SOCKET John Walshaw 1998-2000. University of Sussex, U.K. --------------------------------------------------------- EXAMPLE SOCKET OUTPUT: ---------------------- The following is the result of running SOCKET on the hemagglutinin structure 1htm (Bullough et al., 1994), using a packing-cutoff of 7.0Å and no helix-extension, with the QUIET option (-q). If -q is omitted, then additional output listing the residues constituting each knob-in-hole interaction, lists of knobs, lists of cyclic arrangements of knobs, and (crude) interhelical angles, is provided. In this annotation, raw output is enclosed by <<<<<<....>>>>>> Firstly, miscellaneous info: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< SOCKET v2.17 16-11-00 John Walshaw, University of Sussex using cutoff of 7.0 Angstroms for centre of mass distances attempting to open "pdb1htm.ent" opened "pdb1htm.ent" (input) file name implies standard PDB entry, code 1htm opened "1htm.dssp" (input) Found beginning of residue data There are 259 alpha-helical residues in this structure chain A starts at residue 12 chain B starts at residue 40 chain C starts at residue 11 chain D starts at residue 40 chain E starts at residue 10 chain F starts at residue 40 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Most knob sidechains will be in contact with 4 'hole' sidechains (contacts are determined by the packing cutoff). Cases where there are more than 4 within this distance (distances are measured between the centres of mass of each sidechain) are reported, and 'proper' holes of 4 sidechains are selected from them. If there are many cases of sidechain with > 4 other sidechains in contact, then the packing-cutoff is too big. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< 5 sidechains in contact with residue 108 (PHE 63D, helix 3) residue 108 (PHE 63:D) has > 4 contacts; looking for holes contacts: 0) LYS 58:B 1) THR 59:B 2) LYS 62:B 3) PHE 63:B 4) ILE 66:B - includes hole: THR 59:B LYS 62:B PHE 63:B ILE 66:B >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'Daisy chains' are groups of 3 or more residues, one on each helix, which form a cyclic-complementary interaction. These are the basis of coiled coils with order > 2, ie which have more than 2 helices. The list below specifies which helices are involved in these cyclic arrangements. The knob numbers can be ignored (they are independent of residue number). Helix numbering starts at zero (sorry). <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< daisy chain 0 : knobs 2 (helix 0) 21 (helix 6) 31 (helix 3) daisy chain 1 : knobs 4 (helix 0) 24 (helix 6) 34 (helix 3) daisy chain 2 : knobs 6 (helix 0) 25 (helix 6) 35 (helix 3) daisy chain 3 : knobs 7 (helix 0) 26 (helix 6) 36 (helix 3) daisy chain 4 : knobs 8 (helix 3) 15 (helix 0) 37 (helix 6) daisy chain 5 : knobs 9 (helix 3) 16 (helix 0) 38 (helix 6) daisy chain 6 : knobs 10 (helix 3) 17 (helix 0) 39 (helix 6) daisy chain 7 : knobs 11 (helix 3) 18 (helix 0) 40 (helix 6) daisy chain 8 : knobs 12 (helix 3) 19 (helix 0) 41 (helix 6) daisy chain 9 : knobs 13 (helix 3) 20 (helix 0) 42 (helix 6) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The following lists pairs of adjacent helices which interact with knobs-into-holes. Initially, such pairs are listed as pseudo coiled-coils, which are preliminarily numbered in sequence starting from zero. As is apparent from the previous list, in this case helices 0, 3 and 6 constitute a 3-stranded coiled coil. Therefore, adjacent helix pairs 0/3, 0/6 and 3/6 do not themselves constitute true 2-stranded coiled coils - they are subsets of the 3-stranded coiled coil (ie coiled coil #3). So of the 4 listed below, only #3 is treated as a real coiled coil. The frequency is the number of layers of knobs-into-holes interactions. