Contacts of the helix formed by residues 392 - 412 (chain C) in PDB entry 3MDY
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 392 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ALA* 3.4 37.9 - - + -
328C ILE 3.9 0.4 - - - -
329C ALA* 3.6 17.9 - - + -
355C VAL* 3.4 31.4 - - + -
356C LYS 3.9 4.3 - - - -
357C PHE* 3.7 44.9 - + + -
389C ARG 4.9 0.2 + - - -
390C ASN 4.3 1.0 + - - -
391C HIS* 1.3 69.9 - - - +
393C GLN* 1.3 71.2 + - + +
395C TYR* 2.9 34.8 + + - +
396C ILE* 3.5 25.2 + - + -
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Residues in contact with GLN 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C HIS* 3.1 9.3 - - + -
392C PHE* 1.3 84.6 - - + +
394C SER* 1.3 61.7 + - - +
396C ILE* 3.2 27.5 + - - +
397C MET* 3.0 47.3 + - + +
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Residues in contact with SER 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLU* 4.5 3.4 - - - +
387C LEU* 3.7 23.3 - - - +
388C ASN* 2.6 39.7 + - - +
391C HIS* 2.9 13.2 + - - +
392C PHE 2.9 0.6 + - - -
393C GLN* 1.3 79.0 - - - +
395C TYR* 1.3 57.6 + - - +
397C MET* 3.4 15.8 + - - +
398C ALA* 3.0 27.9 + - - +
478C PRO* 5.7 0.6 - - - +
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Residues in contact with TYR 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ALA* 3.3 23.1 - - + +
331C ARG* 3.7 37.3 - - + +
355C VAL* 3.9 15.9 - - + -
368C PRO* 3.7 24.7 + - + +
370C THR* 5.1 4.9 - - - -
387C LEU* 3.7 28.9 - - + -
389C ARG* 3.4 37.5 + - - +
391C HIS 4.1 10.5 - - - -
392C PHE* 2.9 31.6 + + + +
394C SER* 1.3 74.0 - - - +
396C ILE* 1.3 61.0 + - - +
398C ALA* 3.3 7.8 + - + +
399C ASP* 3.0 31.5 + - - +
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Residues in contact with ILE 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C HIS* 2.9 62.5 - - + +
328C ILE 3.7 9.9 - - - +
329C ALA* 3.8 8.3 - - + -
392C PHE* 3.5 31.9 - - + +
393C GLN* 3.5 29.8 - - - +
395C TYR* 1.3 74.5 - - - +
397C MET* 1.3 67.3 + - + +
399C ASP* 3.2 13.5 + - - +
400C MET* 3.3 17.5 + - + +
483C THR* 6.5 1.8 - - + -
484C ALA 6.3 0.4 - - - +
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Residues in contact with MET 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C HIS* 6.2 0.7 - - + -
393C GLN* 3.0 41.8 + - + +
394C SER* 3.8 19.5 - - - +
396C ILE* 1.3 75.4 - - + +
398C ALA* 1.3 65.7 + - - +
400C MET* 3.3 14.4 + - - +
401C TYR 3.5 0.2 + - - -
478C PRO* 3.3 50.0 - - + +
479C ALA* 3.8 11.0 - - + +
481C ARG* 3.0 27.7 + - + +
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Residues in contact with ALA 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ARG* 6.3 1.3 - - + -
379C PRO* 3.8 21.9 - - + +
381C GLU* 3.9 5.1 + - - +
382C VAL* 4.4 4.0 - - + -
387C LEU* 4.3 11.9 - - + -
394C SER 3.0 17.9 + - - +
395C TYR* 3.5 10.5 - - + +
396C ILE 3.2 0.2 - - - -
397C MET* 1.3 75.1 - - - +
399C ASP* 1.3 66.9 + - - +
400C MET 3.1 0.9 + - - -
401C TYR* 3.3 13.2 + - - +
402C SER* 3.4 13.8 + - - -
481C ARG* 3.7 10.1 - - - +
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Residues in contact with ASP 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LEU* 3.8 0.9 - - + +
316C HIS* 2.8 29.6 + - + +
329C ALA* 3.6 1.2 - - - -
330C HIS* 2.8 28.5 + - - +
331C ARG* 2.9 29.9 + - - -
333C LEU* 3.6 19.4 + - + +
395C TYR 3.0 15.9 + - - +
396C ILE 3.2 10.7 + - - +
398C ALA* 1.3 78.8 - - - +
400C MET* 1.3 58.5 + - - +
402C SER* 3.1 7.8 + - - -
403C PHE* 2.9 24.1 + - - +
