Contacts of the helix formed by residues 159 - 183 (chain F) in PDB entry 5JRE
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 ASN 159 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E TYR* 3.0 8.0 + - - +
16E GLU* 3.2 17.2 + - - +
19E LYS* 4.3 14.1 - - - +
109F TRP* 3.9 20.1 - - + -
113F PHE* 3.6 15.4 - - - -
157F LEU 3.8 0.2 - - - -
158F LYS* 1.3 75.2 - - - +
160F PHE* 1.3 62.0 + - - +
161F ASP* 3.0 31.8 + - - +
162F LEU* 3.0 21.8 + - + +
163F ARG* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 160 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F LYS 3.4 4.7 + - - -
159F ASN* 1.3 72.6 - - - +
161F ASP* 1.3 74.3 + - - +
163F ARG* 3.3 25.3 + - + +
164F ARG* 3.1 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F PHE* 3.8 22.2 - - + -
159F ASN* 3.0 12.8 + - - +
160F PHE* 1.3 84.4 - - - +
162F LEU* 1.3 62.6 + - - +
164F ARG* 3.1 32.9 + - - +
165F LYS* 3.2 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E TYR* 3.6 32.1 - - + +
109F TRP* 4.9 2.9 - - + -
112F LEU* 3.9 17.9 - - + +
113F PHE* 3.6 53.4 - - + +
157F LEU* 3.7 30.5 - - + +
159F ASN* 3.0 29.4 + - + +
161F ASP* 1.3 77.9 - - - +
163F ARG* 1.3 61.7 + - - +
165F LYS* 3.1 20.5 + - + +
166F LEU 3.3 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.9 29.2 - - - +
30A SER* 4.0 24.2 + - - -
34A LYS* 5.6 1.0 - - - +
78A ILE* 6.0 8.3 - - - +
82A GLU* 5.8 0.2 + - - -
157F LEU* 3.2 37.2 - - + +
158F LYS 3.8 12.6 + - - -
159F ASN 2.9 19.1 + - - +
160F PHE* 3.3 27.0 + - + +
162F LEU* 1.3 75.0 - - - +
164F ARG* 1.3 61.8 + - - +
166F LEU* 3.3 27.8 + - + +
167F ASP* 3.4 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F PHE* 3.1 46.3 + - + +
161F ASP* 3.1 39.3 + - - +
162F LEU 3.2 0.2 - - - -
163F ARG* 1.3 73.7 - - + +
165F LYS* 1.3 61.2 + - + +
167F ASP* 3.2 14.8 + - - +
168F TYR* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F GLN* 3.8 6.6 - - - +
113F PHE* 3.7 39.9 - - - +
116F GLY* 3.7 35.4 - - - +
117F ASP* 3.0 24.1 + - - +
152F LEU* 5.5 2.0 - - + -
161F ASP* 3.2 16.0 + - - +
162F LEU* 3.1 18.7 + - + +
164F ARG* 1.3 76.2 - - - +
166F LEU* 1.3 57.3 + - - +
168F TYR* 3.2 13.3 + - + +
169F VAL* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.8 34.5 - - + -
149F TYR* 3.5 26.9 - - + +
152F LEU* 3.5 36.4 - - + +
153F LEU* 3.6 24.9 - - + +
157F LEU* 4.4 9.2 - - + -
162F LEU 3.3 9.9 + - - +
163F ARG* 3.3 20.6 - - + +
165F LYS* 1.3 77.5 - - - +
167F ASP* 1.3 59.2 + - - +
169F VAL* 3.3 10.8 + - - +
170F SER 3.2 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.5 27.6 + - - -
149F TYR* 5.6 0.5 + - - -
163F ARG 3.4 13.3 + - - +
164F ARG* 3.2 17.0 + - + +
166F LEU* 1.3 74.4 - - - +
168F TYR* 1.3 65.8 + - - +
