Contacts of the helix formed by residues 211 - 226 (chain C) in PDB entry 5HVO
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 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C PHE* 3.3 5.1 - - - +
210C HIS* 1.3 93.2 - - + +
212C TYR* 1.3 64.0 + - - +
213C ASP* 3.5 6.6 + - - +
214C TYR* 3.2 48.4 + - + +
215C ALA* 3.3 9.4 + - - +
246C ALA* 3.6 8.1 - - - -
248C PRO* 5.9 0.2 - - + -
388C MET* 4.9 2.2 - - + -
413C GLY* 4.3 19.1 - - - +
416C GLN* 3.5 29.2 + - - +
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Residues in contact with TYR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A THR* 3.3 34.5 - - + -
232A PRO* 3.2 34.3 + - + +
233A SER* 2.3 31.7 + - - -
234A SER* 5.4 0.4 - - - -
211C THR* 1.3 74.5 - - - +
213C ASP* 1.3 59.1 + - - +
215C ALA* 3.3 10.0 + - + +
216C ARG* 2.8 30.1 + - - +
232C PRO 5.5 2.5 - - - -
233C SER* 6.0 1.1 - - - -
244C VAL 5.6 0.9 - - - -
245C GLY* 4.7 5.8 - - - -
246C ALA* 3.6 35.6 + - + +
416C GLN* 5.1 1.4 + - - -
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Residues in contact with ASP 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C THR* 3.2 8.5 + - - +
212C TYR* 1.3 78.1 - - - +
214C TYR* 1.3 67.1 + - + +
216C ARG* 3.1 35.4 + - - +
217C HIS* 2.9 28.6 + - - -
416C GLN* 3.1 25.1 + - - +
186D GLU* 4.6 12.3 - - - +
224D HIS* 4.7 7.2 + - - -
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Residues in contact with TYR 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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180C THR 3.9 7.6 - - - -
181C PRO* 3.6 29.5 - - + +
182C PHE* 3.5 36.6 - - - +
209C PHE* 3.8 13.5 - - + -
210C HIS* 3.8 17.3 - - + -
211C THR* 3.2 32.5 + - + +
213C ASP* 1.3 81.8 - - + +
215C ALA* 1.3 63.8 + - - +
217C HIS* 3.2 4.5 + + - +
218C PHE* 3.0 23.6 + - - +
386C ASP 3.1 14.2 + - - -
387C GLY* 2.7 30.6 + - - -
411C PHE 5.0 1.9 + - - -
413C GLY* 3.6 8.8 + - - -
186D GLU* 5.8 1.6 - - - -
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Residues in contact with ALA 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PHE* 3.7 20.3 - - + -
211C THR 3.3 8.3 + - - +
212C TYR* 3.3 17.0 + - + +
213C ASP 3.2 0.2 - - - -
214C TYR* 1.3 80.7 - - - +
216C ARG* 1.3 57.0 + - - +
218C PHE* 3.1 2.8 + - - +
219C LEU* 2.8 38.2 + - + +
244C VAL* 3.8 21.8 - - + -
245C GLY* 4.5 10.5 - - - +
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Residues in contact with ARG 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TYR 2.8 13.3 + - - +
213C ASP* 3.1 36.9 + - - +
215C ALA* 1.3 76.5 - - - +
217C HIS* 1.3 88.6 + - - +
219C LEU* 3.4 10.5 + - - +
220C SER* 3.0 25.1 + - - -
185D SER* 5.5 3.8 + - - -
186D GLU* 4.8 2.2 + - - -
220D SER* 5.5 2.2 + - - -
224D HIS* 3.8 29.4 + - - -
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Residues in contact with HIS 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 4.1 1.6 - - - -
182C PHE* 3.4 20.2 - - + +
183C PRO 3.2 17.9 - - - +
184C SER* 3.5 22.8 - - - +
185C SER 4.6 2.8 + - - +
213C ASP* 2.9 23.5 + - + -
214C TYR* 3.2 7.8 + + - +
216C ARG* 1.3 101.3 + - - +
218C PHE* 1.3 57.4 + - - +
220C SER* 3.4 7.2 + - - -
221C SER* 3.0 31.9 + - - -
184D SER* 5.2 1.3 - - - -
185D SER* 5.6 2.5 - - - -
186D GLU* 2.5 44.9 + - + +
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Residues in contact with PHE 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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154C MET* 6.0 1.8 - - + -
182C PHE* 3.6 24.6 - + + -
198C LEU* 3.6 29.4 - - + -
201C VAL* 4.7 11.7 - - + -
202C LEU* 4.1 11.4 - - + -
207C ILE* 3.8 25.4 - - + -
209C PHE* 3.5 31.0 - + + -
214C TYR 3.0 13.5 + - - +
