Contacts of the helix formed by residues 219 - 235 (chain E) in PDB entry 3FZ7
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 PHE 219 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E PHE* 5.1 0.7 - + - -
217E TYR* 3.8 28.5 - + + -
218E GLU* 1.3 70.3 - - - +
220E PRO* 1.3 70.9 - - + +
221E GLN* 3.3 1.1 - - + +
222E PRO* 3.3 27.4 - - + +
223E LEU* 3.5 17.5 - - - +
258E ILE* 3.8 30.7 - - + -
372E ASP 3.4 25.8 - - - -
373E GLU* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 220 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E PRO* 4.3 3.8 - - + -
209E PHE* 4.3 7.9 - - + -
218E GLU 3.2 11.2 - - - +
219E PHE* 1.3 85.3 - - + +
221E GLN* 1.3 57.4 + - - +
223E LEU* 3.4 6.3 + - + -
224E HIS* 2.7 30.5 + - - +
240E MET* 3.6 14.2 - - + +
242E ILE* 3.7 28.7 - - + -
258E ILE* 5.6 0.4 - - + -
259E VAL 4.6 1.1 - - - +
260E TRP* 3.5 37.2 - - + +
264E LEU* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E PHE* 3.3 1.0 - - + +
220E PRO* 1.3 80.0 - - - +
222E PRO* 1.4 67.9 - - + +
224E HIS* 2.8 19.1 + - - +
225E ASP* 3.0 28.0 + - - +
259E VAL* 3.6 36.7 + - - +
264E LEU* 3.7 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 222 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E PRO* 4.1 20.5 - - + +
219E PHE* 3.3 27.4 - - + +
221E GLN* 1.4 94.3 - - + +
223E LEU* 1.3 61.7 + - + +
225E ASP* 3.4 12.5 + - - +
226E ALA* 3.3 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E MET* 3.8 37.5 - - + +
190E ASP 3.8 7.9 - - - +
191E PRO* 3.6 33.7 - - + -
194E MET* 3.7 19.9 - - - +
207E PRO* 3.9 22.4 - - + -
218E GLU* 5.0 4.7 - - + -
219E PHE 3.5 18.8 - - - +
220E PRO* 3.4 2.2 + - + +
221E GLN 3.2 0.4 - - - -
222E PRO* 1.3 76.9 - - + +
224E HIS* 1.3 62.2 + - - +
226E ALA* 3.4 5.3 + - - +
227E LEU* 3.2 25.3 + - - +
240E MET* 3.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 224 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E PRO 2.7 21.9 + - - +
221E GLN* 2.8 11.1 + - - +
223E LEU* 1.3 73.3 - - - +
225E ASP* 1.3 67.5 + - - +
227E LEU* 3.1 7.9 + - - +
228E ASP* 3.0 45.8 + - - +
240E MET* 4.3 11.7 - - - -
264E LEU* 3.5 29.0 - - + +
265E PRO* 3.3 25.1 - - + +
266E ARG* 3.0 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221E GLN* 3.0 32.8 + - - +
222E PRO* 3.6 13.8 - - - +
224E HIS* 1.3 81.1 + - - +
226E ALA* 1.3 61.1 + - - +
228E ASP* 3.1 14.8 + - - +
229E LYS* 3.0 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E PRO* 4.1 15.5 - - + -
194E MET* 4.0 6.5 - - + -
195E ILE* 3.6 25.8 - - + +
222E PRO 3.3 9.4 + - - +
223E LEU 3.6 9.0 - - - +
224E HIS 3.2 0.6 - - - -
225E ASP* 1.3 78.3 - - - +
227E LEU* 1.3 52.0 + - - +
229E LYS* 3.2 11.2 + - - +
230E PHE* 2.7 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E MET* 3.5 23.3 - - + -
195E ILE* 4.1 8.1 - - + -
198E CYS* 4.4 9.9 - - - -
205E VAL* 4.4 5.8 - - + -
223E LEU 3.2 13.6 + - - +
224E HIS 3.1 8.4 + - - +
226E ALA* 1.3 73.7 - - - +
228E ASP* 1.3 60.5 + - - +
230E PHE* 3.4 6.1 + - + +
231E GLN* 3.0 23.7 + - - +
236E ILE 4.6 1.7 - - - +
238E ILE* 3.6 45.5 + - + +
240E MET* 3.8 31.0 - - + -
266E ARG* 3.6 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 228 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E HIS* 3.0 32.8 + - - +
225E ASP* 3.1 15.6 + - - +
227E LEU* 1.3 76.0 - - - +
229E LYS* 1.3 59.6 + - - +
231E GLN* 3.3 3.6 + - - +
232E ALA* 2.9 28.2 + - - +
266E ARG* 2.6 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E ASP 3.0 11.8 + - - +
226E ALA* 3.4 12.6 - - - +
228E ASP* 1.3 75.4 - - - +
230E PHE* 1.3 54.7 - - - +
232E ALA* 3.2 8.1 + - + +
233E ASP* 2.7 67.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E ILE* 3.6 44.2 - - + -
198E CYS* 3.8 25.6 - - + -
199E ASP* 4.6 0.4 - - - -
226E ALA 2.7 15.7 + - - +
227E LEU* 3.4 9.4 - - + +
228E ASP 3.2 0.2 - - - -
229E LYS* 1.3 78.3 - - - +
231E GLN* 1.3 52.5 + - - +
233E ASP* 3.4 4.2 + - + +
234E THR* 2.8 65.5 + - + +
236E ILE* 3.7 35.4 - - + -
238E ILE* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E LEU 3.0 15.2 + - - +
228E ASP 3.7 4.3 - - - +
230E PHE* 1.3 72.2 - - - +
232E ALA* 1.3 64.1 + - - +
235E GLY* 2.7 35.6 + - - -
236E ILE 3.4 25.3 + - - +
237E ASP* 3.6 30.8 + - - +
266E ARG* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E ASP 2.9 14.7 + - - +
229E LYS* 3.3 13.9 - - + +
231E GLN* 1.3 80.6 - - - +
233E ASP* 1.3 65.3 + - - +
235E GLY 4.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E LYS* 2.7 55.3 + - - +
230E PHE* 3.9 6.1 - - + +
231E GLN 3.2 0.2 - - - -
232E ALA* 1.3 77.1 - - - +
234E THR* 1.3 68.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E PHE* 2.8 43.0 + - + +
233E ASP* 1.3 88.8 - - + +
235E GLY* 1.3 59.3 + - - +
236E ILE* 3.1 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E GLN* 2.7 32.1 + - - +
232E ALA 4.4 1.0 + - - -
234E THR* 1.3 71.4 - - - +
236E ILE* 1.3 61.8 + - - +
237E ASP* 3.7 4.7 + - - +
----------------------------------------------------------
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