RIBOSOMAL PROTEIN 'A' (L12).
  9. RLA$BACSU             0.62     1    68    53   122    68     1     2   122 50S RIBOSOMAL PROTEIN BL9 ('A' TYPE).
 10. RLA$SPIOL             0.60     1    67   121   188    67     1     1   189 CHLOROPLAST RIBOSOMAL PROTEIN L12 PRECURSOR ('A' TYP
 11. RLA$STRGR             0.57     1    68    58   125    68     0     0   125 50 RIBOSOMAL PROTEIN SA1 ('A' TYPE).
 12. H1D$RAT               0.41     7    66    10    73    59     2     6   216 HISTONE H1D.
 13. H11$MOUSE             0.37     7    66    15    73    59     1     1   211 HISTONE H1.1.
 14. H12$CAEEL             0.36     3    66   125   189    64     1     1   190 HISTONE H1.2.
 15. H1D$HUMAN             0.36     7    68    15    75    61     1     1   212 HISTONE H1D.
 16. H1C$HUMAN             0.36     7    66    16    74    59     1     1   220 HISTONE H1C.

     ..............................................................................................................................
####
CC    Structure superposition
NB    1  blocks
NC    3 structures per block
                                  1ctf                                                                            

    HSP   PDB A  STRUCT     PHI    PSI   ACC |HSP   PDB A  STRUCT     PHI    PSI   ACC |HSP   PDB A  STRUCT     PHI    PSI   ACC |
   |-----------------------------------------|-----------------------------------------|-----------------------------------------|
  1.   1   53 E            360.0  138.7  189 |
  2.   2   54 F E     -A  -123.6  163.6   57 |
  3.   3   55 D E     -   -115.5  144.6   47 |
  4.   4   56 V E     -AB -115.7  121.8    0 |
  5.   5   57 I E     -AB -116.2  131.3   18 |
  6.   6   58 L E     +AB  -86.7  107.0    0 |
  7.   7   59 K E     -    -84.1  -38.5   82 |
  8.   8   60 A E     - B -167.4  146.8   37 |
  9.   9   61 A   >   +   -116.1  -18.2    6 |
 10.  10   62 G G >  S-     53.2 -129.3   44 |
 11.  11   63 A G 3  S+    -77.7   -4.8  106 |
 12.  12   64 N G <>  +   -101.9   24.9   78 |
 13.  13   65 K H <>  +    -57.4  -37.1   74 |
 14.  14   66 V H  > S+    -61.1  -50.4  124 |
 15.  15   67 A H  > S+    -60.6  -46.8   44 |
 16.  16   68 V H  X S+    -65.2  -43.0    0 |
 17.  17   69 I H  X S+    -58.9  -40.5   16 |
 18.  18   70 K H  X S+    -59.2  -50.4  159 |
 19.  19   71 A H  X S+    -62.1  -46.5   27 |
 20.  20   72 V H  X S+    -62.9  -38.6    0 |
 21.  21   73 R H  X S+    -67.6  -38.7  106 |
 22.  22   74 G H  < S+    -69.7  -34.4   69 |
