Contacts of the helix formed by residues 212 - 222 (chain E) in PDB entry 5ZR1
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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E GLU* 2.8 21.7 + - + +
209E LEU* 4.2 5.6 - - + +
210E MET 3.1 13.5 - - - +
211E GLU* 1.3 77.0 - - - +
213E SER* 1.3 72.4 + - - +
214E CYS* 3.3 17.2 + - - +
215E LEU* 3.9 1.7 + - - +
216E ARG* 3.4 12.5 + - - +
263E ASP* 4.8 6.4 - - - +
266E TRP* 3.1 37.6 + - + +
267E PRO* 5.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLN* 6.4 2.0 - - - -
211E GLU 3.5 3.8 + - - -
212E ASP* 1.3 78.3 + - - +
214E CYS* 1.3 55.4 + - - +
216E ARG* 3.5 13.7 - - - +
217E LYS* 2.6 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E ASP* 3.3 17.0 + - - +
213E SER* 1.3 78.4 - - - +
215E LEU* 1.3 62.0 + - - +
217E LYS* 4.3 5.3 - - - +
218E ARG* 3.4 17.5 + - - +
267E PRO* 4.0 28.7 - - + -
270E VAL* 3.3 35.8 - - + +
271E SER* 5.1 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E LEU 3.5 24.7 - - - +
210E MET* 4.7 8.1 - - - +
212E ASP 3.9 4.0 + - - +
214E CYS* 1.3 77.6 - - - +
216E ARG* 1.3 63.7 + - - +
217E LYS 3.6 0.2 + - - -
218E ARG 3.7 1.9 + - - -
219E ILE* 3.3 45.1 - - + +
232E PHE* 4.8 14.1 - - + +
235E VAL* 4.5 20.4 - - + -
236E ALA* 5.4 1.1 - - + -
266E TRP* 3.6 29.0 - - + +
270E VAL* 3.7 20.6 - - + +
273E ILE* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E MET 4.2 10.9 + - - +
211E GLU* 3.1 41.2 + - - +
212E ASP 3.4 11.8 + - - +
213E SER* 3.1 18.7 + - - +
215E LEU* 1.3 81.9 - - - +
217E LYS* 1.3 62.9 + - + +
219E ILE* 4.1 4.0 + - - +
220E ILE* 3.9 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E SER* 2.6 40.1 + - - +
214E CYS* 4.3 5.6 - - - +
216E ARG* 1.3 76.7 - - + +
218E ARG* 1.3 64.5 + - - +
220E ILE* 3.3 9.0 - - + +
221E GLU* 3.2 52.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 218 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214E CYS* 3.4 16.0 + - - +
215E LEU 3.7 2.0 + - - +
216E ARG 3.4 0.4 - - - -
217E LYS* 1.3 79.4 - - - +
219E ILE* 1.3 58.9 + - + +
221E GLU* 4.5 5.8 - - - -
222E GLU* 2.6 70.5 + - + +
270E VAL* 3.2 28.6 + - + -
271E SER* 3.3 34.2 + - - +
272E ARG* 4.7 0.6 - - - +
273E ILE* 3.0 36.4 + - + +
274E THR* 4.2 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E LEU* 3.3 41.4 + - + +
216E ARG 4.8 1.8 - - - +
217E LYS 3.4 0.4 - - - -
218E ARG* 1.3 78.1 - - + +
220E ILE* 1.3 64.1 + - + +
222E GLU* 4.6 3.1 - - - -
223E GLN* 3.9 0.5 + - - -
224E ILE* 3.0 46.2 + - - +
225E THR* 4.3 4.8 + - - -
227E CYS* 4.5 13.9 - - + -
232E PHE* 3.5 39.7 - - + -
235E VAL* 6.3 0.2 - - + -
273E ILE* 4.4 17.9 - - + -
278E ILE* 5.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216E ARG* 3.9 15.0 + - + +
217E LYS* 3.3 15.5 - - + +
219E ILE* 1.3 81.7 - - + +
221E GLU* 1.3 73.0 + - + +
223E GLN* 3.5 16.1 + - - +
225E THR* 5.7 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E LYS* 3.2 46.4 + - - +
218E ARG* 3.1 5.8 + - - +
220E ILE* 1.3 83.4 - - + +
222E GLU* 1.3 62.4 + - - +
223E GLN* 3.2 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 222 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E ARG* 2.6 61.6 + - + +
219E ILE* 4.6 2.9 - - - +
220E ILE 3.4 0.2 - - - -
221E GLU* 1.3 72.7 - - - +
223E GLN* 1.3 68.1 + - - +
224E ILE* 3.3 27.4 - - + +
273E ILE 4.6 5.2 - - - +
274E THR* 4.0 19.0 + - + +
----------------------------------------------------------
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