Contacts of the helix formed by residues 392 - 413 (chain C) in PDB entry 1IAS
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 HIS 392 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ASN* 3.1 19.9 + - - +
390C MET 4.8 1.6 - - - -
391C LYS* 1.3 112.7 + - + +
393C PHE* 1.3 67.1 + - - +
394C GLU* 3.0 9.4 - - + +
395C SER* 2.8 36.1 + - - +
396C PHE* 4.3 3.1 + - - -
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Residues in contact with PHE 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ALA* 3.5 35.0 - - + -
329C ILE 3.8 2.9 - - - -
330C ALA* 3.7 26.2 - - + -
356C VAL* 3.5 32.1 - - + -
357C ARG 4.3 2.9 - - - -
358C HIS* 3.6 46.8 - + + +
365C ILE* 5.3 10.8 - - + +
391C LYS 3.8 4.2 + - - -
392C HIS* 1.3 70.7 - - - +
394C GLU* 1.3 66.4 + - + +
396C PHE* 3.0 34.4 + + - +
397C LYS* 3.5 28.1 + - + -
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Residues in contact with GLU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C HIS* 3.0 8.0 + - + -
393C PHE* 1.3 81.4 - - + +
395C SER* 1.3 62.7 + - - +
397C LYS* 3.0 46.1 + - - +
398C ARG* 3.0 61.9 + - - +
484C THR* 6.0 2.1 - - - +
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Residues in contact with SER 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C GLU* 4.2 4.2 - - - +
388C ILE* 3.6 26.9 - - - +
389C ASN* 2.6 33.4 + - - +
390C MET* 5.0 0.2 - - - -
392C HIS* 2.8 17.0 + - - +
394C GLU* 1.3 77.4 - - - +
396C PHE* 1.3 60.2 + - - +
398C ARG* 3.4 16.7 + - - +
399C ALA* 3.1 25.8 + - - +
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Residues in contact with PHE 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ALA* 3.5 21.5 - - + -
332C ARG* 3.7 28.3 + - + +
356C VAL* 4.2 10.3 - - + -
365C ILE* 4.8 12.8 - - + -
370C ASN* 4.4 13.5 - - - -
388C ILE* 4.6 8.3 - - + -
390C MET* 3.5 64.6 - - + -
392C HIS 4.3 4.9 - - - -
393C PHE* 3.0 34.2 + + - +
395C SER* 1.3 74.3 - - - +
397C LYS* 1.3 66.1 + - - +
399C ALA* 3.2 8.7 + - + +
400C ASP* 3.1 25.1 + - - +
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Residues in contact with LYS 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C HIS* 3.3 68.9 + - + +
318C MET* 5.4 0.6 - - - +
319C GLU* 6.3 0.4 - - - +
328C ALA* 4.5 2.1 - - - +
330C ALA* 4.7 0.2 - - - -
393C PHE* 3.5 33.8 + - + +
394C GLU* 3.0 39.4 + - - +
396C PHE* 1.3 77.2 - - - +
398C ARG* 1.3 63.3 + - + +
400C ASP* 3.1 18.8 + - - +
401C ILE* 3.2 9.9 + - + +
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Residues in contact with ARG 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C GLU* 4.6 2.0 - - - +
392C HIS* 6.4 0.2 - - - +
394C GLU* 3.0 46.6 + - - +
395C SER* 3.5 14.3 + - - +
397C LYS* 1.3 75.3 - - + +
399C ALA* 1.3 66.0 + - - +
401C ILE* 3.1 19.8 + - - +
402C TYR 3.2 9.9 + - - -
479C GLY* 3.5 24.0 - - - +
480C ALA* 3.4 36.8 + - - +
482C ARG* 3.2 23.6 + - + +
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Residues in contact with ALA 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ARG* 6.4 1.6 - - - -
378C TYR 5.2 0.5 - - - +
380C ALA* 3.9 28.7 + - + +
382C GLU* 4.2 2.7 + - - +
383C VAL* 4.2 16.2 - - + -
388C ILE* 5.1 1.6 - - + -
395C SER 3.1 14.4 + - - +
396C PHE* 3.2 11.8 + - + +
398C ARG* 1.3 75.0 - - - +
400C ASP* 1.3 63.8 + - - +
402C TYR* 3.4 5.0 + - - +
403C ALA* 3.3 20.8 + - - +
482C ARG* 3.9 2.0 - - - +
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Residues in contact with ASP 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C LEU* 4.1 9.4 - - + -
