Contacts of the helix formed by residues 209 - 220 (chain C) in PDB entry 4HRE
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 ASP 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C ALA* 3.1 27.9 + - + +
205C ARG* 3.3 21.5 + - - +
208C THR* 1.3 73.0 - - - +
210C VAL* 1.3 65.8 + - - +
211C PRO* 3.8 13.0 - - - +
212C LYS* 2.5 55.7 + - - +
213C TRP* 3.8 2.9 + - - -
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Residues in contact with VAL 210 (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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166C ASP* 3.5 37.9 - - + +
208C THR* 3.7 24.1 + - + +
209C ASP* 1.3 68.4 - - - +
211C PRO* 1.4 68.1 - - + +
212C LYS 3.0 2.5 - - - -
213C TRP* 2.7 29.1 + - + +
214C ILE* 3.1 25.1 + - + -
248C VAL* 4.6 6.3 - - + -
252C LEU* 4.1 19.5 - - + -
256C PHE* 4.3 11.0 - - + -
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Residues in contact with PRO 211 (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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166C ASP* 4.8 5.4 - - - +
169C LYS* 5.3 15.0 - - + +
209C ASP* 3.8 10.8 - - - +
210C VAL* 1.4 93.0 - - + +
212C LYS* 1.3 51.9 + - + +
214C ILE* 3.1 16.0 + - + +
215C SER* 2.4 39.9 + - - -
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Residues in contact with LYS 212 (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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197C GLU* 3.4 37.6 - - + +
201C ALA* 3.8 13.7 - - + +
209C ASP* 2.5 43.1 + - - +
210C VAL 2.9 0.4 + - - -
211C PRO* 1.3 81.2 - - + +
213C TRP* 1.3 61.8 + - + +
215C SER* 3.4 14.8 + - - +
216C ILE* 3.5 21.9 + - - +
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Residues in contact with TRP 213 (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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197C GLU 5.2 0.2 - - - -
198C LEU* 3.0 47.6 + - + +
201C ALA* 4.3 11.0 - - + -
202C GLY* 3.9 25.4 - - - +
208C THR* 4.7 11.2 - - + -
209C ASP 3.8 2.7 + - - -
210C VAL* 2.7 18.2 + - + +
212C LYS* 1.3 75.2 - - + +
214C ILE* 1.3 64.1 + - - +
216C ILE* 3.6 0.7 + - - +
217C MET* 3.1 39.3 + - + +
232C TYR* 5.1 0.7 - - - -
240C MET* 3.9 22.2 - - + -
243C SER* 4.3 4.0 - - - -
244C ILE* 4.0 27.4 - - + -
247C GLU* 3.6 28.7 - - + -
248C VAL* 4.5 13.9 - - + -
256C PHE* 3.8 29.8 - + + -
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Residues in contact with ILE 214 (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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166C ASP 3.9 5.6 - - - +
169C LYS* 3.6 34.8 - - + +
170C LEU* 3.7 16.8 - - + +
173C ALA* 3.8 28.9 - - + -
210C VAL* 3.1 23.3 + - + +
211C PRO* 3.5 13.9 - - + +
213C TRP* 1.3 76.3 - - - +
215C SER* 1.3 64.1 + - - +
217C MET* 5.1 0.2 - - - -
218C THR* 2.9 37.3 + - + +
256C PHE* 3.8 19.7 - - + -
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Residues in contact with SER 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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197C GLU* 6.0 1.3 - - - -
211C PRO* 2.4 27.6 + - - +
212C LYS* 3.4 13.0 + - - +
213C TRP 3.3 0.2 - - - -
214C ILE* 1.3 75.1 - - - +
216C ILE* 1.3 67.0 + - - +
218C THR* 3.5 3.2 + - - -
219C GLU* 2.9 48.6 + - - +
220C ARG* 5.1 0.9 - - - -
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Residues in contact with ILE 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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194C ASP* 3.5 48.7 - - + +
197C GLU* 3.6 29.2 - - + +
198C LEU* 4.0 24.9 - - + +
212C LYS 3.5 13.7 + - - +
213C TRP 4.1 2.9 - - - +
214C ILE 3.4 0.2 - - - -
215C SER* 1.3 81.7 - - - +
217C MET* 1.3 60.3 + - + +
220C ARG* 3.2 48.7 + - + +
225C LEU* 3.7 20.6 - - + +
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Residues in contact with MET 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 ARG* 2.5 34.0 + - - -
198C LEU* 3.6 29.6 - - + -
213C TRP* 3.1 29.2 + - + +
214C ILE* 4.4 0.7 - - - +
216C ILE* 1.3 80.5 - - + +
218C THR* 1.3 53.0 + - + +
225C LEU* 3.6 9.5 - - + +
229C PHE* 4.4 16.2 - - + -
240C MET* 4.0 28.0 - - + -
244C ILE* 5.2 0.9 - - + -
256C PHE* 3.6 28.3 - - + -
259C LEU* 4.0 17.0 - - + +
260C VAL* 4.1 18.8 - - + -
263C ILE* 4.2 3.5 - - + +
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Residues in contact with THR 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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170C LEU* 4.1 7.9 - - + -
173C ALA* 3.9 35.9 - - + +
174C LEU* 3.9 25.7 - - + +
178C ARG 5.0 0.2 - - - -
179C ARG* 3.2 36.2 + - - +
214C ILE* 2.9 28.2 + - + +
215C SER* 3.5 4.0 + - - -
217C MET* 1.3 78.4 - - - +
219C GLU* 1.3 67.4 + - - +
259C LEU* 5.2 0.7 - - + -
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Residues in contact with GLU 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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178C ARG 5.5 1.6 - - - +
179C ARG* 4.7 2.9 - - - +
180C ALA* 2.8 34.8 + - - +
215C SER* 2.9 38.4 + - - +
218C THR* 1.3 77.6 + - - +
220C ARG* 1.3 79.9 + - - +
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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 ARG* 2.3 36.7 + - - +
180C ALA* 4.6 2.5 - - - -
182C ASP* 5.3 2.9 - - - -
190C LEU* 3.7 31.2 - - - +
194C ASP* 3.0 39.9 + - - +
197C GLU* 5.6 2.0 + - - -
215C SER* 4.8 0.8 + - - -
216C ILE* 3.2 35.9 + - + +
219C GLU* 1.3 106.1 + - - +
221C SER* 1.3 60.4 + - - +
224C HIS* 3.8 16.8 - - + -
225C LEU* 3.7 14.5 - - + +
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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