Pages 1–8 1wuv Evolutionary trace report by report maker April 13, 2009

4.3.1 Alistat 7 4.3.2 CE 7 4.3.3 DSSP 7 4.3.4 HSSP 7 4.3.5 LaTex 7 4.3.6 Muscle 7 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 1wuv): Title: Crystal structure of native gladiata lectin (cgl) : a tetrameric cona-like lectin Compound: Mol id: 1; molecule: concanavalin a; chain: a, d, g, j; synonym: lectin Organism, scientific name: Canavalia Gladiata; 1wuv contains a single unique chain 1wuvA (237 residues long) and its homologues 1wuvJ, 1wuvD, and 1wuvG. CONTENTS 2 CHAIN 1WUVA 1 Introduction 1 2.1 P81461 overview 2 Chain 1wuvA 1 From SwissProt, id P81461, 99% identical to 1wuvA: 2.1 P81461 overview 1 Description: Concanavalin A (Con A). 2.2 Multiple sequence alignment for 1wuvA 1 Organism, scientific name: Canavalia virosa. 2.3 Residue ranking in 1wuvA 1 : Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.4 Top ranking residues in 1wuvA and their position on Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core the structure 2 eudicotyledons; ; eurosids I; ; ; Papilionoi- 2.4.1 Clustering of residues at 25% coverage. 2 deae; Phaseoleae; Canavalia. 2.4.2 Overlap with known functional surfaces at Function: Glucose/D-mannose specific lectin. 25% coverage. 2 Subunit: Homotetramer. 2.4.3 Possible novel functional surfaces at 25% Miscellaneous: Binds one manganese (or other transition metal) ion coverage. 5 and one calcium ion. The metal ions are essential for the saccharide- binding and cell-agglutinating activities. 3 Notes on using trace results 6 Similarity: Belongs to the leguminous lectin family. 3.1 Coverage 6 About: This Swiss-Prot entry is copyright. It is produced through a 3.2 Known substitutions 6 collaboration between the Swiss Institute of Bioinformatics and the 3.3 Surface 6 EMBL outstation - the European Bioinformatics Institute. There are 3.4 Number of contacts 6 no restrictions on its use as long as its content is in no way modified 3.5 Annotation 6 and this statement is not removed. 3.6 Mutation suggestions 6 2.2 Multiple sequence alignment for 1wuvA 4 Appendix 7 For the chain 1wuvA, the alignment 1wuvA.msf (attached) with 25 4.1 File formats 7 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 7 database, and fragments shorter than 75% of the query as well as 4.3 Credits 7 duplicate sequences were removed. It can be found in the attachment

1 Lichtarge lab 2006 Fig. 1. Residues 1-118 in 1wuvA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.)

Fig. 2. Residues 119-237 in 1wuvA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.)

Fig. 3. Residues in 1wuvA, colored by their relative importance. Clockwise: front, back, top and bottom views. to this report, under the name of 1wuvA.msf. Its statistics, from the alistat program are the following: 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Format: MSF top 25% of all residues, this time colored according to clusters they Number of sequences: 25 belong to. The clusters in Fig.4 are composed of the residues listed Total number of residues: 5516 Smallest: 182 Largest: 237 Average length: 220.6 Alignment length: 237 Average identity: 39% Most related pair: 98% Most unrelated pair: 19% Most distant seq: 30%

Furthermore, 3% of residues show as conserved in this alignment. The alignment consists of 36% eukaryotic ( 36% plantae) sequences. (Descriptions of some sequences were not readily availa- ble.) The file containing the sequence descriptions can be found in the attachment, under the name 1wuvA.descr. 2.3 Residue ranking in 1wuvA The 1wuvA sequence is shown in Figs. 1–2, with each residue colo- red according to its estimated importance. The full listing of residues in 1wuvA can be found in the file called 1wuvA.ranks sorted in the attachment. 2.4 Top ranking residues in 1wuvA and their position on the structure In the following we consider residues ranking among top 25% of Fig. 4. Residues in 1wuvA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for residues in the protein . Figure 3 shows residues in 1wuvA colored the coloring scheme). Clockwise: front, back, top and bottom views. The by their importance: bright red and yellow indicate more conser- corresponding Pymol script is attached. ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. in Table 1.

