Contacts of the helix formed by residues 277 - 306 (chain C) in PDB entry 2YVX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 277 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ALA* 1.3 76.3 - - - +
278C PRO* 1.4 65.2 - - - +
279C VAL* 3.0 4.3 - - - -
280C ALA* 2.6 35.2 + - - +
281C LEU 3.4 2.4 + - - -
358D LYS* 4.6 0.7 - - - -
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Residues in contact with PRO 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU 6.3 0.2 - - - -
386B LEU* 5.6 15.3 - - + +
387B LEU* 5.9 1.3 - - + +
388B PRO* 5.3 15.0 - - + -
276C ALA 3.8 0.6 - - - +
277C GLY* 1.4 79.4 - - - +
279C VAL* 1.3 65.8 + - + +
281C LEU* 4.7 4.0 - - + +
282C TRP* 3.0 26.4 + - - +
358D LYS* 3.6 42.6 - - + +
361D GLY* 4.9 4.9 - - - -
362D VAL* 3.4 23.8 - - + +
365D LEU* 5.5 6.7 - - + -
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Residues in contact with VAL 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TYR* 4.2 23.8 - - + -
384B PRO* 2.8 41.7 - - + +
385B LEU* 5.3 0.4 - - - -
387B LEU* 4.3 18.8 - - + -
277C GLY 2.8 5.6 + - - -
278C PRO* 1.3 79.2 - - + +
280C ALA* 1.3 59.4 + - - +
282C TRP* 3.4 10.6 - - + +
283C LEU* 3.1 34.0 + - + +
365D LEU* 5.7 6.1 - - + -
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ALA* 4.1 12.3 - - + -
277C GLY* 2.6 28.0 + - - +
279C VAL* 1.3 70.5 - - - +
281C LEU* 1.3 67.2 + - - +
283C LEU* 2.9 34.7 - - + +
284C ALA* 3.5 4.0 + - - +
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL 5.8 0.2 - - - +
273C TYR* 3.3 41.1 - - + +
276C ALA* 3.1 44.4 - - + +
277C GLY 3.4 2.2 + - - +
278C PRO* 4.0 1.8 - - + +
280C ALA* 1.3 79.4 - - - +
282C TRP* 1.3 68.6 + - - +
284C ALA* 3.0 2.9 + - - +
285C ARG* 2.8 38.0 + - + +
337D LEU* 5.1 8.7 - - + -
358D LYS* 4.2 9.0 - - + +
359D GLU* 4.0 16.6 - - - +
362D VAL* 3.8 15.5 - - + -
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Residues in contact with TRP 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TYR* 6.3 4.3 - + - -
278C PRO 3.0 20.0 + - - +
279C VAL* 3.4 13.0 - - + +
281C LEU* 1.3 80.4 - - - +
283C LEU* 1.3 97.6 + - + +
284C ALA 2.9 0.3 + - - -
285C ARG* 4.7 3.1 - - - -
286C VAL* 3.0 36.5 + - + +
362D VAL* 3.6 9.1 - - + +
365D LEU* 3.1 63.4 + - + +
366D LEU* 3.6 16.1 - - + +
369D THR* 3.3 37.3 + - + -
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TYR* 5.9 2.2 - - - +
279C VAL* 3.1 26.4 + - + +
280C ALA* 2.9 31.9 - - + +
282C TRP* 1.3 97.3 - - + +
284C ALA* 1.3 73.8 + - + +
286C VAL* 3.6 3.9 - - - +
287C ARG* 3.2 46.4 + - - +
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Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C VAL* 5.6 0.4 - - - -
267C ASP* 5.0 10.1 + - - +
268C VAL* 3.4 34.8 - - + -
271C LEU* 5.7 0.9 - - + -
280C ALA 4.1 6.5 - - - +
281C LEU* 3.0 8.2 + - - +
282C TRP 2.9 3.4 + - - -
283C LEU* 1.3 81.9 - - + +
285C ARG* 1.3 59.9 + - + +
286C VAL 3.2 1.3 - - - -
287C ARG* 2.7 35.7 + - - +
288C TRP* 3.5 6.1 + - - +
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Residues in contact with ARG 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ALA* 3.4 6.2 - - - +
