Contacts of the helix formed by residues 243 - 253 (chain F) in PDB entry 2R6C
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 243 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377C MET* 4.6 25.5 - - - +
241F GLU 3.8 2.8 + - - -
242F MET* 1.3 79.0 - - - +
244F ALA* 1.3 64.8 - - - +
245F GLN* 3.3 5.7 - - - +
246F GLN* 3.1 29.7 + - - +
247F LEU* 3.3 20.3 + - - +
292F ASP* 4.1 10.8 - - - -
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Residues in contact with ALA 244 (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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239F SER* 4.5 0.2 - - - -
243F SER* 1.3 74.7 - - - +
245F GLN* 1.3 72.4 + - + +
247F LEU* 3.7 5.2 - - - +
248F VAL* 3.3 25.5 + - - +
290F ILE* 3.9 30.0 - - + +
292F ASP* 3.6 34.7 + - + +
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Residues in contact with GLN 245 (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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243F SER* 3.3 4.7 + - - +
244F ALA* 1.3 91.3 - - + +
246F GLN* 1.3 59.3 + - - +
247F LEU 3.1 5.2 - - - -
248F VAL* 3.8 14.2 + - + +
249F MET* 3.5 22.0 + - - +
292F ASP* 5.1 3.0 + - - -
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Residues in contact with GLN 246 (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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376C MET* 3.2 51.5 - - - +
377C MET* 4.8 1.0 + - - +
242F MET* 3.4 30.0 - - - +
243F SER* 3.1 26.0 + - - +
245F GLN* 1.3 77.5 - - - +
247F LEU* 1.3 60.2 + - - +
249F MET* 3.9 21.1 - - + +
250F ARG* 3.5 36.8 + - - +
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Residues in contact with LEU 247 (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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217F THR* 5.6 2.7 - - + -
221F LEU* 3.6 38.4 - - + +
237F ILE* 4.2 12.6 - - + -
239F SER* 3.5 28.7 - - - +
242F MET* 3.7 15.5 - - + -
243F SER 3.3 15.8 + - - +
244F ALA* 3.7 5.2 - - - +
246F GLN* 1.3 79.8 - - - +
248F VAL* 1.3 68.1 + - - +
249F MET 3.4 0.2 - - - -
250F ARG* 3.1 14.5 + - - +
251F MET* 3.3 21.3 + - + +
290F ILE* 4.0 29.8 - - + -
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Residues in contact with VAL 248 (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 ALA 3.3 18.3 + - - +
245F GLN* 3.8 12.7 + - + +
246F GLN 3.6 0.2 - - - -
247F LEU* 1.3 75.6 - - - +
249F MET* 1.3 51.2 + - + +
251F MET* 2.9 15.4 + - + +
252F LEU* 2.7 49.6 + - + -
283F LEU* 4.5 11.9 - - + -
290F ILE* 3.8 20.4 - - + -
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Residues in contact with MET 249 (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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245F GLN 3.5 15.0 - - - +
246F GLN* 3.9 30.7 - - + +
247F LEU 3.4 0.2 - - - -
248F VAL* 1.3 76.8 - - + +
250F ARG* 1.3 60.5 + - - +
252F LEU* 2.8 12.0 + - + -
253F CYS* 2.5 43.3 + - - -
263F LEU* 4.3 25.8 - - + -
264F ARG* 4.5 32.1 - - + +
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Residues in contact with ARG 250 (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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374C ARG* 6.2 1.2 - - - +
376C MET* 5.0 6.7 - - - +
218F ALA* 6.2 1.3 - - - -
221F LEU* 4.3 15.0 - - + +
222F ASN* 5.0 2.4 + - - -
242F MET* 3.5 31.5 - - - +
246F GLN* 3.5 37.4 + - - +
247F LEU 3.1 11.9 + - - +
249F MET* 1.3 82.6 - - + +
251F MET* 1.3 56.2 + - - +
253F CYS* 4.4 5.2 - - - -
254F ALA* 3.6 16.8 + - - +
264F ARG* 4.0 27.6 - - - +
436F ASN* 3.3 36.5 + - - +
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Residues in contact with MET 251 (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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221F LEU* 4.9 17.7 - - + +
224F ALA 6.1 0.2 - - - -
225F GLN* 3.1 48.3 + - + +
237F ILE* 5.3 2.5 - - + -
247F LEU* 3.3 27.1 + - + +
248F VAL* 2.9 24.0 + - + +
250F ARG* 1.3 76.2 - - - +
252F LEU* 1.3 63.6 + - - +
253F CYS 3.4 0.2 - - - -
254F ALA* 3.8 2.5 - - - -
255F GLU* 3.4 7.1 + - - +
283F LEU* 3.9 24.0 - - + +
288F ILE* 3.4 49.1 - - + -
290F ILE* 4.5 1.3 - - + -
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Residues in contact with LEU 252 (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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248F VAL* 2.7 30.1 + - + +
249F MET* 3.5 12.1 - - + +
251F MET* 1.3 72.1 - - - +
253F CYS* 1.3 65.0 + - - +
255F GLU* 3.0 16.9 + - + +
258F ILE* 3.5 19.7 - - + +
263F LEU* 5.0 5.8 - - + -
276F LEU* 3.7 24.2 - - + -
279F ALA* 3.5 41.1 - - + +
280F MET* 3.8 16.6 - - + +
283F LEU* 3.8 17.5 - - + -
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Residues in contact with CYS 253 (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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249F MET* 2.5 39.2 + - - +
250F ARG* 4.3 7.2 - - - +
252F LEU* 1.3 73.0 - - - +
254F ALA* 1.3 57.1 + - - +
255F GLU 3.0 16.1 - - - +
257F ASN* 3.9 2.1 - - - -
258F ILE* 3.4 28.4 + - - +
259F ASN* 3.5 33.9 - - + +
263F LEU* 4.4 12.8 - - - -
264F ARG* 5.2 6.1 - - - -
434F GLU 5.2 0.4 - - - +
435F TYR* 3.3 17.9 - - - +
436F ASN* 4.8 3.6 - - + -
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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