317C HIS* 2.8 26.3 + - + +
330C ALA* 3.5 4.4 - - - +
331C HIS* 2.8 33.9 + - - +
332C ARG* 2.9 26.3 + - - -
333C ASP 4.3 2.3 + - - -
334C LEU* 3.9 10.2 + - + +
396C PHE 3.1 12.2 + - - +
397C LYS 3.2 10.3 - - - +
398C ARG 3.1 0.2 - - - -
399C ALA* 1.3 78.8 - - - +
401C ILE* 1.3 58.1 + - - +
403C ALA* 3.3 7.2 + - - +
404C MET* 2.9 26.9 + - - +
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Residues in contact with ILE 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C LEU* 3.8 21.8 - - + -
317C HIS* 4.3 4.3 - - + +
397C LYS 3.4 14.8 - - - +
398C ARG* 3.1 10.7 + - - +
400C ASP* 1.3 74.5 - - - +
402C TYR* 1.3 66.7 + - - +
404C MET* 3.0 6.3 + - + +
405C GLY* 2.8 20.3 + - - -
474C CYS* 3.5 31.9 - - + -
482C ARG* 4.4 5.8 - - + -
483C LEU 3.5 23.1 - - - +
484C THR* 4.2 1.1 - - - -
485C ALA* 3.6 31.4 - - + +
488C ILE* 4.3 8.1 - - + -
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Residues in contact with TYR 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ARG 4.9 0.2 + - - -
378C TYR 3.2 13.2 - - - -
379C MET 3.2 24.4 + - - -
380C ALA* 3.4 17.0 - - + -
381C PRO* 3.8 22.4 - - + -
398C ARG 3.2 3.0 + - - -
399C ALA 3.6 7.2 - - - +
400C ASP 3.3 0.2 - - - -
401C ILE* 1.3 78.7 - - - +
403C ALA* 1.3 63.5 + - - +
405C GLY* 3.2 9.9 + - - -
406C LEU* 3.2 28.7 + - + +
428C TYR* 2.6 42.2 + - - -
445C VAL* 3.9 6.6 - - - +
451C ARG* 4.4 8.5 - - - -
474C CYS 3.5 20.1 + - - +
475C TRP* 3.7 27.7 + + - -
482C ARG* 3.9 17.7 - - - +
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Residues in contact with ALA 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C LEU* 3.8 29.8 - - + +
378C TYR* 3.9 21.3 - - + +
399C ALA 3.3 8.1 + - - +
400C ASP* 3.3 8.1 + - - +
401C ILE 3.2 0.4 - - - -
402C TYR* 1.3 80.2 - - - +
404C MET* 1.3 67.7 + - - +
405C GLY 3.0 1.8 - - - -
406C LEU* 3.0 19.6 + - - +
407C VAL* 3.0 17.2 + - - +
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Residues in contact with MET 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C THR* 3.2 47.3 - - + +
310C ALA* 3.3 18.2 - - - +
313C LEU* 3.5 32.8 - - + -
334C LEU* 4.2 9.1 - - + +
400C ASP 2.9 15.2 + - - +
401C ILE* 3.0 11.6 + - + +
403C ALA* 1.3 76.3 - - - +
405C GLY* 1.3 57.5 + - - +
407C VAL* 3.3 9.6 + - + +
408C PHE* 3.0 50.6 + - + -
474C CYS* 5.8 0.9 - - - -
485C ALA* 5.7 1.6 - - - -
488C ILE* 4.6 16.4 - - + -
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Residues in contact with GLY 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C ILE 2.8 13.0 + - - -
402C TYR 3.6 4.3 - - - -
403C ALA 3.0 0.6 - - - -
404C MET* 1.3 76.7 - - - +
406C LEU* 1.3 64.9 + - - +
408C PHE* 3.0 10.7 + - - +
409C TRP* 3.0 21.0 + - - +
471C MET* 4.3 5.5 - - - +
474C CYS* 4.1 16.8 - - - -
475C TRP* 3.5 16.5 - - - -
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Residues in contact with LEU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ARG 4.0 6.5 - - - +
378C TYR* 3.8 31.4 - - + +
402C TYR* 3.2 38.7 + - + +
403C ALA* 3.0 7.2 + - - +
405C GLY* 1.3 75.4 - - - +
407C VAL* 1.3 61.3 + - - +
409C TRP* 3.1 9.5 - - - +
410C GLU* 3.1 26.4 + - - +
427C PRO* 3.6 20.8 - - + +
428C TYR* 4.1 9.2 - - + +
452C PRO* 3.8 27.6 - - + -
475C TRP* 3.4 22.4 - - + +
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Residues in contact with VAL 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 3.7 30.1 - - + -
309C THR* 5.3 3.4 - - + -
334C LEU* 4.9 1.1 - - + -
335C LYS* 3.8 14.6 - - - +
