Contacts of the helix formed by residues 221 - 237 (chain E) in PDB entry 3IZ0
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 HIS 221 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E GLU* 3.1 30.2 + - + +
214E GLU* 5.1 0.2 - - - +
220E MET* 1.3 93.4 + - + +
222E ASN* 1.3 59.3 + - - +
223E LYS 3.2 3.4 - - - -
224E LEU* 2.9 29.7 + - + +
225E PHE* 3.1 9.2 + - - +
257E LEU* 3.9 33.4 - - + +
258E PHE* 4.3 17.4 - + - -
138F TYR* 3.4 9.0 + - - +
142F LEU* 4.0 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 222 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E GLY 3.6 6.9 + - - +
213E GLU 2.8 25.7 + - - +
214E GLU* 4.1 1.1 - - - +
215E THR* 3.1 28.1 + - - +
219E ILE* 3.9 10.9 - - + +
220E MET 3.5 0.4 - - - -
221E HIS* 1.3 71.1 - - - +
223E LYS* 1.3 55.6 + - - +
225E PHE* 3.9 14.5 - - - -
226E LEU* 2.8 45.2 + - - +
56F VAL 3.3 21.7 + - - +
57F TYR* 3.5 22.2 + - - +
58F GLY* 3.8 1.8 - - - +
131F ARG* 4.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E GLY 4.6 4.3 + - - +
213E GLU* 3.6 26.2 + - - +
221E HIS 3.2 0.2 - - - -
222E ASN* 1.3 77.6 - - - +
224E LEU* 1.3 62.2 + - + +
226E LEU* 4.4 6.9 - - - +
227E ASP* 3.5 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E GLU* 4.7 0.4 + - - -
221E HIS* 2.9 20.2 + - + +
223E LYS* 1.3 81.7 - - + +
225E PHE* 1.3 59.4 + - - +
227E ASP* 3.5 3.1 + - + +
228E TYR* 3.1 26.1 + - + +
250E LEU* 4.0 18.2 - - + -
253E LYS* 3.5 46.7 - - + +
254E LEU* 4.0 24.7 - - + -
257E LEU* 4.7 9.9 - - + -
138F TYR* 3.9 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 225 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E ILE* 3.3 44.4 - - + -
221E HIS 3.1 7.6 + - - +
222E ASN* 3.2 16.6 + - - +
224E LEU* 1.3 74.5 - - - +
226E LEU* 1.3 57.9 + - + +
228E TYR* 3.1 5.8 + + - +
229E THR* 2.6 61.5 + - - -
131F ARG* 3.5 42.8 - - + -
134F CYS* 3.6 11.0 - - + -
135F ARG* 3.5 27.4 - - + -
138F TYR* 3.5 32.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E ASN* 2.8 35.4 + - - +
223E LYS* 4.4 6.1 - - - +
225E PHE* 1.3 76.8 - - + +
227E ASP* 1.3 58.2 + - - +
229E THR* 4.3 5.4 - - - -
230E ILE* 2.8 56.8 + - + +
56F VAL* 3.7 35.4 - - + +
57F TYR* 3.5 36.1 - - + +
98F ILE* 5.5 1.6 - - + -
127F PHE* 4.8 8.7 - - + -
131F ARG* 5.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 227 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E LYS* 3.5 20.0 + - - +
224E LEU* 3.7 6.5 - - + +
225E PHE 3.2 0.4 - - - -
226E LEU* 1.3 77.8 - - - +
228E TYR* 1.3 65.0 + - - +
230E ILE* 4.0 6.8 - - - +
231E LYS* 3.1 58.8 + - - +
249E GLU* 4.5 0.5 - - - +
253E LYS* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 228 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E LEU* 3.1 13.2 + - + +
225E PHE* 3.3 22.4 - + - +
227E ASP* 1.3 81.4 + - - +
229E THR* 1.3 59.6 + - - +
231E LYS* 3.2 8.3 + - - +
232E CYS* 2.9 54.2 + - - -
243E PHE* 5.1 1.6 - - - +
