Contacts of the helix formed by residues 418 - 432 (chain C) in PDB entry 4AY6
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 418 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385C ALA* 3.5 34.8 - - + -
386C ASP* 3.2 33.4 - - + -
389C SER* 3.6 17.9 - - - -
411C ALA* 4.7 3.8 - - + +
412C ILE* 5.0 0.2 - - - +
415C ASN* 3.0 37.0 + - + +
416C PRO 3.5 0.2 - - - -
417C ALA* 1.3 73.6 - - - +
419C ALA* 1.3 64.1 + - - +
420C ASP* 4.0 24.9 - - + -
421C ALA* 3.9 25.4 + - + +
422C HIS* 3.2 20.5 + - - -
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Residues in contact with ALA 419 (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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417C ALA 3.1 4.5 + - - +
418C PHE* 1.3 76.9 - - - +
420C ASP* 1.3 70.0 + - - +
422C HIS* 3.2 15.2 + - - +
423C SER* 3.2 10.4 + - - -
445C ALA* 3.6 27.1 - - - +
448C LEU* 4.0 15.5 - - + -
449C LYS* 3.7 24.2 - - + +
452C PHE* 4.2 5.6 - - + -
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Residues in contact with ASP 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ASP* 4.4 6.1 - - - +
389C SER* 4.0 8.3 - - - +
418C PHE* 3.6 29.1 - - + -
419C ALA* 1.3 73.8 - - - +
421C ALA* 1.3 60.0 + - - +
423C SER* 3.3 1.9 + - - -
424C ASN* 2.8 38.6 + - - +
449C LYS* 3.1 28.1 + - - -
452C PHE* 3.6 23.1 - - + -
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Residues in contact with ALA 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C SER* 4.1 9.7 + - - +
408C TYR* 4.0 14.1 - - - +
411C ALA* 4.1 10.1 - - + -
412C ILE* 3.5 26.5 - - + +
418C PHE* 3.9 23.7 + - + +
419C ALA 3.3 0.6 - - - -
420C ASP* 1.3 77.3 - - - +
422C HIS* 1.3 54.4 + - - +
424C ASN* 3.3 5.3 + - - +
425C LEU* 2.8 36.0 + - - +
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Residues in contact with HIS 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ILE* 3.9 37.1 - - + +
416C PRO 3.2 20.7 + - - -
418C PHE 3.2 24.2 - - - -
419C ALA 3.2 7.8 + - - +
421C ALA* 1.3 78.2 - - - +
423C SER* 1.3 56.6 + - - +
425C LEU* 3.7 3.0 + - - +
426C ALA* 3.1 20.8 + - - +
441C SER* 3.5 24.6 + - - +
444C THR* 3.8 23.1 - - + +
445C ALA* 3.7 15.3 - - + -
448C LEU* 3.4 19.3 - - + +
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Residues in contact with SER 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ALA 3.2 3.6 + - - -
420C ASP 3.5 7.0 - - - -
422C HIS* 1.3 76.0 - - - +
424C ASN* 1.3 70.7 + - - +
426C ALA* 2.9 15.6 + - - +
427C SER* 2.9 16.9 + - - -
442C TYR* 3.7 19.0 - - - -
445C ALA* 3.8 9.6 - - - +
452C PHE* 3.8 29.2 - - - -
454C ASP* 5.0 3.5 - - - +
455C ALA* 4.1 12.9 + - - +
458C ASN* 5.1 1.2 + - - -
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Residues in contact with ASN 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C SER* 2.7 45.1 + - - -
393C ASN* 3.5 23.5 + - - +
396C LYS* 5.0 0.5 + - - -
408C TYR* 3.4 32.3 + - + -
420C ASP* 2.8 21.0 + - - +
421C ALA 3.6 4.0 - - - +
423C SER* 1.3 74.3 + - - +
425C LEU* 1.3 63.7 + - - +
427C SER* 3.4 12.2 + - - -
428C ILE* 3.3 14.2 + - - +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LEU* 3.8 27.1 - - + -
408C TYR* 3.9 16.3 - - + -
409C THR* 4.4 18.6 - - + +
412C ILE* 4.3 16.8 - - + -
