Pages 1–8 3c1o Evolutionary trace report by report maker January 4, 2010

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 3c1o): Title: The multiple phenylpropene synthases in both clarkia breweri and petunia hybrida represent two distinct lineages CONTENTS Compound: Mol id: 1; molecule: eugenol synthase; chain: a; synonym: brewer’s clarkia; engineered: yes 1 Introduction 1 Organism, scientific name: Clarkia Breweri; 3c1o contains a single unique chain 3c1oA (314 residues long). 2 Chain 3c1oA 1 2.1 O49820 overview 1 2.2 Multiple sequence alignment for 3c1oA 1 2.3 Residue ranking in 3c1oA 1 2.4 Top ranking residues in 3c1oA and their position on the structure 2 2 CHAIN 3C1OA 2.4.1 Clustering of residues at 25% coverage. 2 2.1 O49820 overview 2.4.2 Overlap with known functional surfaces at 25% coverage. 2 From SwissProt, id O49820, 57% identical to 3c1oA: 2.4.3 Possible novel functional surfaces at 25% Description: Isoflavone reductase-like protein. coverage. 3 Organism, scientific name: Citrus paradisi (Grapefruit). Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 3 Notes on using trace results 6 Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 3.1 Coverage 6 eudicots; rosids; eurosids II; Sapindales; Rutaceae; Citrus. 3.2 Known substitutions 6 3.3 Surface 6 3.4 Number of contacts 6 3.5 Annotation 6 2.2 Multiple sequence alignment for 3c1oA 3.6 Mutation suggestions 7 For the chain 3c1oA, the alignment 3c1oA.msf (attached) with 134 sequences was used. The alignment was downloaded from the HSSP 4 Appendix 7 database, and fragments shorter than 75% of the query as well as 4.1 File formats 7 duplicate sequences were removed. It can be found in the attachment 4.2 Color schemes used 7 to this report, under the name of 3c1oA.msf. Its statistics, from the 4.3 Credits 7 alistat program are the following:

1 Lichtarge lab 2006 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.

Fig. 1. Residues 1-157 in 3c1oA colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.)

Fig. 2. Residues 158-314 in 3c1oA colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.)

Fig. 3. Residues in 3c1oA, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 134 Total number of residues: 40367 Smallest: 239 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Largest: 314 top 25% of all residues, this time colored according to clusters they Average length: 301.2 belong to. The clusters in Fig.4 are composed of the residues listed Alignment length: 314 in Table 1. Average identity: 48% Most related pair: 99% Table 1. Most unrelated pair: 23% cluster size member Most distant seq: 46% color residues red 57 5,20,21,28,31,33,54,55,60,64 68,75,76,78,79,80,90,93,96 Furthermore, <1% of residues show as conserved in this ali- 97,98,100,101,102,104,105 gnment. 106,108,109,110,111,112,114 The alignment consists of 35% eukaryotic ( 35% plantae) 115,123,124,128,131,135,139 sequences. (Descriptions of some sequences were not readily availa- 144,146,189,191,193,196,202 ble.) The file containing the sequence descriptions can be found in 207,208,211,214,217,284,288 the attachment, under the name 3c1oA.descr. 289,290,294 blue 6 170,228,229,231,236,238 2.3 Residue ranking in 3c1oA yellow 4 176,178,179,180 The 3c1oA sequence is shown in Figs. 1–2, with each residue colored green 4 8,10,11,14 according to its estimated importance. The full listing of residues purple 2 247,265 in 3c1oA can be found in the file called 3c1oA.ranks sorted in the attachment. Table 1. Clusters of top ranking residues in 3c1oA. 2.4 Top ranking residues in 3c1oA and their position on the structure 2.4.2 Overlap with known functional surfaces at 25% coverage. In the following we consider residues ranking among top 25% of The name of the ligand is composed of the source PDB identifier residues in the protein . Figure 3 shows residues in 3c1oA colored and the heteroatom name used in that file.