2 Table 1. cluster size member color residues red 46 4,5,6,7,8,9,10,14,19,20,24 26,27,28,29,30,31,34,37,40 45,46,48,49,50,51,52,54,55 56,60,61,62,63,64,74,75,76 77,79,80,81,85,86,87,89 blue 11 92,93,94,95,97,98,102,104 106,108,109 yellow 3 111,113,114

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

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. Manganese (ii) ion binding site. Table 2 lists the top 25% of resi- dues at the interface with 1wuvAMN239 (manganese (ii) ion). 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 (%) bb (A˚ ) 10 D D(100) 0.04 4/0 2.14 24 H H(100) 0.04 5/0 2.13 19 D D(95) 0.08 5/1 2.26 N(4) 8 E E(95) 0.09 4/0 2.18 T(4) 34 S S(95) 0.10 1/0 4.12 X(4)

Table 2. The top 25% of residues in 1wuvA at the interface with manga- nese (ii) ion.(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 3. res type disruptive mutations 10 D (R)(FWH)(KYVCAG)(TQM) 24 H (E)(TQMD)(SNKVCLAPIG)(YR) 19 D (R)(FWH)(Y)(VCAG) 8 E (FWH)(R)(YVA)(KCG) 34 S (KR)(FQMWH)(YE)(NLPI)

Table 3. List of disruptive mutations for the top 25% of residues in 1wuvA, that are at the interface with manganese (ii) ion.

Figure 5 shows residues in 1wuvA colored by their importance, at the interface with 1wuvAMN239. Interface with 1wuvG1.By analogy with 1wuvG – 1wuvG1 inter- face. Table 4 lists the top 25% of residues at the interface with

3 Table 4. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) D(11) T(44) N(4) Q(4) 64 V V(76) 0.23 15/2 3.08 F(8) I(8) K(4) R(4) 51 H S(35) 0.24 23/0 3.54 W(20) H(35) I(4) V(4) 55 N T(28) 0.25 22/0 3.56 N(56) D(16)

Table 4. The top 25% of residues in 1wuvA at the interface with 1wuvG1. Fig. 5. Residues in 1wuvA, at the interface with manganese (ii) ion, colored (Field names: res: residue number in the PDB entry; type: amino acid type; by their relative importance. The ligand (manganese (ii) ion) is colored green. substs: substitutions seen in the alignment; with the percentage of each type Atoms further than 30A˚ away from the geometric center of the ligand, as well in the bracket; noc/bb: number of contacts with the ligand, with the number of as on the line of sight to the ligand were removed. (See Appendix for the contacts realized through backbone atoms given in the bracket; dist: distance coloring scheme for the protein chain 1wuvA.) of closest apporach to the ligand. )

1wuvG1. The following table (Table 5) suggests possible disruptive Table 5. replacements for these residues (see Section 3.6). res type disruptive mutations Table 4. 108 S (KR)(FQMWH)(E)(NYLPI) res type subst’s cvg noc/ dist 75 V (YR)(KE)(H)(QD) (%) bb (A˚ ) 76 S (K)(R)(QM)(FNELWPHI) 108 S S(95) 0.04 5/0 3.97 60 R (T)(Y)(D)(SECG) G(4) 62 S (R)(K)(H)(FQW) 75 V L(64) 0.12 1/1 4.76 63 A (Y)(R)(KE)(H) V(35) 74 T (R)(K)(H)(FW) 76 S S(83) 0.13 8/0 3.48 49 T (R)(FKW)(H)(M) Y(16) 64 V (Y)(E)(D)(KR) 60 R N(52) 0.14 48/0 2.36 51 H (E)(Q)(D)(K) R(40) 55 N (Y)(FWH)(R)(TVA) I(8) 62 S S(88) 0.16 20/3 3.23 T(4) Table 5. List of disruptive mutations for the top 25% of residues in D(4) 1wuvA, that are at the interface with 1wuvG1. A(4) 63 A V(56) 0.18 4/4 3.63 Figure 6 shows residues in 1wuvA colored by their importance, at the A(40) interface with 1wuvG1. M(4) Calcium ion binding site. Table 6 lists the top 25% of residues at 74 T S(40) 0.20 8/0 3.71 the interface with 1wuvACA240 (calcium ion). The following table N(16) (Table 7) suggests possible disruptive replacements for these residues T(40) (see Section 3.6). L(4) 49 T H(35) 0.21 4/0 4.50 continued in next column

