Contacts of the helix formed by residues 220 - 231 (chain F) in PDB entry 4DEM
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 220 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215F THR* 4.9 0.4 - - + -
216F ALA* 3.1 8.6 + - - +
218F TYR 3.4 0.2 - - - -
219F SER* 1.3 100.3 - - - +
221F TYR* 1.3 68.2 + - - +
222F LEU 3.4 0.4 - - - -
223F PRO* 3.5 11.4 - - - +
224F ILE* 3.7 9.0 + - - +
246F LEU* 3.4 39.1 - - + +
249F MET* 4.0 12.6 - - + -
250F GLY* 3.4 17.3 - - - -
253F PHE* 3.5 47.6 - + + -
358F LEU* 3.9 35.2 - - + +
362F ILE* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 221 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F LEU* 3.6 19.1 - - + +
177F SER* 5.2 2.7 - - - -
180F GLN* 5.8 0.9 - - - -
216F ALA 3.4 2.9 + - - +
217F PHE* 3.3 25.9 + + - +
220F PHE* 1.3 78.8 - - - +
222F LEU* 1.3 60.0 + - - +
224F ILE* 3.7 0.5 - - - +
225F ALA* 2.8 54.0 + - + +
229F TYR* 4.4 5.4 + - - -
239F HIS* 2.7 47.4 + - - +
242F ALA* 5.0 3.1 - - + -
243F LYS* 3.7 49.7 + - + -
246F LEU* 3.9 14.3 - - + +
247F LEU* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F VAL* 3.9 18.6 - - + -
109F LEU* 3.5 32.3 - - + -
173F LEU* 3.6 28.8 - - + +
174F PHE* 4.1 31.2 - - + -
177F SER* 3.8 16.8 - - - +
217F PHE 2.9 11.6 + - - +
218F TYR* 3.4 20.2 - - - +
221F TYR* 1.3 80.6 - - - +
223F PRO* 1.3 63.6 - - + +
225F ALA* 4.5 1.8 - - - -
226F ALA* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 223 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ARG* 3.5 29.6 - - + +
77F THR* 3.9 16.6 - - + -
78F VAL* 3.6 23.7 - - + +
106F VAL* 4.6 3.6 - - + -
218F TYR 3.4 12.6 - - - +
219F SER 3.5 18.4 - - - +
220F PHE* 3.5 11.9 - - - +
222F LEU* 1.3 100.2 - - + +
224F ILE* 1.3 62.6 + - - +
226F ALA* 3.4 3.2 + - + +
227F ALA* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F THR* 3.4 26.9 - - + -
81F ALA* 3.7 19.7 - - + -
85F LEU* 5.4 0.4 - - + -
220F PHE 3.7 11.4 - - - +
221F TYR 3.4 0.8 + - - -
222F LEU 3.3 0.4 - - - -
223F PRO* 1.3 74.9 - - - +
225F ALA* 1.3 60.2 + - - +
227F ALA* 3.1 5.6 + - - +
228F MET* 2.8 49.9 + - + +
242F ALA* 4.9 0.4 - - + -
246F LEU* 3.6 36.1 - - + -
350F LEU* 5.2 1.1 - - + -
354F VAL* 3.7 27.4 - - + +
355F PHE* 4.7 6.3 - - + -
358F LEU* 4.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F LEU* 3.8 14.1 - - + -
221F TYR* 2.8 60.8 + - + +
224F ILE* 1.3 74.3 - - - +
226F ALA* 1.3 56.7 + - - +
228F MET* 3.2 7.4 + - - +
229F TYR* 2.9 34.9 + - + -
239F HIS* 3.7 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F VAL* 4.6 3.8 - - + -
102F VAL* 3.9 21.1 - - + -
106F VAL* 5.5 0.2 - - + -
170F LEU* 3.7 17.8 - - + +
173F LEU* 3.5 13.0 - - + +
174F PHE* 4.9 5.8 - - + -
222F LEU* 2.9 22.1 + - + +
223F PRO* 3.6 7.4 - - + +
224F ILE 3.2 0.4 - - - -
225F ALA* 1.3 72.4 - - - +
227F ALA* 1.3 58.1 + - - +
229F TYR* 3.2 3.8 + - - +
230F MET* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F VAL* 3.7 17.2 - - - +
81F ALA* 3.6 32.3 - - + -
82F PHE* 3.8 13.1 - - + +
85F LEU* 4.2 3.7 - - + +
223F PRO 3.2 6.8 + - - +
224F ILE 3.1 6.8 + - - +
226F ALA* 1.3 75.5 - - - +
228F MET* 1.3 67.0 + - - +
230F MET* 3.2 12.1 + - - +
231F ALA* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 228 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F LEU* 3.9 21.1 - - + +
221F TYR* 5.7 0.4 - - - -
224F ILE* 2.8 34.0 + - + +
225F ALA* 3.4 14.6 - - - +
227F ALA* 1.3 76.3 - - - +
229F TYR* 1.4 60.7 + - - +
231F ALA* 3.0 8.4 + - - -
233F ILE* 2.8 60.6 + - + +
238F GLU* 3.7 31.0 - - + +
239F HIS* 3.8 16.2 - - + +
242F ALA* 3.9 13.0 - - - -
350F LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 229 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F TYR* 3.5 23.3 - - + +
169F ASN* 3.5 49.5 + - + -
170F LEU* 4.2 11.0 - - + -
173F LEU* 4.0 28.6 - - + +
221F TYR* 4.4 3.2 + - - -
225F ALA* 2.9 25.4 + - + -
226F ALA 3.7 4.7 - - - +
228F MET* 1.4 72.3 - - - +
230F MET* 1.3 63.1 + - - +
232F GLY* 3.1 13.3 + - - -
233F ILE 3.9 2.5 - - - +
234F ASP* 3.9 23.9 + - + +
239F HIS* 3.4 36.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 230 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F VAL* 4.7 5.6 - - - -
82F PHE* 4.0 29.6 - - + -
86F VAL* 4.8 0.7 - - - +
98F ARG* 3.6 13.9 - - + +
99F ALA* 3.6 33.4 - - - +
102F VAL* 3.8 31.2 - - + -
166F TYR* 3.6 52.7 - - + +
170F LEU* 4.2 4.3 - - + -
226F ALA 2.9 22.4 + - - +
227F ALA* 3.2 5.6 + - - +
229F TYR* 1.3 76.6 - - - +
231F ALA* 1.3 59.6 + - - +
232F GLY 3.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F LEU* 3.9 24.8 - - + +
86F VAL* 3.6 27.1 - - + +
227F ALA 2.9 16.4 + - - +
228F MET 3.0 5.6 + - - +
230F MET* 1.3 74.6 - - - +
232F GLY* 1.3 59.7 + - - +
233F ILE* 3.3 13.1 + - + +
----------------------------------------------------------
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