2 Table 2. continued res type subst’s cvg noc/ dist antn (%) bb (A˚ ) S(2) Y(2) A(2)G .(2) 151 N YN(85) 0.25 8/8 2.78 site H(5) G(2)S .(2) A(1)F

Table 2. The top 25% of residues in 3c1oA at the interface with NAP.(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. )

Table 3. Fig. 4. Residues in 3c1oA, colored according to the cluster they belong to: res type disruptive red, followed by blue and yellow are the largest clusters (see Appendix for mutations the coloring scheme). Clockwise: front, back, top and bottom views. The 8 G (KER)(FQMWHD)(NLPI)(Y) corresponding Pymol script is attached. 11 G (KER)(FQMWHD)(NLPI)(Y) 14 G (KER)(FQMWHD)(NLPI)(Y) 111 F (K)(E)(Q)(D) NAP binding site. Table 2 lists the top 25% of residues at the 131 K (FYW)(VA)(H)(T) interface with 3c1oANAP401 (nap). The following table (Table 3) 33 R (T)(D)(Y)(SCG) suggests possible disruptive replacements for these residues (see 10 T (R)(K)(H)(FW) Section 3.6). 112 G (KER)(FWH)(D)(M) 109 S (K)(R)(FQMWH)(YE) Table 2. 110 D (R)(H)(FW)(K) res type subst’s cvg noc/ dist antn 157 F (K)(E)(Q)(R) (%) bb (A˚ ) 151 N (Y)(E)(R)(TH) 8 G G(99). 0.03 15/15 3.58 site 11 G G(99). 0.03 20/20 2.95 site 14 G G(99). 0.03 1/1 4.43 Table 3. List of disruptive mutations for the top 25% of residues in 3c1oA, that are at the interface with NAP. 111 F .F(94) 0.06 16/10 3.00 Y(5) 131 K K(97)S. 0.06 10/0 2.83 site Figure 5 shows residues in 3c1oA colored by their importance, at the TE interface with 3c1oANAP401. 33 R R(97)XM 0.07 77/1 2.83 site Interface with 3c1oA1.Table 4 lists the top 25% of residues at . the interface with 3c1oA1. The following table (Table 5) suggests 10 T T(95) 0.09 29/12 2.58 site possible disruptive replacements for these residues (see Section 3.6). S(2)M. Table 4. 112 G .G(97)E 0.10 6/6 3.71 res type subst’s cvg noc/ dist antn AR (%) bb (A˚ ) 109 S .S(95) 0.12 14/5 2.71 site 33 R R(97)XM 0.07 1/0 4.77 site A(2)R . 110 D .E(92) 0.15 10/10 3.33 site D(5)AS 157 F L(6) 0.23 6/0 3.12 site Table 4. The top 25% of residues in 3c1oA at the interface with 3c1oA1. F(61) (Field names: res: residue number in the PDB entry; type: amino acid type; P(20) 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 continued in next column contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. )

3 Table 5. res type disruptive mutations 33 R (T)(D)(Y)(SCG)

Table 5. List of disruptive mutations for the top 25% of residues in 3c1oA, that are at the interface with 3c1oA1.

Fig. 5. Residues in 3c1oA, at the interface with NAP, colored by their relative importance. The ligand (NAP) 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 3c1oA.)

Fig. 6. Residues in 3c1oA, at the interface with 3c1oA1, colored by their rela- tive importance. 3c1oA1 is shown in backbone representation (See Appendix for the coloring scheme for the protein chain 3c1oA.)

Figure 6 shows residues in 3c1oA colored by their importance, at the interface with 3c1oA1. 2.4.3 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 3c1oA surface, away from (or susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 3c1o. It is shown in Fig. 7. The right panel shows (in blue) the rest of the larger cluster this surface belongs to. The residues belonging to this surface ”patch” are listed in Table 6, while Table 7 suggests possible disruptive replacements for these residues (see Section 3.6). Table 6. res type substitutions(%) cvg antn 8 G G(99). 0.03 site 11 G G(99). 0.03 site 33 R R(97)XM. 0.07 site 10 T T(95)S(2)M. 0.09 site 60 G G(90)A(9) 0.10 31 Y L(89)Y(7)F(1)M. 0.12 64 E D(83)E(9)N(3) 0.14 continued in next column

