Contacts of the helix formed by residues 212 - 225 (chain C) in PDB entry 1Z6Z
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 212 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LYS* 3.8 49.3 + - + +
210C SER* 3.4 1.7 - - - +
211C VAL* 1.3 78.1 - - - +
213C PRO* 1.4 69.4 - - - +
214C ASP* 3.4 16.7 + - - +
215C MET* 3.1 33.0 + - + +
216C ARG* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C VAL 3.3 9.6 - - - +
212C ASP* 1.4 91.6 - - - +
214C ASP* 1.3 58.2 + - - +
216C ARG* 3.9 29.1 - - + +
217C LYS* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ASP* 3.1 17.4 + - - +
213C PRO* 1.3 80.3 - - - +
215C MET* 1.3 61.4 + - - +
217C LYS* 3.7 4.9 + - - +
218C GLY* 3.0 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C PHE* 4.1 37.0 - - + -
162C LYS* 5.3 4.7 - - + +
164C TRP* 4.1 34.3 - - + +
210C SER* 4.3 9.4 - - - +
212C ASP* 3.1 28.3 + - + +
214C ASP* 1.3 78.6 - - - +
216C ARG* 1.3 59.1 + - - +
218C GLY* 3.2 4.4 + - - -
219C LEU* 2.9 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ALA 5.0 0.9 - - - -
207C ARG 3.7 18.6 - - - +
208C GLU* 3.7 23.8 - - - +
209C THR 4.5 0.4 - - - -
210C SER* 2.7 50.7 + - - +
211C VAL* 3.3 17.6 + - - +
212C ASP 3.1 9.4 + - - +
213C PRO* 3.9 26.6 - - - +
214C ASP 3.5 0.2 - - - -
215C MET* 1.3 74.4 - - - +
217C LYS* 1.3 57.2 + - - +
219C LEU* 3.4 4.4 + - - +
220C GLN* 3.0 43.6 + - - +
----------------------------------------------------------
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 PRO 3.0 18.7 + - - +
214C ASP* 4.0 6.1 - - - +
216C ARG* 1.3 75.1 - - - +
218C GLY* 1.3 58.3 + - - +
220C GLN* 3.2 12.4 + - - +
221C GLU* 2.9 40.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
214C ASP 3.0 16.3 + - - -
215C MET* 3.2 6.7 + - - -
217C LYS* 1.3 77.2 - - - +
219C LEU* 1.3 57.5 + - - +
221C GLU* 3.3 17.0 + - - +
222C LEU* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C TRP* 4.0 20.2 - - + -
197C PRO* 6.2 0.2 - - + -
203C GLN* 3.4 24.9 - - - +
206C ALA* 3.6 44.0 - - + +
207C ARG* 3.6 23.0 + - + +
215C MET* 2.9 31.7 + - + +
216C ARG 3.8 3.4 - - - +
218C GLY* 1.3 74.5 - - - +
220C GLN* 1.3 64.7 + - - +
222C LEU* 3.3 19.8 + - + +
223C LYS* 3.2 17.3 + - - +
228C LEU* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ARG* 3.1 44.4 + - + +
208C GLU* 5.1 2.6 - - - +
216C ARG* 3.0 29.4 + - - +
217C LYS* 3.6 10.3 - - - +
219C LEU* 1.3 73.4 - - - +
221C GLU* 1.3 65.5 + - - +
223C LYS* 3.4 3.0 + - - +
224C ALA* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LYS* 2.9 21.8 + - + +
218C GLY* 3.3 16.1 - - - +
220C GLN* 1.3 76.9 - - - +
222C LEU* 1.3 62.8 - - - +
224C ALA* 4.1 4.4 - - - +
225C LYS* 2.9 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C PRO* 4.0 20.2 - - + -
218C GLY 3.0 13.1 + - - +
219C LEU* 3.3 29.2 - - + +
220C GLN 3.2 0.2 - - - -
221C GLU* 1.3 78.4 - - - +
223C LYS* 1.3 62.0 + - - +
225C LYS* 4.0 1.3 - - - -
226C GLY 3.3 1.9 + - - -
227C LYS* 3.1 60.2 + - + +
228C LEU* 3.7 23.4 + - + -
256C TYR* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ASP* 4.7 14.1 - - - +
207C ARG* 3.9 35.5 - - - +
219C LEU 3.2 8.8 + - - +
220C GLN* 3.4 7.4 + - - +
222C LEU* 1.3 77.9 - - - +
224C ALA* 1.3 62.7 + - - +
226C GLY* 3.1 14.6 + - - -
228C LEU* 3.8 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C GLN 3.0 17.7 + - - +
221C GLU* 4.1 4.5 - - - +
223C LYS* 1.3 78.5 - - - +
225C LYS* 1.3 60.8 + - + +
226C GLY* 3.1 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C GLU* 2.9 60.2 + - - +
222C LEU* 4.2 4.0 - - - +
223C LYS 3.4 0.2 - - - -
224C ALA* 1.3 77.4 - - + +
226C GLY* 1.3 61.1 + - - +
227C LYS* 3.3 26.9 - - + -
----------------------------------------------------------
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