170F SER* 3.2 9.3 + - - -
171F ASN* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F GLY 3.7 23.8 - - - -
117F ASP* 4.3 15.7 + - - -
119F ALA* 4.5 4.5 - - + -
120F GLY* 3.2 37.9 + - - -
164F ARG 3.0 12.6 + - - +
165F LYS* 3.2 11.2 - - + +
167F ASP* 1.3 76.3 - - - +
169F VAL* 1.3 64.5 + - - +
171F ASN* 3.1 14.7 + - + +
172F ILE* 3.0 41.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
116F GLY 4.5 10.1 - - - +
119F ALA* 4.0 28.0 - - + -
145F LEU* 4.0 21.5 - - + +
148F LEU* 4.7 10.1 - - + -
149F TYR* 4.0 20.6 - - + +
152F LEU* 4.3 19.7 - - + -
165F LYS 2.9 19.1 + - - +
166F LEU* 3.5 8.3 - - - +
167F ASP 3.2 0.2 - - - -
168F TYR* 1.3 75.2 - - + +
170F SER* 1.3 63.7 + - - +
172F ILE* 3.1 4.2 + - - +
173F ILE* 3.0 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 4.6 10.4 + - - +
149F TYR* 3.8 25.9 + - - -
166F LEU 3.2 4.6 + - - -
167F ASP* 3.4 11.9 - - - -
169F VAL* 1.3 80.2 - - - +
171F ASN* 1.3 63.6 + - - +
173F ILE* 3.4 14.0 + - - +
174F ASN* 3.2 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 171 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F ASP* 3.0 24.1 + - - +
168F TYR* 3.1 13.4 + - + +
170F SER* 1.3 76.5 + - - +
172F ILE* 1.3 67.3 - - + +
174F ASN* 3.2 14.9 + - - +
175F LYS* 3.1 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ALA* 3.5 35.0 - - + +
120F GLY* 4.2 7.4 - - - -
123F LEU* 3.8 31.5 - - + +
145F LEU* 3.7 18.2 - - + -
168F TYR* 3.0 44.6 + - + +
169F VAL 3.1 7.4 + - - +
171F ASN* 1.3 77.6 - - + +
173F ILE* 1.3 63.5 + - - +
175F LYS* 3.1 11.3 + - + +
176F LEU* 3.0 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 4.1 15.5 - - - +
142F LYS* 4.6 7.0 - - + +
145F LEU* 3.7 45.8 - - + +
146F GLU* 3.9 26.9 - - + +
149F TYR* 4.2 10.1 - - + -
169F VAL* 3.0 28.4 + - + +
170F SER* 3.6 11.9 - - - +
171F ASN 3.2 0.2 - - - -
172F ILE* 1.3 76.6 - - - +
174F ASN* 1.3 57.3 + - - +
176F LEU* 3.3 8.4 + - - +
177F ILE* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 174 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY 5.8 2.0 + - - -
123A LEU* 6.2 4.5 - - + +
124A ARG* 3.3 35.7 + - - +
175A LYS* 5.8 2.1 + - - +
179A PHE* 5.9 0.3 - - - -
170F SER* 3.2 19.6 + - - -
171F ASN* 3.5 17.1 + - - +
172F ILE 3.2 0.2 - - - -
173F ILE* 1.3 77.2 - - - +
175F LYS* 1.3 61.2 + - + +
177F ILE* 3.4 8.2 + - - +
178F GLU* 3.1 22.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
175A LYS* 6.1 2.5 - - - +
123F LEU* 4.3 25.1 - - + -
171F ASN* 3.1 15.8 + - + +
172F ILE* 3.1 13.2 + - + +
174F ASN* 1.3 73.4 - - + +
176F LEU* 1.3 66.4 + - - +
178F GLU* 3.3 18.4 - - - +
179F PHE* 3.0 45.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ILE* 5.5 0.2 - - + -
123F LEU* 4.0 18.3 - - + +
