Contacts of the helix formed by residues 279 - 289 (chain A) in PDB entry 3ORY
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 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A VAL* 1.3 69.3 - - - +
280A VAL* 1.3 62.5 + - - +
281A ILE* 3.7 6.2 + - - +
282A ALA* 3.2 31.4 + - + +
283A ILE* 3.1 28.0 + - + +
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ASP* 4.9 0.3 - - - +
235A ILE* 3.6 26.3 - - + +
246A PHE* 4.1 17.0 - - + -
264A ILE* 4.0 19.1 - - + -
265A GLU* 3.4 28.0 + - - +
278A VAL* 3.1 26.9 + - + +
279A ASP* 1.3 72.3 - - - +
281A ILE* 1.3 60.1 + - - +
283A ILE* 3.5 6.9 + - - -
284A LYS* 3.0 28.1 + - - +
356A PO4 3.8 15.8 + - - +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU* 3.6 32.5 - - + +
279A ASP* 3.2 7.2 + - - +
280A VAL* 1.3 74.7 - - - +
282A ALA* 1.3 60.8 + - - +
284A LYS* 3.3 12.8 + - - +
285A LYS* 2.9 54.8 + - + +
356A PO4 3.8 22.2 - - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASP* 3.2 33.0 + - + +
281A ILE* 1.3 79.0 - - - +
283A ILE* 1.3 58.3 + - + +
285A LYS* 3.4 8.4 + - - +
286A TYR* 2.9 29.1 + - - +
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ILE* 3.7 22.9 - - + -
239A THR* 4.0 8.1 - - - +
241A TYR* 3.6 35.0 - - + +
242A ASN* 4.1 8.7 - - - +
278A VAL* 3.4 33.0 - - + -
279A ASP* 3.1 13.9 + - + +
280A VAL* 3.8 7.6 - - - +
281A ILE 3.3 0.2 - - - -
282A ALA* 1.3 74.1 - - + +
284A LYS* 1.3 66.5 + - - +
286A TYR* 3.2 6.5 + - - +
287A PHE* 3.0 42.0 + - + -
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLU* 2.8 49.5 + - + +
231A ILE* 3.8 24.0 - - + +
232A ASP* 3.6 17.3 - - - +
235A ILE* 3.5 8.4 - - + +
280A VAL 3.0 18.3 + - - +
281A ILE* 3.5 16.6 - - - +
283A ILE* 1.3 75.9 - - - +
285A LYS* 1.3 72.7 + - - +
287A PHE* 3.1 5.5 + - - +
288A LEU* 3.0 24.7 + - + +
356A PO4 3.0 33.8 + - - +
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLU* 5.9 1.4 + - - -
281A ILE* 2.9 42.3 + - + +
282A ALA* 3.9 6.5 - - - +
284A LYS* 1.3 86.9 - - - +
286A TYR* 1.3 61.8 + - - +
288A LEU* 3.4 15.9 + - + +
289A GLN* 3.1 24.1 + - - +
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Residues in contact with TYR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ALA* 3.7 3.6 - - - +
156A GLU* 2.6 41.0 + - - -
183A PHE* 4.1 5.8 - + - -
241A TYR* 3.4 27.9 + + + -
282A ALA 2.9 18.2 + - - +
283A ILE* 3.5 6.7 - - - +
284A LYS 3.2 0.2 - - - -
285A LYS* 1.3 74.3 - - - +
287A PHE* 1.3 71.3 + + - +
289A GLN 2.9 8.7 + - - +
290A PRO* 2.9 37.0 - - + +
291A GLN* 3.0 43.0 + - + +
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Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 5.8 1.3 - - + -
179A ASP* 4.8 3.1 - - + -
182A LEU* 3.7 44.6 - - + +
183A PHE* 3.5 61.0 - + - -
231A ILE* 3.7 26.7 - - + -
235A ILE* 5.3 0.2 - - + -
239A THR* 3.8 29.6 - - + -
241A TYR* 4.4 11.4 - + - -
283A ILE* 3.0 43.0 + - + -
284A LYS 3.5 7.4 - - - +
286A TYR* 1.3 78.6 - + - +
288A LEU* 1.3 61.4 + - - +
290A PRO* 3.4 11.3 - - - +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS* 4.8 9.5 + - - -
227A LEU* 4.0 21.8 - - + -
228A GLU* 3.7 36.3 - - + +
231A ILE* 3.7 20.0 - - + -
284A LYS* 3.0 20.4 + - + +
285A LYS* 3.6 21.3 - - + +
286A TYR 3.1 0.2 - - - -
287A PHE* 1.3 78.3 - - - +
289A GLN* 1.3 68.1 + - + +
290A PRO* 3.6 4.3 - - - +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LYS 3.1 11.7 + - - +
286A TYR* 2.9 15.5 + - - +
288A LEU* 1.3 88.7 - - + +
290A PRO* 1.3 66.7 - - - +
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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