Today s subjects: Virtual bond representation Coordination number Contact maps Sidechain packing: is it an instrumental way of selecting and consolidating a fold? ASA of proteins Interatomic distances for hard sphere... PDB
Virtual bond representation
Virtual bond representation of the protein backbone. Dotted lines are the virtual bonds connecting successive α-carbons. This representation takes advantage of the planarity of the three successive backbone bonds, Cαi-1-Ci, Ci-Ni and Ni-Cαi corresponding to each amino acid. The lengths of the virtual bonds are fixed to the extent that the bond lengths and bond angles are fixed and the amide bond adheres to the trans conformation.
Interatomic Distances for Hard-sphere Potentials As used in Ramachandran plots {Ramachandran, Ramakrishnan, et al. 1963 ID: 501}.
Atomic Interactions Strong bonded interactions b Non bonded interactions r U = K( b b ) 0 2 θ U = K( θ θ ) 0 2 U = A r 12 B r 6 q 1 q 2 φ U = K( 1 cos( nφ)) = q1q r U 2
One could also include soft potentials (attractions) to the hard sphere potentials the intrinsic torsional potentials of the respective bonds N-Cα and Cα- C. They are threefold symmetric with minima at trans, gauche+ and gauche- states. repulsive attractive ionic
Number distribution of virtual bond torsions NA(ϕi, ϕi+1) for A = Gly, and Pro.
Coupling between virtual bond torsion and bending angles. The surfaces represent the number distributions from 150 PDB structures, irrespective of residue type.
Amino acid sidechains prefer angles near their ideal rotational isomeric states In addition to φ and ψ angles, proteins also have freedom in the side chain rotational angles. Moving along the side chain away from the backbone defines carbons identified as Cβ, Cγ, etc., and rotational angles as χ1, χ2, etc.; Two examples, Trp and Lys, illustrating the definition of the torsion angles χ1, χ2, etc. of amino acid side chains in proteins, along with the labels α, β, γ δ, etc. assigned to successive atoms for distinguishing their position along the sidechain. Nitrogen atoms are shown in black. Backbone atoms are on the right end in each case.
Distribution of the χ1 sidechain torsion angles for amino acids in α-helical and β-sheet regions compiled from 150 high resolution protein structures. The ordinate represents the total number of observations for each interval of size χ1 = 100. Note the relatively low probability of the gauchestate (χ1 = 60 o) for side chains on α-helices.
Coordination number (z) defines the number of neighbors (nonbonded) on the first coordination shell Distance from the center of the residue 6.8 Å Z = 7 in the core Z is 4 on the surface Z is smaller in small size proteins
Contact maps Gives information about the structure of the protein
x 8 x x 7 x x 6 x x 5 x x 4 x x x 3 x x x 2 x x 1 8 7 6 5 4 3 2 1 helix Antiparallel strand Parallel strand Residues i and j are in contact if distance between their alpha carbons is less than 7 A
Accesible surface areas (ASA)
(A) (B)
Hydrophobicity of proteins
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Yearly added structures to PDB As of Tuesday Feb 28, 2006, there are 35343 Structures
