Contacts of the helix formed by residues 341 - 368 (chain C) in PDB entry 2VIG
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 PHE 341 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C GLN 5.2 0.4 - - - -
269C ASP* 3.5 35.9 - - + -
270C MET* 4.0 11.0 - - + -
273C ILE* 4.1 19.3 - - + -
331C ALA* 4.0 6.1 - - - +
334C LEU* 3.9 18.4 - - + -
335C LYS* 3.5 40.6 - - + -
339C LYS 3.4 16.4 - - - -
340C PRO* 1.3 75.6 - - + +
342C ILE* 1.3 64.2 + - + +
344C GLU* 3.2 14.1 - - + -
345C ALA* 2.8 33.5 + - + +
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Residues in contact with ILE 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C GLN* 6.5 0.4 - - + -
269C ASP* 3.5 39.6 - - - +
272C ARG* 5.4 1.1 + - - +
340C PRO* 3.9 4.6 - - + +
341C PHE* 1.3 80.5 - - + +
343C LYS* 1.3 62.5 + - - +
344C GLU* 3.8 0.6 + - - -
345C ALA* 4.0 2.6 - - - +
346C ALA* 3.2 23.2 + - - +
401C VAL* 3.8 14.1 - - + +
405C HIS* 3.2 41.7 - - + +
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Residues in contact with LYS 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 2.7 42.7 + - - +
330C ARG* 4.7 0.6 - - - +
341C PHE 3.4 0.2 - - - -
342C ILE* 1.3 80.6 - - - +
344C GLU* 1.3 85.9 + - - +
346C ALA* 3.3 6.3 + - - +
347C MET* 3.0 42.4 + - + +
401C VAL* 5.0 3.6 - - - -
402C ILE* 4.2 24.9 - - + +
405C HIS* 3.9 31.0 - - + -
406C LEU* 5.0 12.0 - - + +
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Residues in contact with GLU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C LEU* 4.1 2.9 - - - +
330C ARG* 3.6 36.5 + - - +
331C ALA* 3.7 14.5 - - + +
334C LEU* 3.3 33.8 - - + +
340C PRO 3.7 5.1 - - - +
341C PHE* 3.2 22.7 + - - +
342C ILE 3.8 0.3 + - - -
343C LYS* 1.3 103.4 + - - +
345C ALA* 1.3 56.4 + - - +
347C MET* 3.6 2.9 + - - +
348C ALA* 3.1 27.0 + - - +
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Residues in contact with ALA 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ASP* 3.4 29.6 - - - +
272C ARG* 4.0 12.0 - - + +
273C ILE* 4.0 13.5 - - + -
331C ALA* 3.9 8.4 - - - +
341C PHE* 2.8 24.9 + - + +
342C ILE 4.0 3.4 - - - +
344C GLU* 1.3 70.3 - - - +
346C ALA* 1.3 61.2 + - - +
348C ALA* 3.4 3.5 + - - +
349C LYS* 3.0 31.0 + - - +
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Residues in contact with ALA 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ARG* 4.7 4.6 - - - +
342C ILE 3.2 16.5 + - - +
343C LYS 3.6 4.0 - - - +
345C ALA* 1.3 80.2 - - - +
347C MET* 1.3 56.5 + - - +
349C LYS* 3.5 0.4 + - - -
350C LEU* 3.0 32.6 + - - +
398C GLN* 3.2 30.2 - - - +
401C VAL* 3.9 19.7 - - + -
402C ILE* 3.9 14.1 - - + -
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Residues in contact with MET 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA* 3.7 4.3 - - + -
319A LEU* 3.5 48.1 - - + +
322A GLU* 3.3 29.6 - - - +
327C LEU* 4.3 3.4 - - + -
330C ARG* 3.4 26.9 - - - +
343C LYS* 3.0 29.4 + - + +
344C GLU* 3.7 6.1 - - - +
346C ALA* 1.3 77.9 - - - +
348C ALA* 1.3 56.9 + - - +
350C LEU* 3.7 1.2 - - - +
351C ALA* 2.8 33.1 + - - +
402C ILE* 3.6 38.8 - - + -
