Contacts of the helix formed by residues 278 - 286 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245F ARG 3.6 20.6 - - - +
246F LYS* 3.7 21.6 - - - +
274F GLU* 3.1 39.1 + - - +
275F GLY 3.5 3.4 - - - -
277F ARG* 1.3 96.2 - - + +
279F PHE* 1.3 63.2 + - - +
280F ASP* 3.3 3.4 - - - -
281F GLU* 3.2 40.3 + - + +
282F ILE* 3.2 20.2 + - + +
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Residues in contact with PHE 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270F ILE* 4.0 17.5 - - + -
275F GLY 3.1 8.5 + - - +
276F VAL* 3.2 19.5 + - - +
277F ARG 3.3 1.4 + - - -
278F ARG* 1.3 76.9 - - - +
280F ASP* 1.3 56.1 + - - +
282F ILE* 3.1 5.0 + - - +
283F LEU* 2.7 47.9 + - + +
289F ILE* 3.6 29.8 - - + -
311F MET* 4.3 9.0 - - + -
312F MET* 3.4 35.0 - - + -
315F ARG* 3.8 44.0 - - + +
316F CYS* 3.8 24.2 - - - -
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Residues in contact with ASP 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F ARG 5.1 1.3 + - - +
278F ARG 3.3 1.1 - - - -
279F PHE* 1.3 81.5 - - - +
281F GLU* 1.3 62.1 + - - +
283F LEU* 3.4 7.6 + - - +
284F GLU* 3.4 22.0 + - - +
315F ARG* 2.8 39.9 + - - +
318F ARG* 5.0 3.6 + - - -
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Residues in contact with GLU 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F LYS* 3.3 14.9 - - - +
247F ALA* 2.8 38.1 + - + +
248F SER 4.7 0.3 + - - -
278F ARG* 3.2 40.2 + - + +
280F ASP* 1.3 76.8 - - - +
282F ILE* 1.3 64.4 + - - +
284F GLU* 3.9 9.0 + - - +
285F ALA* 3.3 23.4 + - - +
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Residues in contact with ILE 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F ILE* 3.9 12.3 - - + +
245F ARG 3.7 25.6 - - - +
246F LYS* 3.8 21.5 - - - +
247F ALA* 3.9 3.1 - - - +
250F VAL* 4.2 1.6 - - + -
268F SER* 3.8 18.2 - - - -
270F ILE* 4.1 9.9 - - + -
275F GLY* 3.3 31.2 - - - +
278F ARG 3.2 12.0 + - - +
279F PHE* 3.1 7.9 + - - +
281F GLU* 1.3 76.2 - - - +
283F LEU* 1.3 54.3 + - - +
285F ALA* 3.2 6.0 + - - +
286F SER* 2.6 46.3 + - - +
289F ILE* 3.9 9.9 - - + -
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Residues in contact with LEU 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F PHE* 2.7 41.7 + - + +
280F ASP* 3.7 7.6 - - - +
281F GLU 3.3 0.2 - - - -
282F ILE* 1.3 73.9 - - - +
284F GLU* 1.3 58.5 + - - +
286F SER* 3.1 14.9 + - - +
288F GLY 5.4 0.9 - - - -
289F ILE* 3.9 16.6 - - + -
315F ARG* 3.9 26.2 - - + +
316F CYS* 3.6 26.7 - - - -
318F ARG* 6.0 1.3 - - - +
319F ALA* 4.2 11.4 - - + -
321F LYS* 3.0 39.1 + - + +
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Residues in contact with GLU 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F HIS* 5.7 1.6 + - - -
280F ASP 3.4 11.5 + - - +
281F GLU* 4.0 12.1 - - - +
282F ILE 3.5 0.2 - - - -
283F LEU* 1.3 79.3 - - + +
285F ALA* 1.3 65.3 + - - +
321F LYS* 3.3 19.7 + - - +
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Residues in contact with ALA 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F ALA* 4.1 11.9 - - + -
250F VAL* 3.4 17.9 - - + +
251F HIS* 4.0 26.0 + - + +
254F ARG* 2.7 30.0 + - - -
281F GLU 3.3 19.0 + - - +
282F ILE 3.2 4.6 + - - +
283F LEU 3.1 0.4 - - - -
284F GLU* 1.3 85.1 - - - +
286F SER* 1.3 51.3 + - - +
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Residues in contact with SER 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F VAL* 3.6 9.8 - - - +
254F ARG* 4.0 3.4 - - - +
266F ILE 3.7 4.0 - - - -
268F SER* 2.6 28.5 + - - -
282F ILE* 2.6 22.1 + - - +
283F LEU* 3.1 5.8 + - - +
285F ALA* 1.3 79.5 - - - +
287F ASP* 1.3 62.0 + - - +
288F GLY 3.2 23.3 - - - -
289F ILE* 4.4 2.7 - - - -
321F LYS* 2.8 27.5 + - - +
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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