Contacts of the helix formed by residues 408 - 424 (chain C) in PDB entry 5Y3R
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 TYR 408 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C LEU* 3.1 38.6 - - + +
361C ILE* 3.2 26.3 - - + +
362C ALA* 3.3 37.9 - - + -
366C TYR* 3.5 3.2 + - - +
406C ARG* 3.2 34.6 - - + +
407C VAL* 1.3 80.8 - - + +
409C GLN* 1.3 72.1 - - - +
410C MET 3.1 0.2 - - - -
411C PRO* 3.1 16.2 - - + +
412C SER* 2.2 35.7 + - - +
449C TYR* 5.9 1.0 - - - -
453C MET* 5.1 22.0 - - + -
457C CYS* 6.2 1.3 - - - -
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Residues in contact with GLN 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ILE* 3.6 27.9 - - - +
362C ALA* 5.5 1.6 - - - +
364C ARG* 3.8 8.1 - - - +
395C MET* 3.2 32.0 - - + +
399C GLN* 3.7 2.4 + - - +
406C ARG 3.0 34.5 + - - +
407C VAL 3.3 0.2 - - - +
408C TYR* 1.3 84.2 - - + +
410C MET* 1.3 88.1 + - + +
412C SER* 2.8 21.1 - - - -
413C PHE* 3.0 41.5 + - - -
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Residues in contact with MET 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C MET 4.0 0.9 - - - -
396C PHE* 3.8 23.3 - - + +
399C GLN* 3.2 41.7 - - + +
406C ARG 4.3 2.5 - - - +
407C VAL* 2.2 34.0 + - - +
409C GLN* 1.3 75.7 - - + +
411C PRO* 1.3 53.7 - - + +
413C PHE* 2.2 72.6 + - + +
414C LEU* 2.8 2.5 + - - -
438C LEU* 4.6 10.8 - - + +
441C MET* 6.2 3.4 - - + -
442C GLN* 4.5 24.9 - - + -
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Residues in contact with PRO 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C TYR* 4.3 3.8 - - - +
407C VAL 2.8 23.6 - - - +
408C TYR* 3.1 26.2 - - + +
410C MET* 1.3 77.0 - - + +
412C SER* 1.3 54.7 + - - +
414C LEU* 2.4 32.7 + - + -
415C GLN* 2.8 18.0 + - - +
442C GLN* 4.8 10.9 - - + +
449C TYR* 6.6 0.4 - - + -
456C VAL* 5.9 5.6 - - + -
457C CYS* 4.9 17.5 - - - +
460C ALA* 3.8 22.2 - - + -
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Residues in contact with SER 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C ALA* 4.1 11.6 - - - -
365C GLY* 4.9 9.2 - - - -
366C TYR* 2.3 46.7 + - - -
408C TYR 2.2 28.7 + - - -
409C GLN* 2.8 15.7 + - - -
411C PRO* 1.3 76.6 - - - +
413C PHE* 1.3 66.1 + - - -
416C SER* 2.8 24.4 + - - -
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Residues in contact with PHE 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ARG* 4.7 7.0 - - - -
365C GLY* 6.1 4.5 - - - -
391C ARG* 4.9 0.4 - - + -
392C CYS* 2.9 63.7 - - + -
395C MET* 3.2 10.3 - - + -
396C PHE 4.4 0.7 - - - -
409C GLN* 3.0 34.3 - - - -
410C MET* 2.2 54.6 + - + +
412C SER* 1.3 67.0 - - - +
414C LEU* 1.3 59.7 + - - +
416C SER* 2.1 28.4 + - - -
417C VAL* 2.9 14.6 + - - +
438C LEU* 4.0 22.7 - - + -
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Residues in contact with LEU 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C MET 2.8 4.1 + - - +
411C PRO* 2.4 24.3 + - + +
413C PHE* 1.3 69.7 - - - +
415C GLN* 1.3 70.2 + - - +
416C SER 2.7 2.5 + - - -
417C VAL* 2.7 23.0 + - + +
418C ALA* 2.8 10.2 + - + +
438C LEU* 6.3 1.3 - - + -
439C VAL* 3.9 23.1 - - + -
442C GLN* 3.3 34.1 - - - +
460C ALA* 3.4 14.8 - - + +
461C ILE* 3.4 28.3 - - + +
464C VAL* 3.8 27.4 - - + +
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Residues in contact with GLN 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C TYR* 5.1 12.0 - - + -
369C PHE* 5.2 0.3 - - - -
411C PRO* 2.8 11.8 + - - +
412C SER 4.8 0.2 - - - +
414C LEU* 1.3 73.8 - - - +
416C SER* 1.3 67.0 + - - +
418C ALA* 3.0 9.9 - - - +
419C SER* 3.0 18.9 + - - -
456C VAL* 3.9 10.8 + - - +
459C ARG* 3.1 27.0 + - - +
460C ALA* 3.0 43.7 - - + +
463C LYS* 3.3 22.9 - - + +
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Residues in contact with SER 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C GLY* 4.9 6.7 - - - -
366C TYR* 5.8 2.5 - - - -
369C PHE* 4.2 28.0 - - - -
388C LEU* 6.0 6.2 - - - +
392C CYS* 5.4 3.3 - - - -