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Residues in contact with ALA 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ARG 5.5 0.2 - - - +
273C ILE* 5.7 1.8 - - - -
276C ALA* 3.7 8.1 - - + -
324C ALA 4.9 0.6 - - - +
327C LEU* 3.5 30.4 - - - +
328C THR* 3.5 21.0 + - - +
331C ALA* 4.5 2.7 - - + -
344C GLU 3.1 17.9 + - - +
345C ALA* 3.8 7.2 - - - +
347C MET* 1.3 74.5 - - - +
349C LYS* 1.3 59.1 + - - +
351C ALA* 4.0 0.2 - - - +
352C ALA* 2.8 35.3 + - - +
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Residues in contact with LYS 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ARG* 3.6 31.0 - - + +
275C ILE* 3.9 19.7 - - + -
276C ALA* 3.8 9.7 - - - +
279C ALA* 5.5 0.2 - - - +
345C ALA 3.0 17.1 + - - +
346C ALA 4.0 2.9 - - - +
348C ALA* 1.3 74.7 - - - +
350C LEU* 1.3 58.9 + - - +
352C ALA* 4.0 0.3 - - - +
353C SER* 3.0 35.0 + - - +
388C THR 2.6 28.1 + - - +
389C GLU* 3.9 8.9 + - - +
391C TYR 2.9 27.0 + - - -
392C GLU* 4.3 4.3 - - - -
393C GLY 3.0 18.1 + - - -
394C THR 4.7 0.6 - - - -
395C SER* 4.8 0.6 + - - +
398C GLN* 3.7 19.5 - - + +
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Residues in contact with LEU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ALA* 6.0 0.9 - - + +
316A ASP* 5.0 1.6 - - - +
319A LEU* 3.8 17.9 - - + -
346C ALA 3.0 19.4 + - - +
347C MET 3.7 2.7 - - - +
349C LYS* 1.3 74.8 - - - +
351C ALA* 1.3 65.9 + - - +
353C SER* 3.2 5.5 + - - -
354C GLU* 3.2 50.3 + - - +
395C SER* 3.8 31.4 - - - +
398C GLN* 4.1 7.6 - - + +
399C ARG* 3.7 30.3 - - + +
402C ILE* 3.6 25.4 - - + -
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.3 12.1 - - + +
323A SER* 5.9 0.2 - - - +
323C SER* 6.4 0.2 - - - -
324C ALA* 4.0 12.5 - - + +
327C LEU* 3.4 25.6 - - + -
347C MET 2.8 22.7 + - - +
348C ALA 4.0 1.8 - - - +
350C LEU* 1.3 73.8 - - - +
352C ALA* 1.3 57.9 + - - +
354C GLU* 3.9 3.2 - - - +
355C ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ALA* 3.4 31.6 - - + +
279C ALA* 3.6 10.0 - - + +
280C LEU* 3.8 17.3 - - + -
283C ALA* 5.3 0.3 - - - +
324C ALA* 3.7 11.0 - - + +
328C THR* 4.7 0.9 - - - +
348C ALA 2.8 21.7 + - - +
351C ALA* 1.3 71.7 - - - +
353C SER* 1.3 59.9 + - - +
355C ALA* 3.3 2.9 + - - +
356C ALA* 2.8 30.7 + - - +
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Residues in contact with SER 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ALA* 3.9 3.8 - - - +
349C LYS* 3.0 21.6 + - - -
350C LEU* 3.2 9.0 + - - -
352C ALA* 1.3 77.1 - - - +
354C GLU* 1.3 62.8 + - - +
356C ALA* 3.4 3.5 + - - +
357C THR* 3.1 21.7 + - - -
388C THR* 3.1 51.2 + - - -
389C GLU* 3.8 19.3 - - - +
395C SER* 4.2 3.3 + - - -
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Residues in contact with GLU 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 5.9 1.2 - - - +
350C LEU* 3.2 22.7 + - - +
351C ALA* 4.2 3.0 - - - +
353C SER* 1.3 80.3 + - - +
355C ALA* 1.3 63.3 + - - +
357C THR* 3.4 3.1 + - - +
358C ALA* 3.0 25.4 + - - +
389C GLU* 3.7 21.5 - - + +
395C SER* 3.7 11.1 + - - +
399C ARG* 3.1 42.1 + - - -
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Residues in contact with ALA 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 6.3 0.2 - - + -
