Contacts of the helix formed by residues 228 - 249 (chain F) in PDB entry 1FPY
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 MET 228 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F ALA* 3.5 39.0 - - + +
111F ALA* 4.2 7.0 - - + -
112F GLU* 3.9 17.8 + - + +
124F VAL* 3.0 16.8 + - + -
126F PHE* 3.4 42.8 - - + -
226F ASN 3.2 2.5 + - - -
227F THR* 1.3 70.5 - - - +
229F THR* 1.3 63.9 + - - +
231F LYS* 3.3 2.8 + - - +
232F ALA* 3.2 17.0 + - - +
371F PHE* 3.5 30.9 - - + +
372F ALA* 3.7 23.8 - - + +
375F LEU* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ARG* 4.6 23.8 - - + +
108F ALA* 3.5 33.0 + - + +
109F LYS* 3.8 25.0 + - + -
112F GLU* 3.1 25.1 + - - +
227F THR* 3.0 1.8 + - - -
228F MET* 1.3 70.3 - - - +
230F LYS* 1.3 67.5 + - - +
231F LYS 3.2 0.7 + - - -
232F ALA* 3.2 7.8 + - - +
233F ASP* 3.2 21.5 + - - +
368F TYR* 4.0 4.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 230 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F ASN* 3.3 34.8 - - - +
227F THR* 3.0 26.0 + - - +
229F THR* 1.3 77.8 - - - +
231F LYS* 1.3 57.4 + - - +
233F ASP* 3.0 19.0 - - + +
234F GLU* 3.0 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F PHE* 3.5 22.0 - - + +
128F PRO* 3.3 37.9 - - + -
204F LEU* 5.0 0.8 - - - +
223F THR* 3.3 27.6 + - - -
224F ARG 2.7 29.1 + - - +
225F PHE* 4.3 1.1 - - - +
226F ASN* 4.0 15.4 - - + +
227F THR 2.9 11.9 + - - +
228F MET 3.6 8.3 - - - +
230F LYS* 1.3 75.1 - - - +
232F ALA* 1.3 60.5 + - - +
234F GLU* 3.0 30.8 + - + +
235F ILE* 2.8 32.6 + - - +
371F PHE* 4.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F MET* 3.2 7.0 + - + +
229F THR* 3.2 4.0 + - - +
231F LYS* 1.3 77.8 - - - +
233F ASP* 1.3 61.6 + - - +
235F ILE* 3.4 4.8 + - - +
236F GLN* 3.3 23.0 + - - +
367F PRO* 3.4 22.3 - - + +
368F TYR* 3.2 38.3 - - + +
371F PHE* 3.6 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F THR* 4.4 5.2 - - - +
88F ARG* 3.4 15.8 + - - +
105F ARG* 2.9 37.1 + - - -
229F THR* 3.2 13.3 + - - +
230F LYS* 3.0 22.8 + - + +
232F ALA* 1.3 76.9 - - - +
234F GLU* 1.3 58.6 + - + +
236F GLN* 2.9 24.2 + - - +
237F ILE* 3.0 19.4 + - + +
368F TYR* 2.6 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F GLY 4.3 11.8 - - - +
204F LEU* 3.5 40.4 - - + +
205F VAL 5.1 1.4 + - - -
224F ARG 3.8 5.2 - - - +
226F ASN* 3.4 23.9 + - - +
230F LYS* 3.1 19.5 - - + +
231F LYS* 3.0 39.5 + - + +
233F ASP* 1.3 80.9 - - + +
235F ILE* 1.3 52.9 + - - +
237F ILE* 3.2 5.7 + - + +
238F TYR* 2.7 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F PRO* 4.2 13.5 - - + +
130F PRO* 3.9 17.3 - - + -
223F THR* 5.6 2.0 - - - +
231F LYS* 2.8 21.9 + - - +
232F ALA* 3.4 8.5 - - - +
233F ASP 3.0 0.2 + - - -
234F GLU* 1.3 74.1 - - - +
236F GLN* 1.3 66.3 + - - +
238F TYR* 3.1 9.5 + - + +
239F LYS* 2.9 40.9 + - + +