 23.  23   75 A H  < S+    -82.8  -26.4   48 |
 24.  24   76 T H  < S-   -118.0  -24.3   44 |
 25.  25   77 G    <  +     85.1    5.9   67 |
 26.  26   78 L       -    -62.3  151.6   63 |
 27.  27   79 G    >  -    -73.3  168.4   28 |
 28.  28   80 L H  > S+    -60.6  -49.2   96 |
 29.  29   81 K H  > S+    -58.4  -42.9  124 |
 30.  30   82 E H  > S+    -66.0  -46.7   80 |
 31.  31   83 A H  X S+    -65.4  -40.2    0 |
 32.  32   84 K H  X S+    -63.3  -44.1   74 |
 33.  33   85 D H  X S+    -65.8  -37.4   71 |
 34.  34   86 L H >< S+    -68.4  -42.1   36 |
 35.  35   87 V H >< S+    -68.2  -37.0    1 |
 36.  36   88 E H 3< S+    -73.7  -10.6  106 |
 37.  37   89 S T << S-   -103.7   12.9   78 |
 38.  38   90 A   <   +    -62.0  148.0   32 |
 39.  39   91 P S    S+    -65.4  140.9   85 |
 40.  40   92 A E     -A  -148.5  139.4   22 |
 41.  41   93 A E     +A   -80.2  108.0   49 |
 42.  42   94 L E     +    -82.1  -41.9   22 |
 43.  43   95 K E     -A  -138.9  128.1   89 |
 44.  44   96 E E     +   -125.3  148.8  129 |
 45.  45   97 G E    S+     71.2   34.1   41 |
 46.  46   98 V E     -A   -98.4  159.1   18 |
 47.  47   99 S    >  -    -72.5  166.2   57 |
 48.  48  100 K H  > S+    -55.6  -45.6  125 |
 49.  49  101 D H  > S+    -67.9  -36.8  122 |
 50.  50  102 D H  > S+    -68.5  -41.2  105 |
 51.  51  103 A H  X S+    -66.2  -41.4    0 |
 52.  52  104 E H  X S+    -68.7  -40.9   66 |
 53.  53  105 A H  X S+    -65.9  -41.8   61 |
 54.  54  106 L H  X S+    -67.1  -42.4   20 |
 55.  55  107 K H  X S+    -55.3  -51.8   52 |
 56.  56  108 K H  X S+    -62.1  -42.0  129 |
 57.  57  109 A H  X S+    -62.2  -45.3   41 |
 58.  58  110 L H  X>S+    -70.4  -38.1    0 |
 59.  59  111 E H ><5S+    -59.8  -46.2   96 |
 60.  60  112 E H 3<5S+    -63.6  -30.2  166 |
 61.  61  113 A H 3<5S-    -75.9  -18.4   21 |
 62.  62  114 G T <<5S+    111.5   18.5   25 |
 63.  63  115 A     < -    -95.8  155.5   10 |
 64.  64  116 E E     +B   -90.7  116.0  119 |
 65.  65  117 V E     -B  -127.1  153.9   20 |
 66.  66  118 E E     -B  -130.6  144.5   83 |
 67.  67  119 V E      B  -117.8  127.9   37 |
 68.  68  120 K           -133.3  360.0  151 |
   |-----------------------------------------|-----------------------------------------|-----------------------------------------|
####


$$$$
CC   Sequence alignments  -  from 1
NB   1 blocks
NC   120 sequences per block

     .........|.........|.........|.........|.........|.........|.........|.........|.........|.........|.........|.........|......
