Contacts of the helix formed by residues 274 - 286 (chain G) in PDB entry 3EXF
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 THR 274 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270G VAL* 4.8 5.2 - - + +
273G ARG* 1.3 76.9 - - - +
275G ARG* 1.3 70.4 + - - +
276G GLU* 3.2 21.6 + - - +
277G GLU* 3.2 25.5 + - - +
278G ILE* 3.8 6.9 - - - +
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Residues in contact with ARG 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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270G VAL* 3.2 39.9 - - + +
273G ARG 5.1 0.2 - - - +
274G THR* 1.3 78.6 - - - +
276G GLU* 1.3 57.6 + - - +
278G ILE* 3.4 18.6 + - + +
279G GLN* 2.9 30.4 + - - +
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Residues in contact with GLU 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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274G THR* 3.2 18.5 + - - +
275G ARG* 1.3 77.7 - - - +
277G GLU* 1.3 62.5 + - - +
279G GLN* 3.2 14.3 - - + +
280G GLU* 2.7 52.0 + - - +
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Residues in contact with GLU 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G ARG* 3.1 27.4 + - - +
198G TYR* 2.6 29.2 + - - -
258G TYR* 3.0 21.1 + - + +
273G ARG* 4.5 8.7 - - - +
274G THR* 3.2 16.1 + - - +
276G GLU* 1.3 90.1 + - + +
278G ILE* 1.3 61.5 + - - +
280G GLU* 3.8 4.5 - - - +
281G VAL* 3.1 26.2 + - + +
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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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258G TYR* 3.9 17.3 - - + +
260G TYR* 3.7 39.6 - - + +
269G GLY 4.2 7.0 - - - +
273G ARG* 3.3 37.7 - - + +
274G THR 3.8 13.7 - - - +
275G ARG* 3.4 18.1 + - + +
277G GLU* 1.3 72.7 - - - +
279G GLN* 1.3 59.3 + - - +
281G VAL* 3.4 2.6 + - - +
282G ARG* 3.0 28.8 + - - +
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Residues in contact with GLN 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 ARG 2.9 18.9 + - - +
276G GLU* 3.2 15.7 - - + +
278G ILE* 1.3 76.6 - - - +
280G GLU* 1.3 60.6 - - + +
282G ARG* 3.4 6.9 + - - +
283G SER* 3.0 30.8 + - - +
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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 GLU* 2.7 34.6 + - - +
277G GLU* 3.8 6.1 - - - +
278G ILE 3.1 0.4 - - - -
279G GLN* 1.3 79.6 - - + +
281G VAL* 1.3 60.1 + - + +
282G ARG 3.1 0.4 - - - -
283G SER* 3.3 8.5 + - - +
284G LYS* 2.9 59.6 + - + +
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Residues in contact with VAL 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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197G ARG* 4.5 12.6 - - - +
228G MET* 4.2 14.1 - - + -
258G TYR* 4.0 42.6 - - + -
260G TYR* 4.0 15.3 - - + -
277G GLU* 3.1 20.0 + - + +
278G ILE 3.4 4.2 + - - +
280G GLU* 1.3 76.8 - - + +
282G ARG* 1.3 58.4 + - - +
284G LYS* 5.3 0.4 - - - -
285G SER* 3.0 37.5 + - - +
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Residues in contact with ARG 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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43G ARG* 3.4 28.3 - - - +
47G LEU* 6.2 3.2 - - - +
66G ASP* 5.0 5.1 + - - -
260G TYR* 3.5 48.1 - - + +
278G ILE* 3.0 18.0 + - + +
279G GLN* 3.8 7.9 - - - +
280G GLU 3.1 0.2 - - - -
281G VAL* 1.3 79.6 - - - +
283G SER* 1.3 62.6 + - - +
286G ASP* 3.6 20.9 + - - +
289G MET* 5.1 14.4 - - - +
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Residues in contact with SER 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 GLN* 3.0 22.7 + - - +
280G GLU* 3.3 13.3 + - - +
282G ARG* 1.3 79.0 - - - +
284G LYS* 1.3 67.4 + - - +
285G SER 3.5 0.2 + - - -
286G ASP 4.9 0.9 + - - -
289G MET* 5.7 5.2 - - - +
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Residues in contact with LYS 284 (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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280G GLU* 2.9 47.1 + - + +
281G VAL* 5.3 0.2 - - - -
283G SER* 1.3 77.3 + - - +
285G SER* 1.3 65.5 + - - +
290G LEU* 4.3 8.8 - - - +
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Residues in contact with SER 285 (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 MET* 3.2 29.8 - - - +
281G VAL* 3.0 25.6 + - - +
283G SER 3.3 0.6 + - - -
284G LYS* 1.3 84.5 - - - +
286G ASP* 1.3 69.4 + - - +
287G PRO 3.4 0.2 - - - -
290G LEU* 4.0 21.5 - - - +
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Residues in contact with ASP 286 (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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43G ARG* 2.8 44.2 + - - -
260G TYR* 2.5 30.6 + - - +
282G ARG* 3.6 20.9 + - + +
283G SER 4.9 0.4 + - - -
285G SER* 1.3 77.7 - - - +
287G PRO* 1.4 64.0 - - - +
288G ILE* 3.6 14.1 - - - +
289G MET* 3.7 29.9 + - + +
290G LEU* 2.9 29.9 + - - +
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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