(1) Amino Acid Sequences

1p3hN is a chain of M. tuberculosis GroEs and the others are chains of E.coli GroES. They have 37% sequence identity as shown below.

	1         2         3         4         5         6         7         8         9        10 1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
1p3hN Others	AKVNIKPLEDKILVQANEAETTTASGLVIPDTAKEKPQEGTVVAVGPGRWDEDGEKRIPLDVAEGDTVIYSKYGGTEIKYNGEEYLILSARDVLAVVSK    || || |   |   | ||  | | |    |  |   | | ||| ||  | ||                 ||    |   || || |  | || |     MNIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA
	<=  Base Loop  =>                 <=R =>                      <=T=>

*"<=Base Loop=>" ,  "<=R=>", and "<=T=>" indicate the position of the base loop, the roof loop, and the 79-83 turn respectively.

Although the structural variations for the base loop in E. coli GroES are almost negligible (whole protein Cα RMSDs 0.42 ± 0.13 Å), the corresponding DALI sequence alignments with M. tuberculosis GroES show remarkable variation in this region. [1]

(A) Structure of 1p3hN	(B) The D2 code of 1p3hN	(C) Structural variations of GroES.

(A) Figure 5 of ref. [8].
(B) Residues are colored according to their D² code:  '0' in blue, 'A' in red, 'B' and 'Q' in orange, 'G' in green, and 'R' in yellow.
(C) The 'master-slave' alignments by DALI with 1p3hN as master, where residues of the base loop are shown in red, the roof loop in blue, and the 79-83 turn in yellow.

(A) D2 code-variable residues.	(B) HMM-SA -variable residues.	(C) Stride-variable residues	(D) Alignment blocks assigned by FATCAT

(A) The 'master-slave' alignments by DALI with 1p3hN as master, where residues with different D²-codes are colored accordingly:  '0' in blue, 'A' in red, 'B' and 'Q' in orange, 'G' in green, and 'R' in yellow.
(B) The structure of 1p3hN only is shown, where residues with different HMM-SA codes are shown in blue.
(C) The structure of 1p3h-N only is shown, where residues with different Stride codes are shown in blue.
(D) Alignment blocks are colored as follows: residues in block1 in red and residues in block2 in blue if multiple alignment blocks are assigned by FATCAT.

(2) D² encoding

The D² code of the residues which do not have the same D² code as the corresponding residue of 1p3hN is shown in the following figure.
Note that chains of 1pcq are assigned the same D² code-sequence. 1pf9O and 1pf9R are also assigned the same D² code-sequence.

	1         2         3         4         5         6         7         8         9        10 1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
1p3hN 1aonO 1aonP 1aonS 1pf9O 1pf9R 1svtO 1pcqO 1pcqP 1pcqQ 1pcqR 1pcqS	--0000000R000000R00R000QBR0000RQBR0G000000R000R0000QBRB00O00RG00R000000RGR000000RR0000000QABG0000--           G     0    1G0R0RGR 0RR  0 RG   0      R RRG0  0 RG0 R0     R0QBG       G                          G     0    1G1R0RGR 0RR  0 3G   0      R RRG   0 RG0  0     R0QBG                                 G     0    1G1R0RGR 00R  0  G   0      R RRG0  0 RG0 R0     R0QBG           G     0    RG0R0RGRR00R G0 RG   0      R RRG0  0 RG0  0      0QBG           G     0    RG0R0RGRR00R G0 RG   0      R RRG0  0 RG0  0      0QBG           G     0 R RPG0R0RG  0RR0G0 RG   0      R1RR00  0 RG0  0O    R0QBG           G     0   RPG0R0RG  0RR0 0 RG   0      R RR00  0 RG0  0O    R0QBG           G     0   RPG0R0RG  0RR0 0 RG   0      R RR00  0 RG0  0O    R0QBG           G     0   RPG0R0RG  0RR0 0 RG   0      R RR00  0 RG0  0O    R0QBG           G     0   RPG0R0RG  0RR0 0 RG   0      R RR00  0 RG0  0O    R0QBG           G     0   RPG0R0RG  0RR0 0 RG   0      R RR00  0 RG0  0O    R0QBG
	<=  Base Loop  =>                 <=R =>                      <=T=>

(A) Chains of 1aon	(B) Chains of 1pcq	(C) The other chains

The 'master-slave' alignments by DALI with 1p3hN as master, where residues with different D2-codes are colored accordingly:  '0' in blue, 'A' in red, 'B' and 'Q' in orange, 'G' in green, and 'R' in yellow. 1p3hN is not shown in the figures.