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HEADER MICROTUBULES 23-SEP-97 1TUB TITLE TUBULIN ALPHA-BETA DIMER, ELECTRON DIFFRACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUBULIN; COMPND 3 CHAIN: A, B; COMPND 4 BIOLOGICAL_UNIT: DIMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGAN: BRAIN KEYWDS MICROTUBULES, ALPHA-TUBULIN, BETA-TUBULIN, GTPASE EXPDTA ELECTRON DIFFRACTION AUTHOR E.NOGALES,K.H.DOWNING REVDAT 3 18-NOV-98 1TUBB 3 HET REMARK TITLE HETATM REVDAT 3 2 3 DBREF HEADER LINK SOURCE REVDAT 3 3 3 KEYWDS HELIX REVDAT 2 21-OCT-98 1TUBA 3 REMARK HETATM CONECT LINK REVDAT 1 07-OCT-98 1TUB 0 JRNL AUTH E.NOGALES,S.G.WOLF,K.H.DOWNING JRNL TITL STRUCTURE OF THE ALPHA BETA TUBULIN DIMER BY JRNL TITL 2 ELECTRON CRYSTALLOGRAPHY JRNL REF NATURE V. 391 199 1998 JRNL REFN ASTM NATUAS UK ISSN 0028-0836 0006 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.NOGALES,S.G.WOLF,K.H.DOWNING REMARK 1 TITL ERRATUM. STRUCTURE OF THE ALPHA BETA TUBULIN DIMER REMARK 1 TITL 2 BY ELECTRON CRYSTALLOGRAPHY REMARK 1 REF NATURE V. 393 191 1998 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 0006 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.NOGALES,K.H.DOWNING,L.A.AMOS,J.LOWE REMARK 1 TITL TUBULIN AND FTSZ FORM A DISTINCT FAMILY OF GTPASES REMARK 1 REF NAT.STRUCT.BIOL. V. 5 451 1998 REMARK 1 REFN ASTM NSBIEW US ISSN 1072-8368 2024 REMARK 2 REMARK 2 RESOLUTION. 3.7 ANGSTROMS. REMARK 3
SEQRES 1 A 440 MET ARG GLU CYS ILE SER ILE HIS VAL GLY GLN ALA GLY SEQRES 2 A 440 VAL GLN ILE GLY ASN ALA CYS TRP GLU LEU TYR CYS LEU SEQRES 3 A 440 GLU HIS GLY ILE GLN PRO ASP GLY GLN MET PRO SER ASP SEQRES 4 A 440 LYS THR ILE GLY GLY GLY ASP ASP SER PHE ASN THR PHE SEQRES 5 A 440 PHE SER GLU THR GLY ALA GLY LYS HIS VAL PRO ARG ALA SEQRES 6 A 440 VAL PHE VAL ASP LEU GLU PRO THR VAL ILE ASP GLU VAL SEQRES 7 A 440 ARG THR GLY THR TYR ARG GLN LEU PHE HIS PRO GLU GLN SEQRES 8 A 440 LEU ILE THR GLY LYS GLU ASP ALA ALA ASN ASN TYR ALA SEQRES 9 A 440 ARG GLY HIS TYR THR ILE GLY LYS GLU ILE ILE ASP LEU SEQRES 10 A 440 VAL LEU ASP ARG ILE ARG LYS LEU ALA ASP GLN CYS THR SEQRES 11 A 440 GLY LEU GLN GLY PHE SER VAL PHE HIS SER PHE GLY GLY SEQRES 12 A 440 GLY THR GLY SER GLY PHE THR SER LEU LEU MET GLU ARG SEQRES 13 A 440 LEU SER VAL ASP TYR GLY LYS LYS SER LYS LEU GLU PHE SEQRES 14 A 440 SER ILE TYR PRO ALA PRO GLN VAL SER THR ALA VAL VAL SEQRES 15 A 440 GLU PRO TYR ASN SER ILE LEU THR THR HIS THR THR LEU SEQRES 16 A 440 GLU HIS SER ASP CYS ALA PHE MET VAL ASP ASN GLU ALA.... HET GTP A 500 32 HET GDP B 500 28 HET TXL B 1 58 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM TXL TAXOTERE FORMUL 3 GTP C10 H16 N5 O14 P3 FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 TXL C43 H53 N1 O14
HELIX 1 1 ALA A 12 LEU A 23 1 12 HELIX 2 2 VAL A 74 ARG A 79 1 6 HELIX 3 3 GLY A 111 ASP A 127 1 17 HELIX 4 4 GLY A 146 TYR A 161 1 16 HELIX 5 5 VAL A 182 THR A 193 1 12 HELIX 6 6 ASN A 206 ARG A 215 1 10 HELIX 7 7 THR A 225 THR A 239 1 15 HELIX 8 8 LEU A 252 LEU A 259 1 8 HELIX 9 9 VAL A 288 CYS A 295 1 8 HELIX 10 10 PRO A 325 THR A 337 1 13 HELIX 11 11 ALA A 385 LEU A 397 1 13 HELIX 12 12 PHE A 418 GLU A 433 1 16 HELIX 13 21 CYS B 12 VAL B 23 1 12 HELIX 14 22 THR B 74 ARG B 79 1 6 HELIX 15 23 GLY B 111 GLU B 127 1 17 HELIX 16 24 GLY B 146 TYR B 161 1 16 HELIX 17 25 VAL B 182 GLN B 193 1 12 HELIX 18 26 