Contacts of the helix formed by residues 214 - 226 (chain C) in PDB entry 3RCY
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 THR 214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C GLY* 3.5 26.2 - - - +
178C HIS* 3.1 15.3 + - - +
179C MET* 4.3 6.2 + - + +
213C PHE* 1.3 76.5 - - - +
215C THR* 1.3 59.8 + - - +
216C ALA* 3.8 9.4 + - - +
217C GLY* 3.0 20.8 + - - -
218C ALA* 2.8 26.3 + - - +
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Residues in contact with THR 215 (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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214C THR* 1.3 70.4 - - - +
216C ALA* 1.3 65.1 + - - +
218C ALA* 3.3 2.9 + - - +
219C ILE* 3.0 38.2 + - + +
237C VAL* 3.9 12.5 - - - +
244C ALA* 3.3 44.5 + - - +
247C GLN* 3.7 29.2 + - + +
248C VAL* 3.7 6.5 - - + -
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Residues in contact with ALA 216 (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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179C MET* 4.1 18.2 - - + -
214C THR* 3.8 8.0 + - - +
215C THR* 1.3 78.4 - - - +
217C GLY* 1.3 56.6 + - - +
219C ILE* 3.3 10.0 + - - +
220C ARG* 3.1 32.9 + - + +
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Residues in contact with GLY 217 (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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179C MET* 3.6 7.5 - - - -
180C PRO* 3.4 32.5 - - - +
213C PHE* 4.1 4.7 - - - -
214C THR* 3.0 18.6 + - - -
216C ALA* 1.3 74.9 - - - +
218C ALA* 1.3 57.9 + - - +
220C ARG* 3.4 1.1 + - - +
221C LEU* 3.0 30.5 + - - +
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Residues in contact with ALA 218 (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 PHE* 3.6 6.3 - - - +
214C THR 2.8 19.2 + - - +
215C THR 3.3 4.7 + - - +
217C GLY* 1.3 72.3 - - - +
219C ILE* 1.3 58.7 + - - +
222C GLY* 2.8 15.6 + - - -
233C TYR* 2.6 34.0 + - - +
236C PRO* 3.6 26.5 - - + +
237C VAL* 4.0 1.1 - - + -
248C VAL* 3.8 21.1 - - + -
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Residues in contact with ILE 219 (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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215C THR* 3.0 34.6 + - + +
216C ALA* 3.7 7.9 - - - +
218C ALA* 1.3 75.0 - - - +
220C ARG* 1.3 67.0 + - + +
222C GLY* 3.8 0.2 - - - -
223C GLN* 3.0 38.1 + - + +
247C GLN* 4.2 6.3 - - + +
248C VAL* 4.1 13.0 - - - -
251C ALA* 3.6 42.0 - - + +
252C VAL* 3.9 7.4 - - + +
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Residues in contact with ARG 220 (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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179C MET* 3.5 39.9 - - - +
180C PRO* 4.1 7.7 + - + +
182C MET* 3.5 29.9 - - - +
185C ILE* 3.5 24.8 - - + +
216C ALA* 3.1 18.9 + - + +
217C GLY* 3.8 4.5 - - - +
219C ILE* 1.3 75.2 - - + +
221C LEU* 1.3 63.2 + - - +
223C GLN* 3.3 29.6 - - - +
224C ALA* 3.6 8.8 + - - +
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Residues in contact with LEU 221 (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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169C ALA* 3.9 5.8 - - + -
180C PRO* 4.6 5.6 - - + -
184C ASP 4.4 1.8 - - - +
185C ILE* 4.0 30.0 - - + +
188C SER* 3.5 31.0 - - - +
207C PHE* 3.8 24.9 - - + -
213C PHE* 3.5 31.2 - - + -
217C GLY 3.0 17.4 + - - +
220C ARG* 1.3 73.8 - - - +
222C GLY* 1.3 66.1 + - - +
224C ALA* 3.2 14.5 + - - +
225C ILE* 3.4 13.5 + - + +
233C TYR* 3.6 15.0 - - + +
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Residues in contact with GLY 222 (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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218C ALA 2.8 19.6 + - - -
219C ILE 3.3 1.1 + - - -
221C LEU* 1.3 77.6 - - - +
223C GLN* 1.3 61.4 + - - +
225C ILE* 3.2 20.5 + - - +
226C GLU* 3.2 19.0 + - - +
233C TYR* 3.7 17.0 + - - -
252C VAL* 4.1 6.5 - - - -
254C ILE* 3.5 6.3 - - - +
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Residues in contact with GLN 223 (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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219C ILE* 3.0 33.4 + - + +
220C ARG* 3.3 27.8 - - - +
222C GLY* 1.3 75.0 - - - +
224C ALA* 1.3 64.7 + - + +
225C ILE 3.4 0.7 + - - -
226C GLU* 3.6 34.5 + - - +
227C PRO* 3.9 4.7 - - - +
251C ALA 5.7 2.0 - - - +
252C VAL* 4.4 2.9 - - + +
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Residues in contact with ALA 224 (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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185C ILE* 3.6 29.8 - - + -
189C VAL* 3.6 22.3 - - + +
220C ARG 3.9 5.4 - - - +
221C LEU 3.2 10.5 + - - +
222C GLY 3.2 1.4 - - - -
223C GLN* 1.3 83.0 - - + +
225C ILE* 1.3 59.7 + - + +
227C PRO* 3.5 13.2 - - - +
228C TYR* 4.1 4.9 - - - -
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Residues in contact with ILE 225 (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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188C SER* 4.0 29.2 - - - +
189C VAL* 4.3 6.1 - - + +
192C CYS* 3.9 21.3 - - - -
207C PHE* 3.6 42.4 - - + -
221C LEU* 3.7 13.7 - - + +
222C GLY* 3.2 16.8 + - - +
224C ALA* 1.3 78.3 - - - +
226C GLU* 1.3 65.2 + - - +
227C PRO* 3.2 4.0 - - - -
228C TYR* 3.1 20.3 + - - +
230C PRO* 3.4 16.2 - - + +
233C TYR* 4.7 5.4 - - + -
254C ILE* 3.7 17.3 - - + -
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Residues in contact with GLU 226 (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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222C GLY 3.2 11.4 + - - +
223C GLN* 3.7 27.7 - - - +
224C ALA 3.5 0.2 - - - -
225C ILE* 1.3 76.7 - - - +
227C PRO* 1.4 67.5 - - + +
228C TYR 3.0 2.0 + - - -
229C SER* 3.1 14.6 + - - -
230C PRO* 4.0 2.0 - - - +
251C ALA 4.4 1.7 - - - +
252C VAL* 3.4 10.4 - - - +
253C ARG* 2.7 50.2 + - + +
254C ILE* 3.8 21.3 - - + -
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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