Contacts of the helix formed by residues 400 - 415 (chain C) in PDB entry 4AY5
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 ASP 400 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395C LEU* 2.9 41.2 + - + +
398C MET* 3.1 10.0 + - + +
399C GLN* 1.3 74.5 - - - +
401C VAL* 1.3 59.1 + - - +
402C GLN* 3.2 12.8 - - - +
403C GLY* 2.9 23.9 + - - -
404C ALA* 3.2 13.7 + - - +
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Residues in contact with VAL 401 (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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395C LEU 5.1 0.2 - - - -
396C LYS* 5.1 4.0 - - + +
399C GLN 3.2 9.8 + - - +
400C ASP* 1.3 71.0 - - - +
402C GLN* 1.3 74.8 + - + +
404C ALA* 3.0 7.7 + - - +
405C LEU* 2.8 27.7 + - + +
428C ILE* 4.1 32.8 - - + -
432C SER* 5.3 5.2 - - - +
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Residues in contact with GLN 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C ASP* 3.2 11.0 - - - +
401C VAL* 1.3 85.0 - - + +
403C GLY* 1.3 62.7 + - - +
405C LEU* 3.2 19.1 - - - +
406C GLN* 2.8 37.3 + - - +
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Residues in contact with GLY 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C LEU* 3.6 12.3 - - - -
400C ASP* 2.9 26.8 + - - -
402C GLN* 1.3 70.3 - - - +
404C ALA* 1.3 68.2 + - - +
405C LEU 2.9 1.6 - - - -
406C GLN* 2.6 29.6 + - - +
407C CYS* 3.0 12.8 + - - -
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Residues in contact with ALA 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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392C GLY* 3.3 31.2 - - - +
395C LEU* 3.7 6.0 - - - +
396C LYS* 3.6 24.7 - - + +
400C ASP 3.2 8.4 + - - +
401C VAL* 3.0 9.8 + - - +
403C GLY* 1.3 73.4 - - - +
405C LEU* 1.3 65.6 + - - +
407C CYS* 3.0 5.4 + - - +
408C TYR* 3.0 34.2 + - + -
428C ILE* 4.7 3.6 - - + -
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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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401C VAL* 2.8 16.2 + - + +
402C GLN* 3.2 14.8 - - - +
404C ALA* 1.3 79.1 - - - +
406C GLN* 1.3 61.5 + - - +
408C TYR* 3.2 4.6 + - + +
409C THR* 2.7 32.1 + - + +
425C LEU* 3.6 31.4 - - + -
428C ILE* 4.1 27.3 - - + +
429C HIS* 6.0 3.4 - - + +
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Residues in contact with GLN 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C GLN* 2.8 38.3 + - - +
403C GLY* 2.6 20.8 + - - +
405C LEU* 1.3 74.6 - - - +
407C CYS* 1.3 52.5 + - - +
409C THR* 2.9 8.2 + - - +
410C ARG* 2.8 57.3 + - - +
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Residues in contact with CYS 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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388C TYR* 3.3 33.4 - - + +
391C MET* 3.6 28.9 - - - -
392C GLY* 3.6 13.0 - - - -
395C LEU* 3.7 17.9 - - - -
403C GLY 3.0 16.8 + - - -
404C ALA 3.0 6.4 + - - +
406C GLN* 1.3 76.4 - - - +
408C TYR* 1.3 69.4 + - - +
410C ARG* 3.0 3.8 + - - +
411C ALA* 2.8 24.5 + - - +
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Residues in contact with TYR 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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389C SER* 3.2 31.9 - - - +
392C GLY* 3.5 13.6 + - - -
393C ASN* 2.6 32.3 + - - -
396C LYS* 3.8 14.4 + - - +
404C ALA* 3.0 20.5 + - + -
405C LEU* 3.8 7.9 - - + +
407C CYS* 1.3 82.7 - - - +
409C THR* 1.3 63.4 + - - +
411C ALA* 3.2 6.9 + - - +
412C ILE* 3.2 25.6 + - - +
421C ALA* 3.9 12.5 - - - +
424C ASN* 3.4 38.8 + - + +
425C LEU* 4.0 12.6 - - + -
428C ILE* 3.4 29.8 - - + -
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Residues in contact with THR 409 (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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405C LEU* 2.7 25.0 + - + +
406C GLN* 2.9 15.1 + - - +
408C TYR* 1.3 77.3 - - - +
410C ARG* 1.3 60.8 + - - +
412C ILE* 3.1 17.8 + - + +
413C GLN* 3.1 17.2 + - - +
425C LEU* 5.0 20.2 - - + -
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Residues in contact with ARG 410 (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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388C TYR* 3.6 39.3 + - + -
406C GLN* 2.8 49.9 + - - +
407C CYS* 3.0 3.5 + - - +
409C THR* 1.3 72.3 - - - +
411C ALA* 1.3 56.1 + - - +
413C GLN* 3.0 18.5 + - + +
414C ILE* 2.8 49.0 + - + +
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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
----------------------------------------------------------
385C ALA* 3.8 26.8 - - - +
388C TYR* 3.8 12.0 - - + +
389C SER* 4.1 6.3 - - - +
407C CYS 2.8 11.4 + - - +
408C TYR 3.4 9.6 - - - +
410C ARG* 1.3 75.2 - - - +
412C ILE* 1.3 57.4 + - - +
414C ILE* 3.4 5.7 + - - +
415C ASN* 2.9 30.7 + - - +
418C PHE* 4.4 4.6 - - + +
421C ALA* 3.9 16.8 - - + -
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Residues in contact with ILE 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 TYR 3.2 16.2 - - - +
409C THR* 3.1 11.1 + - + +
411C ALA* 1.3 77.8 - - - +
413C GLN* 1.3 59.1 + - - +
415C ASN 3.9 5.6 - - - -
416C PRO* 3.0 31.3 - - + +
418C PHE* 5.5 0.2 - - - -
421C ALA* 3.5 15.0 - - + +
422C HIS* 3.4 63.3 - - + +
425C LEU* 4.7 14.1 - - + -
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Residues in contact with GLN 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C THR* 3.1 10.7 + - - +
410C ARG* 3.3 28.2 + - + +
412C ILE* 1.3 79.9 - - - +
414C ILE* 1.3 64.5 + - + +
415C ASN 3.5 0.2 + - - -
416C PRO* 4.0 9.5 - - - +
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Residues in contact with ILE 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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382C PRO 3.9 10.3 - - - +
383C THR* 4.1 27.8 - - - +
385C ALA* 4.4 5.6 - - + -
388C TYR* 3.3 40.4 - - + +
410C ARG* 2.8 29.5 + - + +
411C ALA* 3.7 3.8 - - - +
413C GLN* 1.3 78.9 - - + +
415C ASN* 1.3 64.1 + - + +
416C PRO* 3.8 3.0 - - - +
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Residues in contact with ASN 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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385C ALA* 4.0 17.1 - - + +
411C ALA 2.9 12.5 + - - +
412C ILE* 3.2 6.1 - - - +
414C ILE* 1.3 84.8 - - + +
416C PRO* 1.3 62.9 - - - +
417C ALA* 2.8 29.9 + - - +
418C PHE* 2.9 39.0 + - + +
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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