421C ALA 2.8 21.4 + - - +
422C HIS* 3.7 5.2 - - - +
424C ASN* 1.3 70.0 - - - +
426C ALA* 1.3 65.4 + - - +
428C ILE* 2.9 17.9 + - - +
429C HIS* 3.3 28.3 + - + +
441C SER* 3.5 21.1 - - - +
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C HIS 3.1 5.7 + - - +
423C SER 2.9 13.9 + - - +
425C LEU* 1.3 74.8 - - - +
427C SER* 1.3 55.8 + - - +
429C HIS* 3.1 9.0 + - - +
430C LYS* 2.9 24.8 + - - +
438C ALA* 3.3 33.1 - - - +
441C SER* 3.4 18.3 - - - -
442C TYR* 3.6 22.2 - - + +
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Residues in contact with SER 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LYS* 3.6 17.0 - - - -
423C SER* 2.9 17.1 + - - -
424C ASN* 3.5 14.3 + - - -
425C LEU 3.1 0.2 - - - -
426C ALA* 1.3 72.1 - - - +
428C ILE* 1.3 64.7 + - - +
430C LYS* 3.4 5.4 + - - +
431C ASP* 3.1 29.3 + - - +
442C TYR* 2.8 23.3 + - - -
458C ASN* 4.2 7.8 + - - -
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Residues in contact with ILE 428 (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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396C LYS* 3.7 37.0 - - + +
401C VAL* 4.2 25.1 - - + +
404C ALA* 4.9 6.3 - - + -
405C LEU* 4.0 24.9 - - + -
408C TYR* 3.5 32.8 - - + -
424C ASN 3.3 2.4 + - - +
425C LEU 2.9 8.3 + - - +
427C SER* 1.3 75.1 - - - +
429C HIS* 1.3 67.8 + - + +
431C ASP* 3.1 8.2 + - + +
432C SER* 2.9 34.6 + - - +
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Residues in contact with HIS 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C LEU* 5.7 3.0 - - + +
425C LEU* 3.3 43.2 + - + +
426C ALA* 3.1 10.5 + - - +
428C ILE* 1.3 82.1 - - + +
430C LYS* 1.3 62.8 + - - +
432C SER* 3.1 1.8 + - - -
433C GLY 3.1 11.4 + - - -
434C ASN* 2.9 55.4 + - - +
437C GLU* 3.7 27.7 - - + +
438C ALA* 3.8 8.1 - - + -
441C SER* 5.0 1.6 - - - -
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Residues in contact with LYS 430 (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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426C ALA 2.9 12.3 + - - +
427C SER* 3.5 11.7 - - - +
429C HIS* 1.3 77.3 - - - +
431C ASP* 1.3 64.2 + - - +
433C GLY* 2.8 21.0 + - - -
435C ILE* 4.1 12.6 - - + +
438C ALA* 3.7 8.9 - - + +
442C TYR* 4.2 11.9 - - - +
458C ASN* 3.7 33.2 - - + +
461C HIS* 2.7 39.3 + - - -
462C CYS* 3.7 15.0 - - - -
465C ILE* 3.8 11.9 - - - +
499C HIS* 5.1 3.9 - - - -
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Residues in contact with ASP 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LYS* 3.3 27.8 + - - -
427C SER* 3.1 12.9 + - - +
428C ILE* 3.1 10.8 + - + +
430C LYS* 1.3 81.1 - - - +
432C SER* 1.3 60.0 + - - +
433C GLY* 3.1 5.9 + - - -
1399G SER* 3.4 27.6 + - - -
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Residues in contact with SER 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C VAL* 5.7 1.7 - - - +
428C ILE* 2.9 26.7 + - - +
429C HIS* 3.1 5.0 + - - -
431C ASP* 1.3 76.3 - - - +
433C GLY* 1.3 63.8 + - - +
434C ASN* 3.1 18.9 + - - +
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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
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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