Pages 1–8 1z8d Evolutionary trace report by report maker October 30, 2009

4.3.1 Alistat 7 4.3.2 CE 7 4.3.3 DSSP 7 4.3.4 HSSP 8 4.3.5 LaTex 8 4.3.6 Muscle 8 4.3.7 Pymol 8 4.4 Note about ET Viewer 8 4.5 Citing this work 8 4.6 About report maker 8 4.7 Attachments 8

1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1z8d): Title: Crystal structure of human muscle glycogen phosphorylase a with amp and glucose Compound: Mol id: 1; molecule: glycogen phosphorylase, muscle form; chain: a; synonym: myophosphorylase; ec: 2.4.1.1; enginee- red: yes; mutation: yes Organism, scientific name: Homo Sapiens; 1z8d contains a single unique chain 1z8dA (821 residues long). CONTENTS

1 Introduction 1 2 CHAIN 1Z8DA 2.1 P11217 overview 2 Chain 1z8dA 1 2.1 P11217 overview 1 From SwissProt, id P11217, 95% identical to 1z8dA: 2.2 Multiple sequence alignment for 1z8dA 1 Description: Glycogen phosphorylase, muscle form (EC 2.4.1.1) 2.3 Residue ranking in 1z8dA 1 (Myophosphorylase). 2.4 Top ranking residues in 1z8dA and their position on Organism, scientific name: Homo sapiens (Human). the structure 2 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 2.4.1 Clustering of residues at 25% coverage. 2 Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; 2.4.2 Overlap with known functional surfaces at Catarrhini; Hominidae; Homo. 25% coverage. 3 Function: Phosphorylase is an important allosteric enzyme in carbo- 2.4.3 Possible novel functional surfaces at 25% hydrate metabolism. Enzymes from different sources differ in their coverage. 5 regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties. 3 Notes on using trace results 6 Catalytic activity: (1,4-alpha-D-glucosyl)(n) + phosphate = (1,4- 3.1 Coverage 6 alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate. 3.2 Known substitutions 6 Cofactor: Pyridoxal phosphate. 3.3 Surface 6 Enzyme regulation: Activity of phosphorylase is controlled both 3.4 Number of contacts 7 by allosteric means (through the noncovalent binding of metaboli- 3.5 Annotation 7 tes) and by covalent modification. Thus AMP allosterically activates, 3.6 Mutation suggestions 7 whereas ATP, ADP, and glucose-6-phosphate allosterically inhibit, phosphorylase B. 4 Appendix 7 Subunit: Homodimer. Dimers associate into a tetramer to form the 4.1 File formats 7 enzymatically active phosphorylase A. 4.2 Color schemes used 7 Ptm: Phosphorylation of Ser-14 converts phosphorylase B (unphos- 4.3 Credits 7 phorylated) to phosphorylase A.

1 Lichtarge lab 2006 Disease: Defects in PYGM are the cause of glycogen storage disease V (GSD-V) [MIM:232600]; also known as McArdle’s disease. GSD- V is a form of autosomal recessive myopathy characterized by exercise intolerance, muscle cramps, and recurrent myoglobinuria. Similarity: Belongs to the glycogen phosphorylase family. About: This Swiss-Prot entry is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are no restrictions on its use as long as its content is in no way modified and this statement is not removed.

2.2 Multiple sequence alignment for 1z8dA For the chain 1z8dA, the alignment 1z8dA.msf (attached) with 516 sequences was used. The alignment was downloaded from the HSSP database, and fragments shorter than 75% of the query as well as duplicate sequences were removed. It can be found in the attachment to this report, under the name of 1z8dA.msf. Its statistics, from the Fig. 1. Residues 2-288 in 1z8dA colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.) alistat program are the following:

Format: MSF Number of sequences: 516 Total number of residues: 404536 Smallest: 715 Largest: 821 Average length: 784.0 Alignment length: 821 Average identity: 46% Most related pair: 99% Most unrelated pair: 26% Most distant seq: 46%

Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 9% eukaryotic ( 2% vertebrata, <1% arthropoda, 2% fungi, 2% plantae), and 12% prokaryotic sequences. (Descriptions of some sequences were not readily available.) The file Fig. 2. Residues 289-561 in 1z8dA colored by their relative importance. (See containing the sequence descriptions can be found in the attachment, Appendix, Fig.11, for the coloring scheme.) under the name 1z8dA.descr.

