Contacts of the helix formed by residues 166 - 184 (chain F) in PDB entry 3J7Y
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 PRO 166 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1878A U 5.9 0.2 - - - +
1879A G 5.2 5.6 - - - +
1885A A 4.5 18.2 - - - +
1886A G 3.9 8.7 - - - +
1896A U 3.4 34.3 - - + +
1897A A 3.8 22.4 - - - +
164F MET 3.9 0.9 - - - +
165F LEU* 1.3 87.9 - - + +
167F MET* 1.3 66.2 + - - +
168F LYS* 4.3 3.1 - - + +
169F VAL* 2.8 40.1 + - + +
170F ARG* 3.1 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1886A G 3.4 51.5 + - + +
165F LEU 3.3 3.8 + - - -
166F PRO* 1.3 69.2 - - - +
168F LYS* 1.3 56.6 + - - +
170F ARG* 3.2 18.0 + - - +
171F ALA* 2.9 26.9 + - - +
276F GLN* 3.3 36.6 - - - +
279F ARG* 3.5 21.3 - - - +
286F PHE* 4.0 17.9 - - + -
62i ILE* 3.6 15.3 - - + +
66i PHE* 3.3 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1879A G 3.8 13.0 - - - +
1880A C 2.7 35.3 + - - +
1884A G 3.4 9.5 + - - -
1885A A 2.7 42.8 + - - +
1886A G 5.9 0.2 - - - +
166F PRO* 3.1 2.2 - - + +
167F MET* 1.3 80.2 - - - +
169F VAL* 1.3 56.5 + - - +
171F ALA* 3.2 8.0 + - - +
172F LEU* 2.9 29.9 + - - +
276F GLN* 3.9 12.9 - - + +
279F ARG* 3.4 27.8 - - - +
280F TYR 5.3 2.0 + - - -
90g ARG* 3.4 34.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1878A U 4.4 7.0 - - - +
1879A G 3.4 40.2 - - - +
95F ILE* 3.9 8.5 - - + +
98F GLN* 3.9 23.1 - - - +
99F VAL* 3.9 5.2 - - + +
165F LEU* 4.3 21.1 - - + -
166F PRO* 2.8 31.0 + - + +
168F LYS* 1.3 75.9 - - - +
170F ARG* 1.3 59.0 + - - +
172F LEU* 3.2 9.3 + - - +
173F GLY* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1886A G 3.0 54.2 + - - -
99F VAL* 4.0 15.8 - - + +
102F TRP* 3.9 30.4 - - + -
164F MET* 3.5 20.3 - - - +
165F LEU* 2.8 43.2 + - + -
166F PRO 3.1 6.1 + - - +
167F MET* 3.2 18.8 + - - +
169F VAL* 1.3 76.5 - - - +
171F ALA* 1.3 61.2 - - - +
173F GLY* 3.2 2.8 + - - -
174F LEU* 3.0 24.8 + - - +
59i ASN* 3.9 19.1 + - - +
62i ILE* 3.9 9.9 - - + +
70i PRO* 3.9 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F MET 2.9 7.8 + - - +
168F LYS 3.3 9.2 - - - +
170F ARG* 1.3 75.7 - - - +
172F LEU* 1.3 59.3 + - - +
174F LEU* 3.2 5.5 + - - +
175F LYS* 2.9 38.1 + - - +
273F LEU* 4.1 13.1 - - + +
276F GLN* 3.4 35.2 - - + -
62i ILE* 3.4 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1879A G 3.6 34.8 - - - +
1880A C 4.0 8.5 - - - +
89F THR* 5.6 8.3 - - + +
90F ALA 5.8 0.2 - - - +
92F ARG* 4.9 3.4 - - + -
95F ILE* 3.4 35.2 - - + -
168F LYS 2.9 12.2 + - - +
169F VAL* 3.3 10.3 - - - +
171F ALA* 1.3 76.9 - - - +
173F GLY* 1.3 52.8 + - - +
175F LYS* 3.2 17.8 + - + +
176F VAL* 2.8 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 173 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ILE* 3.6 21.7 - - - +
96F LEU* 4.5 2.6 - - - +
99F VAL* 4.0 11.2 - - - -
169F VAL 2.9 11.4 + - - -
170F ARG 3.2 4.7 + - - -
172F LEU* 1.3 76.1 - - - +
174F LEU* 1.3 50.5 + - - +
176F VAL* 3.2 6.6 + - - +
177F ALA* 2.8 35.0 + - - +
250F VAL* 3.7 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F ARG 3.0 11.3 + - - +
171F ALA 3.3 9.4 - - - +
173F GLY* 1.3 73.9 - - - +
175F LYS* 1.3 58.8 + - - +
177F ALA* 3.2 4.2 + - - +
178F LEU* 2.9 34.9 + - + +
248F LEU* 3.5 29.2 - - + +
249F ASN* 3.9 20.2 - - - -
250F VAL* 3.7 16.2 - - + +
253F MET* 4.2 4.5 - - - -
273F LEU* 4.0 19.7 - - + -
59i ASN* 3.7 18.6 - - - +
62i ILE* 4.2 7.0 - - + -
63i LEU* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F ASP* 4.4 7.9 - - + +
86F VAL* 3.0 47.2 - - + +
89F THR* 4.2 12.8 - - + +
171F ALA* 2.9 23.1 + - - +
172F LEU* 3.3 19.1 - - + +
174F LEU* 1.3 76.0 - - - +
176F VAL* 1.3 58.1 + - + +
178F LEU* 3.2 4.6 + - - +