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Residues in contact with MET 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C VAL* 4.7 0.7 - - + -
312C LEU* 3.8 22.4 - - + -
316C HIS* 4.0 7.6 - - + +
396C ILE* 3.3 14.8 + - + +
397C MET* 3.3 10.4 + - - +
398C ALA 3.1 1.2 - - - -
399C ASP* 1.3 74.0 - - - +
401C TYR* 1.3 64.3 + - - +
403C PHE* 3.4 15.5 + - + +
404C GLY 3.0 17.0 + - - -
473C CYS* 3.4 28.3 - - + +
481C ARG* 4.5 2.9 - - + -
482C LEU 3.4 22.7 - - - +
483C THR* 4.5 1.6 - - - -
484C ALA* 3.6 37.2 - - + +
487C VAL* 3.8 22.0 - - + -
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Residues in contact with TYR 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ARG 5.0 0.3 + - - -
377C TYR 3.5 20.2 - - - -
378C MET 3.5 13.3 + - - -
379C PRO* 3.5 19.5 - - + -
380C PRO* 4.1 8.5 - - + -
397C MET 3.5 3.2 + - - -
398C ALA 3.3 8.4 + - - +
400C MET* 1.3 74.0 - - - +
402C SER* 1.3 69.0 + - - +
404C GLY* 3.1 11.1 + - - -
405C LEU* 3.3 28.8 + - + +
427C TYR* 2.7 32.8 + - - -
444C VAL* 3.6 12.3 - - + +
450C ARG* 3.7 27.4 - - - -
473C CYS 3.4 10.5 + - - -
474C TRP* 3.6 27.7 - - + +
481C ARG* 3.7 22.9 - - - +
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Residues in contact with SER 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C LEU* 4.0 28.5 + - - -
377C TYR* 2.6 28.4 + - - +
379C PRO* 4.1 3.8 - - - +
398C ALA 3.4 9.7 + - - -
399C ASP* 3.1 11.6 + - - -
401C TYR* 1.3 81.7 - - - +
403C PHE* 1.3 64.0 + - - +
405C LEU* 3.2 17.7 + - - +
406C ILE* 3.3 15.7 + - - +
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Residues in contact with PHE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ALA* 4.0 8.3 - - - -
308C SER* 3.9 22.7 - - - -
309C VAL* 3.6 45.1 - - + -
312C LEU* 3.8 22.4 - - + -
333C LEU* 4.3 6.5 - - + +
338C ILE* 4.9 8.7 - - + -
348C ILE* 6.1 1.1 - - + -
399C ASP 2.9 16.2 + - - +
400C MET* 3.8 16.6 - - + +
401C TYR 3.2 0.4 - - - -
402C SER* 1.3 78.3 - - - +
404C GLY* 1.3 63.0 + - - +
406C ILE* 3.1 22.6 + - + +
407C LEU* 3.0 52.5 + - + +
473C CYS* 5.0 1.1 - - - -
487C VAL* 4.3 4.9 - - + -
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Residues in contact with GLY 404 (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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400C MET 3.0 9.9 + - - -
401C TYR 3.1 5.7 + - - -
403C PHE* 1.3 76.7 - - - +
405C LEU* 1.3 61.2 + - - +
407C LEU* 3.2 17.9 + - - +
408C TRP 3.2 9.9 + - - -
470C MET* 3.7 3.8 - - - +
473C CYS* 3.7 25.9 - - - +
474C TRP* 3.6 18.9 - - - -
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Residues in contact with LEU 405 (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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376C ARG 3.9 7.9 - - - +
377C TYR* 3.7 35.7 - - + -
401C TYR* 3.3 39.3 + - + +
402C SER 3.2 6.0 + - - +
404C GLY* 1.3 76.6 - - - +
406C ILE* 1.3 61.0 + - - +
408C TRP* 3.2 8.9 + - - +
409C GLU* 3.1 24.8 + - - +
426C PRO* 4.1 11.4 - - + +
427C TYR* 3.9 19.1 - - + +
451C PRO* 3.8 27.1 - - + -
474C TRP* 3.7 16.3 - - + -
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Residues in contact with ILE 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU* 3.6 30.7 - - + -
308C SER* 5.8 0.9 - - - +
333C LEU* 4.2 11.2 - - + -
334C LYS* 3.6 32.5 - - - +
335C SER* 4.0 6.1 - - - +
338C ILE* 4.0 16.6 - - + -
377C TYR* 3.9 7.6 - - + -
402C SER 3.8 12.8 - - - +
403C PHE* 3.1 23.1 + - + +
405C LEU* 1.3 72.8 - - - +