(3) HMM-SA encoding

HMM-SA (Hidden Markov Model-Structural Alphabet)  is a collection of 27 structural prototypes of four residues. The HMM-SA code of the residues which do not have the same HMM-SA code as the corresponding residue of 1p3hN is shown in the following figure. See below for the description of each alphabet.

	1         2         3         4         5         6         7         8         9        10 1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
1p3hN 1aonO 1aonP 1aonS 1pf9O 1pf9R 1svtO 1pcqO 1pcqP 1pcqQ 1pcqR 1pcqS	-SNMMNLJUSNLNMNGSKPRNMHaDSLMNHGBDOQKNLXKLGIMLHRJKLHaDEIMLLLPQTYUSLXMXKPOUSLLTTTUFSLXMMXKHBBQGILNT--    J L Y Q MXLLNJLU HESUFUQPRLYGFQMLGQ LK      YPSUDOIKLLKPQMYUSLXMXKPSYBQX XL   QK       V    LX    J L Y Q MX LNJLU KFSUFUQPRLYGFSN GQ L        PSUDQJKL KPQMYCSLXLXKPSYBQXM L    K      EZ    LX    L L Y Q  X LNJLU HESUFUQPRNYGFSM GQ L        PSUDQJKL KPQMYUSLXMXKPSYBQXMXL    K      EZ    LX    L  KY Q MX LNJLF HESURUQPRLYGFQM PQ L        PSUDQJKN KPQNYUSLXMXKPSYBQT XL    K    L  V    LX    J  KY Q MX LNJLF HESURUQPRLYGFQM PQ L   T    PSUDQJKL KPQNYUSLXMXKPSYBQT XL    K       V    LX    L M Y QTMX LNJHFDDQGURUQLLLYGFQM GQ L   T    PSUDSYJL KPQNYCSLXMXKPSYBQN XM    K            PR    R   Y QTMX LNJLFDDESURUQPRLYGFQM GQ L   T    PSUDORYLKKPQNYCSLXMXKPSYBQN XL                 LN    R   Y QTMX LNJLFDDESURUQL LYGFQM PQ L   T    PSUDORYLKKPQNYCSLXMXKPSYBQN XL                 LN    R   Y QTMX LNJLFDDESURUQPRLYGFQM GQ L   T    PSUDORYLKKPQNYCSLXMXKPSYBQN X                  LN    R   Y QTMX LNJLFDDESURUQPRLYGFQM GQ L   T    PSUDORYLKKPQNYCSLXMXKPSYBQN XL                 LX    R   Y QTMX LNJLFDDESURUQL LYGFQM PQ L   T    PSUDORYLKKPQNYCSLXMXKPSYBQN XL                 LN
	<=  Base Loop  =>                 <=R =>                      <=T=>

(4) Secondary structure assignment by Stride

STRIDE [1] is a program to recognize secondary structural elements  in proteins from  their atomic coordinates. It performs the same task as DSSP by Kabsch and Sander but utilizes both hydrogen bond energy and mainchain dihedral angles rather than hydrogen bonds alone. See below for the description of each alphabet.

	1         2         3         4         5         6         7         8         9        10 1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
1p3hN 1aonO 1aonP 1aonS 1pf9O 1pf9R 1svtO 1pcqO 1pcqP 1pcqQ 1pcqR 1pcqS	EEEETTTEEEEEE     BTTTT B  TTTT  EEEEEEEEE   EETTTT  EE    TTTEEEEEETTTTEEEEETTEEEEEEEGGGEEEEEE    C      T      TTTTC    TT  C   T CCB         CT   C  CC   T  BCCBCCC                CCCCCCCC       CB  B      TTTTC    TT  C   T CCB         CT   C  CC   T   CCBBTT                CCCCCBCC  C       C   T    C TTTTC    TT  C   T CCBC        CT   C  CC   T   CCBCTT                CCCCCCCC  C    C      T      TTTTT    TT  C   T CCB         CT   C  CC   T  BCCBBCC                CCCCC C   C    C      T      TTTTT    TT  C   T CCB         CT   C  CC   T  BCCBCCC                CCCCCCC   C    CCCB   B      TTTTC    TT  CCCC  CCB        E T   C       T   CCBCTT                CBTTTTC   C    CCCB   B    B TTTTT    TT  CCCC  CCBBCCC    E T   C       T   CCBCTT                CBTTTTC   C    C      B    B TTTTT    TT  CCCC  CCBBCCC    E T   C       T   CCBCTT                CBTTTTC   C    C      B  CBB TTTTT    TT  CCCC  CCBBCCC    E T   C       T   CCBCTT                CBTTTTC   C    C      B    B TTTTT    TT  CCCC  CCBBCCC    E T   C       T   CCBCTT                CBCCCCC   C    C      B      TTTTT    TT  CCCC  CCB        E T   C       T   CCBCTT                CBCCCCC   C
	<=  Base Loop  =>                 <=R =>                      <=T=>

(5) Flexible structural alignment by FATCAT (Added for reference)

Shown below is the 'master-slave' alignments by FATCAT with 1p3h-N as master, where the numbers below amino acid-sequence indicate the alignment block of the residue. Note that chains of 1pcq, 1pf9, and 1svt are decomposed into three alignment blocks 1, 2, and 3.

