Contacts of the helix formed by residues 297 - 302 (chain N) in PDB entry 2JA7
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 ILE 297 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282N ILE* 6.2 0.9 - - + -
283N VAL* 4.0 27.4 - - + -
286N PHE* 3.6 37.0 - - + -
287N ARG* 4.3 11.4 - - + +
291N ILE* 3.4 29.2 - - + +
293N PRO 3.3 17.2 + - - +
294N ASP* 4.4 4.3 - - - -
296N GLU* 1.3 76.0 - - - +
298N LEU* 1.3 72.7 + - + +
299N GLU 2.9 4.5 - - - -
300N HIS* 2.8 28.3 + - - +
301N ILE* 3.4 16.7 + - + +
318N VAL* 6.1 1.6 - - + -
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Residues in contact with LEU 298 (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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294N ASP* 4.3 2.2 - - + -
295N GLY* 3.3 31.2 - - - +
296N GLU 3.5 0.2 - - - -
297N ILE* 1.3 88.7 - - + +
299N GLU* 1.3 53.4 + - + +
300N HIS 3.3 0.2 - - - -
301N ILE* 3.7 7.4 - - + -
302N CYS* 2.7 36.6 + - - +
311N LEU* 4.8 17.3 - - + +
314N LEU* 3.5 43.1 - - + -
318N VAL* 4.1 21.5 - - + -
4U PHE* 5.3 5.8 - - + -
6U PHE* 4.7 13.5 - - + -
13U MET* 6.2 3.8 - - + -
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Residues in contact with GLU 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295N GLY 2.8 22.9 + - - +
296N GLU* 3.5 15.5 - - + +
297N ILE 2.9 1.0 - - - -
298N LEU* 1.3 75.6 - - - +
300N HIS* 1.3 61.4 + - + +
301N ILE 3.1 5.2 + - - -
302N CYS 3.6 14.8 - - - +
303N TYR* 3.8 10.6 - - - -
305N VAL* 5.2 7.3 - - - +
376N PHE* 5.1 2.7 - - - -
569N TYR* 5.7 0.2 - - - -
571N PRO* 3.1 31.5 - - + +
572N HIS* 3.0 38.1 + - - -
6U PHE* 5.5 3.8 - - + -
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Residues in contact with HIS 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286N PHE* 3.9 18.4 - + + -
291N ILE* 3.1 45.2 - - + +
296N GLU* 3.1 27.3 + - - +
297N ILE* 2.8 9.7 + - - +
299N GLU* 1.3 78.2 - - + +
301N ILE* 1.3 59.2 + - - +
303N TYR* 3.4 18.4 + - - -
372N SER* 5.9 1.8 - - - -
375N ALA* 4.2 5.2 - - + +
376N PHE* 3.0 57.1 - + - +
379N GLY* 3.3 15.8 - - - -
380N TYR 4.2 0.2 + - - -
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Residues in contact with ILE 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282N ILE* 4.2 5.4 - - + -
286N PHE* 3.6 29.2 - - + -
297N ILE* 3.4 22.4 + - + +
298N LEU* 4.0 4.5 - - + +
300N HIS* 1.3 83.7 - - - +
302N CYS* 1.3 60.8 + - + +
303N TYR* 3.8 7.1 - - - -
310N MET* 4.2 1.8 - - - +
314N LEU* 3.8 38.1 - - + -
379N GLY* 4.2 8.7 - - - -
382N ILE* 4.1 30.1 - - + -
383N ASN* 3.4 32.5 - - - +
386N LEU* 4.6 5.2 - - + -
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Residues in contact with CYS 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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298N LEU 2.7 24.1 + - - +
299N GLU* 3.6 12.0 - - - +
301N ILE* 1.3 72.5 - - + +
303N TYR* 1.3 63.6 + - - +
304N ASP 3.1 31.6 + - - -
305N VAL* 5.0 2.4 - - - +
307N ASP* 4.1 6.7 - - - -
310N MET* 4.1 25.1 - - + -
311N LEU* 3.5 33.0 - - + -
314N LEU* 5.0 3.6 - - + -
571N PRO* 4.8 2.4 - - - +
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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