Contacts of the helix formed by residues 299 - 321 (chain C) in PDB entry 3ZXR
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 SER 299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C LEU 2.6 28.9 + - - -
289C MET 2.8 16.9 + - - -
290C TYR 3.8 11.7 - - - -
291C ASP* 3.5 14.9 - - - +
298C LEU* 1.3 75.7 - - - +
300C ASP* 1.3 59.5 + - - +
301C THR* 3.5 4.1 + - - -
302C ALA* 3.3 13.9 + - - +
303C ARG* 2.9 29.3 + - - +
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Residues in contact with ASP 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ASP* 5.2 5.1 + - - +
299C SER* 1.3 71.7 - - - +
301C THR* 1.3 61.1 + - - +
303C ARG* 2.8 40.1 + - - +
304C HIS* 2.9 50.5 + - + +
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Residues in contact with THR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ILE* 4.6 6.5 - - + -
281C LEU* 4.5 12.1 - - + -
288C LEU* 4.1 22.8 + - + +
289C MET* 5.4 1.6 - - - -
299C SER* 3.3 8.4 + - - -
300C ASP* 1.3 79.5 - - - +
302C ALA* 1.3 55.8 + - - +
304C HIS* 4.7 2.7 - - - -
305C TYR* 2.9 28.1 + - - +
391C ILE* 3.5 37.3 - - + +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU 4.6 0.2 + - - -
289C MET* 3.5 55.4 - - + +
298C LEU* 3.8 17.5 - - + -
299C SER* 3.3 10.1 + - - +
301C THR* 1.3 75.4 - - - +
303C ARG* 1.3 66.5 + - - +
305C TYR* 3.1 5.1 + - - +
306C ILE* 3.0 28.1 + - + +
365C LEU* 4.5 0.5 - - - +
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Residues in contact with ARG 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C GLY* 5.9 3.2 - - - -
295C TYR* 6.4 1.3 - - - -
298C LEU* 4.7 11.5 + - + +
299C SER 2.9 15.6 + - - +
300C ASP* 2.8 39.2 + - - +
302C ALA* 1.3 75.3 - - - +
304C HIS* 1.3 65.2 + - - +
306C ILE* 3.3 11.8 + - - +
307C GLY 2.9 22.0 + - - -
342C TYR* 4.1 18.8 - - + +
396C GLU* 2.9 37.4 + - - -
397C PRO* 3.5 23.5 - - + +
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Residues in contact with HIS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C ASP* 2.9 38.4 + - + +
301C THR* 3.9 3.8 - - - +
303C ARG* 1.3 80.5 + - - +
305C TYR* 1.3 58.6 + - - +
307C GLY* 3.1 1.2 + - - -
308C GLY 2.9 23.9 + - - -
390C GLY* 3.4 25.0 - - - +
391C ILE* 3.8 13.0 + - + +
394C LYS* 3.5 42.5 + - + +
395C ILE 3.4 18.5 - - - +
396C GLU* 2.9 28.9 + - - -
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Residues in contact with TYR 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ALA* 5.7 0.3 - - - +
130C PHE* 4.4 3.3 - - - -
279C GLN* 2.8 38.6 + - + +
280C SER 6.1 0.4 - - - -
281C LEU* 3.8 35.1 - - + +
289C MET* 4.9 3.8 - - + -
301C THR 2.9 14.7 + - - +
302C ALA* 3.1 13.7 + - - +
304C HIS* 1.3 73.4 - - - +
306C ILE* 1.3 64.7 + - - +
308C GLY* 3.2 4.0 + - - -
309C LEU* 3.1 33.0 + - + +
365C LEU* 3.5 21.1 - - + -
383C MET 3.7 0.4 + - - -
384C LEU* 3.5 33.7 - - + +
387C GLY* 3.6 38.4 - - - -
388C LEU 4.4 0.2 - - - -
391C ILE* 3.8 2.6 - - + +
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Residues in contact with ILE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C LEU* 3.9 18.6 - - + -
302C ALA 3.0 17.8 + - - +
303C ARG* 3.5 7.9 - - - +
305C TYR* 1.3 73.9 - - - +
307C GLY* 1.3 63.9 + - - +
309C LEU* 3.1 8.9 + - - +
310C LEU* 3.0 34.3 + - + +
342C TYR* 3.8 39.0 - - + -
351C VAL* 4.2 9.4 - - + -
353C ILE* 3.8 29.8 - - + -
365C LEU* 3.7 24.0 - - + -