266C VAL* 4.3 14.6 - - + +
281C LEU* 2.8 33.2 + - + +
282C TRP* 4.0 2.2 - - - +
284C ALA* 1.3 76.1 - - + +
286C VAL* 1.3 57.1 + - - +
288C TRP 3.4 1.7 + - - -
289C LEU* 3.1 13.7 + - - -
330D THR* 4.0 3.0 + - - +
333D GLN* 2.7 68.7 + - - +
334D SER* 3.0 21.8 - - - +
337D LEU* 4.0 18.7 - - + +
359D GLU* 3.4 14.6 + - - -
362D VAL* 4.4 8.9 - - - +
366D LEU* 3.2 29.9 - - + +
402D ASN* 2.7 27.8 + - - +
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Residues in contact with VAL 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C TRP* 3.0 43.5 + - + +
283C LEU 3.6 8.3 - - - +
285C ARG* 1.3 75.4 - - - +
287C ARG* 1.3 71.5 + - - +
288C TRP 3.2 0.2 - - - -
289C LEU* 4.0 4.7 - - - -
290C VAL* 3.5 21.1 + - + +
366D LEU* 3.2 30.3 - - + +
369D THR* 4.2 24.9 - - + +
370D LEU* 4.6 13.0 - - + -
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Residues in contact with ARG 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ASP* 5.9 3.6 - - + +
283C LEU* 3.2 40.8 + - - +
284C ALA* 2.7 20.9 + - - +
286C VAL* 1.3 79.8 - - - +
288C TRP* 1.3 75.1 + - + +
290C VAL* 3.6 3.9 + - - +
291C ILE* 3.5 22.0 + - + +
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Residues in contact with TRP 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LYS 5.8 0.4 - - - -
264C GLY 4.1 12.6 - - - -
265C ALA* 3.0 43.5 - - + -
267C ASP* 3.4 28.8 + - + +
284C ALA 3.5 2.1 + - - +
285C ARG 3.4 1.8 + - - -
287C ARG* 1.3 86.7 - - + +
289C LEU* 1.3 51.7 + - - +
290C VAL 2.4 19.3 + - - -
291C ILE* 3.0 21.1 + - + +
292C LEU* 3.1 34.9 + - + +
421C LEU* 3.4 57.0 - - + -
423C SER* 4.2 11.4 - - - -
426C LEU* 4.5 13.2 - - + -
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ALA* 3.9 3.2 - - + +
285C ARG 3.1 16.1 + - - +
286C VAL* 4.1 10.3 - - + -
287C ARG 3.7 0.2 - - - -
288C TRP* 1.3 73.0 - - - +
290C VAL* 1.3 57.8 + - - +
292C LEU* 4.2 7.4 - - + -
293C ILE* 2.9 32.4 + - + +
326D THR* 3.5 27.1 - - + +
329D ASN* 3.6 25.4 - - + -
330D THR* 3.4 24.2 - - - +
333D GLN* 3.2 32.1 - - + +
366D LEU* 4.9 4.5 - - + -
370D LEU* 3.9 19.9 - - + +
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Residues in contact with VAL 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C VAL* 3.5 23.5 + - + +
287C ARG* 3.8 4.7 - - - +
288C TRP 2.4 11.9 + - - -
289C LEU* 1.3 70.5 - - - +
291C ILE* 1.3 75.7 + - + +
292C LEU 2.9 1.1 - - - -
293C ILE* 2.8 17.4 + - - +
294C LEU* 3.1 20.2 + - + +
369D THR* 5.5 3.8 - - + +
370D LEU* 4.2 16.8 - - + -
373D LEU* 3.5 34.6 - - + +
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Residues in contact with ILE 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ARG* 3.5 12.5 + - + +
288C TRP* 3.0 15.0 + - + +
290C VAL* 1.3 84.5 - - + +
292C LEU* 1.3 63.5 + - + +
294C LEU* 3.1 28.9 + - + +
295C THR* 3.5 15.0 + - + +
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ALA* 6.2 2.5 - - + -
288C TRP* 3.1 32.9 + - + +
289C LEU* 4.0 8.1 - - + +
290C VAL 2.9 0.2 + - - -
291C ILE* 1.3 77.5 - - + +
293C ILE* 1.3 60.0 + - - +
