Contacts of the helix formed by residues 395 - 416 (chain C) in PDB entry 2YWB
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 THR 395 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C LEU* 4.2 5.8 - - - -
393C GLU* 3.4 33.8 + - + +
394C VAL* 1.3 78.6 - - - +
396C GLU* 1.3 65.0 + - - +
397C GLU* 3.5 8.3 + - - +
398C ARG* 3.0 41.0 + - - +
399C LEU* 3.0 14.5 + - - +
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Residues in contact with GLU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C GLY 5.3 1.4 - - - +
271C LYS* 6.1 1.6 - - - +
275C LEU* 3.8 32.1 - - + +
395C THR* 1.3 71.1 - - - +
397C GLU* 1.3 63.6 + - - +
399C LEU* 3.2 14.1 + - - +
400C GLU* 3.0 25.1 + - + +
403C ARG* 3.0 33.9 + - - -
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Residues in contact with GLU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C THR* 3.1 9.0 + - - +
396C GLU* 1.3 78.7 - - - +
398C ARG* 1.3 62.5 + - - +
400C GLU* 3.3 8.9 + - + +
401C ILE* 3.2 35.5 + - + +
446C TYR* 3.4 23.8 + - - -
484C GLU* 5.6 1.5 - - - +
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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
----------------------------------------------------------
390C VAL* 3.9 19.9 - - + +
392C GLY* 4.0 2.6 - - - -
393C GLU* 2.7 58.4 + - - +
395C THR* 3.0 24.6 + - - +
397C GLU* 1.3 76.1 - - - +
399C LEU* 1.3 58.0 + - - +
401C ILE* 3.1 5.3 + - - -
402C LEU* 2.9 27.1 + - - +
429C LEU* 3.5 18.3 - - + +
431C PRO* 3.4 33.3 - - - +
446C TYR* 3.2 33.3 + - + +
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Residues in contact with LEU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C GLY 3.9 19.3 - - - +
245C LEU* 3.9 13.5 - - + -
275C LEU* 4.6 7.0 - - + -
386C LEU* 3.8 36.6 - - + +
390C VAL* 4.4 6.3 - - + -
394C VAL* 3.9 28.3 - - + -
395C THR 3.0 17.2 + - - +
396C GLU* 3.6 22.4 - - - +
398C ARG* 1.3 75.2 - - - +
400C GLU* 1.3 54.2 + - - +
402C LEU* 3.9 4.2 - - - +
403C ARG* 2.7 53.5 + - + +
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Residues in contact with GLU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C GLU* 3.0 14.9 + - + +
397C GLU* 3.4 13.2 - - + +
398C ARG 3.2 0.2 - - - -
399C LEU* 1.3 77.8 - - - +
401C ILE* 1.3 63.8 + - - +
403C ARG* 3.6 23.2 + - - +
404C ARG* 3.0 66.2 + - - +
484C GLU* 5.5 1.9 - - - +
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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
----------------------------------------------------------
397C GLU* 3.2 30.0 + - + +
398C ARG* 3.1 6.8 + - - +
400C GLU* 1.3 83.5 - - - +
402C LEU* 1.3 60.4 + - - +
404C ARG* 3.4 5.6 + - - +
405C ALA* 3.0 24.9 + - - +
429C LEU* 4.1 11.9 - - + -
446C TYR* 3.6 30.7 - - + -
482C VAL* 3.7 23.5 - - + +
484C GLU* 3.6 31.6 - - + +
485C ILE* 3.8 19.1 - - + -
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Residues in contact with LEU 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C LEU* 4.0 22.0 - - + +
389C ARG* 3.3 42.0 - - + +
390C VAL* 3.8 13.2 - - + -
398C ARG 2.9 17.4 + - - +
399C LEU* 3.9 4.5 - - - +
401C ILE* 1.3 76.0 - - - +
403C ARG* 1.3 56.7 + - - +
405C ALA* 3.1 3.0 + - - +
406C ASP* 2.7 40.3 + - + +
427C ALA* 3.5 26.5 - - + +
429C LEU* 4.4 13.2 - - + +
448C LEU* 3.9 22.0 - - + -
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Residues in contact with ARG 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C GLY 4.1 15.4 + - - -
