Contacts of the helix formed by residues 236 - 249 (chain B) in PDB entry 3RIE
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 HIS 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B MET* 2.6 35.4 + - + -
51B TRP* 5.9 0.9 - + - -
52B PRO* 5.5 5.2 - - + -
231B GLU* 3.7 28.4 - - + +
232B SER 3.3 5.5 + - - -
235B ILE* 1.3 98.7 + - + +
237B VAL* 1.3 64.6 - - - +
238B GLY 3.2 2.9 - - - +
239B THR* 3.3 18.8 + - - +
240B ILE* 3.2 24.2 + - - +
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B LEU* 3.3 27.4 - - - +
234B TRP 5.7 0.4 - - - -
235B ILE 3.8 3.1 + - - -
236B HIS* 1.3 72.7 - - - +
238B GLY* 1.4 63.6 + - - +
240B ILE* 3.1 9.6 + - + +
241B LYS* 3.0 28.6 + - + +
313B PHE* 4.1 12.1 - - + -
314B LEU* 3.8 23.6 - - + -
317B GLU* 3.8 35.7 - - + -
601C GOL 6.0 1.3 - - - +
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Residues in contact with GLY 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B HIS 3.2 1.4 - - - -
237B VAL* 1.4 77.1 - - - +
239B THR* 1.3 54.9 + - - +
241B LYS* 3.3 12.9 + - - +
242B ASN* 2.9 36.3 + - - +
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Residues in contact with THR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLU* 3.6 29.1 - - + +
236B HIS* 3.3 28.3 + - - +
238B GLY* 1.3 72.4 - - - +
240B ILE* 1.3 60.7 + - - +
242B ASN* 3.2 11.0 + - + +
243B MET* 2.9 47.5 + - + +
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B CYS* 4.6 8.5 - - - -
231B GLU* 4.0 14.4 - - + -
232B SER 3.9 7.4 - - - +
233B LEU* 3.6 27.8 - - + +
236B HIS 3.2 10.5 + - - +
237B VAL* 3.1 15.1 + - + +
239B THR* 1.3 76.4 - - - +
241B LYS* 1.3 54.7 + - - +
243B MET* 3.3 1.7 + - - +
244B ILE* 2.8 60.0 + - + +
256B TYR* 3.4 47.3 - - + +
314B LEU* 4.5 7.0 - - + -
318B ILE* 4.4 9.6 - - + -
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Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B VAL* 3.0 24.2 + - + +
238B GLY* 3.5 13.7 - - - +
240B ILE* 1.3 76.2 - - - +
242B ASN* 1.3 58.9 + - - +
244B ILE* 3.8 6.5 - - - +
245B GLY* 3.0 26.5 + - - -
317B GLU* 3.2 50.1 + - - +
318B ILE* 4.2 14.6 - - + -
319B GLU* 4.9 6.8 + - - -
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Residues in contact with ASN 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B GLY 2.9 21.5 + - - +
239B THR* 3.5 13.3 + - + +
240B ILE 3.2 0.2 - - - -
241B LYS* 1.3 75.7 - - - +
243B MET* 1.3 60.2 + - + +
245B GLY* 3.4 2.9 + - - -
246B TYR* 2.9 52.2 + - + +
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Residues in contact with MET 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B PHE* 3.5 56.8 - - + +
213B TYR* 4.8 15.8 - - + +
230B CYS* 4.0 20.2 - - - -
231B GLU* 5.2 1.8 - - + +
239B THR* 2.9 39.0 + - + +
240B ILE 3.9 2.7 - - - +
242B ASN* 1.3 70.7 - - + +
244B ILE* 1.3 67.4 + - - +
246B TYR* 3.3 17.9 + - - +
247B ALA* 2.9 25.3 + - - +
272B LEU* 3.9 21.4 - - + +
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Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ILE* 2.8 41.0 + - + +
241B LYS* 3.8 4.9 - - - +
243B MET* 1.3 76.5 - - - +
245B GLY* 1.3 52.5 + - - +
247B ALA* 3.2 2.3 + - - +
248B LYS* 2.8 64.7 + - + +
254B VAL* 4.1 14.8 - - + +
255B GLU* 5.7 1.1 - - - -
256B TYR* 4.4 10.5 - - + -
272B LEU* 3.7 23.8 - - + -
318B ILE* 3.9 38.4 - - + +
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Residues in contact with GLY 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LYS 3.0 14.9 + - - -
242B ASN* 3.6 4.5 - - - -
244B ILE* 1.3 75.3 - - - +
246B TYR* 1.3 63.7 + - - +
248B LYS* 3.2 16.1 + - - +
249B LYS* 3.4 20.3 + - - +
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B PHE 3.7 18.6 - - - -
209B ASN* 4.1 4.9 - - - -
210B GLN* 3.5 69.6 + - + +
213B TYR* 5.1 9.6 - + + -
242B ASN* 2.9 38.2 + - + +
243B MET* 3.7 23.1 - - - +
245B GLY* 1.3 72.2 - - - +
247B ALA* 1.3 65.3 + - - +
248B LYS 3.3 0.2 + - - -
249B LYS* 3.3 11.3 + - - +
250B LEU* 4.0 5.1 - - - +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B TYR* 4.5 9.9 - - + -
243B MET 2.9 18.4 + - - +
244B ILE 3.8 2.7 - - - +
246B TYR* 1.3 77.6 - - - +
248B LYS* 1.3 57.1 + - - +
250B LEU* 3.0 3.9 + - - -
251B PHE* 2.7 39.3 + - + +
254B VAL* 3.8 14.4 - - + -
272B LEU* 4.5 5.6 - - + -
274B CYS* 3.8 29.6 - - - -
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Residues in contact with LYS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ILE* 2.8 34.9 + - + +
245B GLY* 3.7 9.0 - - - +
246B TYR 3.1 0.4 - - - -
247B ALA* 1.3 79.2 - - - +
249B LYS* 1.3 60.4 + - - +
250B LEU 3.1 0.6 + - - -
251B PHE 3.8 11.1 - - - +
254B VAL* 3.7 38.5 + - + +
318B ILE 5.5 4.2 + - - -
319B GLU 6.0 3.2 - - - -
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Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLN* 3.8 20.6 - - - +
245B GLY* 3.4 16.3 + - - +
246B TYR* 3.3 8.4 + - - +
247B ALA 3.2 1.2 - - - -
248B LYS* 1.3 75.8 - - - +
250B LEU* 1.3 64.9 + - + +
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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