Contacts of the helix formed by residues 298 - 307 (chain N) in PDB entry 6NR8
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 298 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236N SER* 5.0 1.8 - - - -
237N LEU* 3.3 29.9 - - + +
238N GLU* 2.9 29.5 - - - +
264N ARG* 5.0 7.0 - - - +
267N ILE* 3.3 24.7 - - + +
296N GLY 3.9 3.0 + - - +
297N ILE* 1.3 80.2 - - - +
299N PRO* 1.3 69.5 - - + +
300N PHE* 3.2 5.6 - - + +
301N SER* 3.1 4.5 + - - +
302N LEU 2.8 22.3 + - - -
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Residues in contact with PRO 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264N ARG* 6.2 0.9 - - - +
297N ILE 4.1 4.0 - - - +
298N ASP* 1.3 85.5 - - + +
300N PHE* 1.3 63.5 + - - +
302N LEU* 3.6 17.8 - - + +
303N ASP* 3.0 30.9 + - - +
342P GLU* 3.3 37.6 - - + +
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Residues in contact with PHE 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264N ARG* 4.5 19.5 - - - +
267N ILE* 4.7 16.4 - - + -
268N GLU* 3.2 31.4 - - - -
271N VAL* 4.9 11.2 - - + -
298N ASP* 3.2 5.3 - - + -
299N PRO* 1.3 83.3 - - - +
301N SER* 1.3 59.4 + - - +
303N ASP* 3.3 15.1 + - + +
304N ALA* 3.0 27.7 + - + +
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Residues in contact with SER 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237N LEU* 3.6 31.9 - - - +
267N ILE* 5.2 2.2 - - - +
271N VAL* 3.3 25.3 - - - +
274N ILE* 6.0 0.2 - - - +
297N ILE* 4.6 4.7 - - - +
298N ASP* 3.1 6.3 + - - +
300N PHE* 1.3 77.9 - - - +
302N LEU* 1.3 61.0 + - - +
303N ASP 3.1 1.6 - - - -
304N ALA* 4.0 7.4 - - - +
305N LEU* 2.8 46.3 + - - +
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Residues in contact with LEU 302 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217N ARG 4.7 8.1 - - - +
218N HIS* 3.4 39.4 - - + +
221N MET* 3.8 19.5 - - + -
297N ILE* 4.1 12.9 - - + +
298N ASP 2.8 15.8 + - - +
299N PRO* 3.6 19.1 - - + +
300N PHE 3.3 0.2 - - - -
301N SER* 1.3 75.9 - - - +
303N ASP* 1.3 60.4 + - - +
305N LEU* 5.2 1.6 - - - -
306N SER* 3.0 27.1 + - - -
312N ALA* 5.5 1.8 - - + -
314N ARG* 3.7 27.6 - - - +
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Residues in contact with ASP 303 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218N HIS* 3.1 23.5 + - - -
299N PRO 3.0 17.0 + - - +
300N PHE* 3.4 16.6 - - + +
301N SER 3.1 0.6 - - - -
302N LEU* 1.3 77.1 - - - +
304N ALA* 1.3 63.0 + - - +
306N SER* 4.5 0.2 - - - -
307N LYS* 3.3 50.8 + - + +
341P LEU* 5.9 2.9 - - - +
342P GLU* 5.5 1.4 - - - +
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Residues in contact with ALA 304 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271N VAL* 3.7 28.5 - - + -
275N ILE* 3.9 13.9 - - + +
300N PHE* 3.0 23.5 + - + +
301N SER* 3.2 1.5 + - - +
303N ASP* 1.3 77.6 - - - +
305N LEU* 1.3 63.6 + - - +
307N LYS* 4.7 3.1 - - - +
308N GLU* 3.7 17.0 + - - +
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Residues in contact with LEU 305 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271N VAL* 3.7 16.2 - - + -
274N ILE* 3.7 35.0 - - + -
275N ILE* 4.1 4.7 - - + -
291N VAL* 4.6 14.6 - - + -
297N ILE* 5.3 5.6 - - + -
301N SER* 2.8 39.5 + - - +
302N LEU* 5.0 0.7 - - - +
304N ALA* 1.3 72.5 - - - +
306N SER* 1.3 64.8 + - - +
308N GLU* 3.2 12.0 + - - +
310N ILE* 3.2 39.0 + - + +
312N ALA* 3.9 28.0 - - + -
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Residues in contact with SER 306 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218N HIS* 3.3 30.7 - - - +
220N ASP* 2.9 22.1 - - - +
221N MET* 3.3 34.1 - - - +
302N LEU* 3.0 22.7 + - - +
304N ALA 3.5 0.4 - - - -
305N LEU* 1.3 78.9 - - - +
307N LYS* 1.3 58.1 + - - +
309N GLY* 3.1 14.2 + - - -
310N ILE 3.8 8.9 + - - -
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Residues in contact with LYS 307 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218N HIS* 3.6 18.0 + - - +
220N ASP* 3.3 30.3 + - + +
303N ASP* 3.3 37.4 + - + +
304N ALA* 4.7 3.1 - - - +
306N SER* 1.3 75.0 - - - +
308N GLU* 1.3 63.5 + - - +
309N GLY 3.5 0.2 + - - -
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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