Contacts of the helix formed by residues 403 - 410 (chain C) in PDB entry 3HN8
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 ASN 403 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375C LEU 5.0 2.5 - - - -
376C ALA* 5.1 12.3 - - + +
378C ARG 4.6 7.9 + - - -
379C LYS* 5.3 0.4 - - - +
402C ASP* 1.3 93.9 + - - +
404C LEU* 1.3 64.7 + - - +
405C LEU* 3.3 5.7 + - + +
406C GLU* 3.5 37.3 + - - +
407C LEU* 3.1 20.1 - - - +
452C LYS* 6.0 1.1 - - - +
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Residues in contact with LEU 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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305C LEU* 4.5 9.8 - - + +
314C LEU* 3.5 27.8 - - + -
341C LEU* 4.3 4.3 - - + -
375C LEU* 3.9 27.7 + - + +
378C ARG* 4.1 25.1 - - + +
379C LYS 4.2 1.3 - - - -
380C LEU* 3.7 40.4 - - + +
401C LEU* 3.7 25.4 - - + +
402C ASP 2.8 5.5 + - - +
403C ASN* 1.3 71.3 - - - +
405C LEU* 1.3 69.1 + - - +
407C LEU* 3.2 8.4 + - + +
408C ALA* 3.1 21.4 + - - +
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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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307C TYR* 5.0 4.5 - - + -
309C TYR* 4.6 12.3 - - + +
372C LEU* 3.8 20.6 - - + -
375C LEU* 3.8 38.5 + - + +
376C ALA* 5.4 3.8 - - + +
403C ASN* 3.3 4.2 - - + -
404C LEU* 1.3 78.6 - - - +
406C GLU* 1.3 68.6 + - + +
408C ALA* 3.2 2.4 + - + +
409C GLU* 3.0 59.7 + - + +
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Residues in contact with GLU 406 (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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406A GLU* 3.1 30.6 - - - +
403C ASN* 3.5 33.0 + - - +
404C LEU 3.3 0.4 - - - -
405C LEU* 1.3 92.2 - - + +
407C LEU* 1.3 65.4 + - + +
408C ALA 3.4 0.2 + - - -
409C GLU* 3.6 12.0 + - - +
410C GLN 3.9 10.7 + - - +
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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 LEU* 4.0 21.3 - - + +
401C LEU* 3.6 42.4 - - + -
402C ASP* 4.0 9.0 - - + +
403C ASN* 3.1 33.2 - - - +
404C LEU* 3.2 9.0 + - - +
406C GLU* 1.3 80.7 - - + +
408C ALA* 1.3 61.8 + - - +
410C GLN 3.4 15.5 - - - +
411C PRO* 5.0 2.3 - - - +
416C LEU* 3.6 31.6 - - + +
418C ARG* 4.1 14.4 - - - +
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Residues in contact with ALA 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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305C LEU* 3.1 33.3 - - + +
306C ARG* 3.8 21.2 - - - +
307C TYR* 3.9 19.2 + - + +
314C LEU* 5.0 3.4 - - + -
375C LEU* 5.8 0.7 - - + -
404C LEU 3.1 12.9 + - - +
405C LEU* 3.8 3.4 - - + +
407C LEU* 1.3 79.0 - - - +
409C GLU* 1.3 54.7 + - - +
410C GLN* 2.7 20.1 + - - -
411C PRO 4.6 3.3 - - - +
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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
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557A LYS* 5.3 6.8 + - - +
558A PRO 5.8 0.3 - - - +
309C TYR* 3.9 22.9 + - - +
405C LEU* 3.0 41.7 + - + +
406C GLU* 4.1 9.1 - - - +
407C LEU 3.5 0.6 - - - -
408C ALA* 1.3 74.7 - - - +
410C GLN* 1.3 87.5 + - - +
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Residues in contact with GLN 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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414A ARG* 5.2 6.9 + - - +
557A LYS* 6.0 2.4 - - - +
406C GLU 3.9 7.3 + - - +
407C LEU* 3.4 14.4 - - - +
408C ALA 2.7 8.7 + - - -
409C GLU* 1.3 86.5 + - - +
411C PRO* 1.3 77.1 - - + +
412C PRO* 4.8 6.7 - - + -
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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