246C LEU 3.9 14.6 + - - +
247C ARG* 5.9 0.2 - - - +
248C LEU* 3.8 44.2 + - + +
386C LEU* 3.5 23.3 - - + +
396C GLU* 3.0 26.0 + - - -
399C LEU* 2.7 47.2 + - - +
400C GLU* 3.6 27.5 + - - +
402C LEU* 1.3 71.7 - - - +
404C ARG* 1.3 58.0 + - + +
406C ASP* 3.8 4.3 - - - +
407C ASP* 3.0 30.5 + - - +
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Residues in contact with ARG 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLY* 6.2 0.9 - - - -
248C LEU* 4.6 12.6 - - + -
400C GLU* 3.0 46.9 + - - +
401C ILE* 3.6 5.8 - - - +
402C LEU 3.1 0.6 - - - -
403C ARG* 1.3 76.1 - - + +
405C ALA* 1.3 64.2 + - - +
407C ASP* 3.4 5.7 + - - +
408C ILE* 3.1 29.0 + - + +
481C ARG* 2.5 42.0 + - - +
482C VAL* 4.0 18.1 - - + +
483C PRO* 4.2 4.4 - - - +
484C GLU* 3.7 25.1 + - - -
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Residues in contact with ALA 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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401C ILE 3.0 11.9 + - - +
402C LEU 3.8 2.7 - - - +
404C ARG* 1.3 74.8 - - - +
406C ASP* 1.3 63.7 + - - +
408C ILE* 3.1 7.0 + - - +
409C PHE* 3.0 23.8 + - - +
448C LEU* 3.5 35.7 - - + -
478C ILE* 4.2 8.7 - - + +
482C VAL* 4.1 8.2 - - + +
485C ILE* 3.6 21.8 - - + -
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Residues in contact with ASP 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ARG* 2.8 58.9 + - - +
248C LEU 5.5 0.3 + - - -
386C LEU* 5.0 6.9 - - + +
389C ARG* 4.2 2.6 + - - -
402C LEU* 2.7 32.1 + - + +
403C ARG* 3.8 5.6 - - - +
405C ALA* 1.3 74.4 - - - +
407C ASP* 1.3 57.9 + - - +
409C PHE* 3.4 4.9 + - - +
410C THR* 2.9 30.8 + - - -
426C LEU* 4.4 0.9 - - - -
427C ALA* 4.1 24.1 + - + +
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Residues in contact with ASP 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU 4.5 0.2 - - - +
118A GLY* 3.9 1.2 - - - -
119A GLU* 3.4 25.8 + - - +
172A LYS* 3.0 36.9 + - - -
248C LEU* 4.2 27.0 - - + +
403C ARG 3.0 18.4 + - - +
404C ARG* 3.7 5.1 - - - +
406C ASP* 1.3 76.0 + - - +
408C ILE* 1.3 61.3 + - - +
410C THR* 3.9 7.2 - - - +
411C SER* 2.9 35.4 + - - -
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Residues in contact with ILE 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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119A GLU* 3.7 27.3 - - + +
404C ARG* 3.1 17.3 + - + +
405C ALA 3.1 7.3 + - - +
407C ASP* 1.3 77.5 - - - +
409C PHE* 1.3 63.1 + - - +
411C SER* 3.4 4.7 + - - -
412C LEU* 3.0 25.1 + - + +
474C ALA* 4.9 2.7 - - - +
477C ARG* 3.7 33.9 + - + +
478C ILE* 3.8 18.6 - - + -
481C ARG* 3.8 31.6 - - + +
482C VAL* 3.9 17.0 - - + -
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Residues in contact with PHE 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C ALA 3.0 16.1 + - - +
406C ASP* 3.7 7.9 - - - +
408C ILE* 1.3 78.6 - - - +
410C THR* 1.3 65.4 + - - +
412C LEU* 3.5 3.4 + - - +
413C LEU* 3.1 42.6 + - + +
425C ALA* 4.0 11.7 - - + -
426C LEU* 3.6 39.9 - - - -
427C ALA* 4.7 2.9 - - + -
450C LEU* 3.8 48.0 - - + -
451C ARG 4.4 4.0 - - - -
452C ALA* 4.8 9.6 - - + -
466C LEU* 5.1 4.3 - - + -
470C PHE* 4.0 28.5 - + - -
471C LEU* 5.6 0.9 - - + -
474C ALA* 4.5 7.0 - - + -
478C ILE* 4.6 3.8 - - + -
490C TYR* 5.3 1.3 - + - -
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Residues in contact with THR 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ARG* 3.4 28.5 + - - +