268F MET* 3.4 34.1 - - + -
363F PRO 6.0 0.2 - - - +
367F PRO* 3.3 26.5 - - + -
371F PHE* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 236 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F THR* 3.1 33.1 + - - +
26F GLY 2.9 28.4 + - - +
28F GLU* 3.6 25.2 - - - +
88F ARG* 3.6 19.1 - - - +
232F ALA 3.4 13.5 - - - +
233F ASP 2.9 8.3 + - - +
235F ILE* 1.3 77.1 - - - +
237F ILE* 1.3 62.9 + - - +
239F LYS* 3.4 18.2 + - - +
240F TYR* 3.0 23.4 + - - +
367F PRO* 3.8 18.9 - - - +
368F TYR* 4.2 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F GLU* 5.3 1.6 - - - +
73F THR 6.0 1.3 - - - +
75F VAL* 5.3 7.2 - - + -
88F ARG* 4.0 18.6 - - - +
199F MET* 5.2 0.9 - - - +
202F MET* 4.0 51.6 - - + +
204F LEU* 3.6 23.3 - - + -
233F ASP* 3.0 20.4 + - + +
234F GLU* 3.5 11.7 - - + +
235F ILE 3.2 0.2 - - - -
236F GLN* 1.3 75.2 - - - +
238F TYR* 1.3 54.1 + - - +
240F TYR* 3.0 7.9 + - - +
241F VAL* 2.8 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 238 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F PRO* 2.9 42.2 + - + -
132F PHE* 3.5 6.6 - + - -
199F MET* 3.2 32.9 - - + +
204F LEU* 4.2 7.4 - - + -
221F VAL* 2.9 48.9 + - + +
223F THR* 4.3 17.7 - - + -
234F GLU 2.7 17.3 + - - +
235F ILE* 3.1 14.8 - - + +
237F ILE* 1.3 74.8 - - - +
239F LYS* 1.3 58.8 + - + +
241F VAL* 3.1 2.5 + - - +
242F VAL* 2.8 46.2 + - + +
255F PHE* 3.7 22.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F GLY* 5.0 5.7 + - - -
27F LYS* 6.1 0.7 - - - +
130F PRO* 6.2 0.9 - - + -
235F ILE* 2.9 40.5 + - + +
236F GLN* 3.8 19.5 + - - +
238F TYR* 1.3 75.6 - - + +
240F TYR* 1.3 57.9 + - - +
242F VAL* 3.7 0.2 - - - +
243F HIS* 2.7 42.9 + - + +
255F PHE* 3.6 46.2 - - + -
268F MET* 6.1 0.7 - - + -
363F PRO* 3.3 25.5 + - - -
364F ALA 5.0 1.8 + - - -
365F ALA 4.3 8.3 + - - -
367F PRO* 5.0 0.8 - - - +
468L VAL* 3.3 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 240 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E VAL* 4.2 18.4 - - + -
183E PRO* 3.5 20.6 - - + +
20F ARG* 3.4 25.8 + - - +
28F GLU* 4.1 7.9 - - - +
77F ASP* 2.6 32.4 + - - -
79F PHE* 3.4 25.7 - + - -
80F PHE* 3.2 21.1 - - - -
202F MET* 4.5 17.3 - - + -
236F GLN 3.0 14.1 + - - +
237F ILE* 3.3 10.1 - - - +
239F LYS* 1.3 77.3 - - - +
241F VAL* 1.3 64.9 + - - +
243F HIS* 3.6 2.9 - - - +
244F ASN* 2.9 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F PHE* 3.8 9.4 - - + -
195F MET* 3.6 28.7 - - - +
198F VAL* 3.6 26.7 - - + -
199F MET* 3.7 18.4 - - + -
202F MET* 3.5 30.7 - - - -
237F ILE* 2.8 23.7 + - + +
238F TYR 3.5 6.3 - - - +
240F TYR* 1.3 70.6 - - + +
242F VAL* 1.3 58.1 + - - +
245F VAL* 2.8 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F PHE* 3.9 24.0 - - + -
195F MET* 3.3 24.2 - - + +
199F MET* 3.6 19.5 - - + -
238F TYR* 2.8 41.6 + - + +