126F SER* 3.9 25.4 - - - +
130F LEU* 6.4 0.2 - - + -
138F ALA* 3.8 21.3 - - + +
141F ALA* 3.9 10.8 - - + -
142F LYS* 3.5 37.0 - - + +
145F LEU* 4.0 17.9 - - + -
172F ILE 3.0 10.6 + - - +
173F ILE* 3.5 10.1 - - - +
175F LYS* 1.3 74.5 - - - +
177F ILE* 1.3 66.0 + - - +
179F PHE* 3.1 15.1 + - + +
180F ILE* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 4.0 28.5 - - - +
127A SER* 3.7 27.8 - - - +
128A GLU* 6.1 1.6 - - + +
131A ILE* 4.5 10.5 - - + +
179A PHE* 5.7 1.1 - - + -
142F LYS* 3.4 34.1 - - + -
173F ILE* 2.9 33.8 + - + +
174F ASN* 3.6 9.0 - - - +
175F LYS 3.4 0.2 - - - -
176F LEU* 1.3 75.5 - - - +
178F GLU* 1.3 56.6 + - - +
180F ILE* 3.2 9.9 + - - +
181F ILE* 2.9 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LYS* 2.8 33.0 + - - +
178A GLU* 4.6 11.5 - - - +
179A PHE* 3.8 34.2 - - + -
182A TRP* 6.1 0.2 - - - -
175C LYS* 5.9 0.8 + - - -
174F ASN 3.1 13.4 + - - +
175F LYS* 3.3 21.4 - - - +
177F ILE* 1.3 77.2 - - - +
179F PHE* 1.3 79.5 + - - +
181F ILE* 3.2 4.8 + - - +
182F TRP* 3.0 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F LEU* 3.7 24.9 - - + -
126F SER 6.1 0.4 - - - -
127F SER* 3.5 26.9 - - - -
130F LEU* 3.6 34.8 - - + +
175F LYS* 3.0 35.5 + - + -
176F LEU* 3.1 13.9 + - + +
178F GLU* 1.3 98.7 - - - +
180F ILE* 1.3 61.5 + - + +
182F TRP* 3.4 16.7 + - - +
183F LYS* 3.5 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 5.2 15.0 - - + -
130F LEU* 5.6 0.4 - - + -
135F ILE* 3.7 9.8 - - + +
138F ALA* 3.7 43.3 - - + +
139F LYS* 4.0 36.3 - - + +
142F LYS* 4.1 21.3 - - + -
176F LEU* 2.9 24.3 + - + +
177F ILE* 3.5 7.6 - - - +
179F PHE* 1.3 75.2 - - + +
181F ILE* 1.3 66.6 + - - +
183F LYS 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 4.2 13.2 - - - +
130A LEU* 4.6 9.6 - - + -
131A ILE* 4.8 12.8 - - + +
179A PHE* 4.0 48.5 - - + -
182A TRP* 4.5 13.9 - - + +
183A LYS* 4.4 35.3 - - + +
177F ILE* 2.9 35.1 + - + +
178F GLU* 3.6 7.4 - - - +
180F ILE* 1.3 73.4 - - - +
182F TRP* 1.3 69.4 + - - +
183F LYS 3.0 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 182 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TRP* 3.5 55.9 - + + +
178C GLU* 5.3 9.8 + - - +
130F LEU* 4.4 20.2 - - + -
178F GLU 3.0 13.4 + - - +
179F PHE* 3.6 15.7 - - - +
180F ILE 3.3 0.2 - - - -
181F ILE* 1.3 80.2 - - - +
183F LYS* 1.3 78.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS* 5.6 3.8 + - - -
130F LEU* 4.6 9.6 - - + -
133F GLY* 5.0 10.5 - - - +
135F ILE* 3.4 45.3 - - + +
179F PHE 3.5 4.4 + - - +
180F ILE 3.0 19.3 + - - +
181F ILE 3.8 4.3 - - - +
182F TRP* 1.3 103.9 - - + +
----------------------------------------------------------
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