Contacts of the helix formed by residues 213 - 224 (chain C) in PDB entry 5DQZ
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 LEU 213 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ARG* 3.6 53.6 - - - +
188C TYR* 5.3 4.7 - - + -
192C GLU* 4.0 16.8 - - - +
202C PRO* 3.3 9.9 - - + -
211C LYS* 3.1 2.0 - - - +
212C PRO* 1.3 92.4 - - + +
214C SER* 1.3 59.1 + - - +
215C PHE 3.4 0.2 - - - -
216C VAL* 3.0 21.4 + - + -
217C TYR* 2.8 61.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PRO 3.1 3.0 + - - -
203C ALA 3.5 15.4 + - - -
205C GLY* 3.7 7.6 - - - -
208C HIS* 3.3 20.7 - - - +
209C THR* 3.5 3.4 + - - -
210C GLY 3.5 6.6 + - - -
211C LYS* 2.7 37.7 + - - +
213C LEU* 1.3 75.2 - - - +
215C PHE* 1.3 58.2 + - - +
217C TYR* 3.0 16.7 + - - +
218C ASP* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 3.4 18.4 - - - -
119C MET* 4.2 6.5 - - + -
195C ILE* 3.6 24.9 - - + -
200C TYR* 4.2 11.7 - + + -
201C ALA 3.8 6.7 - - - +
202C PRO* 2.9 13.9 + - + +
204C ILE 3.3 21.1 - - - +
205C GLY* 3.9 3.1 - - - -
206C PHE* 3.8 27.1 - + - -
214C SER* 1.3 75.1 - - - +
216C VAL* 1.3 65.1 + - - +
218C ASP* 3.2 7.4 + - + +
219C ILE* 3.0 54.9 + - + +
268C ILE* 4.1 21.1 - - + -
271C VAL* 5.0 0.7 - - + -
272C LEU* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C TYR* 3.9 43.3 - - + +
191C THR* 4.0 8.7 - - - +
192C GLU* 4.2 12.3 - - + +
195C ILE* 3.6 18.6 - - + +
202C PRO* 3.7 27.1 - - + -
213C LEU* 3.0 30.3 + - + +
215C PHE* 1.3 77.5 - - - +
217C TYR* 1.3 57.5 + - + +
220C ALA* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C TYR* 3.6 42.4 - + - +
208C HIS* 3.5 35.2 - + + +
211C LYS* 4.2 23.2 - - + +
212C PRO* 6.0 0.9 - - - +
213C LEU* 2.8 50.9 + - + +
214C SER* 3.0 11.4 + - - +
216C VAL* 1.3 77.7 - - - +
218C ASP* 1.3 63.0 + - - +
221C ASP* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C MET* 3.7 22.4 - - + +
205C GLY* 3.6 3.6 - - - -
206C PHE* 2.6 36.1 + - - +
207C VAL* 3.1 14.6 + - - +
208C HIS* 3.0 35.3 + - - -
214C SER 3.0 14.5 + - - +
215C PHE* 3.2 10.9 + - + +
217C TYR* 1.3 77.6 - - - +
219C ILE* 1.3 63.4 + - - +
221C ASP* 3.2 4.7 + - - +
222C ILE* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C MET* 5.0 1.6 - - + -
191C THR* 3.8 20.4 - - + -
195C ILE* 4.2 5.2 - - + -
215C PHE* 3.0 44.2 + - + +
218C ASP* 1.3 80.4 - - - +
220C ALA* 1.3 64.1 + - - +
222C ILE* 3.1 34.7 + - + +
223C ILE* 3.7 7.1 + - - +
264C LEU* 4.1 8.3 - - + -
267C LEU* 3.8 19.8 - - + +
268C ILE* 3.9 34.5 - - + -
271C VAL* 4.4 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LEU* 3.7 18.2 - - + +
188C TYR* 3.4 33.2 - - + -
191C THR* 4.1 12.1 - - + +
216C VAL 2.9 20.2 + - - +
217C TYR 4.1 0.2 - - - +
219C ILE* 1.3 79.2 - - - +
221C ASP* 1.3 58.5 + - - +
223C ILE* 3.1 5.8 + - - +
224C LYS* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ARG* 3.1 41.0 + - - +
141C GLU* 3.7 9.5 - - - +
188C TYR* 4.0 9.0 + - - -
208C HIS* 3.2 26.5 + - + -
217C TYR* 2.9 25.0 + - - +
218C ASP* 3.6 5.4 - - - +
220C ALA* 1.3 75.6 - - - +
222C ILE* 1.3 62.5 + - - +
223C ILE 3.4 0.2 + - - -
224C LYS* 3.2 40.1 + - - +
225C PHE* 4.7 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C MET* 3.9 32.5 - - + +
122C LEU* 4.1 22.8 - - + +
123C ARG* 3.8 27.4 - - + +
218C ASP 3.1 14.2 + - - +
219C ILE* 3.2 21.3 - - + +
220C ALA 3.1 0.8 - - - -
221C ASP* 1.3 80.7 - - + +
223C ILE* 1.3 68.1 + - + +
225C PHE 5.5 0.3 + - - -
226C ASP* 3.7 12.8 - - - +
267C LEU* 4.3 13.5 - - + -
271C VAL* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LEU* 3.9 25.6 - - + -
191C THR* 5.2 0.7 - - - +
219C ILE 4.1 6.3 - - - +
220C ALA* 3.1 8.3 + - - +
222C ILE* 1.3 92.3 - - + +
224C LYS* 1.3 67.3 + - - +
225C PHE 3.3 2.2 - - - -
226C ASP* 3.1 15.2 + - + +
227C THR* 2.9 38.0 + - - +
260C THR* 4.1 21.5 - - + -
264C LEU* 4.3 17.3 - - + -
267C LEU* 4.3 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ARG* 5.2 0.4 - - - +
149C TYR* 5.0 6.3 + - - -
180C ILE* 6.3 0.4 - - + -
184C THR* 4.2 26.6 + - + +
187C LEU* 3.7 15.3 - - + -
188C TYR* 4.0 11.8 + - + +
220C ALA 2.9 16.7 + - - +
221C ASP* 3.2 35.5 + - - +
222C ILE 3.7 1.6 - - - -
223C ILE* 1.3 75.7 - - - +
225C PHE* 1.3 83.2 + - + +
227C THR 3.3 0.5 + - - -
228C VAL* 3.0 31.9 + - + +
229C VAL* 3.3 27.9 + - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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