412C SER 2.8 17.8 + - - -
413C PHE* 2.1 38.8 + - - -
414C LEU 2.7 3.2 + - - -
415C GLN* 1.3 80.7 - - - +
417C VAL* 1.3 67.6 + - - +
418C ALA 2.7 0.2 + - - -
419C SER* 3.0 2.3 + - - -
420C VAL* 3.0 25.9 + - - +
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Residues in contact with VAL 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ILE* 3.9 28.5 - - + -
392C CYS* 6.0 0.4 - - - -
413C PHE 3.0 16.6 - - - +
414C LEU* 2.7 21.8 + - + +
416C SER* 1.3 85.2 + - - +
418C ALA* 1.3 65.8 + - - +
420C VAL* 3.0 13.9 - - + +
421C LEU* 2.9 44.3 + - + +
431C TYR* 5.7 3.1 - - + -
435C LEU* 5.1 17.5 - - + -
438C LEU* 5.6 6.7 - - + -
439C VAL* 6.4 0.4 - - + -
464C VAL* 5.9 3.4 - - + -
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Residues in contact with ALA 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C LEU* 2.8 11.8 + - + +
415C GLN* 3.0 15.5 - - - +
417C VAL* 1.3 75.5 - - + +
419C SER* 1.3 69.1 + - - +
421C LEU* 2.8 15.4 + - - +
422C LEU* 2.8 15.2 + - - +
463C LYS* 3.6 36.8 - - + +
464C VAL* 4.6 7.4 - - - +
467C ALA* 4.4 9.7 - - + +
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Residues in contact with SER 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C PHE* 3.3 34.4 - - - -
373C CYS 4.3 3.3 - - - +
415C GLN 3.0 7.6 + - - -
418C ALA* 1.3 76.8 - - - +
420C VAL* 1.3 67.0 + - - +
422C LEU* 3.7 10.3 - - - +
423C TYR* 3.0 21.1 + - - +
463C LYS* 2.8 31.1 + - - +
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Residues in contact with VAL 420 (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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369C PHE* 4.4 11.4 - - + -
372C PRO* 4.9 11.0 - - + +
373C CYS 5.0 4.3 - - - -
385C TYR* 4.0 32.3 - - + -
388C LEU* 6.0 4.3 - - + -
389C ILE* 6.0 1.6 - - + -
416C SER* 3.0 19.4 + - - +
417C VAL* 3.0 20.6 - - + +
418C ALA 2.9 0.2 + - - -
419C SER* 1.3 81.3 - - - +
421C LEU* 1.3 78.8 + - + +
423C TYR* 3.0 21.9 - - - +
424C LEU* 3.5 10.1 + - + +
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Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C TYR* 6.0 0.9 - - + -
417C VAL* 3.2 33.9 - - + +
418C ALA 2.8 5.6 + - - +
420C VAL* 1.3 86.3 - - + +
422C LEU* 1.3 59.3 + - - +
423C TYR 3.0 1.6 - - - -
424C LEU* 2.5 47.9 + - + +
425C ASP* 5.0 0.2 - - - +
428C PRO* 3.5 33.0 - - + -
431C TYR* 5.2 11.7 - - + -
435C LEU* 4.7 17.7 - - + -
467C ALA* 5.2 6.1 - - + -
471C LYS* 6.2 0.2 - - - -
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Residues in contact with LEU 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ALA 2.8 16.7 + - - +
419C SER* 3.7 12.3 - - - +
421C LEU* 1.3 76.7 - - - +
423C TYR* 1.3 61.4 + - - +
424C LEU 3.3 2.9 + - - -
425C ASP* 4.7 2.9 - - - +
463C LYS* 5.0 11.0 - - + +
466C LEU* 4.3 28.0 - - + +
467C ALA* 4.3 22.5 - - + +
470C ALA* 3.4 36.2 - - + +
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Residues in contact with TYR 423 (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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373C CYS 4.3 8.5 - - - +
374C LYS* 3.3 33.7 - - + -
376C ILE* 3.5 26.5 - - + +
377C ASN* 2.3 51.4 + - - -
419C SER 3.0 13.2 + - - +
420C VAL 3.0 12.3 - - - +
422C LEU* 1.3 79.3 - - - +
424C LEU* 1.3 82.2 + - + +
425C ASP* 3.6 3.3 + - - -
426C THR* 5.8 1.2 - - + +
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Residues in contact with LEU 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ILE* 5.5 3.6 - - + -
385C TYR* 5.1 15.9 - - + +
420C VAL* 3.8 11.2 - - + +
421C LEU* 2.5 53.6 + - + +
422C LEU 4.4 0.2 - - - -
423C TYR* 1.3 99.1 - - + +
425C ASP* 1.3 64.1 + - - +
426C THR* 3.1 27.1 - - + +
427C VAL 4.8 1.9 + - - -
428C PRO* 3.7 27.5 - - + +
471C LYS* 5.5 4.5 - - - -
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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
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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