Contacts of the helix formed by residues 270 - 279 (chain G) in PDB entry 2R9R
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 TYR 270 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57G TRP* 3.9 21.2 + + - -
58G VAL* 3.6 46.4 - - + +
264G ARG* 3.6 32.1 - - + +
265G ALA 4.4 3.8 - - - +
267G LEU* 3.1 34.1 + - + +
268G LYS 4.0 5.2 - - - -
269G GLY* 1.3 86.3 - - - +
271G GLN* 1.3 56.3 + - - +
272G TRP* 3.1 26.9 - + - +
273G LEU* 2.9 27.1 + - + +
274G LYS* 3.2 10.2 + - - +
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Residues in contact with GLN 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265G ALA 5.6 0.2 - - - -
267G LEU 4.1 2.7 + - - +
268G LYS* 3.5 37.8 - - + +
269G GLY* 3.4 6.7 - - - +
270G TYR* 1.3 78.2 - - - +
272G TRP* 1.3 62.8 + - + +
274G LYS* 2.8 37.7 + - - +
275G ASP* 3.0 38.8 + - - +
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Residues in contact with TRP 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G TRP* 4.1 27.4 - + - -
248G CYS* 4.4 8.3 - - - -
264G ARG* 6.0 0.2 - - - -
269G GLY 3.6 23.8 + - - -
270G TYR* 3.8 22.9 - + - +
271G GLN* 1.3 80.0 - - - +
273G LEU* 1.3 91.6 + - + +
275G ASP* 3.7 10.1 + - - +
276G LYS* 3.2 51.5 + - + +
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Residues in contact with LEU 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247G ALA 4.8 0.2 - - - +
248G CYS* 4.0 26.7 - - + +
250G ILE* 4.1 13.9 - - + -
255G TYR* 4.7 0.7 - - - +
264G ARG* 3.7 39.5 - - + -
265G ALA* 3.9 15.0 - - + +
270G TYR* 2.9 12.5 + - + +
272G TRP* 1.3 107.5 - - + +
274G LYS* 1.3 60.2 + - - +
276G LYS* 3.4 6.7 + - + +
277G ILE* 3.0 50.2 + - + +
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Residues in contact with LYS 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259G ILE* 3.9 17.7 - - + -
265G ALA* 3.7 28.6 - - - +
270G TYR 3.2 4.5 + - - +
271G GLN* 2.8 39.2 + - - +
273G LEU* 1.3 78.0 - - - +
275G ASP* 1.3 73.9 + - - +
277G ILE* 3.2 2.4 + - - +
278G LEU* 3.0 52.1 + - + +
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Residues in contact with ASP 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271G GLN* 3.0 30.4 + - - +
272G TRP* 4.0 8.1 - - - +
274G LYS* 1.3 90.0 + - - +
276G LYS* 1.3 57.7 + - + +
278G LEU* 3.8 3.4 - - - +
279G SER* 2.8 33.6 + - - -
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Residues in contact with LYS 276 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G ILE* 5.7 4.0 - - + -
272G TRP* 3.2 40.4 + - + +
273G LEU* 3.8 10.5 - - + +
274G LYS 3.3 0.4 - - - -
275G ASP* 1.3 76.5 - - + +
277G ILE* 1.3 62.3 + - + +
279G SER* 3.0 20.2 + - - -
281G GLU* 5.3 0.3 - - - +
282G GLY* 3.1 14.4 + - - -
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Residues in contact with ILE 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G ILE* 3.6 29.4 - - + -
255G TYR* 3.5 58.3 - - + -
259G ILE* 4.3 1.3 - - + -
265G ALA* 3.7 20.4 - - + -
273G LEU* 3.0 30.7 + - + +
274G LYS* 3.2 5.1 + - - +
276G LYS* 1.3 77.9 - - - +
278G LEU* 1.3 62.5 + - + +
282G GLY* 3.4 14.3 - - - +
283G ARG* 2.7 40.2 + - - +
286G GLN* 5.3 0.7 - - - +
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Residues in contact with LEU 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258G GLY* 4.4 16.4 - - - -
259G ILE* 3.9 27.1 - - + -
274G LYS* 3.0 42.1 + - + +
275G ASP* 4.3 3.4 - - - +
277G ILE* 1.3 79.1 - - + +
279G SER* 1.3 66.4 + - - +
283G ARG* 3.3 23.2 - - - +
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Residues in contact with SER 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275G ASP 2.8 17.1 + - - -
276G LYS* 3.0 21.8 + - - -
277G ILE 3.4 0.4 - - - -
278G LEU* 1.3 81.8 - - - +
280G GLU* 1.3 66.1 + - - +
281G GLU* 3.8 7.3 + - - +
282G GLY 3.1 6.6 + - - -
283G ARG* 3.0 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