2.3 Residue ranking in 1z8dA The 1z8dA sequence is shown in Figs. 1–3, with each residue colored according to its estimated importance. The full listing of residues in 1z8dA can be found in the file called 1z8dA.ranks sorted in the attachment.

2.4 Top ranking residues in 1z8dA and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 4 shows residues in 1z8dA colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment.

2.4.1 Clustering of residues at 25% coverage. Fig. 5 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.5 are composed of the residues listed Fig. 3. Residues 562-836 in 1z8dA colored by their relative importance. (See in Table 1. Appendix, Fig.11, for the coloring scheme.)

2 Table 1. cluster size member color residues red 196 84,86,88,89,90,92,93,101,126 128,129,131,132,133,134,135 136,137,138,139,140,141,142 143,145,146,148,156,157,158 159,160,161,164,165,166,168 175,177,180,182,189,204,215 223,225,227,232,241,242,243 244,279,280,281,283,288,291 292,293,295,296,297,298,302 336,337,338,339,340,341,342 348,351,353,355,364,374,375 376,377,378,379,380,382,383 384,385,387,396,397,398,441 442,444,453,454,455,456,459 462,468,471,476,479,481,482 483,484,485,487,489,490,491 496,499,538,542,563,564,566 568,569,571,572,573,574,575 576,578,579,601,607,608,609 Fig. 4. Residues in 1z8dA, colored by their relative importance. Clockwise: 610,611,612,613,616,617,620 front, back, top and bottom views. 644,647,648,650,653,654,658 659,661,663,664,665,666,667 668,669,670,672,673,674,675 676,677,678,679,680,681,684 685,686,688,690,691,693,694 695,696,698,699,711,712,769 771,776,780,797,811,812,813 814,815,820,824,825 blue 3 704,707,804 yellow 3 587,631,633 green 2 406,407

Table 1. Clusters of top ranking residues in 1z8dA.

2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Glucose binding site. Table 2 lists the top 25% of residues at the interface with 1z8dGLC901 (glucose). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist Fig. 5. Residues in 1z8dA, colored according to the cluster they belong to: (%) bb (A˚ ) red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The 377 H H(100) 0.01 37/14 2.70 corresponding Pymol script is attached. 484 N N(99)A 0.02 10/0 2.87 672 E E(99)Q 0.02 14/3 2.69 674 S S(99)G 0.02 20/14 3.14 675 G G(99)D 0.02 12/12 2.75 136 L L(99)G. 0.04 17/11 3.37 139 L L(99)Q. 0.04 8/0 3.48 continued in next column

3 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) 676 T T(99)Q 0.04 5/1 4.08 680 X K(99)CX 0.04 1/0 4.95 135 G G(99)E. 0.06 15/15 3.72 D 574 K K(99).R 0.07 1/0 4.92 673 A A(99)G 0.07 11/6 3.62 455 V V(99).T 0.08 7/0 3.20 A 573 Y Y(99).C 0.08 5/0 3.12 S 283 D D(99)GA 0.11 1/0 4.67 SEN

Table 2. The top 25% of residues in 1z8dA at the interface with glu- cose.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the num- ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Fig. 6. Residues in 1z8dA, at the interface with glucose, colored by their relative importance. The ligand (glucose) is colored green. Atoms further than Table 3. 30A˚ away from the geometric center of the ligand, as well as on the line of res type disruptive sight to the ligand were removed. (See Appendix for the coloring scheme for mutations the protein chain 1z8dA.) 377 H (E)(TQMD)(SNKVCLAPIG)(YR) 484 N (Y)(H)(FTEWR)(SCDG) 672 E (FWH)(Y)(VCAG)(TR) Table 4. continued 674 S (KR)(FQMWH)(E)(NYLPI) res type subst’s cvg noc/ dist 675 G (R)(K)(FWH)(EQM) (%) bb (A˚ ) 136 L (R)(Y)(H)(TKE) H(1)NC 139 L (Y)(R)(TH)(CG) 676 T (FWHR)(K)(M)(EQLPI) Table 4. The top 25% of residues in 1z8dA at the interface with 680 X (Y)(E)(R)(FW) AMP.(Field names: res: residue number in the PDB entry; type: amino acid 135 G (R)(FKWH)(QM)(YE) type; substs: substitutions seen in the alignment; with the percentage of each 574 K (Y)(T)(FW)(VCAG) type in the bracket; noc/bb: number of contacts with the ligand, with the num- 673 A (KER)(Y)(QHD)(N) ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) 455 V (KR)(E)(Y)(QH) 573 Y (K)(QM)(R)(NELPI) 283 D (R)(H)(FW)(Y) Table 5. res type disruptive Table 3. List of disruptive mutations for the top 25% of residues in mutations 1z8dA, that are at the interface with glucose. 242 R (D)(E)(T)(YLPI)