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< coiled coil 0: 2 helices 0 6 frequency 5 (subset of coiled coil 3) coiled coil 1: 2 helices 0 3 frequency 8 (subset of coiled coil 3) coiled coil 2: 2 helices 3 6 frequency 3 (subset of coiled coil 3) coiled coil 3: 3 helices 0 3 6 frequency 10 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> A summary of the helices (and daisy-chains if present) belonging to each coiled coil: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< helix 0 is in a 3-stranded coiled coil helix 3 is in a 3-stranded coiled coil helix 6 is in a 3-stranded coiled coil daisy chain 0 is in coiled coil 3 daisy chain 1 is in coiled coil 3 daisy chain 2 is in coiled coil 3 daisy chain 3 is in coiled coil 3 daisy chain 4 is in coiled coil 3 daisy chain 5 is in coiled coil 3 daisy chain 6 is in coiled coil 3 daisy chain 7 is in coiled coil 3 daisy chain 8 is in coiled coil 3 daisy chain 9 is in coiled coil 3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Details of each true coiled coil (a single one in this case) are then given. The coiled coils are numbered in Roman numerals in sequence, but the preliminary serial number (see above) is also given for reference to the above lists. N.B. The inter-helical angles are not strictly measured between the true helical axes - they are an indicator of the relative orienation (parallel or antiparallel) of helices. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< angle between helices 0 and 3 is 12.242 parallel angle between helices 0 and 6 is 12.659 parallel angle between helices 3 and 6 is 11.437 parallel this coiled coil is parallel >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The first (and in this case only) coiled coil is #3 from the preliminary list. The topology (orientation + order) is specified; the maximum length is the longest stretch of knobs-into-holes packing in a single helix. The mean length is caluclated from the stretches of knobs-into-holes packing in all the helices. In heterotypic coiled coils with order > 2, some pairs of helices can have considerably longer knobs-into-holes packing regions than others in the same coiled coil, forming essentially 2-stranded interactions beyond the layers of cyclic interactions. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< 1htm 7.0 0 coiled coil (i) 3 (parallel 3-stranded, length max 55 mean 55.00): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Within each coiled coil, each helix is identified by a single letter (V, W, X, Y or Z), so that the hole-helix for each knob can be specified (in the 'partner' line). The register of each knob is calculated explicitly for each knob residue, and the intervening residues have their register filled in in sequence. This means that discontinuities in the register will appear at knob positions only. In this example, there are two structural discontinuities in the heptad repeat. Complementary knobs have a 'knobtype' of 3 or higher. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< assigning heptad to helix 0 (X) 41-104:B extent of coiled coil packing: 41- 95:B sequence TQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALEN register defgabcdefgabcdefgabcdabcdefgabcdefgabcdefgabcdefgdefga partner ----Z--Y--YZ----------Z------Z--Y--YZ--Y---Z------Y-------!----- knobtype ----4--4--44----------4------4--4--44--4---4------4-------2----- assigning heptad to helix 3 (Y) 41-101:D extent of coiled coil packing: 41- 95:D sequence TQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVA register defgabcdefgabcdefgabcdabcdefgabcdefgabcdefgabcdefgdefga partner ----X--Z--ZX--Z-------X------X--Z---X--Z---X------Z-------!-- knobtype ----4--4--44--2-------4------4--4---4--4---4------4-------2-- assigning heptad to helix 6 (Z) 41-104:F extent of coiled coil packing: 41- 95:F sequence TQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALEN register defgabcdefgabcdefgabcdabcdefgabcdefgabcdefgabcdefgdefga partner ----Y--X--XY--X-------Y------Y--X---Y--X---Y------X-------!----- knobtype ----4--4--44--2-------4------4--4---4--4---4------4-------2----- 1htm c 7.00 e 0 result 1 COILED COILS PRESENT (+ 3 helix groups are either pairs with too few complementary knob in hole interactions or are subsets of larger coiled coils) Finished >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> References 1htm PDB structure: Bullough,P.A., Hughson,F.M., Skehel, J.J. & Wiley, D.C. (1994) Nature 371 37