4 Table 8. res type substitutions(%) cvg antn 111 F .F(94)Y(5) 0.06 131 K K(97)S.TE 0.06 site 108 P .P(97)AH 0.08 90 Q Q(97)R(1)L 0.09 112 G .G(97)EAR 0.10 123 P P(92)M(2)L(1)R. 0.10 A(1)E 109 S .S(95)A(2)R 0.12 site 110 D .E(92)D(5)AS 0.15 site 124 F A(35)F(9)G(41) 0.21 Fig. 7. A possible active surface on the chain 3c1oA. The larger cluster it V(8)D(2)MI.T belongs to is shown in blue. 128 L L(9)Y(29)F(55) 0.21 C(1)IV(1). Table 6. continued 115 E .V(60)E(5)P(24) 0.24 res type substitutions(%) cvg antn I(3)SY(1)LT(1) G(2) 151 N YN(85)H(5)G(2)S 0.25 site .(2)A(1)F Table 6. Residues forming surface ”patch” in 3c1oA. Table 8. Residues forming surface ”patch” in 3c1oA.

Table 7. res type disruptive Table 9. mutations res type disruptive 8 G (KER)(FQMWHD)(NLPI)(Y) mutations 11 G (KER)(FQMWHD)(NLPI)(Y) 111 F (K)(E)(Q)(D) 33 R (T)(D)(Y)(SCG) 131 K (FYW)(VA)(H)(T) 10 T (R)(K)(H)(FW) 108 P (YR)(T)(E)(KH) 60 G (KER)(QHD)(FYMW)(N) 90 Q (Y)(T)(FWH)(SCG) 31 Y (K)(Q)(R)(E) 112 G (KER)(FWH)(D)(M) 64 E (FWH)(R)(Y)(VA) 123 P (Y)(R)(H)(T) 109 S (K)(R)(FQMWH)(YE) Table 7. Disruptive mutations for the surface patch in 3c1oA. 110 D (R)(H)(FW)(K) 124 F (K)(E)(R)(Q) 128 L (R)(Y)(K)(H) Another group of surface residues is shown in Fig.8. The right panel 115 E (H)(R)(FW)(Y) shows (in blue) the rest of the larger cluster this surface belongs to. 151 N (Y)(E)(R)(TH)

Table 9. Disruptive mutations for the surface patch in 3c1oA.

Another group of surface residues is shown in Fig.9. The right panel shows (in blue) the rest of the larger cluster this surface belongs to.

Fig. 8. Another possible active surface on the chain 3c1oA. The larger cluster it belongs to is shown in blue.

The residues belonging to this surface ”patch” are listed in Table 8, while Table 9 suggests possible disruptive replacements for these residues (see Section 3.6). Fig. 9. Another possible active surface on the chain 3c1oA. The larger cluster it belongs to is shown in blue.

5 The residues belonging to this surface ”patch” are listed in Table 10, Table 11. continued while Table 11 suggests possible disruptive replacements for these res type disruptive residues (see Section 3.6). mutations Table 10. Table 11. Disruptive mutations for the surface patch in 3c1oA. res type substitutions(%) cvg 191 D .D(98)A 0.02 202 D .D(97)AH 0.04 Another group of surface residues is shown in Fig.10. The residues 207 N .N(98)D 0.04 97 I I(94)M(5) 0.05 104 K K(96)R(2)Q(1) 0.05 214 P .P(83)L(15) 0.06 289 Y Y(97)F(1).K 0.10 76 D D(88)E(9)N(1) 0.11 208 R .K(88)R(8)EN(1) 0.11 290 P P(97)A.QH 0.12 288 L L(94)A(2).VT 0.13 105 R LR(95)K(2)E 0.16 284 E E(94)N(1)D(2)G. 0.18 102 N N(59)T(34)S(2) 0.19 C(2)G 144 P P(94)S(2).(1)VA 0.19 101 G G(89)N(4)VR(1) 0.20 K(3) 294 F Y(74)F(23)H. 0.20 98 K R(1)K(91)NA(2) 0.22 H(1)TQE 100 A A(64)V(29)G(1)L 0.24 I(2)S

Table 10. Residues forming surface ”patch” in 3c1oA. Fig. 10. Another possible active surface on the chain 3c1oA.