	1         2         3         4         5         6         7         8         9        10 1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
1p3hN 1aonO 1aonP 1aonS 1pf9O 1pf9R 1svtO 1pcqO 1pcqP 1pcqQ 1pcqR 1pcqS	VNIKPLEDKILVQANEA-ETTT----ASGLVIPDTAKEKPQEGTVVAVGPGRWDEDGEKRIPLDVAEGDTVIYSKYG-GTEIKYNGEEYLILSARDVLAVVSK   MNIRPLHDRVIVKRKEV-ETKSAGGIVLTGSAAAK----STRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111-1111    111111111    1111111111111111 111111111111111111111 1111111111111111111111111   MNIRPLHDRVIVKRKEV-ETKSAGGIVLTGSAAAK----STRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111-1111    111111111    1111111111111111 111111111111111111111 1111111111111111111111111   MNIRPLHDRVIVKRKEV-ETKSAGGIVLTGSAAAK----STRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111-1111    111111111    1111111111111111 111111111111111111111 1111111111111111111111111   MNIRPLHDRVIVKRKEVETKSA----GGIVLTGSAAAKS-TRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111 2222----2222222222222 333333333333333 33333333333333333333 33333333333333333333333333   MNIRPLHDRVIVKRKEVETKSA----GGIVLTGSAAAKS-TRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111 2222----2222222222222 333333333333333 33333333333333333333 33333333333333333333333333   MNIRPLHDRVIVKRKEVETKSA----GGIVLTGSAAAKS-TRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111 2222----2222222222222 333333333333333 33333333333333333333 33333333333333333333333333   MNIRPLHDRVIVKRKEVETKSA----GGIVLTGSAAAKS-TRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111 2222----2222222222222 333333333333333 33333333333333333333 33333333333333333333333333   MNIRPLHDRVIVKRKEVETKSA----GGIVLTGSAAAKS-TRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111 2222----2222222222222 333333333333333 33333333333333333333 33333333333333333333333333   MNIRPLHDRVIVKRKEVETKSA----GGIVLTGSAAAKS-TRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111 2222----2222222222222 333333333333333 33333333333333333333 33333333333333333333333333   MNIRPLHDRVIVKRKEVETKSA----GGIVLTGSAAAKS-TRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111 2222----2222222222222 333333333333333 33333333333333333333 33333333333333333333333333   MNIRPLHDRVIVKRKEVETKSA----GGIVLTGSAAAKS-TRGEVLAVGNGRILE-NGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA   11111111111111111 2222----2222222222222 333333333333333 33333333333333333333 33333333333333333333333333
	<=     Base Loop    =>                 <= R =>                      <=T=>

[The D² codes]

• 0 = DDDDD    (Extended strand, small blue spheres)
• 1 = DDDDU
• 2 = DDDUD
• 3 = DDDUU
• 8 = DUDDD
• 9 = DUDDU
• A = DUDUD    (Helix, large red spheres)
• B = DUDUU    (C-cap, large orange spheres)
• G = UDDDD    (Large green spheres)
• H = UDDDU
• I = UDDUD
• J = UDDUU
• O = UUDDD
• P = UUDDU
• Q = UUDUD    (N-cap, large orange spheres)
• R = UUDUU    (Turn, large yellow spheres)

[The HMM-SA code]

• Alpha helix: A, a, V, W, Z, B, C, D
• 3-helix (3/10 helix): B, E, H
• 5 helix (pi helix): C
• Extended structures: L, N, M, T, X:
• Turn I: Z, B, C, D, E, O, S, Q, P, H
• Turn II: U, S
• Turn I' and  II': F, U
• Turn VIa and VIb: F
• Turn IV: R, Q, I, F, U, G
  
• Turn VIII : I, P, G
  
• Coil (None of the above): G, Y, J, K, L, D, S, Q

[The Stride code]

• H = alpha helix
• B or b = isolated bridge
• E = extended conformation
• G = 3-helix (3/10 helix)
• I = 5 helix (pi helix)
• T = Turn
• C = coil (None of the above)