4 Fig. 6. Residues in 1wuvA, at the interface with 1wuvG1, colored by their Fig. 7. Residues in 1wuvA, at the interface with calcium ion, colored by their relative importance. 1wuvG1 is shown in backbone representation (See relative importance. The ligand (calcium ion) is colored green. Atoms further Appendix for the coloring scheme for the protein chain 1wuvA.) 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 1wuvA.) Table 6. res type subst’s cvg noc/ dist (%) bb (A˚ ) Interface with 1wuvD.Table 8 lists the top 25% of residues at 10 D D(100) 0.04 4/0 2.43 the interface with 1wuvD. The following table (Table 9) suggests 24 H H(100) 0.04 2/0 4.52 possible disruptive replacements for these residues (see Section 3.6). 19 D D(95) 0.08 4/0 2.37 Table 8. N(4) res type subst’s cvg noc/ dist 14 N N(88) 0.14 6/2 2.41 (%) bb (A˚ ) D(11) 98 G G(92) 0.14 1/1 4.72 S(8) Table 6. The top 25% of residues in 1wuvA at the interface with calcium ion.(Field names: res: residue number in the PDB entry; type: amino acid Table 8. The top 25% of residues in 1wuvA at the interface with 1wuvD. type; substs: substitutions seen in the alignment; with the percentage of each (Field names: res: residue number in the PDB entry; type: amino acid type; type in the bracket; noc/bb: number of contacts with the ligand, with the num- substs: substitutions seen in the alignment; with the percentage of each type ber of contacts realized through backbone atoms given in the bracket; dist: in the bracket; noc/bb: number of contacts with the ligand, with the number of distance of closest apporach to the ligand. ) contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. )

Table 7. res type disruptive Table 9. mutations res type disruptive 10 D (R)(FWH)(KYVCAG)(TQM) mutations 24 H (E)(TQMD)(SNKVCLAPIG)(YR) 98 G (KR)(E)(FQMWH)(D) 19 D (R)(FWH)(Y)(VCAG) 14 N (Y)(FWH)(TR)(VCAG) Table 9. List of disruptive mutations for the top 25% of residues in 1wuvA, that are at the interface with 1wuvD. Table 7. List of disruptive mutations for the top 25% of residues in 1wuvA, that are at the interface with calcium ion. Figure 8 shows residues in 1wuvA colored by their importance, at the interface with 1wuvD. Figure 7 shows residues in 1wuvA colored by their importance, at the 2.4.3 Possible novel functional surfaces at 25% coverage. One interface with 1wuvACA240. group of residues is conserved on the 1wuvA surface, away from (or

5 Table 10. continued res type substitutions(%) cvg 81 L L(100) 0.04 85 L L(100) 0.04 86 P P(92)T(4)G(4) 0.06 87 E E(92)P(4)D(4) 0.06 19 D D(95)N(4) 0.08 77 Y Y(95)T(4) 0.08 7 V V(95)L(4) 0.09 34 S S(95)X(4) 0.10 20 P P(92)I(4)A(4) 0.11 75 V L(64)V(35) 0.12 79 V V(92)I(8) 0.12 56 S S(92)A(4)N(4) 0.13 76 S S(83)Y(16) 0.13 14 N N(88)D(11) 0.14 60 R N(52)R(40)I(8) 0.14 62 S S(88)T(4)D(4) 0.16 A(4) 29 I I(83)X(4)N(4) 0.17 V(8) 30 K N(64)K(32)X(4) 0.17 Fig. 8. Residues in 1wuvA, at the interface with 1wuvD, colored by their rela- 63 A V(56)A(40)M(4) 0.18 tive importance. 1wuvD is shown in backbone representation (See Appendix 74 T S(40)N(16)T(40) 0.20 for the coloring scheme for the protein chain 1wuvA.) L(4) 5 V I(23)V(68)F(8) 0.21 49 T H(35)D(11)T(44) 0.21 susbtantially larger than) other functional sites and interfaces reco- N(4)Q(4) gnizable in PDB entry 1wuv. It is shown in Fig. 9. The right panel 64 V V(76)F(8)I(8) 0.23 shows (in blue) the rest of the larger cluster this surface belongs to. K(4)R(4) 51 H S(35)W(20)H(35) 0.24 I(4)V(4) 37 T T(71)N(8)K(4) 0.25 S(11)I(4) 55 N T(28)N(56)D(16) 0.25

Table 10. Residues forming surface ”patch” in 1wuvA.