ASN B 206 ARG B 215 1 10 HELIX 19 27 GLY B 225 THR B 239 1 15 HELIX 20 28 LEU B 252 MET B 259 1 8 HELIX 21 29 VAL B 288 MET B 295 1 8 HELIX 22 30 MET B 325 ASN B 337 1 13 HELIX 23 31 GLN B 385 ALA B 397 1 13 HELIX 24 32 PHE B 418 GLN B 433 1 16 SHEET 1 A 6 ILE A 93 LYS A 96 0 SHEET 2 A 6 ALA A 65 LEU A 70 1 N VAL A 66 O ILE A 93 SHEET 3 A 6 GLU A 3 HIS A 8 1 N CYS A 4 O ALA A 65 SHEET 4 A 6 GLY A 134 SER A 140 1 N PHE A 135 O GLU A 3 SHEET 5 A 6 LYS A 166 ILE A 171 1 N LEU A 167 O GLY A 134 SHEET 6 A 6 CYS A 200 VAL A 204 1 N ALA A 201 O LYS A 166 SHEET 1 B 4 HIS A 266 ALA A 273 0 SHEET 2 B 4 ARG A 373 ASN A 380-1 N ALA A 374 O HIS A 266 SHEET 3 B 4 ALA A 314 ARG A 320-1 N CYS A 315 O ARG A 373 SHEET 4 B 4 PHE A 351 ASN A 356 1 N LYS A 352 O ALA A 314 SHEET 1 C 6 VAL B 93 GLN B 96 0 SHEET 2 C 6 ALA B 65 LEU B 70 1 N ILE B 66 O VAL B 93
ATOM 1 N MET A 1-26.006 52.343-25.121 1.00 20.00 N ATOM 2 CA MET A 1-25.759 52.677-23.728 1.00 20.00 C ATOM 3 C MET A 1-26.559 53.689-24.177 1.00 20.00 C ATOM 4 O MET A 1-26.668 54.651-23.359 1.00 20.00 O ATOM 5 CB MET A 1-24.344 52.329-23.334 1.00 20.00 C ATOM 6 CG MET A 1-24.068 50.890-23.389 1.00 20.00 C ATOM 7 SD MET A 1-22.458 50.493-22.812 1.00 20.00 S ATOM 8 CE MET A 1-21.258 51.213-23.870 1.00 20.00 C ATOM 9 N ARG A 2-26.730 52.760-25.298 1.00 20.00 N ATOM 10 CA ARG A 2-27.391 52.415-26.712 1.00 20.00 C ATOM 11 C ARG A 2-28.773 51.786-26.637 1.00 20.00 C ATOM 12 O ARG A 2-29.066 50.784-27.282 1.00 20.00 O ATOM 13 CB ARG A 2-26.672 51.189-27.422 1.00 20.00 C ATOM 14 CG ARG A 2-25.232 51.386-27.936 1.00 20.00 C ATOM 15 CD ARG A 2-24.609 50.189-28.659 1.00 20.00 C ATOM 16 NE ARG A 2-23.214 50.398-29.087 1.00 20.00 N ATOM 17 CZ ARG A 2-22.449 49.540-29.750 1.00 20.00 C ATOM 18 NH1 ARG A 2-22.910 48.381-30.090 1.00 20.00 N ATOM 19 NH2 ARG A 2-21.192 49.766-30.118 1.00 20.00 N ATOM 20 N GLU A 3-29.539 52.412-25.872 1.00 20.00 N ATOM 21 CA GLU A 3-30.855 52.028-25.580 1.00 20.00 C ATOM 22 C GLU A 3-31.714 52.018-26.804 1.00 20.00 C ATOM 23 O GLU A 3-31.462 52.681-27.800 1.00 20.00 O ATOM 24 CB GLU A 3-31.476 52.978-24.615 1.00 20.00 C ATOM 25 CG GLU A 3-30.661 53.172-23.354 1.00 20.00 C ATOM 26 CD GLU A 3-31.275 54.158-22.421 1.00 20.00 C ATOM 27 OE1 GLU A 3-32.324 54.765-22.784 1.00 20.00 O ATOM 28 OE2 GLU A 3-30.745 54.383-21.276 1.00 20.00 O ATOM 29 N CYS A 4-32.691 51.242-26.661 1.00 20.00 N ATOM 30 CA CYS A 4-33.749 51.193-27.597 1.00 20.00 C ATOM 31 C CYS A 4-34.838 51.966-26.942 1.00 20.00 C ATOM 32 O CYS A 4-34.791 52.239-25.736 1.00 20.00 O ATOM 33 CB CYS A 4-34.167 49.797-27.837 1.00 20.00 C ATOM 34 SG CYS A 4-32.974 48.892-28.890 1.00 20.00 S
Sequence information
>1TUB:A PDBID CHAIN SEQUENCE MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRT GTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVD YGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR GDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSV >1TUB:B PDBID CHAIN SEQUENCE MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGP FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYP DRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGR MSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG EGMDEMEFTEAESNMNDLVSEYQQYQD
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