Contacts of the helix formed by residues 267 - 279 (chain L) in PDB entry 1OEY
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 LEU 267 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265L PRO 3.9 1.2 + - - -
266L LEU* 1.3 71.6 - - - +
268L LYS* 1.3 64.1 + - + +
270L LEU* 3.2 5.6 + - + +
271L LEU* 3.0 35.1 + - + +
285L LEU* 4.1 22.2 - - + -
297L LEU* 4.3 20.9 - - + +
298L LEU* 3.6 32.8 - - - +
299L SER* 3.7 7.0 - - - +
300L ASP* 2.9 19.2 + - - +
303L VAL* 4.0 25.2 - - + +
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Residues in contact with LYS 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266L LEU* 3.1 10.7 - - + +
267L LEU* 1.3 81.2 - - + +
269L ASP* 1.3 59.2 + - - +
271L LEU* 3.4 29.7 + - + +
272L GLU* 3.0 27.9 + - - +
300L ASP* 4.4 1.0 + - - -
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Residues in contact with ASP 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265L PRO* 4.2 9.4 - - + +
266L LEU* 3.1 46.2 + - - +
268L LYS* 1.3 77.2 - - - +
270L LEU* 1.3 58.9 + - - +
272L GLU* 3.5 6.2 + - - +
273L LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240L LEU* 4.7 6.7 - - + -
265L PRO* 3.9 30.1 - - + -
266L LEU 3.3 7.1 + - - +
267L LEU* 3.2 6.6 + - + +
269L ASP* 1.3 76.6 - - - +
271L LEU* 1.3 59.5 + - - +
273L LEU* 3.3 12.9 + - + +
274L THR* 2.9 32.6 + - - -
285L LEU* 3.4 20.0 - - + -
297L LEU* 4.4 2.9 - - + -
303L VAL* 4.2 26.0 - - + -
306L MSE 4.3 5.6 - - + -
322L TRP* 4.0 17.3 - - + -
324L LEU* 4.2 28.4 - - + +
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Residues in contact with LEU 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267L LEU* 3.0 32.4 + - + +
268L LYS* 3.4 35.9 + - + +
270L LEU* 1.3 72.4 - - - +
272L GLU* 1.3 60.8 + - - +
274L THR* 3.4 4.5 + - - -
275L ARG* 2.9 28.2 + - - +
280L ARG 5.0 1.4 - - - +
281L GLU* 5.7 2.4 - - - +
283L ILE* 3.8 31.8 - - + +
285L LEU* 3.9 16.8 - - + +
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Residues in contact with GLU 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268L LYS 3.0 16.9 + - - +
269L ASP* 3.9 6.5 - - - +
270L LEU 3.3 0.2 - - - -
271L LEU* 1.3 73.6 - - - +
273L LEU* 1.3 64.5 + - - +
275L ARG* 3.3 36.4 + - - -
276L ARG* 3.0 47.5 + - - +
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Residues in contact with LEU 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L LEU* 4.3 19.1 - - + -
242L VAL* 5.3 1.3 - - + -
255L ILE* 4.4 19.5 - - + -
257L VAL* 3.9 28.5 - - + -
269L ASP 3.0 18.1 + - - +
270L LEU* 3.3 15.0 + - + +
272L GLU* 1.3 74.3 - - - +
274L THR* 1.3 68.5 + - - +
276L ARG* 3.3 10.5 + - - +
277L GLU* 2.9 40.2 + - + +
278L PHE* 5.2 3.8 - - + -
324L LEU* 5.1 5.6 - - + -
326L ILE* 5.9 0.2 - - + -
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Residues in contact with THR 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270L LEU 2.9 17.6 + - - -
271L LEU* 3.6 7.9 - - - -
273L LEU* 1.3 81.3 - - - +
275L ARG* 1.3 66.3 + - - +
278L PHE* 2.9 35.1 + - + +
279L GLN 3.5 0.9 + - - -
280L ARG* 4.1 5.7 + - + +
283L ILE* 3.9 29.8 - - + -
285L LEU* 3.7 15.1 - - - +
324L LEU* 4.3 2.9 - - - +
326L ILE* 3.8 29.0 - - + +
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Residues in contact with ARG 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271L LEU 2.9 17.5 + - - +
272L GLU* 3.6 32.6 + - - +
274L THR* 1.3 75.6 - - - +
276L ARG* 1.3 58.3 + - - +
279L GLN* 2.9 30.9 + - - +
280L ARG 3.6 17.0 + - - +
281L GLU* 3.8 40.3 + - + -
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Residues in contact with ARG 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272L GLU* 3.0 46.0 + - - +
273L LEU* 3.7 8.1 - - - +
274L THR 3.2 0.2 - - - -
275L ARG* 1.3 78.8 - - - +
277L GLU* 1.3 74.3 + - - +
279L GLN* 4.5 7.3 + - - +
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Residues in contact with GLU 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253L LYS* 4.1 17.4 + - - -
255L ILE* 3.5 43.3 - - + +
256L ALA 5.0 2.1 + - - +
273L LEU* 2.9 23.3 + - + +
276L ARG* 1.3 94.1 - - + +
278L PHE* 1.3 81.7 + - + +
279L GLN* 3.7 2.1 - - - +
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Residues in contact with PHE 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L VAL* 3.9 20.6 - - + -
244L TYR* 4.0 49.7 + + + +
253L LYS* 4.2 25.6 - - + -
255L ILE* 4.2 20.0 - - + -
273L LEU* 5.2 2.2 - - + -
274L THR* 2.9 23.3 + - + +
277L GLU* 1.3 94.4 - - + +
279L GLN* 1.3 74.0 + - - +
280L ARG* 3.2 13.2 + - + +
326L ILE* 3.4 29.4 - - + -
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Residues in contact with GLN 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274L THR 3.5 0.2 + - - -
275L ARG* 2.9 23.4 + - - +
276L ARG 4.6 8.3 - - - +
277L GLU 5.1 1.8 - - - +
278L PHE* 1.3 81.7 - - - +
280L ARG* 1.3 60.1 + - - +
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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