Contacts of the helix formed by residues 271 - 283 (chain G) in PDB entry 2EG5
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 SER 271 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228G CYS* 4.5 0.9 - - - -
229G LYS* 4.1 26.0 - - - +
269G ILE 4.1 0.2 + - - -
270G PRO* 1.3 76.8 - - - +
272G ALA* 1.3 65.8 + - - +
273G GLU* 3.6 17.7 + - - +
274G GLU* 3.1 43.7 + - - +
275G VAL* 3.2 12.5 + - - +
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Residues in contact with ALA 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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228G CYS* 4.3 9.8 - - - +
229G LYS 5.6 0.4 + - - -
270G PRO 4.0 0.6 + - - -
271G SER* 1.3 72.0 - - - +
273G GLU* 1.3 70.2 + - - +
275G VAL* 3.3 4.8 + - - +
276G LYS* 3.1 23.7 + - - +
290G LEU* 4.9 7.2 - - + +
292G THR* 4.0 20.9 - - + -
359G LEU* 3.8 27.9 - - + +
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Residues in contact with GLU 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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271G SER* 3.6 19.7 + - - +
272G ALA* 1.3 83.9 + - - +
274G GLU* 1.3 56.5 + - + +
276G LYS* 3.4 9.2 + - + +
277G CYS* 3.0 32.0 + - - +
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Residues in contact with GLU 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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198G LEU* 3.7 27.8 - - + +
201G PHE* 5.2 2.0 - - + -
229G LYS* 4.2 6.2 - - - -
268G TYR* 2.6 30.9 + - - -
270G PRO* 3.4 9.0 - - + +
271G SER* 3.1 37.1 + - - +
273G GLU* 1.3 73.1 - - + +
275G VAL* 1.3 67.3 + - - +
277G CYS* 4.0 5.8 - - - +
278G ILE* 3.1 32.4 + - + +
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Residues in contact with VAL 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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201G PHE* 4.2 8.7 - - + -
205G PHE* 3.7 25.9 - - + -
226G CYS* 5.2 7.4 - - + -
228G CYS* 5.7 1.1 - - + -
270G PRO* 3.6 31.4 - - + -
271G SER 3.2 7.4 + - - +
272G ALA 3.7 7.4 - - - +
274G GLU* 1.3 77.1 - - - +
276G LYS* 1.3 58.0 + - - +
278G ILE* 3.3 2.3 + - - +
279G VAL* 3.0 35.5 + - + +
290G LEU* 6.3 0.2 - - + -
359G LEU* 4.1 34.3 - - + -
361G ILE* 4.6 11.2 - - + -
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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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272G ALA 3.1 16.6 + - - +
273G GLU* 3.7 8.3 - - + +
275G VAL* 1.3 78.0 - - - +
277G CYS* 1.3 59.3 + - - +
279G VAL* 3.5 7.8 + - - +
280G GLU* 2.9 57.8 + - - +
287G ILE* 4.0 21.4 - - + +
290G LEU* 4.1 23.5 - - + +
361G ILE* 5.2 0.9 - - - -
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Residues in contact with CYS 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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273G GLU 3.0 18.4 + - - +
274G GLU* 4.0 6.5 - - - +
276G LYS* 1.3 78.1 - - - +
278G ILE* 1.3 60.0 + - - +
280G GLU* 3.2 12.1 + - - +
281G GLU* 2.8 32.1 + - - +
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Residues in contact with ILE 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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198G LEU* 5.4 1.6 - - + -
201G PHE* 3.5 35.7 - - + -
202G THR* 3.7 29.8 - - + +
205G PHE* 3.6 20.2 - - + -
206G THR* 3.5 26.5 - - - +
209G LEU* 4.3 4.5 - - + -
274G GLU* 3.1 21.0 + - + +
275G VAL 3.7 3.4 - - - +
277G CYS* 1.3 76.9 - - - +
279G VAL* 1.3 65.4 + - - +
281G GLU* 4.2 6.3 - - + -
282G GLU* 2.9 24.6 + - - +
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Residues in contact with VAL 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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205G PHE* 3.9 19.7 - - + -
209G LEU* 3.8 16.8 - - + -
275G VAL* 3.0 20.8 + - + +
276G LYS 3.7 6.7 - - - +
278G ILE* 1.3 75.6 - - - +
280G GLU* 1.3 63.6 + - - +
282G GLU* 3.9 3.3 - - - +
283G GLY* 3.2 18.2 + - - -
284G SER 4.9 0.2 + - - -
285G PHE* 4.1 23.5 + - + +
287G ILE* 3.7 27.8 - - + -
361G ILE* 4.2 19.1 - - + -
363G LEU* 4.2 13.9 - - + -
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Residues in contact with GLU 280 (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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276G LYS* 2.9 49.1 + - - +
277G CYS* 3.7 9.0 - - - +
279G VAL* 1.3 77.7 - - + +
281G GLU* 1.3 62.2 + - - +
283G GLY* 3.4 13.4 + - - -
285G PHE 5.5 2.2 - - - -
287G ILE* 4.1 14.5 - - + +
366G LYS* 5.7 0.9 + - - -
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Residues in contact with GLU 281 (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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210G ARG* 5.3 0.5 + - - -
277G CYS* 2.8 20.2 + - - +
278G ILE* 3.7 8.1 - - + +
280G GLU* 1.3 77.0 - - - +
282G GLU* 1.3 66.9 + - - +
283G GLY* 3.3 1.2 + - - -
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Residues in contact with GLU 282 (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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206G THR* 3.2 35.3 - - + +
209G LEU* 3.6 25.8 - - + -
210G ARG* 2.7 65.0 + - - +
278G ILE* 2.9 17.7 + - - +
279G VAL 3.9 3.6 - - - +
281G GLU* 1.3 77.5 - - - +
283G GLY* 1.3 57.3 + - - +
284G SER* 2.3 41.4 + - - +
285G PHE* 5.0 2.0 - - + -
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Residues in contact with GLY 283 (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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279G VAL 3.2 13.1 + - - -
280G GLU* 3.7 12.6 - - - -
281G GLU 3.2 2.3 - - - -
282G GLU* 1.3 75.3 - - - +
284G SER* 1.3 60.8 + - - +
285G PHE 3.3 3.7 + - - -
366G LYS* 3.6 28.7 + - - +
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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