Contacts of the helix formed by residues 211 - 218 (chain C) in PDB entry 5E9W
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 211 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LYS* 2.7 44.8 + - - +
184C ILE* 4.2 7.2 - - + +
203C ASP* 4.0 15.3 + - - +
206C CYS 5.4 1.2 + - - -
209C GLY 3.1 1.0 - - - -
210C GLY* 1.3 75.0 - - - +
212C LEU* 1.3 64.9 + - - +
213C LEU 3.3 3.4 - - - -
214C LYS* 2.9 40.3 + - + +
215C TRP* 3.1 31.3 + - - +
282C SER* 4.7 1.7 + - - -
284C GLN* 3.6 14.9 - - - +
501C SAH 4.1 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ASP* 6.2 0.2 - - - +
209C GLY* 3.1 28.9 + - - +
211C ASP* 1.3 76.7 - - - +
213C LEU* 1.3 58.7 + - + +
215C TRP* 3.1 9.5 + - - +
216C LYS* 2.9 26.3 + - - +
223C LEU* 3.8 24.9 - - + -
225C CYS* 4.1 13.9 - - - -
236C CYS* 3.6 26.2 - - - +
239C ARG* 3.7 22.2 - - + -
240C TYR* 3.7 18.4 - - + +
243C MET* 3.9 14.1 - - - -
253C PHE* 3.7 14.8 - - + -
257C PHE* 5.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C GLY 5.1 2.7 - - - +
210C GLY 5.0 7.2 + - - +
211C ASP 3.3 0.6 - - - -
212C LEU* 1.3 76.5 - - + +
214C LYS* 1.3 60.9 + - + +
216C LYS* 3.3 4.3 + - + +
217C LYS* 2.9 34.5 + - + +
239C ARG* 5.1 14.1 - - - +
243C MET* 3.2 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C ASN* 2.6 53.4 + - - -
180C LYS* 4.0 5.2 - - + -
181C SER* 3.4 27.4 - - - +
184C ILE* 4.1 21.5 - - + +
188C LEU* 4.7 4.0 - - - +
210C GLY 2.9 17.1 + - - +
211C ASP* 2.9 37.6 + - - +
213C LEU* 1.3 79.6 - - + +
215C TRP* 1.3 58.5 + - - +
217C LYS* 3.5 3.8 + - - +
218C GLY* 3.0 23.4 + - - -
415C MET* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ILE* 3.5 42.8 - - + -
188C LEU* 3.9 17.5 - - + -
201C VAL* 3.6 29.8 - - + -
203C ASP* 3.8 17.8 + - - -
211C ASP* 3.1 30.8 + - + +
212C LEU 3.1 6.3 + - - +
214C LYS* 1.3 74.3 - - - +
216C LYS* 1.3 65.8 + - - +
218C GLY* 3.2 1.6 + - - +
219C ARG 3.2 14.9 + - - -
220C ILE* 3.4 47.6 + - + +
223C LEU* 4.0 20.5 - - + +
253C PHE* 3.7 9.4 - - + -
280C ILE* 4.3 13.0 - - + -
282C SER* 3.5 28.3 - - - -
315C ILE* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C LEU 2.9 13.8 + - - +
213C LEU* 3.6 12.6 - - + +
214C LYS 3.2 0.2 - - - -
215C TRP* 1.3 78.7 - - - +
217C LYS* 1.3 73.9 - - + +
219C ARG* 3.1 22.4 + - - +
243C MET* 3.7 31.6 - - + -
244C LYS* 6.4 0.2 - - - +
249C SER* 5.2 4.3 - - - -
250C GLU* 4.5 26.1 - - - +
251C TYR 4.2 22.8 + - - +
252C ILE* 3.8 18.8 - - + +
253C PHE* 3.5 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C LEU* 2.9 19.1 + - + +
214C LYS* 4.2 3.6 - - - +
216C LYS* 1.3 90.5 - - + +
218C GLY* 1.3 58.6 + - - +
219C ARG* 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LEU* 3.5 28.0 - - - +
192C ARG* 2.6 41.3 + - - -
214C LYS 3.0 11.5 + - - -
215C TRP 3.2 2.6 + - - -
216C LYS 3.2 0.6 - - - -
217C LYS* 1.3 76.8 - - - +
219C ARG* 1.3 56.3 + - - +
220C ILE* 3.3 3.0 + - - +
----------------------------------------------------------
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