283C ALA* 5.1 2.5 - - + -
320C ALA* 3.8 35.9 - - + +
321C LEU* 4.6 1.8 - - + +
324C ALA* 4.5 2.2 - - + -
351C ALA 2.9 20.2 + - - +
352C ALA* 3.6 7.0 - - - +
354C GLU* 1.3 77.7 - - - +
356C ALA* 1.3 56.0 + - - +
358C ALA* 4.5 4.9 - - - -
359C ILE* 2.8 45.6 + - + +
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Residues in contact with ALA 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ALA* 3.6 27.4 - - + +
282C ILE* 4.4 6.1 - - + +
283C ALA* 3.8 14.3 - - + +
352C ALA 2.8 20.9 + - - +
353C SER 3.5 6.1 - - - +
355C ALA* 1.3 71.5 - - - +
357C THR* 1.3 57.9 + - - +
359C ILE* 4.3 0.3 - - - +
360C SER* 2.8 31.7 + - - -
385C ALA* 3.4 17.8 - - + +
388C THR* 4.3 3.1 - - - +
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Residues in contact with THR 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C SER 3.1 11.7 + - - -
354C GLU* 4.0 2.9 - - - +
355C ALA 3.2 0.4 - - - -
356C ALA* 1.3 74.5 - - - +
358C ALA* 1.3 64.9 + - - +
360C SER* 3.1 7.4 + - - -
361C HIS* 3.1 24.4 + - + +
382C TYR* 4.2 3.8 + - + -
385C ALA* 3.8 19.6 + - - +
386C ARG* 3.9 4.3 - - - -
389C GLU* 2.7 32.7 + - - +
361D HIS* 3.8 15.3 - - + +
382D TYR* 3.9 15.2 + - - +
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Residues in contact with ALA 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C MET* 5.7 0.2 - - - -
320C ALA* 6.0 3.4 - - + -
354C GLU 3.0 18.2 + - - +
355C ALA* 3.9 5.8 - - - +
357C THR* 1.3 78.7 - - - +
359C ILE* 1.3 63.3 + - + +
361C HIS* 3.5 6.1 + - - +
362C GLN* 3.2 29.4 + - + +
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Residues in contact with ILE 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ALA* 3.6 35.4 - - + +
286C ALA* 4.1 2.9 - - + -
287C LEU* 4.0 10.5 - - + +
317C MET* 3.3 62.4 - - + +
320C ALA* 4.5 4.0 - - + -
321C LEU* 3.7 20.2 - - + +
355C ALA* 2.8 37.1 + - + +
356C ALA 4.3 1.8 - - - +
358C ALA* 1.3 73.7 - - + +
360C SER* 1.3 58.5 + - - +
362C GLN 3.2 1.2 + - - -
363C ALA* 2.8 28.2 + - - +
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Residues in contact with SER 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ILE* 5.1 1.8 - - - -
286C ALA* 4.0 14.4 - - - -
356C ALA 2.8 23.3 + - - -
357C THR* 3.1 9.5 + - - -
359C ILE* 1.3 74.6 - - - +
361C HIS* 1.3 63.0 + - - +
363C ALA* 3.4 3.6 + - - +
364C ILE* 3.2 24.9 + - - +
378C ALA 4.6 1.6 - - - +
381C HIS* 3.8 14.6 - - - -
382C TYR* 3.4 38.0 - - - +
385C ALA* 3.6 6.4 - - - +
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Residues in contact with HIS 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C THR* 3.1 19.3 + - + +
358C ALA* 3.6 7.4 - - - +
359C ILE 3.3 0.2 - - - -
360C SER* 1.3 76.5 + - - +
362C GLN* 1.3 85.8 + - - +
364C ILE* 3.3 2.9 + - - +
365C GLN* 3.1 10.7 + - - -
382C TYR* 3.5 30.0 - + + -
357D THR* 3.8 9.7 - - + +
386D ARG* 2.7 55.5 + - - +
389D GLU* 2.7 39.2 + - - -
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Residues in contact with GLN 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C LYS* 2.9 43.9 + - + +