239F LYS 3.7 0.4 - - - +
241F VAL* 1.3 72.8 - - - +
243F HIS* 1.3 65.4 + - - +
246F ALA* 3.0 26.3 + - - +
253F ALA* 3.8 18.4 - - + -
255F PHE* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 243 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E HIS* 3.7 21.5 - + - -
183E PRO 5.2 0.4 - - - +
184E PRO* 4.0 22.8 - - + +
27F LYS* 3.9 20.3 + - - -
239F LYS* 2.7 30.3 + - + +
240F TYR* 3.6 3.9 - - - +
242F VAL* 1.3 74.0 - - - +
244F ASN* 1.3 59.4 + - - +
246F ALA* 3.5 3.3 - - - +
247F HIS* 3.1 25.3 + - - +
252F THR* 5.7 0.2 - - - -
253F ALA* 3.2 38.4 + - + -
254F THR* 4.5 2.2 - - - -
255F PHE* 3.7 19.3 - + - -
467L SER 4.4 3.0 + - - -
468L VAL 3.4 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 244 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E PRO* 3.2 28.6 - - - +
184E PRO* 3.6 13.7 - - - +
79F PHE* 3.5 34.5 - - + +
80F PHE* 5.9 0.4 - - - -
240F TYR* 2.9 53.9 + - - +
243F HIS* 1.3 72.3 - - - +
245F VAL* 1.3 66.4 + - - +
246F ALA 3.1 1.3 - - - -
247F HIS* 3.2 9.7 + - - +
248F ARG* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F PHE* 3.6 22.2 - - + -
191F ILE* 4.2 5.6 - - + +
194F GLU* 4.0 12.8 - - + +
195F MET* 3.6 28.3 - - + +
198F VAL* 4.2 15.3 - - + -
241F VAL* 2.8 36.5 + - + +
244F ASN* 1.3 70.3 - - - +
246F ALA* 1.3 63.7 + - - +
248F ARG* 3.1 9.3 + - - +
249F PHE* 3.0 47.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F LEU* 3.8 28.3 - - + -
191F ILE* 5.1 3.4 - - - -
195F MET* 4.0 5.1 - - + +
242F VAL 3.0 18.5 + - - +
243F HIS 3.5 5.2 - - - +
245F VAL* 1.3 77.0 - - - +
247F HIS* 1.3 57.5 + - - +
249F PHE* 2.9 10.7 + - - -
251F LYS* 2.7 38.3 + - - +
253F ALA* 3.8 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 247 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E LYS* 4.8 20.3 - - + +
171E HIS* 5.8 3.3 - - + -
184E PRO* 4.1 25.2 - - + +
243F HIS 3.1 12.6 + - - +
244F ASN* 3.2 16.1 + - - +
246F ALA* 1.3 80.7 - - - +
248F ARG* 1.3 62.5 + - + +
250F GLY* 2.8 25.5 + - - -
251F LYS 3.3 13.5 + - - +
252F THR* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 248 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F PRO 5.5 1.8 + - - -
79F PHE* 4.1 30.8 - - + +
194F GLU* 3.3 26.1 + - - -
198F VAL* 5.5 1.6 - - - +
244F ASN 2.8 13.5 + - - +
245F VAL* 3.5 17.4 - - - +
247F HIS* 1.3 84.4 - - + +
249F PHE* 1.3 76.2 + - + +
250F GLY 3.1 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 249 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F ASP* 4.5 7.4 - - + -
191F ILE* 3.8 46.2 - - + -
194F GLU* 3.7 29.4 - - + -
245F VAL* 3.0 30.4 + - + +
246F ALA* 2.9 9.7 + - - +
248F ARG* 1.3 99.3 - - + +
250F GLY* 1.3 62.9 + - - +
251F LYS* 3.1 11.3 + - + +
----------------------------------------------------------
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