378C ARG* 5.6 3.8 - - - +
406C ASP* 2.9 21.2 + - - -
407C ASP* 3.9 8.5 - - - +
409C PHE* 1.3 80.8 - - - +
411C SER* 1.3 65.0 + - - +
413C LEU* 3.3 12.7 + - - +
414C ARG* 3.1 51.8 + - - +
419C TYR* 4.1 9.1 - - + -
425C ALA* 5.1 2.4 + - - +
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Residues in contact with SER 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 4.6 13.6 + - - -
171A PRO* 3.7 24.6 - - - +
172A LYS* 3.6 26.0 + - - +
407C ASP* 2.9 22.7 + - - -
408C ILE* 3.8 5.4 - - - -
410C THR* 1.3 76.2 - - - +
412C LEU* 1.3 59.7 + - - +
414C ARG* 3.1 8.1 + - - +
415C GLU* 2.9 28.8 + - - +
477C ARG* 5.7 1.8 - - - -
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Residues in contact with LEU 412 (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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408C ILE* 3.0 17.3 + - + +
409C PHE* 3.9 4.0 - - - +
411C SER* 1.3 73.5 - - - +
413C LEU* 1.3 66.8 + - - +
415C GLU* 3.4 8.9 + - - +
416C TRP* 3.1 36.7 + - - +
470C PHE* 3.2 23.3 - - + -
473C GLU* 3.0 36.3 - - + +
474C ALA* 3.3 41.3 - - + +
477C ARG* 3.6 27.3 - - + +
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Residues in contact with LEU 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C PHE* 3.1 35.6 + - + +
410C THR* 3.5 11.7 - - - +
411C SER 3.2 0.4 - - - -
412C LEU* 1.3 78.3 - - - +
414C ARG* 1.3 59.1 + - - +
416C TRP 3.4 0.3 + - - -
417C GLY 3.1 2.8 + - - -
418C LEU* 2.9 51.6 + - + +
419C TYR* 3.1 21.4 + - + +
422C VAL* 5.3 4.0 - - + -
425C ALA* 3.5 31.0 - - + -
466C LEU* 4.5 10.5 - - + -
470C PHE* 3.3 32.3 - - + -
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Residues in contact with ARG 414 (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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168A ALA* 4.9 4.3 - - - +
171A PRO* 4.3 22.7 - - + +
172A LYS* 6.3 1.8 - - - -
456A GLU* 5.5 0.2 - - - +
247C ARG* 5.8 0.2 - - - +
373C ASP 5.9 0.6 + - - -
374C THR* 4.6 17.1 + - - +
377C LEU* 5.5 2.0 + - - +
378C ARG* 4.0 26.7 - - - +
410C THR* 3.1 32.8 + - - +
411C SER* 3.1 10.3 + - - +
413C LEU* 1.3 73.7 - - - +
415C GLU* 1.3 66.6 + - - +
417C GLY* 3.0 13.8 + - - -
419C TYR* 3.7 55.2 + - + -
420C GLU* 4.9 4.0 + - - -
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Residues in contact with GLU 415 (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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102A LYS* 3.2 20.1 + - - -
121A GLN* 2.9 34.1 + - - +
168A ALA* 3.7 34.7 - - - +
169A HIS* 2.7 36.2 + - + +
171A PRO* 4.4 6.4 - - + +
456A GLU* 3.8 7.3 - - - +
411C SER 2.9 18.9 + - - +
412C LEU* 3.7 11.2 - - - +
414C ARG* 1.3 74.2 - - - +
416C TRP* 1.3 71.5 + - + +
417C GLY 3.5 0.3 + - - -
477C ARG* 3.8 11.6 + - - -
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Residues in contact with TRP 416 (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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102A LYS* 4.9 3.6 - - - +
169A HIS* 6.3 0.2 - - - -
456A GLU* 3.5 20.6 - - - +
465A ARG* 5.7 8.5 - - + -
412C LEU* 3.1 25.0 + - + +
413C LEU 4.1 0.9 - - - +
415C GLU* 1.3 93.3 + - + +
417C GLY* 1.3 61.1 + - - +
418C LEU* 3.4 23.1 + - + +
421C LYS* 5.6 1.0 + - - -
467C PRO* 5.0 8.3 - - + -
469C GLU* 2.6 34.5 - - + -
470C PHE* 3.9 33.4 - + + -
473C GLU* 2.9 31.6 + - - -
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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