Contacts of the helix formed by residues 366 - 370 (chain C) in PDB entry 3OS8
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 GLY 366 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307C ALA* 3.4 12.9 - - - +
364C VAL 3.2 0.4 + - - -
365C PRO* 1.3 71.8 - - - +
367C PHE* 1.3 63.8 + - - +
368C VAL* 3.5 4.4 - - - +
369C ASP* 3.3 27.8 + - - +
370C LEU* 4.0 3.9 - - - +
454C LEU* 5.4 3.3 - - - +
474C HIS* 3.2 27.9 + - - -
478C VAL* 4.2 6.1 - - - -
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Residues in contact with PHE 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ALA* 3.2 41.7 - - + +
362C LYS* 4.0 6.7 - - - -
364C VAL* 3.0 22.3 + - + +
365C PRO 3.3 1.8 + - - -
366C GLY* 1.3 77.9 - - - +
368C VAL* 1.3 61.5 + - - +
369C ASP 3.1 0.2 - - - -
370C LEU* 3.2 25.1 + - + +
375C GLN* 3.5 54.7 - - + +
378C LEU* 3.6 31.9 - - + -
379C LEU* 4.3 6.3 - - + -
453C LEU* 3.8 25.8 - - + -
454C LEU* 4.3 9.1 - - + +
544C LEU* 4.5 7.9 - - + -
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Residues in contact with VAL 368 (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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362C LYS* 3.1 47.8 - - + +
364C VAL 4.5 1.1 + - - +
366C GLY 5.4 1.8 - - - +
367C PHE* 1.3 74.5 - - + +
369C ASP* 1.3 68.0 + - - +
370C LEU 3.1 12.9 + - - +
375C GLN* 3.7 13.3 + - - +
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Residues in contact with ASP 369 (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 SER* 3.1 28.9 + - - -
306C LEU* 4.9 3.7 + - - +
307C ALA* 4.7 1.4 + - - +
366C GLY* 3.3 21.5 + - - +
367C PHE 3.1 0.8 - - - -
368C VAL* 1.3 85.8 - - - +
370C LEU* 1.3 60.9 + - - +
467C LYS* 5.1 4.2 + - - -
471C GLU* 3.9 8.3 - - - +
474C HIS* 3.2 21.6 + - + +
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Residues in contact with LEU 370 (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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366C GLY 4.0 5.2 - - - +
367C PHE* 3.4 25.1 - - + +
368C VAL 3.1 4.1 - - - +
369C ASP* 1.3 82.7 - - - +
371C THR* 1.3 64.0 + - - +
372C ARG 3.7 0.3 + - - -
374C ASP* 4.2 7.4 - - + -
375C GLN* 2.8 26.1 + - + -
378C LEU* 3.5 33.0 - - + -
454C LEU* 4.8 2.5 - - + -
471C GLU* 3.2 41.3 - - + +
474C HIS* 4.0 14.6 - - + -
475C ILE* 3.9 20.2 - - + -
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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