Table 11. res type disruptive belonging to this surface ”patch” are listed in Table 12, while Table mutations 13 suggests possible disruptive replacements for these residues (see 191 D (R)(H)(FW)(Y) Section 3.6). 202 D (R)(FKWH)(YCG)(VQA) Table 12. 207 N (Y)(FWH)(T)(VCARG) res type substitutions(%) cvg 97 I (Y)(R)(TH)(SCG) 178 G .G(98)D 0.01 104 K (Y)(T)(FW)(SVCAG) 229 E E(100) 0.01 214 P (Y)(R)(T)(H) 228 W LW(98)G 0.03 289 Y (K)(QM)(EVA)(NLPI) 231 K K(74)L(21)TYM 0.14 76 D (R)(FWH)(Y)(VCAG) I(1) 208 R (T)(Y)(VCAG)(SD) 238 K K(61)R(37)M 0.16 290 P (Y)(R)(T)(H) 236 F L(83)F(7)I(5)M 0.17 288 L (R)(Y)(H)(K) V(1)A 105 R (T)(Y)(CG)(SVAD) 179 T .D(85)S(4)T(3) 0.22 284 E (FWH)(R)(Y)(VA) N(2)H(2)E 102 N (FYWH)(R)(E)(M) 170 R .(2)P(85)S(5) 0.24 144 P (R)(Y)(H)(K) Q(2)R(2)KA 101 G (E)(D)(FYW)(HR) 176 I .I(77)V(9)L(11) 0.24 294 F (KE)(Q)(D)(T) E 98 K (Y)(FW)(T)(VCAG) 100 A (R)(KY)(E)(H) Table 12. continued in next column Residues forming surface ”patch” in 3c1oA.

6 Table 13. 3.4 Number of contacts res type disruptive Another column worth noting is denoted “noc/bb”; it tells the num- mutations ber of contacts heavy atoms of the residue in question make across 178 G (R)(K)(FWH)(M) the interface, as well as how many of them are realized through the 229 E (FWH)(YVCARG)(T)(SNKLPI) backbone atoms (if all or most contacts are through the backbone, 228 W (KE)(QDR)(T)(SN) mutation presumably won’t have strong impact). Two heavy atoms 231 K (Y)(FTW)(CG)(H) are considered to be “in contact” if their centers are closer than 5A˚ . 238 K (Y)(T)(FW)(SCG) 236 F (KE)(TR)(D)(Q) 3.5 Annotation 179 T (R)(K)(FW)(H) 170 R (TY)(D)(ECG)(S) If the residue annotation is available (either from the pdb file or 176 I (R)(Y)(H)(T) from other sources), another column, with the header “annotation” appears. Annotations carried over from PDB are the following: site (indicating existence of related site record in PDB ), S-S (disulfide Table 13. Disruptive mutations for the surface patch in 3c1oA. bond forming residue), hb (hydrogen bond forming residue, jb (james bond forming residue), and sb (for salt bridge forming residue).

3 NOTES ON USING TRACE RESULTS 3.6 Mutation suggestions 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 an R at that position, it is advisable to try anything, but RVK. Conver- 4 APPENDIX 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 V. The percentage of times the substitution appears in the alignment Files with extension “ranks sorted” are the actual trace results. The is given in the immediately following bracket. No percentage is given fields in the table in this file: 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 alignment# number of the position in the alignment to 100%. • residue# residue number in the PDB file • type amino acid type 3.3 Surface • rank rank of the position according to older version of ET To detect candidates for novel functional interfaces, first we look for • residues that are solvent accessible (according to DSSP program) by variability has two subfields: 2 at least 10A˚ , which is roughly the area needed for one water mole- 1. number of different amino acids appearing in in this column cule to come in the contact with the residue. Furthermore, we require of the alignment that these residues form a “cluster” of residues which have neighbor 2. their type within 5A˚ from any of their heavy atoms. • rho ET score - the smaller this value, the lesser variability of Note, however, that, if our picture of protein evolution is correct, this position across the branches of the tree (and, presumably, the neighboring residues which are not surface accessible might be the greater the importance for the protein) equally important in maintaining the interaction specificity - they • cvg coverage - percentage of the residues on the structure which should not be automatically dropped from consideration when choo- have this rho or smaller sing the set for mutagenesis. (Especially if they form a cluster with the surface residues.) • gaps percentage of gaps in this column

7 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.