215C ALA 3.3 8.5 - - - +
217C HIS* 1.3 75.4 - - - +
219C LEU* 1.3 70.1 + - + +
221C SER* 3.3 2.8 + - - -
222C CYS* 3.1 40.8 + - - -
235C VAL* 4.7 0.4 - - + -
244C VAL* 4.0 26.0 - - + -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ALA* 2.8 30.8 + - + +
216C ARG* 3.8 7.4 - - - +
218C PHE* 1.3 76.4 - - + +
220C SER* 1.3 64.2 + - - +
222C CYS* 3.2 6.1 + - - +
223C SER* 3.0 19.6 + - - -
230C THR* 3.7 21.1 - - - +
231C THR 3.5 17.7 - - - +
232C PRO* 3.7 20.4 - - + +
233C SER* 4.2 1.3 - - - +
234C SER 3.7 23.1 - - - +
235C VAL* 4.0 11.2 - - + -
244C VAL* 3.8 30.5 - - + -
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Residues in contact with SER 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C SER* 3.9 14.7 + - - -
216C ARG* 3.0 19.0 + - - -
217C HIS* 3.6 9.0 - - - -
219C LEU* 1.3 78.8 - - - +
221C SER* 1.3 57.2 + - - +
223C SER* 3.2 8.8 + - - -
224C HIS* 2.9 45.5 + - - -
216D ARG* 5.7 2.1 + - - -
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Residues in contact with SER 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C PHE* 3.6 15.3 - - - -
185C SER* 3.5 25.9 - - - -
188C TYR* 3.9 22.6 - - - +
198C LEU* 4.0 8.7 - - - -
217C HIS 3.0 18.0 + - - -
218C PHE 3.3 5.4 + - - -
220C SER* 1.3 73.5 + - - +
222C CYS* 1.3 58.6 + - - +
224C HIS* 4.6 0.9 - - - +
225C LEU* 2.8 44.1 + - - +
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Residues in contact with CYS 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C LEU* 4.3 12.3 - - - -
202C LEU* 4.1 22.9 - - - -
218C PHE* 3.1 49.8 + - - -
219C LEU* 3.4 9.6 - - - +
221C SER* 1.3 76.3 - - - +
223C SER* 1.3 51.5 + - - +
226C LEU* 2.6 43.0 + - - +
228C LEU* 3.7 9.4 + - + +
230C THR* 4.5 0.4 - - + -
235C VAL* 4.2 18.8 - - + -
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Residues in contact with SER 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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229B VAL* 4.7 15.9 - - - +
219C LEU 3.0 13.8 + - - -
220C SER* 3.2 10.9 + - - -
222C CYS* 1.3 77.6 - - - +
224C HIS* 1.3 72.3 + - - +
226C LEU 2.5 16.7 - - - +
227C GLY* 4.1 2.9 - - - -
228C LEU 3.4 25.3 + - - -
230C THR* 4.1 9.8 - - - +
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Residues in contact with HIS 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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231B THR* 5.4 10.0 - - + +
185C SER* 4.8 9.5 + - - +
220C SER* 2.9 36.2 + - - +
221C SER* 4.4 3.1 - - - +
223C SER* 1.3 92.5 + - - +
225C LEU* 1.3 68.8 + - + +
226C LEU 4.1 0.9 - - - +
213D ASP* 5.1 4.9 + - - -
216D ARG* 4.4 26.4 + - - -
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Residues in contact with LEU 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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185C SER* 5.8 2.0 - - - +
188C TYR* 3.7 32.5 - - + -
189C ARG* 4.2 22.0 - - + +
194C ARG* 3.7 50.0 - - + +
195C GLY* 5.8 1.8 - - - -
198C LEU* 4.0 7.6 - - + -
221C SER* 2.8 29.0 + - - +
224C HIS* 1.3 80.2 - - + +
226C LEU* 1.3 64.8 + - + +
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Residues in contact with LEU 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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195C GLY* 4.5 14.6 - - - -
198C LEU* 4.0 21.8 - - + -
199C ARG* 4.2 31.4 - - + +
202C LEU* 3.8 29.2 - - + -
222C CYS* 2.6 15.7 + - - +
223C SER 2.5 29.8 - - - +
224C HIS 3.8 0.8 - - - +
225C LEU* 1.3 86.3 - - + +
227C GLY* 1.3 53.7 + - - +
228C LEU* 2.9 19.9 + - + -
237C TYR* 5.0 4.5 - - + -
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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