Table 11. res type disruptive mutations 31 S (KR)(FQMWH)(NYELPI)(D) Fig. 9. A possible active surface on the chain 1wuvA. The larger cluster it 54 Y (K)(QM)(NEVLAPIR)(D) belongs to is shown in blue. 61 L (YR)(TH)(SKECG)(FQWD) 80 D (R)(FWH)(KYVCAG)(TQM) 81 L (YR)(TH)(SKECG)(FQWD) The residues belonging to this surface ”patch” are listed in Table 10, while Table 11 suggests possible disruptive replacements for these 85 L (YR)(TH)(SKECG)(FQWD) 86 P (R)(H)(Y)(K) residues (see Section 3.6). 87 E (H)(FW)(R)(Y) Table 10. 19 D (R)(FWH)(Y)(VCAG) res type substitutions(%) cvg 77 Y (K)(QM)(R)(NELPI) 31 S S(100) 0.04 7 V (YR)(KE)(H)(QD) 54 Y Y(100) 0.04 34 S (KR)(FQMWH)(YE)(NLPI) 61 L L(100) 0.04 20 P (YR)(H)(T)(KE) 80 D D(100) 0.04 continued in next column continued in next column

6 Table 11. continued that these residues form a “cluster” of residues which have neighbor res type disruptive within 5A˚ from any of their heavy atoms. mutations Note, however, that, if our picture of protein evolution is correct, 75 V (YR)(KE)(H)(QD) the neighboring residues which are not surface accessible might be 79 V (YR)(KE)(H)(QD) equally important in maintaining the interaction specificity - they 56 S (R)(K)(H)(FW) should not be automatically dropped from consideration when choo- 76 S (K)(R)(QM)(FNELWPHI) sing the set for mutagenesis. (Especially if they form a cluster with 14 N (Y)(FWH)(TR)(VCAG) the surface residues.) 60 R (T)(Y)(D)(SECG) 62 S (R)(K)(H)(FQW) 3.4 Number of contacts 29 I (Y)(R)(H)(T) Another column worth noting is denoted “noc/bb”; it tells the num- 30 K (Y)(FW)(T)(SVCAG) ber of contacts heavy atoms of the residue in question make across 63 A (Y)(R)(KE)(H) the interface, as well as how many of them are realized through the 74 T (R)(K)(H)(FW) backbone atoms (if all or most contacts are through the backbone, 5 V (KE)(R)(Y)(QD) mutation presumably won’t have strong impact). Two heavy atoms 49 T (R)(FKW)(H)(M) are considered to be “in contact” if their centers are closer than 5A˚ . 64 V (Y)(E)(D)(KR) 51 H (E)(Q)(D)(K) 3.5 Annotation 37 T (R)(FWH)(K)(M) If the residue annotation is available (either from the pdb file or 55 N (Y)(FWH)(R)(TVA) from other sources), another column, with the header “annotation” appears. Annotations carried over from PDB are the following: site Table 11. Disruptive mutations for the surface patch in 1wuvA. (indicating existence of related site record in PDB ), S-S (disulfide 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 Trace results are commonly expressed in terms of coverage: the resi- they are meant to be disruptive to the interaction of the protein due is important if its “coverage” is small - that is if it belongs to with its ligand. The attempt is made to complement the following some small top percentage of residues [100% is all of the residues properties: small [AV GSTC], medium [LPNQDEMIK], large in a chain], according to trace. The ET results are presented in the [WFYHR], hydrophobic [LPVAMWFI], polar [GTCY ]; posi- form of a table, usually limited to top 25% percent of residues (or tively [KHR], or negatively [DE] charged, aromatic [WFYH], to some nearby percentage), sorted by the strength of the presumed long aliphatic chain [EKRQM], OH-group possession [SDETY ], evolutionary pressure. (I.e., the smaller the coverage, the stronger the and NH2 group possession [NQRK]. The suggestions are listed pressure on the residue.) Starting from the top of that list, mutating a according to how different they appear to be from the original amino couple of residues should affect the protein somehow, with the exact acid, and they are grouped in round brackets if they appear equally effects to be determined experimentally. disruptive. From left to right, each bracketed group of amino acid types resembles more strongly the original (i.e. is, presumably, less 3.2 Known substitutions disruptive) These suggestions are tentative - they might prove disrup- One of the table columns is “substitutions” - other amino acid types tive to the fold rather than to the interaction. Many researcher will seen at the same position in the alignment. These amino acid types choose, however, the straightforward alanine mutations, especially in may be interchangeable at that position in the protein, so if one wants the beginning stages of their investigation. to affect the protein by a point mutation, they should be avoided. For example if the substitutions are “RVK” and the original protein has 4 APPENDIX an R at that position, it is advisable to try anything, but RVK. Conver- sely, when looking for substitutions which will not affect the protein, 4.1 File formats one may try replacing, R with K, or (perhaps more surprisingly), with Files with extension “ranks sorted” are the actual trace results. The V. The percentage of times the substitution appears in the alignment fields in the table in this file: 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 guide - due to rounding errors these percentages often do not add up • residue# residue number in the PDB file to 100%. • type amino acid type • rank 3.3 Surface rank of the position according to older version of ET • 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 2 of the alignment at least 10A˚ , which is roughly the area needed for one water mole- cule to come in the contact with the residue. Furthermore, we require 2. their type

