Contacts of the helix formed by residues 219 - 235 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PHE* 4.8 1.1 - + - -
217C TYR* 3.9 35.9 - + + -
218C GLU* 1.3 71.6 - - - +
220C PRO* 1.3 68.8 - - + +
221C GLN* 3.3 1.3 - - + +
222C PRO* 3.4 25.6 - - + +
223C LEU* 3.5 16.7 - - - +
258C ILE* 3.9 32.5 - - + -
372C ASP 3.2 26.7 - - - -
373C GLU* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C PRO* 4.3 5.8 - - + -
209C PHE* 4.2 7.2 - - + -
218C GLU 3.2 10.8 - - - +
219C PHE* 1.3 85.4 - - + +
221C GLN* 1.3 61.8 + - - +
223C LEU* 3.1 9.0 + - + +
224C HIS* 2.7 29.3 + - - +
240C MET* 3.4 13.1 - - + +
242C ILE* 3.8 26.2 - - + -
258C ILE* 5.5 0.4 - - + -
259C VAL 4.5 0.9 - - - +
260C TRP* 3.7 36.8 - - + +
264C LEU* 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C PHE* 4.7 0.9 - - + +
220C PRO* 1.3 79.4 - - - +
222C PRO* 1.4 73.6 - - + +
224C HIS* 3.0 13.5 + - - +
225C ASP* 3.0 27.4 + - - +
259C VAL* 3.7 40.1 + - - +
264C LEU* 3.8 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C PRO* 4.2 20.7 - - + +
219C PHE* 3.4 28.9 - - + +
221C GLN* 1.4 94.6 - - + +
223C LEU* 1.3 60.0 + - + +
225C ASP* 3.6 13.6 + - + +
226C ALA* 3.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C MET* 3.8 32.5 - - + +
190C ASP 3.9 0.9 - - - -
191C PRO* 3.6 35.2 - - + -
194C MET* 3.4 27.6 - - + +
207C PRO* 3.9 29.8 - - + -
218C GLU* 4.9 5.2 - - + -
219C PHE 3.5 19.3 - - - +
220C PRO* 3.1 2.8 + - + +
222C PRO* 1.3 77.0 - - + +
224C HIS* 1.3 57.2 + - - +
226C ALA* 3.2 3.0 + - - +
227C LEU* 3.0 25.3 + - - +
240C MET* 3.3 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C PRO 2.7 13.3 + - - +
221C GLN* 3.2 13.9 - - + +
223C LEU* 1.3 73.6 - - - +
225C ASP* 1.3 70.4 + - - +
227C LEU* 3.2 6.3 + - - +
228C ASP* 2.9 46.1 + - - +
240C MET* 4.0 13.5 - - + -
264C LEU* 3.5 29.7 - - + +
265C PRO* 3.4 28.2 - - + -
266C ARG* 2.9 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C GLN* 3.0 31.3 + - - +
222C PRO* 3.7 12.8 - - + +
224C HIS* 1.3 81.0 + - - +
226C ALA* 1.3 61.7 + - - +
228C ASP* 3.0 13.6 + - - +
229C LYS* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C PRO* 4.1 15.7 - - + -
194C MET* 3.8 5.8 - - + -
195C ILE* 3.5 27.6 - - + +
222C PRO 3.3 9.7 + - - +
223C LEU 3.2 10.0 + - - +
225C ASP* 1.3 77.0 - - - +
227C LEU* 1.3 53.3 + - - +
229C LYS* 3.3 10.2 + - + +
230C PHE* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C MET* 3.7 19.3 - - + -
195C ILE* 4.2 8.1 - - + -
198C CYS* 4.2 7.4 - - - -
205C VAL* 4.3 6.7 - - + -
223C LEU 3.0 13.3 + - - +
224C HIS 3.7 2.7 - - - +
226C ALA* 1.3 75.7 - - - +
228C ASP* 1.3 57.1 + - - +
230C PHE* 3.5 6.0 - - + +
231C GLN* 3.0 22.7 + - - +
236C ILE 4.7 1.4 - - - +
238C ILE* 3.6 55.4 + - + +
239C ASP 4.4 0.7 - - - +
240C MET* 4.2 33.4 - - + -
266C ARG* 3.6 29.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C HIS* 2.9 31.9 + - - +
225C ASP* 3.0 14.6 + - - +
227C LEU* 1.3 73.8 - - - +
229C LYS* 1.3 60.3 + - - +
231C GLN* 3.1 5.0 + - - +
232C ALA* 2.9 28.3 + - - +
266C ARG* 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ASP 3.0 12.2 + - - +
226C ALA* 3.6 11.0 - - + +
228C ASP* 1.3 74.3 - - - +
230C PHE* 1.3 58.6 + - - +
232C ALA* 3.8 6.6 - - + +
233C ASP* 2.9 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ILE* 3.6 42.6 - - + -
198C CYS* 3.7 26.0 - - + -
199C ASP* 4.6 0.2 - - - -
226C ALA 2.7 21.2 + - - +
227C LEU* 3.5 9.0 - - + +
228C ASP 3.1 0.2 - - - -
229C LYS* 1.3 73.4 - - - +
231C GLN* 1.3 53.2 + - - +
233C ASP* 3.2 5.9 + - + +
234C THR* 2.7 59.4 + - + -
236C ILE* 3.7 38.1 - - + -
238C ILE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LEU 3.0 14.1 + - - +
228C ASP 3.1 5.8 + - - +
230C PHE* 1.3 72.4 - - - +
232C ALA* 1.3 65.4 + - - +
235C GLY* 2.9 30.8 + - - +
236C ILE 3.2 25.9 + - - +
237C ASP* 3.4 29.7 + - - +
266C ARG* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C ASP 2.9 18.4 + - - +
229C LYS* 3.9 9.0 - - + +
230C PHE 3.4 0.2 - - - -
231C GLN* 1.3 72.9 - - - +
233C ASP* 1.3 65.4 + - - +
234C THR 3.7 0.2 + - - -
235C GLY 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LYS* 2.9 51.7 + - - +
230C PHE* 3.7 7.0 - - + +
231C GLN 3.1 0.2 - - - -
232C ALA* 1.3 85.1 - - - +
234C THR* 1.3 67.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 2.7 43.8 + - + +
233C ASP* 1.3 87.8 - - + +
235C GLY* 1.3 59.1 + - - +
236C ILE* 3.1 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C GLN* 2.9 24.5 + - - +
232C ALA 4.7 0.2 - - - -
233C ASP 3.9 0.4 - - - -
234C THR* 1.3 76.8 - - - +
236C ILE* 1.3 62.7 + - - +
237C ASP* 3.4 5.9 + - - +
----------------------------------------------------------
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