COVERAGE 4.3.4 HSSP Whenever available, report maker uses HSSP ali- gnment as a starting point for the analysis (sequences shorter than V 75% of the query are taken out, however); R. Schneider, A. de 100% 50% 30% 5% 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/

4.3.5 LaTex The text for this report was processed using LATEX; V Leslie Lamport, “LaTeX: A Document Preparation System Addison- RELATIVE IMPORTANCE Wesley,” Reading, Mass. (1986). 4.3.6 Muscle When making alignments “from scratch”, report Fig. 11. Coloring scheme used to color residues by their relative importance. 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. 4.2 Color schemes used http://www.drive5.com/muscle/ The following color scheme is used in figures with residues colored by cluster size: black is a single-residue cluster; clusters composed of 4.3.7 Pymol The figures in this report were produced using more than one residue colored according to this hierarchy (ordered Pymol. The scripts can be found in the attachment. Pymol by descending size): red, blue, yellow, green, purple, azure, tur- is an open-source application copyrighted by DeLano Scien- quoise, brown, coral, magenta, LightSalmon, SkyBlue, violet, gold, 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 evolutionary pressure they experience can be seen in Fig. 11. 4.4 Note about ET Viewer 4.3 Credits Dan Morgan from the Lichtarge lab has developed a visualization 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- stics include the format, the number of sequences, the total number http://mammoth.bcm.tmc.edu/traceview/ of residues, the average and range of the sequence lengths, and the alignment length (e.g. including gap characters). Also shown are The viewer is self-unpacking and self-installing. Input files to be used some percent identities. A percent pairwise alignment identity is defi- with ETV (extension .etvx) can be found in the attachment to the ned as (idents / MIN(len1, len2)) where idents is the number of main report. exact identities and len1, len2 are the unaligned lengths of the two sequences. The ”average percent identity”, ”most related pair”, and 4.5 Citing this work ”most unrelated pair” of the alignment are the average, maximum, The method used to rank residues and make predictions in this report and minimum of all (N)(N-1)/2 pairs, respectively. The ”most distant can be found in Mihalek, I., I. Res,ˇ O. Lichtarge. (2004). ”A Family of seq” is calculated by finding the maximum pairwise identity (best Evolution-Entropy Hybrid Methods for Ranking of Protein Residues relative) for all N sequences, then finding the minimum of these N by Importance” J. Mol. Bio. 336: 1265-82. For the original version numbers (hence, the most outlying sequence). alistat is copyrighted of ET see O. Lichtarge, H.Bourne and F. Cohen (1996). ”An Evolu- by HHMI/Washington University School of Medicine, 1992-2001, tionary Trace Method Defines Binding Surfaces Common to Protein and freely distributed under the GNU General Public License. Families” J. Mol. Bio. 257: 342-358. 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 (CE) of the optimal path . Protein Engineering 11(9) 739-747. 4.6 About report maker 4.3.3 DSSP In this work a residue is considered solvent accessi- report maker was written in 2006 by Ivana Mihalek. The 1D ran- ble if the DSSP program finds it exposed to water by at least 10A˚ 2, king visualization program was written by Ivica Res.ˇ report maker which is roughly the area needed for one water molecule to come in is copyrighted by Lichtarge Lab, Baylor College of Medicine, the contact with the residue. DSSP is copyrighted by W. Kabsch, C. Houston.

8 4.7 Attachments • 3c1oA.msf - the multiple sequence alignment used for the chain The following files should accompany this report: 3c1oA • 3c1oA.descr - description of sequences used in 3c1oA msf • 3c1oA.complex.pdb - coordinates of 3c1oA with all of its • 3c1oA.ranks sorted - full listing of residues and their ranking interacting partners for 3c1oA • 3c1oA.etvx - ET viewer input file for 3c1oA • 3c1oA.3c1oANAP401.if.pml - Pymol script for Figure 5 • 3c1oA.cluster report.summary - Cluster report summary for • 3c1oA.cbcvg - used by other 3c1oA – related pymol scripts 3c1oA • 3c1oA.3c1oA1.if.pml - Pymol script for Figure 6 • 3c1oA.ranks - Ranks file in sequence order for 3c1oA • 3c1oA.clusters - Cluster descriptions for 3c1oA

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