164:
methods are more accurate in predicting the structures of proteins with low contact orders. This may be partly because low contact order proteins tend to be small, but is likely to be explained by the smaller number of possible long-range residue-residue interactions to be considered during
157:
is the total number of residues in the protein. The value of contact order typically ranges from 5% to 25% for single-domain proteins, with lower contact order belonging to mainly helical proteins, and higher contact order belonging to proteins with a high beta-sheet content.
192:
has produced transition-state models whose contact order is close to that of the folded state in proteins that are small and fast-folding. Further, contact orders in transition states as well as those in native states are highly correlated with overall folding time.
132:
275:
Plaxco, Kevin W; Simons, Kim T; Baker, David (April 1998). "Contact order, transition state placement and the refolding rates of single domain proteins".
455:
Paci, E; Lindorff-Larsen, K; Dobson, CM; Karplus, M; Vendruscolo, M (2005). "Transition state contact orders correlate with protein folding rates".
177:
method overproduce low-contact-order structure predictions compared to the distributions observed in experimentally determined protein structures.
64:
420:
Pandit, AD; Jha, A; Freed, KF; Sosnick, TR (2006). "Small proteins fold through transition states with native-like topologies".
235:"Contact order, transition state placement and the refolding rates of single domain proteins11Edited by P. E. Wright"
180:
The percentage of the natively folded contact order can also be used as a measure of the "nativeness" of folding
161:
196:
In addition to their role in structure prediction, contact orders can themselves be predicted based on a
39:
in the folded protein divided by the total length of the protein. Higher contact orders indicate longer
555:
234:
364:
Zuo, G; Wang, J; Wang, W (2006). "Folding with downhill behavior and low cooperativity of proteins".
48:
550:
52:
8:
166:
522:
495:
389:
341:
316:
201:
197:
189:
185:
170:
32:
200:, which can be useful in classifying the fold of a novel sequence with some degree of
527:
472:
437:
381:
346:
292:
254:
393:
517:
507:
491:
464:
429:
373:
336:
328:
284:
246:
213:
181:
44:
40:
36:
35:. It is calculated as the average sequence distance between residues that form
468:
433:
544:
314:
258:
512:
315:
Bonneau, Richard; Ruczinski, Ingo; Tsai, Jerry; Baker, David (August 2002).
531:
476:
441:
385:
350:
288:
250:
174:
29:
296:
55:
associated with the formation of local as opposed to nonlocal contacts.
377:
332:
43:, and low contact order has been suggested as a predictor of potential
25:
145:
is the sequence separation, in residues, between contacting residues
410:
2nd ed. Cold Spring Harbor
Laboratory Press: Cold Spring Harbor, NY.
21:
454:
274:
51:
barrier. This effect is thought to be due to the lower loss of
127:{\displaystyle CO={1 \over {L\cdot N}}\sum ^{N}\Delta S_{i,j}}
233:
Plaxco, Kevin W; Simons, Kim T; Baker, David (1998-04-10).
173:. Even successful structure prediction methods such as the
317:"Contact order and ab initio protein structure prediction"
496:"Protein contact order prediction from primary sequences"
419:
67:
58:
Relative contact order (CO) is formally defined as:
489:
126:
232:
542:
408:Bioinformatics: Sequence and Genome Analysis
363:
47:, or protein folding that occurs without a
24:is a measure of the locality of the inter-
521:
511:
340:
310:
308:
306:
270:
268:
543:
490:Shi, Yi; Zhou, Jianjun; Arndt, David;
303:
413:
265:
216:: topological arrangement of contacts
400:
448:
13:
483:
357:
141:is the total number of contacts, Δ
105:
14:
567:
226:
1:
220:
277:Journal of Molecular Biology
239:Journal of Molecular Biology
169:procedures that minimize an
162:Protein structure prediction
7:
207:
10:
572:
28:contacts in the protein's
469:10.1016/j.jmb.2005.06.081
434:10.1016/j.jmb.2006.06.041
513:10.1186/1471-2105-9-255
494:; Lin, Guohui (2008).
289:10.1006/jmbi.1998.1645
251:10.1006/jmbi.1998.1645
128:
53:conformational entropy
129:
204:to known sequences.