Figure 6 shows residues in 1z8dA colored by their importance, at the Table 5. List of disruptive mutations for the top 25% of residues in interface with 1z8dGLC901. 1z8dA, that are at the interface with AMP. AMP binding site. Table 4 lists the top 25% of residues at the interface with 1z8dAMP900 (amp). The following table (Table 5) Figure 7 shows residues in 1z8dA colored by their importance, at the suggests possible disruptive replacements for these residues (see interface with 1z8dAMP900. Section 3.6). Adenine binding site. Table 6 lists the top 25% of residues at the Table 4. interface with 1z8dADE902 (adenine). The following table (Table res type subst’s cvg noc/ dist 7) suggests possible disruptive replacements for these residues (see (%) bb (A˚ ) Section 3.6). 242 R R(95)T 0.15 3/0 4.04 continued in next column

4 Table 7. continued res type disruptive mutations 610 A (E)(K)(R)(Y) 612 G (R)(K)(E)(H)

Table 7. List of disruptive mutations for the top 25% of residues in 1z8dA, that are at the interface with adenine.

Fig. 7. Residues in 1z8dA, at the interface with AMP, colored by their rela- tive importance. The ligand (AMP) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1z8dA.)

Table 6. res type subst’s cvg noc/ dist (%) bb (A˚ ) 613 Y Y(99)D. 0.10 59/17 3.29 H Fig. 8. Residues in 1z8dA, at the interface with adenine, colored by their 283 D D(99)GA 0.11 2/2 4.92 relative importance. The ligand (adenine) is colored green. Atoms further than SEN 30A˚ away from the geometric center of the ligand, as well as on the line of 610 A A(89) 0.17 4/1 3.37 sight to the ligand were removed. (See Appendix for the coloring scheme for S(4)R the protein chain 1z8dA.) F(5).YN 612 G G(66)L 0.24 13/13 3.27 S(14) Figure 8 shows residues in 1z8dA colored by their importance, at the A(13) interface with 1z8dADE902. T(5).I Interface with 1z8dA1.Table 8 lists the top 25% of residues at the interface with 1z8dA1. The following table (Table 9) suggests Table 6. The top 25% of residues in 1z8dA at the interface with ade- possible disruptive replacements for these residues (see Section 3.6). nine.(Field names: res: residue number in the PDB entry; type: amino acid Table 8. type; substs: substitutions seen in the alignment; with the percentage of each res type subst’s cvg noc/ dist type in the bracket; noc/bb: number of contacts with the ligand, with the num- ˚ ber of contacts realized through backbone atoms given in the bracket; dist: (%) bb (A) distance of closest apporach to the ligand. ) 164 G G(100) 0.01 1/1 4.07 166 F F(99). 0.02 14/4 3.46 280 Y Y(99)F 0.05 17/1 4.08 Table 7. 281 P P(99)D 0.05 12/0 3.78 res type disruptive 279 L L(99)PV 0.08 4/4 4.30 mutations D 613 Y (K)(QM)(VA)(NLPIR) 291 L L(98).T 0.11 4/0 4.17 283 D (R)(H)(FW)(Y) MIA continued in next column continued in next column

5 Table 8. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) 177 E E(98)AT 0.13 5/0 4.02 611 P P(77) 0.19 12/0 3.90 S(8) A(13).T LI 165 I M(18) 0.23 1/1 4.80 I(38) L(40)S F(1)Q