179F THR* 2.9 27.3 + - - +
273F LEU* 3.0 37.1 + - + -
274F LEU* 4.5 3.8 - - - +
276F GLN* 4.9 2.8 - - - +
277F ASP* 2.6 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F THR* 4.7 2.9 - - - +
90F ALA 3.9 7.9 - - - +
91F PRO 2.9 28.7 - - - +
92F ARG* 3.6 21.3 - - + +
95F ILE* 4.7 1.6 - - + -
96F LEU* 3.6 29.2 - - + +
172F LEU* 2.8 39.3 + - + +
173F GLY* 3.4 5.4 - - - +
175F LYS* 1.3 76.6 - - - +
177F ALA* 1.3 58.0 + - - +
179F THR* 2.3 29.3 + - - -
180F VAL* 2.9 17.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F LEU* 4.2 21.8 - - + -
173F GLY 2.8 13.2 + - - +
174F LEU 3.2 8.3 + - - +
176F VAL* 1.3 77.2 - - - +
178F LEU* 1.3 56.3 + - - +
180F VAL* 3.2 4.2 + - - +
181F LYS* 2.9 27.0 + - - +
250F VAL* 4.1 13.5 - - + -
253F MET* 3.3 33.4 - - + +
254F LEU* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F VAL* 3.7 29.8 - - + +
87F PHE* 3.9 33.6 - - + -
174F LEU* 2.9 14.1 + - + +
175F LYS 3.4 7.6 - - - +
177F ALA* 1.3 77.4 - - - +
179F THR* 1.3 61.9 + - - +
181F LYS* 3.2 5.0 + - - +
182F LEU* 3.0 22.7 + - - +
187F LEU* 4.1 4.1 - - + +
248F LEU* 5.1 5.4 - - + -
253F MET* 3.4 8.0 - - + +
259F LEU* 3.5 30.3 - - + -
261F LEU* 4.2 7.0 - - + -
269F LEU* 4.0 23.3 - - + -
273F LEU* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F VAL 3.4 1.5 + - - +
87F PHE 3.4 25.1 - - - +
88F ALA* 4.4 1.1 - - - -
89F THR* 3.2 48.7 + - - +
90F ALA 4.7 0.2 + - - -
91F PRO* 4.6 7.3 + - - +
175F LYS 2.9 19.8 + - - +
176F VAL* 2.3 28.2 + - - +
178F LEU* 1.3 76.0 - - - +
180F VAL* 1.3 57.4 + - - +
182F LEU* 3.2 3.3 + - - +
183F ALA* 2.7 37.0 + - - +
13M LEU* 4.6 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F PRO* 4.7 4.5 - - + +
93F LEU* 4.7 7.0 - - + -
96F LEU* 4.0 18.4 - - + -
176F VAL* 2.9 17.2 + - + +
177F ALA* 3.4 9.6 - - - +
179F THR* 1.3 84.3 + - - +
181F LYS* 1.3 60.6 + - + +
183F ALA* 3.3 6.1 + - - +
184F GLN* 2.8 49.6 + - + +
254F LEU* 6.3 0.4 - - + -
16M LEU* 4.7 13.9 - - + -
22M VAL* 3.5 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177F ALA 2.9 14.8 + - - +
178F LEU* 3.2 10.3 + - - +
180F VAL* 1.3 81.5 - - + +
182F LEU* 1.3 58.4 + - - +
184F GLN* 3.6 1.7 + - - -
185F ASP 3.4 2.6 + - - -
186F ASP* 3.0 50.9 + - + -
187F LEU* 3.1 19.6 + - + -
253F MET* 3.1 39.0 + - + +
254F LEU* 4.7 4.8 + - - +
256F HIS 3.4 20.0 + - - -
257F GLN 4.1 6.0 + - - -
258F THR 4.0 2.7 - - - -
259F LEU* 4.0 28.5 - - + +
21M ARG* 5.8 1.6 - - - +
22M VAL 4.8 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F VAL* 3.7 30.7 - - + -
63F GLN 5.2 1.3 - - - +
64F ALA* 4.8 5.2 - - + -
82F LEU* 4.0 16.8 - - + -
87F PHE* 3.9 18.2 - - + +
178F LEU 3.0 12.9 + - - +
179F THR 3.7 5.8 - - - +
181F LYS* 1.3 74.1 - - - +
183F ALA* 1.3 67.6 + - - +
185F ASP* 3.2 11.1 + - - -
187F LEU* 3.9 19.0 - - + +
114h ASN* 3.5 44.4 - - + +
115h SER* 3.4 13.7 - - - -
118h HIS* 6.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F THR 2.7 21.9 + - - +
180F VAL* 3.6 7.6 - - - +
182F LEU* 1.3 74.0 - - - +
184F GLN* 1.3 57.1 + - - +
185F ASP* 3.3 0.7 + - - +
13M LEU* 4.1 34.5 - - + +
16M LEU* 4.2 15.5 - - + -
17M ARG* 4.0 16.8 - - - +
115h SER* 3.3 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 184 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F VAL* 2.8 34.9 + - + +
181F LYS* 4.2 2.9 - - - +
183F ALA* 1.3 77.3 - - + +
185F ASP* 1.3 63.4 - - - +
186F ASP* 2.9 31.4 - - + +
16M LEU* 2.8 34.9 + - + +
17M ARG* 4.3 5.8 + - - +
18M GLY 4.9 0.2 - - - -
19M LEU 3.7 9.3 + - - -
20M PRO 2.8 30.7 + - - +
21M ARG* 3.9 7.0 - - + +
22M VAL* 3.3 22.7 + - - +
----------------------------------------------------------
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