246E MET* 3.8 24.9 - - + -
247E ASN* 2.7 29.3 + - - -
250E LEU* 3.9 31.2 - - + -
134F CYS* 3.9 29.8 - - + -
137F THR* 3.1 18.1 - - + +
138F TYR* 4.3 7.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E PHE* 2.6 54.6 + - - -
226E LEU* 3.9 7.2 - - - -
228E TYR* 1.3 72.8 - - - +
230E ILE* 1.3 67.1 + - - +
232E CYS* 3.4 3.3 + - - +
233E TYR* 2.9 21.7 + - - +
127F PHE* 4.0 18.4 - - + -
130F PHE* 4.0 3.2 - - + -
131F ARG* 3.4 35.9 - - + -
134F CYS* 3.9 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E LEU* 2.8 43.1 + - + +
227E ASP* 4.0 5.8 - - - +
229E THR* 1.3 71.8 - - - +
231E LYS* 1.3 66.9 + - + +
233E TYR* 2.9 17.8 + - - +
234E GLU* 3.1 31.5 + - + +
57F TYR* 6.1 1.3 - - + -
98F ILE* 3.7 46.0 - - + -
127F PHE* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E ASP* 3.1 48.8 + - - +
228E TYR* 3.5 5.4 - - - +
230E ILE* 1.3 78.9 - - + +
232E CYS* 1.3 61.4 + - - +
234E GLU* 3.3 11.3 + - + +
235E SER* 3.3 19.9 + - - -
246E MET* 4.1 22.6 - - + +
249E GLU* 2.9 40.4 + - - +
253E LYS* 4.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E TYR* 2.9 54.1 + - - +
229E THR 3.6 7.6 - - - +
231E LYS* 1.3 75.8 - - - +
233E TYR* 1.3 57.2 + - - +
235E SER* 3.3 1.1 + - - -
236E PHE* 2.8 30.5 + - - +
243E PHE* 3.4 28.6 - - + -
246E MET* 3.7 16.1 - - - +
130F PHE* 3.7 15.7 - - + -
134F CYS* 4.1 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E THR 2.9 12.2 + - - +
230E ILE* 2.9 13.8 + - + +
232E CYS* 1.3 76.1 - - - +
234E GLU* 1.3 52.7 + - + +
236E PHE* 3.2 21.0 + + - +
237E MET* 2.7 51.5 + - - +
98F ILE* 3.5 26.9 - - + -
99F CYS* 4.7 1.3 + - - -
100F ARG* 4.2 22.9 - - + +
123F GLY 4.8 0.9 + - - -
126F ASN* 3.8 13.0 - - - +
127F PHE* 3.7 41.9 + + + -
130F PHE* 3.2 42.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ILE* 3.1 30.9 + - + +
231E LYS* 3.3 10.1 + - + +
233E TYR* 1.3 74.8 - - + +
235E SER* 1.3 61.5 + - - +
237E MET* 3.3 3.8 + - - +
238E SER* 2.8 27.3 + - - -
100F ARG* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E LYS 3.3 9.4 + - - -
232E CYS 3.5 8.1 - - - -
234E GLU* 1.3 77.2 - - - +
236E PHE* 1.3 58.3 + - - +
238E SER* 2.8 27.0 + - - -
240E ALA* 3.1 33.7 + - - +
242E SER 5.2 0.4 + - - -
243E PHE* 4.4 4.0 - - - -
246E MET* 3.1 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 236 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E CYS 2.8 21.1 + - - +
233E TYR* 3.4 28.0 - + - +
235E SER* 1.3 72.7 - - - +
237E MET* 1.3 72.0 + - + +
239E GLY* 2.9 21.8 + - - -
240E ALA 3.9 14.8 + - - -
243E PHE* 4.0 13.1 - + + -
130F PHE* 3.5 31.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E TYR* 2.7 38.3 + - - +
234E GLU 3.6 6.5 - - - +
235E SER 3.2 0.2 - - - -
236E PHE* 1.3 90.1 - - + +
238E SER* 1.3 58.9 + - - +
239E GLY 3.4 0.4 - - - -
100F ARG* 3.5 56.2 + - + +
----------------------------------------------------------
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