Table 8. The top 25% of residues in 1z8dA at the interface with 1z8dA1. (Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the number of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. )

Table 9. res type disruptive Fig. 9. Residues in 1z8dA, at the interface with 1z8dA1, colored by their rela- mutations tive importance. 1z8dA1 is shown in backbone representation (See Appendix 164 G (KER)(FQMWHD)(NYLPI)(SVA) for the coloring scheme for the protein chain 1z8dA.) 166 F (KE)(TQD)(SNCG)(R) 280 Y (K)(Q)(EM)(NR) 281 P (R)(Y)(H)(T) 279 L (R)(Y)(H)(T) 291 L (R)(Y)(H)(T) 177 E (H)(FWR)(Y)(K) 611 P (R)(Y)(H)(K) 165 I (Y)(R)(H)(T)

Table 9. List of disruptive mutations for the top 25% of residues in 1z8dA, that are at the interface with 1z8dA1.

Figure 9 shows residues in 1z8dA colored by their importance, at the Fig. 10. A possible active surface on the chain 1z8dA. The larger cluster it interface with 1z8dA1. belongs to is shown in blue. 2.4.3 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 1z8dA surface, away from (or Table 10. continued susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 1z8d. It is shown in Fig. 10. The right panel res type substitutions(%) cvg shows (in blue) the rest of the larger cluster this surface belongs to. 204 G G(93)N(1)D(4).T 0.22 The residues belonging to this surface ”patch” are listed in Table 10, HCS while Table 11 suggests possible disruptive replacements for these 215 W W(76)H(6).(8)T 0.22 residues (see Section 3.6). Y(2)NL(3)FSQ(1) GAV Table 10. res type substitutions(%) cvg Table 10. Residues forming surface ”patch” in 1z8dA. 397 P P(99)WTYS 0.13 351 R R(97)H(1).YSCV 0.15 398 R R(94)Q(2)AH(1)E 0.15 Table 11. K res type disruptive 355 D D(94)E(2)TRVQ.K 0.18 mutations AS 397 P (R)(K)(E)(YH) continued in next column continued in next column