407C LEU* 1.3 67.6 + - + +
409C GLU* 3.0 30.2 + - + +
410C VAL* 3.1 14.5 + - + +
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Residues in contact with LEU 407 (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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305C ALA* 3.8 29.2 - - + -
403C PHE* 3.0 48.5 + - + +
404C GLY* 3.2 8.5 + - - +
406C ILE* 1.3 75.0 - - + +
408C TRP* 1.3 57.5 + - - +
410C VAL* 3.3 6.8 + - + +
411C ALA* 2.9 31.0 + - - +
466C MET* 4.2 12.5 - - + +
469C LEU* 4.0 33.2 - - + -
470C MET* 3.8 17.7 - - + +
473C CYS* 4.4 12.8 - - - -
487C VAL* 4.5 2.2 - - + -
491C LEU* 4.8 3.6 - - + -
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Residues in contact with TRP 408 (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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404C GLY 3.2 3.2 + - - -
405C LEU* 3.3 10.8 - - - +
407C LEU* 1.3 78.7 - - - +
409C GLU* 1.3 79.9 + - + +
411C ALA* 3.3 1.2 + - - +
412C ARG* 3.2 66.0 + - - +
424C GLN* 3.6 11.9 - - + -
425C LEU 3.6 16.8 - - - -
426C PRO* 3.6 16.2 - - + -
427C TYR 4.9 0.4 - - - -
428C HIS* 3.9 26.0 - + - -
451C PRO* 3.4 25.0 - - + +
452C SER 2.9 28.2 + - - -
453C PHE* 4.1 7.4 - + - -
457C TRP* 3.9 19.2 - + - -
470C MET* 3.5 22.3 - - - -
474C TRP* 3.9 13.0 - + + -
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Residues in contact with GLU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU* 3.9 12.6 - - + +
335C SER* 2.5 32.6 + - - -
377C TYR* 2.5 35.4 + - - -
405C LEU 3.1 9.3 + - - +
406C ILE* 3.0 19.1 + - - +
408C TRP* 1.3 83.6 - - + +
410C VAL* 1.3 62.6 + - + +
412C ARG* 3.8 12.7 + - - +
413C ARG* 3.9 8.1 - - - +
423C TYR* 2.6 29.1 + - + -
424C GLN 3.6 16.8 - - - +
425C LEU* 3.9 0.2 - - - +
426C PRO* 3.6 16.1 - - + +
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Residues in contact with VAL 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU* 3.8 32.1 - - + -
291C LEU* 3.9 16.2 - - + -
296C LEU* 3.7 24.4 - - + +
301C MET* 4.0 26.5 - - + +
304C LEU* 4.3 8.5 - - + -
305C ALA* 5.1 8.7 - - + +
406C ILE* 3.1 14.7 + - + +
407C LEU* 3.7 8.7 - - + +
409C GLU* 1.3 76.0 - - - +
411C ALA* 1.3 64.9 + - - +
413C ARG* 3.0 18.9 + - - +
414C CYS* 3.7 1.4 + - - +
466C MET* 5.8 0.9 - - + -
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Residues in contact with ALA 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C MET* 4.0 20.9 - - - -
407C LEU 2.9 17.4 + - - +
408C TRP 3.9 0.2 - - - +
410C VAL* 1.3 74.3 - - - +
412C ARG* 1.3 63.8 + - - +
413C ARG 3.0 1.2 + - - -
414C CYS* 3.0 17.2 + - - +
456C ARG* 3.8 6.4 + - - -
457C TRP* 3.4 26.5 + - + -
463C LEU* 4.1 7.4 - - + +
466C MET* 4.5 4.7 - - + +
470C MET* 3.6 15.9 - - + -
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Residues in contact with ARG 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C TRP* 3.2 65.6 + - + +
409C GLU 3.9 7.2 - - - +
410C VAL 3.3 0.2 - - - -
411C ALA* 1.3 77.7 - - - +
413C ARG* 1.3 61.0 + - + +
414C CYS 3.3 0.2 - - - -
421C GLU* 3.3 55.0 + - + +
422C GLU* 3.0 28.8 + - - +
423C TYR* 6.0 0.2 - - - -
424C GLN* 3.5 23.8 - - - +
428C HIS* 4.4 8.5 + - - -
452C SER 5.0 0.8 + - - -
454C PRO* 4.5 9.5 - - + +
456C ARG* 3.1 17.0 + - - -
457C TRP* 3.6 13.4 - - + -
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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) + - + + + + + -
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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