7 http://cl.sdsc.edu/. Shindyalov IN, Bourne PE (1998) ”Protein structure alignment by incremental combinatorial extension (CE) of the optimal path . Protein Engineering 11(9) 739-747. 4.3.3 DSSP In this work a residue is considered solvent accessi- COVERAGE ble if the DSSP program finds it exposed to water by at least 10A˚ 2, which is roughly the area needed for one water molecule to come in V the contact with the residue. DSSP is copyrighted by W. Kabsch, C. 100% 50% 30% 5% Sander and MPI-MF, 1983, 1985, 1988, 1994 1995, CMBI version by [email protected] November 18,2002, http://www.cmbi.kun.nl/gv/dssp/descrip.html.

4.3.4 HSSP Whenever available, report maker uses HSSP ali-

V gnment as a starting point for the analysis (sequences shorter than RELATIVE IMPORTANCE 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. Fig. 10. Coloring scheme used to color residues by their relative importance. http://swift.cmbi.kun.nl/swift/hssp/

4.3.5 LaTex The text for this report was processed using LATEX; • rho ET score - the smaller this value, the lesser variability of Leslie Lamport, “LaTeX: A Document Preparation System Addison- this position across the branches of the tree (and, presumably, Wesley,” Reading, Mass. (1986). the greater the importance for the protein) 4.3.6 Muscle When making alignments “from scratch”, report • cvg coverage - percentage of the residues on the structure which maker uses Muscle alignment program: Edgar, Robert C. (2004), have this rho or smaller ”MUSCLE: multiple sequence alignment with high accuracy and • gaps percentage of gaps in this column high throughput.” Nucleic Acids Research 32(5), 1792-97. 4.2 Color schemes used http://www.drive5.com/muscle/ The following color scheme is used in figures with residues colored 4.3.7 Pymol The figures in this report were produced using by cluster size: black is a single-residue cluster; clusters composed of Pymol. The scripts can be found in the attachment. Pymol more than one residue colored according to this hierarchy (ordered is an open-source application copyrighted by DeLano Scien- by descending size): red, blue, yellow, green, purple, azure, tur- tific LLC (2005). For more information about Pymol see quoise, brown, coral, magenta, LightSalmon, SkyBlue, violet, gold, http://pymol.sourceforge.net/. (Note for Windows bisque, LightSlateBlue, orchid, RosyBrown, MediumAquamarine, users: the attached package needs to be unzipped for Pymol to read DarkOliveGreen, CornflowerBlue, grey55, burlywood, LimeGreen, the scripts and launch the viewer.) tan, DarkOrange, DeepPink, maroon, BlanchedAlmond. 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. 10. Dan Morgan from the Lichtarge lab has developed a visualization 4.3 Credits tool specifically for viewing trace results. If you are interested, please visit: 4.3.1 Alistat alistat reads a multiple sequence alignment from the 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 4.5 Citing this work exact identities and len1, len2 are the unaligned lengths of the two 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. Lichtarge (2006). ”Evolutionary Trace Report Maker: a new type 4.3.2 CE To map ligand binding sites from different of service for comparative analysis of proteins.” Bioinformatics source structures, report maker uses the CE program: 22:1656-7.

8 4.6 About report maker • 1wuvA.clusters - Cluster descriptions for 1wuvA report maker was written in 2006 by Ivana Mihalek. The 1D ran- • 1wuvA.msf - the multiple sequence alignment used for the chain king visualization program was written by Ivica Res.ˇ report maker 1wuvA is copyrighted by Lichtarge Lab, Baylor College of Medicine, • 1wuvA.descr - description of sequences used in 1wuvA msf Houston. • 1wuvA.ranks sorted - full listing of residues and their ranking 4.7 Attachments for 1wuvA The following files should accompany this report: • 1wuvA.1wuvAMN239.if.pml - Pymol script for Figure 5 • • 1wuvA.complex.pdb - coordinates of 1wuvA with all of its 1wuvA.cbcvg - used by other 1wuvA – related pymol scripts interacting partners • 1wuvA.1wuvG1.if.pml - Pymol script for Figure 6 • 1wuvA.etvx - ET viewer input file for 1wuvA • 1wuvA.1wuvACA240.if.pml - Pymol script for Figure 7 • 1wuvA.cluster report.summary - Cluster report summary for • 1wuvA.1wuvD.if.pml - Pymol script for Figure 8 1wuvA • 1wuvA.ranks - Ranks file in sequence order for 1wuvA

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