6 Table 11. continued backbone atoms (if all or most contacts are through the backbone, res type disruptive mutation presumably won’t have strong impact). Two heavy atoms mutations are considered to be “in contact” if their centers are closer than 5A˚ . 351 R (D)(E)(LPI)(T) 398 R (T)(Y)(D)(CG) 3.5 Annotation 355 D (R)(FWH)(Y)(KCG) If the residue annotation is available (either from the pdb file or 204 G (R)(K)(E)(FMW) from other sources), another column, with the header “annotation” 215 W (K)(E)(Q)(D) appears. Annotations carried over from PDB are the following: site (indicating existence of related site record in PDB ), S-S (disulfide Table 11. Disruptive mutations for the surface patch in 1z8dA. bond forming residue), hb (hydrogen bond forming residue, jb (james bond forming residue), and sb (for salt bridge forming residue). 3.6 Mutation suggestions 3 NOTES ON USING TRACE RESULTS Mutation suggestions are completely heuristic and based on comple- 3.1 Coverage mentarity with the substitutions found in the alignment. Note that they are meant to be disruptive to the interaction of the protein Trace results are commonly expressed in terms of coverage: the resi- with its ligand. The attempt is made to complement the following due is important if its “coverage” is small - that is if it belongs to properties: small [AV GSTC], medium [LPNQDEMIK], large some small top percentage of residues [100% is all of the residues [WFYHR], hydrophobic [LPVAMWFI], polar [GTCY ]; posi- in a chain], according to trace. The ET results are presented in the tively [KHR], or negatively [DE] charged, aromatic [WFYH], form of a table, usually limited to top 25% percent of residues (or long aliphatic chain [EKRQM], OH-group possession [SDETY ], to some nearby percentage), sorted by the strength of the presumed and NH2 group possession [NQRK]. The suggestions are listed evolutionary pressure. (I.e., the smaller the coverage, the stronger the according to how different they appear to be from the original amino pressure on the residue.) Starting from the top of that list, mutating a acid, and they are grouped in round brackets if they appear equally couple of residues should affect the protein somehow, with the exact disruptive. From left to right, each bracketed group of amino acid effects to be determined experimentally. types resembles more strongly the original (i.e. is, presumably, less 3.2 Known substitutions disruptive) These suggestions are tentative - they might prove disrup- tive to the fold rather than to the interaction. Many researcher will One of the table columns is “substitutions” - other amino acid types choose, however, the straightforward alanine mutations, especially in seen at the same position in the alignment. These amino acid types the beginning stages of their investigation. may be interchangeable at that position in the protein, so if one wants to affect the protein by a point mutation, they should be avoided. For 4 APPENDIX example if the substitutions are “RVK” and the original protein has an R at that position, it is advisable to try anything, but RVK. Conver- 4.1 File formats sely, when looking for substitutions which will not affect the protein, Files with extension “ranks sorted” are the actual trace results. The one may try replacing, R with K, or (perhaps more surprisingly), with fields in the table in this file: V. The percentage of times the substitution appears in the alignment • is given in the immediately following bracket. No percentage is given alignment# number of the position in the alignment in the cases when it is smaller than 1%. This is meant to be a rough • residue# residue number in the PDB file guide - due to rounding errors these percentages often do not add up • type amino acid type to 100%. • rank rank of the position according to older version of ET 3.3 Surface • variability has two subfields: To detect candidates for novel functional interfaces, first we look for 1. number of different amino acids appearing in in this column residues that are solvent accessible (according to DSSP program) by of the alignment 2 at least 10A˚ , which is roughly the area needed for one water mole- 2. their type cule to come in the contact with the residue. Furthermore, we require • rho ET score - the smaller this value, the lesser variability of that these residues form a “cluster” of residues which have neighbor this position across the branches of the tree (and, presumably, within 5A˚ from any of their heavy atoms. the greater the importance for the protein) Note, however, that, if our picture of protein evolution is correct, • the neighboring residues which are not surface accessible might be cvg coverage - percentage of the residues on the structure which equally important in maintaining the interaction specificity - they have this rho or smaller should not be automatically dropped from consideration when choo- • gaps percentage of gaps in this column sing the set for mutagenesis. (Especially if they form a cluster with the surface residues.) 4.2 Color schemes used The following color scheme is used in figures with residues colored 3.4 Number of contacts by cluster size: black is a single-residue cluster; clusters composed of Another column worth noting is denoted “noc/bb”; it tells the num- more than one residue colored according to this hierarchy (ordered ber of contacts heavy atoms of the residue in question make across by descending size): red, blue, yellow, green, purple, azure, tur- the interface, as well as how many of them are realized through the quoise, brown, coral, magenta, LightSalmon, SkyBlue, violet, gold,

7 75% of the query are taken out, however); R. Schneider, A. de Daruvar, and C. Sander. ”The HSSP database of protein structure- sequence alignments.” Nucleic Acids Res., 25:226–230, 1997.

http://swift.cmbi.kun.nl/swift/hssp/ COVERAGE 4.3.5 LaTex The text for this report was processed using LATEX; V Leslie Lamport, “LaTeX: A Document Preparation System Addison- 100% 50% 30% 5% Wesley,” Reading, Mass. (1986).