397C PRO* 4.3 3.8 - - + -
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Residues in contact with GLY 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ARG 2.9 12.5 + - - -
304C HIS 3.1 5.5 + - - -
306C ILE* 1.3 76.9 - - - +
308C GLY* 1.3 55.3 + - - +
310C LEU* 4.3 1.0 - - - +
311C HIS* 3.0 32.6 + - - +
395C ILE* 3.6 25.9 - - - +
397C PRO* 3.8 19.4 - - - +
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Residues in contact with GLY 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C HIS 2.9 11.5 + - - -
305C TYR 3.2 2.4 + - - -
307C GLY* 1.3 73.7 - - - +
309C LEU* 1.3 56.0 + - - +
311C HIS* 3.2 2.4 + - - -
312C HIS* 2.7 44.1 + - - +
386C ALA 3.3 24.2 - - - -
390C GLY* 3.8 13.1 - - - -
395C ILE* 4.5 1.8 - - - -
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Residues in contact with LEU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C GLN* 4.4 1.1 - - - +
305C TYR* 3.1 29.5 + - + +
306C ILE* 3.1 9.6 + - - +
308C GLY* 1.3 73.0 - - - +
310C LEU* 1.3 61.2 + - + +
312C HIS 3.8 0.3 - - - -
313C ALA* 2.9 30.3 + - - +
316C LEU* 3.9 23.1 - - + +
351C VAL* 4.5 6.5 - - + -
365C LEU* 3.7 30.3 - - + -
367C PHE* 4.2 32.0 - - + -
383C MET* 3.6 34.8 - - + +
386C ALA* 4.2 6.0 + - + -
387C GLY 4.4 0.4 - - - +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C ILE* 3.0 32.6 + - + +
307C GLY* 4.3 3.4 - - - +
309C LEU* 1.3 75.5 - - - +
311C HIS* 1.3 65.7 + - - +
313C ALA* 3.4 15.0 - - + +
314C PRO* 4.3 0.2 - - - +
340C LEU* 3.6 46.6 - - + +
341C VAL* 3.7 17.9 - - - -
342C TYR* 3.7 9.6 - - + +
350C CYS* 3.8 32.1 - - + -
351C VAL* 4.1 11.7 - - + -
367C PHE* 5.0 1.8 - - + -
397C PRO* 4.7 8.7 - - + -
398C GLN* 5.7 4.5 - - + +
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Residues in contact with HIS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C GLY 3.0 21.1 + - - +
308C GLY 3.8 1.6 - - - +
310C LEU* 1.3 77.6 - - - +
312C HIS* 1.3 91.0 + + - +
314C PRO* 3.4 13.5 - - - +
395C ILE* 3.9 28.5 - - + +
429C ARG* 5.4 3.1 + - - -
433C ASP* 5.8 1.4 + - - -
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Residues in contact with HIS 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C GLY* 2.7 29.0 + - - +
309C LEU 3.8 0.4 - - - +
311C HIS* 1.3 94.7 + + - +
313C ALA* 1.3 64.5 + - - +
314C PRO* 3.2 4.2 - - - +
315C SER* 2.9 10.5 + - - -
316C LEU* 2.8 21.0 + - + -
386C ALA* 3.9 30.1 - - + -
389C ASP* 2.7 30.8 + - + -
395C ILE* 4.7 0.4 - - + +
433C ASP* 4.6 11.2 + - - -
436C TYR* 3.4 45.2 - + + +
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Residues in contact with ALA 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C LEU 2.9 15.4 + - - +
310C LEU* 3.4 16.4 - - + +
312C HIS* 1.3 74.9 - - - +
314C PRO* 1.4 68.6 - - + +
315C SER 3.0 1.6 + - - -
316C LEU* 4.0 8.5 - - + -
317C LEU* 3.1 39.0 + - + +
340C LEU* 3.6 27.1 - - + -
367C PHE* 5.6 3.6 - - + -
420C PRO* 5.2 1.8 - - + -
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Residues in contact with PRO 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C LEU 4.3 2.2 - - - +
311C HIS 3.4 13.0 - - - +
312C HIS 3.2 6.5 - - - +
313C ALA* 1.4 92.8 - - + +
315C SER* 1.3 55.4 + - - +
340C LEU* 4.6 11.9 - - + -
420C PRO* 4.3 15.9 - - + +
425C ASP 5.0 0.2 - - - -
426C VAL* 3.5 20.3 - - - +
429C ARG* 3.4 53.2 - - + +