  1. EEEEEEEEEEE      
  2. FFFFFFFFFFF      
  3. DDDDDDDDDDD  P   
  4. VVVVVVLVLVV  V   
  5. IIIGVIVFISI  A   
  6. LLLLLLLLLIL  K   
  7. KKKTAATAADTAEKEK 
  8. AAADSDSDGeGPKAKT 
  9. AAAAAAAIApAAAAAP 
 10. GGGGGGGGGSGPPTPV 
 11. AAAAAAEGSNEAAGVK 
 12. NNNNEQKKQAKEKEKK 
 13. KKKKKKKKKRKKKKKK 
 14. VVIIIIVIIIITKKKA 
 15. AAGNKKNKKSQPAAAK 
 16. VVVVVVVVVVVIAKAK 
 17. IIIIIIIIIIIKKKKA 
 18. KKKKKKKKKKKKKTKG 
 19. AAVEVVVAVAVKPTAA 
 20. VVVVVVVVVVVAAVGT 
 21. RRRRRRRRRRRRGAGA 
 22. GGAAEEEEEAEKVKTG 
 23. AALIIIILILLARKPK 
 24. TTTTTTTTTTTARTRR 
 25. GGGGGGGGGSSgKGKK 
 26. LLLLLLLLLLLaADAA 
 27. GGGGGGGGGGGSSKSS 
 28. LLLLLLLLLLLGGVGG 
 29. KKKKKKKKKKKPPKPP 
 30. EEEEEEEEEEEPPKPP 
 31. AAAAAAAAAAAVVAVV 
 32. KKKKKKKKKKKSSKSS 
 33. DDDDEDAGEEDEESEE 
 34. LLKLVLAVLLLLLPLL 
 35. VVVVVVVVVIVIIKII 
 36. EEDEDDDDDEDTTKTT 
 37. SSG NNGDnGGKKIKK 
 38. AAAAATAAkLTAAaAA 
 39. PPPGPPPPPPPVVpVV 
 40. AASGKKAGLKKAAAAA 
 41. AATKAPTNEKPAAAAA 
 42. LLLVLILVVLVSSKSS 
 43. KKKKKKKKKKLKKKKK 
 44. EEEEEEEEEEEEEVEE 
 45. GGAAGGGGGGKRRARR 
 46. VVVVVIMLIVV  K   
 47. SSSASASSASASSSSS 
 48. KKKKKKKKKKKGGPGG 
 49. DDEADEEEEDEVVAVV 
 50. DDEDEEDDEDASSKSS 
 51. AAAAAAGAAAALLKLL 
 52. EEEEEEDEEEEAAAAA 
 53. AAEAEEEEEDKAAAAA 
 54. LLAMIIAMLAALLPLL 
 55. KKKKKKKKKKAKKKKK 
 56. KKKKAATEAKEKKKKK 
 57. ASQKKAKKKQSAAAAA 
 58. LLLLLLLLLLLLLPLL 
 59. EEVEEEEEEEKAAAAA 
 60. EEEEEEEEEDAAAKAA 
 61. AAAAVAAAVAAAAKAA 
 62. GGGGGGGGGGGGGAGG 
 63. AAAAAAAAAAAYYAYY 
 64. EEEKSKSTSKSDDADD 
 65. VVVVVVVVVVVVVPVV 
 66. EEEEEEEEESEEEKEE 
 67. VVVLVILLVIV   K  
 68. KKKKKKKKK K   N  

     .........|.........|.........|.........|.........|.........|.........|.........|.........|.........|.........|.........|......
%%%%
CC    Chi angles
NB     1  blocks
NC     3  structures per block
                                  1ctf

    HSP   PDB A    CHI1   CHI2   CHI3   CHI4 |HSP   PDB A    CHI1   CHI2   CHI3   CHI4 |HSP   PDB A    CHI1   CHI2   CHI3   CHI4 |
   |-----------------------------------------|-----------------------------------------|-----------------------------------------|
  1.   1   53 E  -72.61 161.99-172.68-999.00 |
  2.   2   54 F  -57.31  87.30-999.00-999.00 |
  3.   3   55 D  -59.09 -18.06-999.00-999.00 |
  4.   4   56 V -178.72-999.00-999.00-999.00 |
  5.   5   57 I  -64.25 118.70-999.00-999.00 |
  6.   6   58 L  164.32  62.27-999.00-999.00 |
  7.   7   59 K  -76.65 -88.76 -40.22 164.87 |
  8.   8   60 A -999.00-999.00-999.00-999.00 |
  9.   9   61 A -999.00-999.00-999.00-999.00 |
 10.  10   62 G -999.00-999.00-999.00-999.00 |
 11.  11   63 A -999.00-999.00-999.00-999.00 |
 12.  12   64 N  -64.02 -37.43-999.00-999.00 |
 13.  13   65 K  -70.81-172.11-177.68  85.82 |