4.3.6 Muscle When making alignments “from scratch”, report maker uses Muscle alignment program: Edgar, Robert C. (2004), ”MUSCLE: multiple sequence alignment with high accuracy and high throughput.” Nucleic Acids Research 32(5), 1792-97. V http://www.drive5.com/muscle/ RELATIVE IMPORTANCE 4.3.7 Pymol The figures in this report were produced using Fig. 11. Coloring scheme used to color residues by their relative importance. Pymol. The scripts can be found in the attachment. Pymol is an open-source application copyrighted by DeLano Scien- tific LLC (2005). For more information about Pymol see bisque, LightSlateBlue, orchid, RosyBrown, MediumAquamarine, http://pymol.sourceforge.net/. (Note for Windows DarkOliveGreen, CornflowerBlue, grey55, burlywood, LimeGreen, users: the attached package needs to be unzipped for Pymol to read tan, DarkOrange, DeepPink, maroon, BlanchedAlmond. the scripts and launch the viewer.) The colors used to distinguish the residues by the estimated 4.4 Note about ET Viewer evolutionary pressure they experience can be seen in Fig. 11. Dan Morgan from the Lichtarge lab has developed a visualization 4.3 Credits tool specifically for viewing trace results. If you are interested, please 4.3.1 Alistat alistat reads a multiple sequence alignment from the visit: file and shows a number of simple statistics about it. These stati- http://mammoth.bcm.tmc.edu/traceview/ stics include the format, the number of sequences, the total number of residues, the average and range of the sequence lengths, and the The viewer is self-unpacking and self-installing. Input files to be used alignment length (e.g. including gap characters). Also shown are with ETV (extension .etvx) can be found in the attachment to the some percent identities. A percent pairwise alignment identity is defi- main report. ned as (idents / MIN(len1, len2)) where idents is the number of exact identities and len1, len2 are the unaligned lengths of the two 4.5 Citing this work sequences. The ”average percent identity”, ”most related pair”, and The method used to rank residues and make predictions in this report ”most unrelated pair” of the alignment are the average, maximum, can be found in Mihalek, I., I. Res,ˇ O. Lichtarge. (2004). ”A Family of and minimum of all (N)(N-1)/2 pairs, respectively. The ”most distant Evolution-Entropy Hybrid Methods for Ranking of Protein Residues seq” is calculated by finding the maximum pairwise identity (best by Importance” J. Mol. Bio. 336: 1265-82. For the original version relative) for all N sequences, then finding the minimum of these N of ET see O. Lichtarge, H.Bourne and F. Cohen (1996). ”An Evolu- numbers (hence, the most outlying sequence). alistat is copyrighted tionary Trace Method Defines Binding Surfaces Common to Protein by HHMI/Washington University School of Medicine, 1992-2001, Families” J. Mol. Bio. 257: 342-358. and freely distributed under the GNU General Public License. report maker itself is described in Mihalek I., I. Res and O. 4.3.2 CE To map ligand binding sites from different Lichtarge (2006). ”Evolutionary Trace Report Maker: a new type source structures, report maker uses the CE program: of service for comparative analysis of proteins.” Bioinformatics http://cl.sdsc.edu/. Shindyalov IN, Bourne PE (1998) 22:1656-7. ”Protein structure alignment by incremental combinatorial extension 4.6 About report maker (CE) of the optimal path . Protein Engineering 11(9) 739-747. report maker was written in 2006 by Ivana Mihalek. The 1D ran- 4.3.3 DSSP In this work a residue is considered solvent accessi- king visualization program was written by Ivica Res.ˇ report maker 2 ble if the DSSP program finds it exposed to water by at least 10A˚ , is copyrighted by Lichtarge Lab, Baylor College of Medicine, which is roughly the area needed for one water molecule to come in Houston. the contact with the residue. DSSP is copyrighted by W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995, CMBI version 4.7 Attachments by [email protected] November 18,2002, The following files should accompany this report: http://www.cmbi.kun.nl/gv/dssp/descrip.html. • 1z8dA.complex.pdb - coordinates of 1z8dA with all of its 4.3.4 HSSP Whenever available, report maker uses HSSP ali- interacting partners gnment as a starting point for the analysis (sequences shorter than • 1z8dA.etvx - ET viewer input file for 1z8dA

8 • 1z8dA.cluster report.summary - Cluster report summary for • 1z8dA.ranks sorted - full listing of residues and their ranking 1z8dA for 1z8dA • 1z8dA.ranks - Ranks file in sequence order for 1z8dA • 1z8dA.1z8dGLC901.if.pml - Pymol script for Figure 6 • 1z8dA.clusters - Cluster descriptions for 1z8dA • 1z8dA.cbcvg - used by other 1z8dA – related pymol scripts • 1z8dA.msf - the multiple sequence alignment used for the chain • 1z8dA.1z8dAMP900.if.pml - Pymol script for Figure 7 1z8dA • 1z8dA.1z8dADE902.if.pml - Pymol script for Figure 8 • 1z8dA.descr - description of sequences used in 1z8dA msf • 1z8dA.1z8dA1.if.pml - Pymol script for Figure 9

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