Contacts of the helix formed by residues 278 - 286 (chain G) in PDB entry 3SRF
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 ARG 278 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245G ARG 4.2 6.7 - - - +
246G LYS* 3.8 26.0 - - - +
274G GLU* 3.1 45.7 + - - +
275G GLY 3.7 3.8 - - - -
277G ARG* 1.3 91.4 - - + +
279G PHE* 1.3 62.9 + - - +
280G ASP* 3.3 3.4 - - - -
281G GLU* 3.3 43.5 + - + +
282G ILE* 3.3 17.1 - - - +
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Residues in contact with PHE 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 4.3 11.0 - - + -
275G GLY 3.3 10.6 + - - +
276G VAL* 3.5 16.8 + - - +
277G ARG 3.5 1.8 + - - -
278G ARG* 1.3 76.4 - - - +
280G ASP* 1.3 61.8 + - - +
282G ILE* 3.3 4.0 + - + +
283G LEU* 2.8 43.6 + - + +
289G ILE* 3.6 29.8 - - + -
311G MET* 4.3 8.7 - - + -
312G MET* 3.6 36.8 - - + -
315G ARG* 3.7 45.1 - - + +
316G CYS* 3.7 25.4 - - - -
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Residues in contact with ASP 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G ARG* 3.3 1.1 - - - -
279G PHE* 1.3 79.9 - - - +
281G GLU* 1.3 61.6 + - - +
283G LEU* 3.6 7.8 + - - +
284G GLU* 3.3 23.1 + - - +
315G ARG* 2.7 41.4 + - - +
318G ARG* 5.3 2.3 + - - -
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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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246G LYS* 3.3 16.5 - - - +
247G ALA* 2.9 39.2 + - + +
278G ARG* 3.3 37.4 + - + +
280G ASP* 1.3 75.6 - - - +
282G ILE* 1.3 67.0 + - - +
284G GLU* 2.9 31.8 - - + +
285G ALA* 3.2 11.8 + - - +
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Residues in contact with ILE 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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244G ILE* 3.8 27.8 - - + +
245G ARG 3.3 30.1 - - - +
246G LYS* 3.8 21.5 - - - +
247G ALA* 4.2 1.1 - - - +
250G VAL* 4.1 6.1 - - + -
268G SER* 3.9 1.6 - - - -
270G ILE* 3.9 7.9 - - + -
275G GLY* 3.7 17.9 - - - +
278G ARG 3.3 14.6 - - - +
279G PHE* 3.3 8.8 + - - +
281G GLU* 1.3 78.2 - - + +
283G LEU* 1.3 59.6 + - - +
285G ALA* 3.4 1.6 + - - +
286G SER* 2.7 37.4 + - - +
289G ILE* 3.9 20.0 - - + -
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Residues in contact with LEU 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G PHE* 2.8 37.8 + - + +
280G ASP* 3.8 7.9 - - - +
282G ILE* 1.3 77.6 - - - +
284G GLU* 1.3 52.0 + - - +
286G SER* 3.2 11.5 + - - +
288G GLY 5.3 1.1 - - - -
289G ILE* 3.7 17.0 - - + +
315G ARG* 3.7 26.5 - - + +
316G CYS* 3.7 26.2 - - - -
319G ALA* 4.0 11.9 - - + -
321G LYS* 2.8 51.5 + - + +
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Residues in contact with GLU 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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247G ALA* 4.7 4.0 - - - +
251G HIS* 5.5 2.1 - - - -
280G ASP 3.3 12.8 + - - +
281G GLU* 2.9 28.7 - - + +
283G LEU* 1.3 78.2 - - - +
285G ALA* 1.3 67.7 + - - +
321G LYS* 3.6 13.6 + - - +
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Residues in contact with ALA 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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247G ALA* 4.4 7.9 - - + -
250G VAL* 3.4 23.1 - - + +
251G HIS* 4.3 22.9 + - + -
254G ARG* 2.8 21.1 + - - -
281G GLU 3.2 17.5 + - - +
282G ILE 4.0 2.9 - - - +
284G GLU* 1.3 85.5 - - - +
286G SER* 1.3 59.8 + - - +
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Residues in contact with SER 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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250G VAL* 3.2 13.0 - - - +
254G ARG* 3.8 4.9 - - - +
266G ILE 4.0 3.6 - - - -
268G SER* 2.6 30.0 + - - -
282G ILE 2.7 21.8 + - - -
283G LEU* 3.2 5.0 + - - +
285G ALA* 1.3 80.2 - - - +
287G ASP* 1.3 63.5 + - - +
288G GLY 3.4 16.2 - - - -
289G ILE* 4.5 2.2 - - - -
321G LYS* 2.8 28.4 + - - +
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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