317C MET* 3.9 23.3 - - + -
358C ALA* 3.2 18.5 + - + +
359C ILE 3.7 3.4 - - - +
361C HIS* 1.3 106.3 + - - +
363C ALA* 1.3 61.6 + - - +
365C GLN* 3.3 11.4 + - - +
366C ILE* 3.0 36.2 + - + +
396D GLU* 5.7 0.2 + - - -
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Residues in contact with ALA 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ALA* 3.5 33.2 - - + +
289C CYS* 5.4 0.7 - - - -
290C ALA* 4.0 16.2 - - + +
317C MET* 4.0 1.8 - - + +
359C ILE 2.8 12.5 + - - +
360C SER 3.5 10.8 - - - +
362C GLN* 1.3 73.8 - - - +
364C ILE* 1.3 66.5 + - - +
366C ILE* 3.4 0.9 + - - +
367C LEU* 3.1 30.2 + - + +
378C ALA* 4.4 12.3 - - + -
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Residues in contact with ILE 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C SER 3.2 9.1 + - - +
361C HIS 3.3 6.9 + - - +
363C ALA* 1.3 77.9 - - - +
365C GLN* 1.3 62.4 - - - +
367C LEU* 3.3 2.1 + - - +
368C GLY* 3.0 21.8 + - - +
371C GLY* 3.5 29.2 - - - +
372C TYR* 5.0 1.3 - - + -
378C ALA* 3.9 15.7 - - - +
379C GLU* 4.0 8.1 - - - -
382C TYR* 3.4 46.4 - - + -
231D LEU* 4.5 6.7 - - + -
386D ARG* 3.4 26.9 - - + +
390D ILE* 3.7 18.8 - - + -
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Residues in contact with GLN 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C LYS* 4.3 7.2 - - - +
361C HIS* 3.1 10.7 + - - +
362C GLN* 3.6 22.0 - - - +
363C ALA 3.1 0.4 - - - -
364C ILE* 1.3 77.2 - - - +
366C ILE* 1.3 56.9 + - - +
368C GLY* 3.2 8.9 + - - -
386D ARG* 3.0 34.9 + - - +
389D GLU* 3.1 27.8 + - - +
390D ILE* 4.0 7.3 - - - +
394D THR* 4.0 7.1 - - - +
395D SER* 3.8 8.8 + - - +
396D GLU* 2.9 39.8 + - - +
501D FAD 2.6 27.3 + - - +
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Residues in contact with ILE 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ALA* 3.9 33.0 - - + +
293C TYR* 3.9 2.8 - - + -
294C ALA* 3.9 16.4 - - + -
304C LEU* 3.6 9.9 - - + +
310C ILE* 4.0 12.1 - - + -
313C LYS* 3.8 30.1 - - + -
314C LEU* 3.9 27.8 - - + -
317C MET* 4.0 10.8 - - - -
362C GLN 3.0 20.5 + - - +
363C ALA 3.9 3.1 - - - +
364C ILE 3.3 0.2 - - - -
365C GLN* 1.3 75.2 - - - +
367C LEU* 1.3 61.5 + - + +
501D FAD 3.1 28.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C CYS* 4.0 17.0 - - - +
290C ALA* 4.2 8.7 - - - -
293C TYR* 3.6 54.0 + - + -
363C ALA 3.1 19.8 + - - +
366C ILE* 1.3 77.1 - - - +
368C GLY* 1.3 62.7 + - - +
369C GLY 3.6 0.3 + - - -
370C MET* 3.4 15.7 + - + +
371C GLY* 3.4 17.0 - - - +
376C MET* 3.7 36.1 - - + -
378C ALA* 3.7 25.4 - - + -
501D FAD 4.3 5.1 + - - +
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Residues in contact with GLY 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ILE 3.0 9.9 + - - +
365C GLN* 3.2 14.4 + - - -
366C ILE 3.2 0.8 - - - -
367C LEU* 1.3 72.5 - - - +
369C GLY* 1.3 61.4 + - - +
371C GLY* 2.9 22.0 + - - -
372C TYR 3.8 2.3 + - - -
390D ILE* 3.8 23.2 - - - +
394D THR* 5.4 0.7 - - - -
501D FAD 3.9 20.2 - - - -
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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).
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