336C SER* 3.8 25.6 - - - +
339C ILE* 4.1 14.1 - - + -
378C TYR* 4.0 1.3 - - + -
403C ALA 3.0 13.9 + - - +
404C MET* 3.4 14.4 - - + +
405C GLY 3.0 0.2 - - - -
406C LEU* 1.3 73.2 - - - +
408C PHE* 1.3 71.1 + - + +
409C TRP 3.0 1.6 - - - -
410C GLU* 2.9 23.9 + - + +
411C ILE* 3.0 21.4 + - + +
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Residues in contact with PHE 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ALA* 3.4 38.8 - - + -
309C THR* 4.4 9.0 - - + -
310C ALA* 4.4 0.4 - - + -
404C MET* 3.0 46.0 + - + -
405C GLY* 3.0 10.3 + - - +
407C VAL* 1.3 77.0 - - + +
409C TRP* 1.3 57.9 + - - +
411C ILE* 3.1 11.8 + - + +
412C ALA* 2.9 30.7 + - - +
467C MET* 3.6 27.7 - - + +
470C ILE* 4.2 18.2 - - + -
471C MET* 4.2 11.7 - - + -
474C CYS* 6.0 0.2 - - - -
488C ILE* 3.7 24.9 - - + -
492C LEU* 3.8 13.2 - - + -
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Residues in contact with TRP 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C GLY 3.0 8.1 + - - +
406C LEU* 3.1 11.7 - - - +
407C VAL 3.0 0.4 - - - -
408C PHE* 1.3 77.1 - - - +
410C GLU* 1.3 79.3 + - + +
411C ILE 3.1 0.5 + - - -
412C ALA 3.5 0.2 + - - -
413C ARG* 3.1 57.5 + - - +
425C GLN 3.1 22.4 - - - -
426C LEU 3.5 10.3 - - - -
427C PRO* 3.6 18.2 - - + -
428C TYR 5.0 0.9 - - - -
429C TYR* 3.6 26.9 - + - -
452C PRO* 3.5 26.3 - - + +
453C ASN* 3.2 28.6 + - + -
455C PRO* 4.5 1.0 - - + +
458C TRP* 3.6 18.8 - + - -
471C MET* 3.1 37.4 - - + +
475C TRP* 3.8 6.5 - + + -
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Residues in contact with GLU 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LEU* 3.8 10.5 - - + +
336C SER* 2.8 23.6 + - - -
378C TYR* 2.6 36.3 + - - -
406C LEU 3.3 9.5 - - - +
407C VAL* 2.9 16.8 + - + +
409C TRP* 1.3 86.3 - - + +
411C ILE* 1.3 62.0 + - - +
413C ARG* 3.6 13.2 - - - +
414C ARG* 3.7 13.0 - - - +
424C TYR* 2.6 38.7 + - + -
425C GLN 4.0 7.0 - - - +
427C PRO* 3.7 18.1 - - + +
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Residues in contact with ILE 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 4.1 21.8 - - + -
292C LEU* 4.0 20.8 - - + +
297C VAL* 4.6 5.0 - - + +
302C MET* 3.7 33.4 - - + +
305C LEU* 4.1 28.9 - - + +
306C ALA* 4.4 10.1 - - + +
309C THR* 5.3 1.1 - - - +
407C VAL* 3.0 19.5 + - + +
408C PHE* 3.3 19.5 - - + +
409C TRP 3.0 0.4 - - - -
410C GLU* 1.3 74.1 - - - +
412C ALA* 1.3 61.4 + - - +
413C ARG 3.1 1.1 - - - -
414C ARG* 2.9 24.4 + - - +
415C CYS* 3.5 6.1 + - - +
467C MET* 4.8 1.6 - - + -
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Residues in contact with ALA 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C MET* 3.9 25.8 - - - -
408C PHE 2.9 17.8 + - - +
411C ILE* 1.3 72.9 - - - +
413C ARG* 1.3 58.6 + - - +
415C CYS* 2.9 25.6 + - - +
457C ARG* 4.1 0.9 + - - -
458C TRP* 3.7 38.1 + - + -
464C LEU* 4.2 7.6 - - + +
467C MET* 4.4 10.5 - - + -
471C MET* 5.0 0.9 - - - -
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Residues in contact with ARG 413 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C TRP* 3.1 58.1 + - - +
410C GLU* 3.6 8.5 - - - +
412C ALA* 1.3 77.3 - - - +
414C ARG* 1.3 61.7 + - + +
415C CYS 3.4 1.0 + - - -
421C HIS* 4.1 1.2 - - - +
422C GLU* 3.0 65.5 + - + +
423C ASP* 2.4 37.4 + - - +
425C GLN* 3.7 18.9 - - - +
429C TYR* 3.0 30.1 + - - -
455C PRO* 5.6 3.6 - - - +
457C ARG* 4.1 0.3 + - - -
458C TRP* 3.5 12.5 - - + -
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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