Contacts of the helix formed by residues 236 - 249 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C MET* 3.0 35.6 + - + +
51C TRP* 3.9 14.2 - + - -
231C GLU* 3.3 37.4 - - + +
232C SER* 2.9 35.1 + - - +
235C ILE* 1.3 106.5 - - + +
237C VAL* 1.3 64.7 + - - +
238C GLY 3.2 2.5 - - - -
239C THR* 3.2 14.6 + - - +
240C ILE* 3.0 24.5 + - + +
265C PRO* 5.3 2.9 - - + -
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Residues in contact with VAL 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B GOL 6.1 0.2 - - - +
233C LEU 3.6 22.9 - - - +
234C TRP 5.6 0.4 - - - -
235C ILE 3.5 4.3 + - - +
236C HIS* 1.3 76.9 - - - +
238C GLY* 1.3 56.5 + - - +
240C ILE* 3.3 7.2 + - + +
241C LYS* 2.8 51.0 + - + +
313C PHE* 4.3 11.7 - - + -
314C LEU* 4.1 19.7 - - + -
317C GLU* 3.8 29.8 - - + +
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Residues in contact with GLY 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C HIS 3.2 1.2 - - - -
237C VAL* 1.3 78.6 - - - +
239C THR* 1.4 55.2 + - - +
241C LYS* 3.9 7.6 - - - +
242C ASN* 3.0 37.3 + - - +
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Residues in contact with THR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C PRO* 4.9 9.0 - - + +
208C PHE* 4.7 12.1 - - + -
230C CYS* 5.1 1.8 - - - -
231C GLU* 4.3 20.6 - - + -
236C HIS* 3.2 22.1 + - - +
238C GLY* 1.4 70.3 - - - +
240C ILE* 1.3 70.0 + - - +
242C ASN* 3.1 8.9 + - + +
243C MET* 2.8 44.1 + - + +
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C CYS* 3.5 26.2 - - - +
231C GLU* 5.0 0.7 - - + -
232C SER 3.7 7.2 - - - +
233C LEU* 3.6 28.0 - - + -
236C HIS* 3.0 22.8 + - + +
237C VAL* 3.3 10.7 + - - +
239C THR* 1.3 77.4 - - - +
241C LYS* 1.3 61.9 + - + +
243C MET* 3.9 0.7 - - - +
244C ILE* 2.9 50.5 + - + +
256C TYR* 3.4 32.3 - - + +
314C LEU* 4.5 16.4 - - + -
318C ILE* 5.0 2.0 - - + -
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Residues in contact with LYS 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C VAL* 2.8 44.4 + - + +
238C GLY* 3.9 6.7 - - - +
240C ILE* 1.3 73.6 - - + +
242C ASN* 1.3 68.8 + - - +
245C GLY* 2.9 20.6 + - - -
314C LEU* 6.4 0.2 - - + -
317C GLU* 3.4 37.1 + - + +
318C ILE* 5.3 1.1 - - + -
320C ASN* 4.0 21.9 + - - +
321C ILE* 3.7 31.9 - - + +
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Residues in contact with ASN 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C GLY 3.0 22.9 + - - +
239C THR* 3.1 9.9 + - + +
241C LYS* 1.3 79.6 - - - +
243C MET* 1.3 61.7 + - + +
245C GLY* 3.3 2.6 + - - -
246C TYR* 3.0 56.9 + - + +
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Residues in contact with MET 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C LEU 4.2 0.4 - - - +
208C PHE* 3.9 39.0 - - + +
213C TYR* 3.4 41.8 - - + +
229C GLN 6.1 0.4 - - - +
230C CYS* 3.8 25.8 - - - -
239C THR* 2.8 36.2 + - + +
240C ILE 4.0 0.2 - - - +
242C ASN* 1.3 71.6 - - - +
244C ILE* 1.3 69.0 + - - +
246C TYR* 3.2 26.5 + - + +
247C ALA* 3.0 23.2 + - - +
272C LEU* 4.1 11.3 - - + +
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C CYS* 5.8 0.2 - - - -
240C ILE* 2.9 37.9 + - + +
243C MET* 1.3 79.1 - - - +
245C GLY* 1.3 56.0 + - - +
247C ALA* 3.1 2.4 + - - +
248C LYS* 2.8 49.8 + - + +
254C VAL* 3.9 16.4 - - + +
255C GLU 5.3 0.9 - - - +
256C TYR* 4.3 13.5 - - + -
272C LEU* 3.6 23.8 - - + -
318C ILE* 3.8 34.5 - - + -
321C ILE* 3.5 20.4 - - + -
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Residues in contact with GLY 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LYS 2.9 15.8 + - - -
242C ASN* 3.6 4.9 - - - -
243C MET 3.2 0.2 - - - -
244C ILE* 1.3 76.8 - - - +
246C TYR* 1.4 63.3 + - - +
248C LYS* 3.4 4.9 + - - +
249C LYS* 3.3 29.8 + - - +
321C ILE* 3.9 17.0 - - - +
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Residues in contact with TYR 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C PHE 3.9 5.6 + - - -
209C ASN* 3.6 26.8 - - - +
210C GLN* 3.0 63.2 + - + +
213C TYR* 4.5 11.0 - - + -
242C ASN* 3.0 41.4 + - + +
243C MET* 3.2 32.0 + - + +
245C GLY* 1.4 74.4 - - - +
247C ALA* 1.3 64.9 + - - +
249C LYS* 3.4 8.1 + - - -
250C LEU* 3.8 6.1 - - - +
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Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C TYR* 4.6 8.3 - - + -
243C MET 3.0 17.1 + - - +
244C ILE 3.7 2.0 - - - +
246C TYR* 1.3 77.9 - - - +
248C LYS* 1.3 59.0 + - - +
250C LEU 3.1 3.5 + - - -
251C PHE* 2.8 39.1 + - + +
254C VAL* 3.7 23.6 - - + -
272C LEU* 4.4 5.4 - - + -
274C CYS* 3.7 25.1 - - - -
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Residues in contact with LYS 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ILE* 2.8 36.3 + - + +
245C GLY* 3.9 5.4 - - - +
246C TYR 3.2 0.4 - - - -
247C ALA* 1.3 75.5 - - - +
249C LYS* 1.3 64.4 + - - +
250C LEU 3.1 1.1 + - - -
251C PHE 3.8 10.7 - - - +
254C VAL* 3.8 25.4 - - + +
318C ILE* 5.1 5.7 + - + +
321C ILE* 4.0 29.1 + - + +
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Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C GLN* 3.6 24.0 - - - +
245C GLY 3.3 19.0 + - - +
246C TYR* 3.8 6.5 - - - +
247C ALA 3.3 1.4 - - - -
248C LYS* 1.3 76.6 - - - +
250C LEU* 1.3 63.1 + - + +
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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