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Residues in contact with SER 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C HIS* 2.9 8.3 + - - +
314C PRO* 1.3 77.1 - - - +
316C LEU* 1.3 67.0 + - - +
317C LEU 3.1 2.5 - - - -
318C ALA* 3.0 23.7 + - - +
319C PHE* 4.4 0.7 + - - -
426C VAL 4.3 4.9 - - - -
429C ARG* 3.8 11.4 - - - +
430C LEU* 3.8 22.6 - - - +
433C ASP* 3.6 20.6 + - - -
436C TYR* 2.7 37.9 + - - -
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C LEU* 3.9 30.7 - - + +
312C HIS* 2.8 19.4 + - + +
313C ALA* 4.0 3.4 - - - -
315C SER* 1.3 77.6 + - - +
317C LEU* 1.3 57.8 + - + +
318C ALA 3.0 0.2 - - - -
319C PHE* 2.9 22.4 + - - +
320C THR* 3.2 21.1 + - + +
367C PHE* 3.8 30.7 - - + -
382C ALA* 3.5 44.4 - - + +
383C MET* 3.6 3.1 - - - +
386C ALA* 4.1 7.9 - - + -
436C TYR* 3.4 12.1 - - - +
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Residues in contact with LEU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ALA* 3.1 28.9 + - + +
315C SER 3.1 0.8 - - - -
316C LEU* 1.3 76.9 - - + +
318C ALA* 1.3 58.4 + - - +
319C PHE 3.1 0.2 - - - -
320C THR* 3.1 19.3 - - - +
321C ASN* 2.7 38.6 + - + +
327C TYR* 3.5 15.3 - - + +
330C LEU* 4.0 17.7 - - + -
340C LEU* 5.9 0.9 - - + -
350C CYS* 6.3 0.4 - - - -
367C PHE* 4.3 11.9 - - + -
369C SER* 3.3 30.3 - - - +
419C THR* 4.9 4.5 - - + -
420C PRO* 3.7 27.1 - - + -
426C VAL* 4.1 7.0 - - + -
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Residues in contact with ALA 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C SER 3.0 16.0 + - - +
316C LEU 3.0 1.6 + - - -
317C LEU* 1.3 77.7 - - - +
319C PHE* 1.3 59.0 + - + +
321C ASN 4.9 0.7 - - - -
322C PRO* 3.5 16.5 - - - +
423C LEU* 5.0 0.2 - - - -
426C VAL* 3.6 27.8 - - + +
427C ILE* 4.0 13.2 - - + +
430C LEU* 3.8 26.9 - - + -
451C TRP* 2.9 20.0 + - - -
455C LYS* 5.3 0.2 - - - -
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Residues in contact with PHE 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C SER 5.0 0.9 - - - -
316C LEU* 2.9 11.0 + - - +
318C ALA* 1.3 81.2 - - + +
320C THR* 1.3 60.7 + - - +
321C ASN 3.5 0.4 - - - -
322C PRO* 3.9 11.9 - - - +
375C ASN 4.7 4.7 + - - +
378C LEU* 4.0 31.1 - - + +
379C ALA* 3.5 16.1 + - - +
382C ALA* 3.9 28.9 - - + -
430C LEU* 3.9 31.0 - - + -
437C LEU* 4.0 11.9 - - + -
443C PHE* 3.8 24.9 - + - -
447C LEU* 4.7 3.6 - - + -
448C ILE* 4.6 7.4 - - + -
451C TRP* 3.4 54.3 - + + -
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Residues in contact with THR 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C MET* 5.4 0.2 - - - +
316C LEU* 3.2 28.2 + - + +
317C LEU* 3.1 23.9 - - - +
319C PHE* 1.3 80.4 - - + +
321C ASN* 1.3 74.9 + - - +
322C PRO* 3.6 3.6 - - - +
367C PHE* 4.2 3.6 - - + -
370C PRO* 3.4 14.3 - - - +
371C ASP 3.1 32.7 + - - +
379C ALA* 4.3 9.6 - - - +
383C MET* 3.8 30.1 - - + -
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Residues in contact with ASN 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C LEU* 2.7 20.4 + - + +
320C THR* 1.3 99.3 + - - +
322C PRO* 1.3 59.9 - - - +
323C THR 3.3 2.4 + - - -
326C SER* 3.4 10.7 + - - -
327C TYR* 2.9 41.4 + - + +
329C ARG* 4.0 4.4 - - - +
330C LEU* 3.8 17.0 - - - +
369C SER* 2.8 43.5 + - - +
371C ASP* 3.5 15.3 + - - -
423C LEU* 3.9 1.4 - - - +
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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