65:
167:global optimization
500:BMC Bioinformatics
406:Mount DM. (2004).
378:10.1002/prot.20857
333:10.1110/ps.3790102
198:sequence alignment
190:molecular dynamics
186:Phi value analysis
124:
33:tertiary structure
556:Protein structure
492:Wishart, David S.
182:transition states
104:
93:
563:
536:
535:
525:
515:
487:
481:
480:
452:
446:
445:
417:
411:
404:
398:
397:
361:
355:
354:
344:
327:(8): 1937–1944.
312:
301:
300:
272:
263:
262:
230:
214:Circuit topology
188:in concert with
133:
131:
130:
125:
123:
122:
103:
95:
94:
92:
78:
45:downhill folding
571:
570:
566:
565:
564:
562:
561:
560:
541:
540:
539:
488:
484:
453:
449:
418:
414:
405:
401:
362:
358:
321:Protein Science
313:
304:
273:
266:
231:
227:
223:
210:
171:energy function
112:
108:
99:
82:
77:
66:
63:
62:
37:native contacts
12:
11:
5:
569:
559:
558:
553:
551:Bioinformatics
538:
537:
482:
463:(3): 495–500.
447:
412:
399:
356:
302:
283:(4): 985–994.
264:
245:(4): 985–994.
224:
222:
219:
218:
217:
209:
206:
135:
134:
121:
118:
115:
111:
107:
102:
98:
91:
88:
85:
81:
76:
73:
70:
9:
6:
4:
3:
2:
568:
557:
554:
552:
549:
548:
546:
533:
529:
524:
519:
514:
509:
505:
501:
497:
493:
486:
478:
474:
470:
466:
462:
458:
451:
443:
439:
435:
431:
428:(4): 755–70.
427:
423:
416:
409:
403:
395:
391:
387:
383:
379:
375:
372:(1): 165–73.
371:
367:
360:
352:
348:
343:
338:
334:
330:
326:
322:
318:
311:
309:
307:
298:
294:
290:
286:
282:
278:
271:
269:
260:
256:
252:
248:
244:
240:
236:
229:
225:
215:
212:
211:
205:
203:
199:
194:
191:
187:
183:
178:
176:
172:
168:
163:
159:
156:
152:
148:
144:
140:
119:
116:
113:
109:
100:
96:
89:
86:
83:
79:
74:
71:
68:
61:
60:
59:
56:
54:
50:
46:
42:
41:folding times
38:
34:
31:
27:
23:
19:
18:contact order
503:
499:
485:
460:
456:
450:
425:
421:
415:
407:
402:
369:
365:
359:
324:
320:
280:
276:
242:
238:
228:
195:
179:
160:
154:
150:
146:
142:
138:
136:
57:
30:native state
17:
15:
49:free energy
545:Categories
457:J Mol Biol
422:J Mol Biol
221:References
26:amino acid
259:0022-2836
106:Δ
97:∑
87:⋅
532:18513429
477:16120445
442:16876194
394:11970404
386:16416404
366:Proteins
351:12142448
208:See also
202:homology
523:2440764
506:: 255.
342:2373674
297:9545386
175:Rosetta
22:protein
530:
520:
475:
440:
392:
384:
349:
339:
295:
257:
153:, and
137:where
390:S2CID
20:of a
528:PMID
473:PMID
438:PMID
382:PMID
347:PMID
293:PMID
255:ISSN
149:and
143:Si,j
16:The
518:PMC
508:doi
465:doi
461:352
430:doi
426:361
374:doi
337:PMC
329:doi
285:doi
281:277
247:doi
243:277
547::
526:.
516:.
502:.
498:.
471:.
459:.
436:.
424:.
388:.
380:.
370:63
368:.
345:.
335:.
325:11
323:.
319:.
305:^
291:.
279:.
267:^
253:.
241:.
237:.
184:.
534:.
510::
504:9
479:.
467::
444:.
432::
396:.
376::
353:.
331::
299:.
287::
261:.
249::
155:L
151:j
147:i
139:N
120:j
117:,
114:i
110:S
101:N
90:N
84:L
80:1
75:=
72:O
69:C
Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.