 14.  14   66 V  170.32-999.00-999.00-999.00 |
 15.  15   67 A -999.00-999.00-999.00-999.00 |
 16.  16   68 V  172.47-999.00-999.00-999.00 |
 17.  17   69 I  -70.23 165.79-999.00-999.00 |
 18.  18   70 K -178.09-164.85 -47.35-173.21 |
 19.  19   71 A -999.00-999.00-999.00-999.00 |
 20.  20   72 V  165.07-999.00-999.00-999.00 |
 21.  21   73 R  -61.09-174.09  68.20-164.58 |
 22.  22   74 G -999.00-999.00-999.00-999.00 |
 23.  23   75 A -999.00-999.00-999.00-999.00 |
 24.  24   76 T   80.88-999.00-999.00-999.00 |
 25.  25   77 G -999.00-999.00-999.00-999.00 |
 26.  26   78 L  -81.74 172.38-999.00-999.00 |
 27.  27   79 G -999.00-999.00-999.00-999.00 |
 28.  28   80 L -178.23  57.02-999.00-999.00 |
 29.  29   81 K  138.28 153.64 158.20  -2.52 |
 30.  30   82 E  -52.66  77.45  21.79-999.00 |
 31.  31   83 A -999.00-999.00-999.00-999.00 |
 32.  32   84 K -178.72 165.86 112.48  11.03 |
 33.  33   85 D  -63.98 154.23-999.00-999.00 |
 34.  34   86 L -161.13 172.82-999.00-999.00 |
 35.  35   87 V  170.29-999.00-999.00-999.00 |
 36.  36   88 E  -58.52 173.19 164.68-999.00 |
 37.  37   89 S  -58.49-999.00-999.00-999.00 |
 38.  38   90 A -999.00-999.00-999.00-999.00 |
 39.  39   91 P -999.00-999.00-999.00-999.00 |
 40.  40   92 A -999.00-999.00-999.00-999.00 |
 41.  41   93 A -999.00-999.00-999.00-999.00 |
 42.  42   94 L  170.46  50.83-999.00-999.00 |
 43.  43   95 K -122.19 175.73 155.28 102.22 |
 44.  44   96 E  -67.59-175.01 153.81-999.00 |
 45.  45   97 G -999.00-999.00-999.00-999.00 |
 46.  46   98 V  -58.55-999.00-999.00-999.00 |
 47.  47   99 S   72.46-999.00-999.00-999.00 |
 48.  48  100 K -156.62 152.31 139.83 -91.07 |
 49.  49  101 D  -58.75 142.85-999.00-999.00 |
 50.  50  102 D  -75.98  -1.29-999.00-999.00 |
 51.  51  103 A -999.00-999.00-999.00-999.00 |
 52.  52  104 E  -71.84 -42.21 142.63-999.00 |
 53.  53  105 A -999.00-999.00-999.00-999.00 |
 54.  54  106 L -171.91  48.76-999.00-999.00 |
 55.  55  107 K -178.51-174.49  72.48 171.31 |
 56.  56  108 K  -78.02-164.45-177.96 155.95 |
 57.  57  109 A -999.00-999.00-999.00-999.00 |
 58.  58  110 L  -67.13 170.67-999.00-999.00 |
 59.  59  111 E  -75.58 174.62 -10.27-999.00 |
 60.  60  112 E  -72.03 166.03-177.67-999.00 |
 61.  61  113 A -999.00-999.00-999.00-999.00 |
 62.  62  114 G -999.00-999.00-999.00-999.00 |
 63.  63  115 A -999.00-999.00-999.00-999.00 |
 64.  64  116 E -173.31-170.67 161.28-999.00 |
 65.  65  117 V -178.65-999.00-999.00-999.00 |
 66.  66  118 E  163.69 166.36-114.87-999.00 |
 67.  67  119 V  166.05-999.00-999.00-999.00 |
 68.  68  120 K  -93.84 169.30  23.53 150.26 |
   |-----------------------------------------|-----------------------------------------|-----------------------------------------|
END.