294C LEU 3.1 4.7 - - - -
295C THR* 3.2 8.5 + - - +
296C GLY* 3.1 22.2 + - - -
423C SER* 5.4 0.7 - - - +
425C PRO* 3.6 24.0 - - + +
426C LEU* 3.8 37.0 - - + +
429C THR* 3.9 13.7 + - + +
329D ASN* 3.0 36.3 - - + +
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Residues in contact with ILE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU* 2.9 21.5 - - + +
290C VAL* 2.8 12.4 + - - +
292C LEU* 1.3 74.3 - - - +
294C LEU* 1.3 58.6 + - - +
296C GLY* 4.2 4.5 - - - +
297C MET* 2.7 29.1 - - + +
429C THR* 5.2 2.0 - - - +
322D VAL* 3.9 16.2 - - + -
325D GLY 4.9 0.2 - - - -
326D THR* 2.6 57.7 - - + +
329D ASN* 3.1 26.9 - - - +
370D LEU* 4.9 6.1 - - + -
373D LEU* 6.2 2.6 - - + +
374D LEU* 5.0 10.5 - - + +
394D LEU* 5.7 3.1 - - + -
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C VAL* 3.1 13.9 + - + +
291C ILE* 3.1 29.8 - - + +
292C LEU 3.1 0.2 - - - -
293C ILE* 1.3 79.1 - - - +
295C THR* 1.3 67.1 + - + +
297C MET* 3.0 28.2 - - + +
298C VAL* 3.6 8.0 + - + +
373D LEU* 6.5 0.2 - - + -
377D LYS* 5.5 10.1 - - - +
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Residues in contact with THR 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ILE* 3.5 15.4 + - + +
292C LEU* 3.2 6.8 + - - +
294C LEU* 1.3 82.1 - - + +
296C GLY* 1.3 61.1 + - - +
298C VAL* 2.9 34.8 + - - +
299C THR* 3.5 4.0 + - - +
426C LEU* 6.0 2.2 - - + +
429C THR* 3.1 25.2 - - - +
430C LEU* 4.7 13.2 - - + +
433C VAL* 4.8 7.0 - - - +
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Residues in contact with GLY 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LEU 3.1 12.0 + - - -
293C ILE* 4.5 4.0 - - - -
295C THR* 1.3 79.1 + - - +
297C MET* 1.3 59.7 + - - +
299C THR* 2.7 28.0 - - - +
429C THR* 4.5 8.5 - - - -
322D VAL* 2.6 37.3 - - - +
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Residues in contact with MET 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ILE* 2.7 27.2 + - + +
294C LEU* 3.0 16.4 - - - +
296C GLY* 1.3 76.2 - - - +
298C VAL* 1.3 63.5 + - - +
299C THR 2.9 1.7 + - - -
300C SER* 2.9 14.0 + - - -
301C SER* 3.4 8.9 + - - -
319D TYR* 6.4 1.3 - - + -
322D VAL* 3.3 16.8 - - + +
373D LEU* 3.7 7.9 - - - +
374D LEU* 3.5 50.3 - - + +
377D LYS* 3.7 42.0 - - + -
378D VAL* 5.1 0.9 - - + +
381D ASP* 5.9 1.3 - - - +
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Residues in contact with VAL 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU* 3.6 12.1 - - + +
295C THR* 2.9 21.3 + - - +
297C MET* 1.3 74.9 - - + +
299C THR* 1.3 60.2 + - - +
300C SER 3.3 0.2 - - - -
301C SER* 3.7 13.0 - - - +
302C ILE* 3.1 43.3 + - + +
433C VAL* 5.5 11.4 - - + +
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Residues in contact with THR 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C THR 3.5 2.2 + - - +
296C GLY* 2.7 45.4 + - - +
298C VAL* 1.3 73.2 - - - +
300C SER* 1.3 73.1 + - - -
302C ILE* 3.8 3.2 + - - +
303C LEU* 3.5 17.3 + - - +
429C THR* 4.9 1.3 - - + +
432C ASP* 4.3 27.1 - - + -
433C VAL* 4.6 17.6 - - + +
436C LEU* 4.1 12.0 - - - +
321D PRO* 2.6 32.6 - - + +
322D VAL* 2.8 7.7 + - - +
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Residues in contact with SER 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C MET 2.9 4.7 + - - -
299C THR* 1.3 83.3 + - - +
301C SER* 1.3 61.8 + - - +
302C ILE 3.3 0.2 - - - -
303C LEU* 3.4 11.7 + - - +
304C GLN* 3.5 10.0 + - - +
318D PHE* 2.4 39.8 + - - +
319D TYR* 3.0 32.6 - - - -
321D PRO* 4.1 1.8 - - - -
322D VAL* 3.3 20.0 - - - -
381D ASP* 5.4 0.2 - - - -
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Residues in contact with SER 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C MET 3.4 4.9 + - - -
298C VAL* 3.3 24.7 + - - +
300C SER* 1.3 77.5 - - - +
302C ILE* 1.3 61.6 + - - +
304C GLN* 3.2 24.1 + - - +
305C GLY 3.5 4.3 + - - -
381D ASP* 4.6 22.5 + - - -
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Residues in contact with ILE 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C VAL* 3.1 32.3 + - + +
299C THR* 4.1 2.9 - - - +
301C SER* 1.3 79.1 - - - +
303C LEU* 1.3 60.1 + - - +
304C GLN 2.7 10.5 + - - -
305C GLY* 3.2 11.4 + - - +
306C PHE* 3.6 23.8 + - + +
433C VAL* 5.4 5.4 - - + +
436C LEU* 3.5 25.8 - - + -
437C LEU* 4.5 28.9 - - + +
440C LEU* 4.9 4.8 - - + +
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Residues in contact with LEU 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C THR 3.5 8.6 + - - +
300C SER* 3.4 13.8 + - - +
302C ILE* 1.3 80.2 - - - +
304C GLN* 1.3 57.2 + - - +
306C PHE 3.9 1.5 - - - +
307C GLU* 4.5 0.7 + - - +
310C LEU* 3.0 42.1 - - + +
320C VAL* 5.2 8.7 - - + -
436C LEU* 3.3 37.0 - - + -
440C LEU* 5.2 9.9 - - + -
318D PHE* 3.7 35.1 - - + +
321D PRO* 4.8 7.9 - - + -
----------------------------------------------------------
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Residues in contact with GLN 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C SER 3.5 2.5 + - - +
301C SER* 3.2 17.4 + - - +
302C ILE 2.7 2.4 - - - -
303C LEU* 1.3 76.7 - - - +
305C GLY* 1.3 55.0 + - - +
306C PHE 2.7 16.6 + - - -
307C GLU* 2.7 39.8 + - + +
318D PHE* 3.3 18.6 - - + -
381D ASP* 4.2 28.0 + - - +
382D GLY* 5.7 0.4 - - - -
383D HIS* 2.9 35.2 + - - -
----------------------------------------------------------
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Residues in contact with GLY 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C SER 3.5 5.8 + - - -
302C ILE* 3.2 7.5 + - - -
304C GLN* 1.3 79.8 - - - +
306C PHE* 1.3 65.2 + - - +
307C GLU* 3.5 2.9 + - - +
308C SER* 5.0 4.7 + - - -
----------------------------------------------------------
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Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ILE* 3.6 20.8 + - + +
303C LEU 4.9 0.4 - - - +
304C GLN 2.7 5.1 + - - -
305C GLY* 1.3 80.1 - - - +
307C GLU* 1.3 51.7 + - - +
308C SER* 3.6 3.6 - - - +
309C VAL* 4.6 10.1 - - + +
310C LEU* 2.7 38.8 + - - +
437C LEU* 5.3 13.7 - - + -
440C LEU* 3.2 47.1 - - + -
441C SER 5.0 0.4 - - - -
444C ARG* 4.0 34.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il