Contacts of the helix formed by residues 159 - 184 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 3.1 8.2 + - - +
16C GLU* 3.2 15.2 + - - +
19C LYS* 4.3 14.1 - - - +
109D TRP* 3.8 20.3 - - + -
113D PHE* 3.5 14.2 - - - -
157D LEU* 4.7 0.2 - - - +
158D LYS* 1.3 74.3 - - - +
160D PHE* 1.3 66.4 + - - +
161D ASP* 2.9 31.8 + - - +
162D LEU* 3.0 23.4 + - + +
163D ARG* 2.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 6.4 1.8 - - + -
158D LYS 3.4 5.3 + - - -
159D ASN* 1.3 74.2 - - - +
161D ASP* 1.3 75.0 + - - +
163D ARG* 3.3 26.4 + - + +
164D ARG* 3.1 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE* 3.7 21.1 - - + -
159D ASN* 2.9 13.3 + - - +
160D PHE* 1.3 84.3 - - - +
162D LEU* 1.3 63.3 + - - +
164D ARG* 3.1 32.7 + - - +
165D LYS* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 3.8 29.6 - - + -
109D TRP* 4.9 3.1 - - + -
112D LEU* 4.0 19.1 - - + +
113D PHE* 3.6 54.7 - - + +
116D GLY* 6.0 0.2 - - - -
157D LEU* 3.7 32.2 - - + +
159D ASN* 3.0 29.3 + - + +
161D ASP* 1.3 75.1 - - - +
163D ARG* 1.3 63.8 + - - +
165D LYS* 3.1 19.9 + - + +
166D LEU 3.3 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.0 29.7 + - - +
30B SER* 3.4 29.7 + - - -
34B LYS* 5.1 3.6 - - - +
78B ILE* 6.0 6.3 - - - +
82B GLU* 5.6 0.6 + - - -
157D LEU* 3.2 37.9 - - + +
158D LYS 3.8 12.3 + - - -
159D ASN 2.9 19.7 + - - +
160D PHE* 3.3 24.7 + - + +
162D LEU* 1.3 75.2 - - - +
164D ARG* 1.3 61.5 + - - +
166D LEU* 3.3 27.2 - - + +
167D ASP* 3.4 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D PHE* 3.1 46.3 + - + +
161D ASP* 3.1 39.5 + - - +
162D LEU 3.2 0.4 - - - -
163D ARG* 1.3 77.7 - - - +
165D LYS* 1.3 57.8 + - + +
167D ASP* 3.2 15.1 + - + +
168D TYR* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D GLN* 3.8 6.8 - - - +
113D PHE* 3.7 50.5 - - - +
116D GLY* 3.7 26.9 - - - +
117D ASP* 3.1 23.7 + - - +
152D LEU* 5.5 1.6 - - + -
161D ASP* 3.2 16.2 + - - +
162D LEU* 3.1 15.9 + - + +
164D ARG* 1.3 73.2 - - + +
166D LEU* 1.3 59.7 + - - +
168D TYR* 3.2 11.7 + - + +
169D VAL* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 6.2 0.4 - - - -
34B LYS* 3.5 36.3 - - + -
149D TYR* 3.5 30.3 - - + +
152D LEU* 3.5 35.8 - - + +
153D LEU* 3.6 28.3 - - + +
157D LEU* 4.4 8.3 - - + -
162D LEU 3.3 8.4 + - - +
163D ARG* 3.3 18.6 - - + +
165D LYS* 1.3 80.3 - - - +
167D ASP* 1.3 59.7 + - - +
169D VAL* 3.3 9.0 + - - +
170D SER 3.2 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS* 3.1 33.3 + - - -
149D TYR* 5.4 1.3 + - - -
163D ARG 3.4 12.3 + - - +
164D ARG* 3.2 16.2 + - - +
166D LEU* 1.3 74.4 - - - +
168D TYR* 1.3 66.3 + - - +
170D SER* 3.2 10.1 + - - -
171D ASN* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D GLY 3.7 24.5 - - - -
117D ASP* 4.2 18.1 + - + -
119D ALA* 4.5 2.2 - - + -
120D GLY* 3.2 36.3 + - - -
124D ARG* 5.3 2.1 + - - -
164D ARG 3.0 13.6 + - - +
165D LYS* 3.2 11.9 + - + +
167D ASP* 1.3 75.9 - - - +
169D VAL* 1.3 65.1 + - + +
171D ASN* 3.1 13.7 + - + +
172D ILE* 2.9 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D GLY* 4.4 11.0 - - - +
119D ALA* 4.0 27.4 - - + -
145D LEU* 4.0 22.9 - - + +
148D LEU* 4.7 9.4 - - + -
149D TYR* 4.0 20.2 - - + +
152D LEU* 4.3 20.9 - - + -
165D LYS 2.9 19.1 + - - +
166D LEU 3.5 7.9 - - - +
167D ASP 3.3 0.2 - - - -
168D TYR* 1.3 74.8 - - + +
170D SER* 1.3 63.5 + - - +
172D ILE* 3.2 4.0 + - - +
173D ILE* 3.0 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D TYR* 3.8 26.7 + - - -
166D LEU 3.2 4.1 + - - -
167D ASP* 3.2 13.0 + - - -
169D VAL* 1.3 81.2 - - - +
171D ASN* 1.3 62.6 + - - +
173D ILE* 3.4 14.0 + - - +
174D ASN* 3.2 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ASP* 3.0 23.3 + - - +
168D TYR* 3.1 13.8 + - + +
170D SER* 1.3 77.2 + - - +
172D ILE* 1.3 68.5 + - + +
174D ASN* 3.2 15.2 + - - +
175D LYS* 3.1 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ALA* 3.5 36.1 - - + +
120D GLY* 4.2 7.6 - - - -
123D LEU* 3.8 31.2 - - + -
145D LEU* 3.7 17.7 - - + -
168D TYR* 2.9 44.1 + - + +
169D VAL 3.5 6.7 - - - +
171D ASN* 1.3 76.5 - - + +
173D ILE* 1.3 64.1 + - - +
175D LYS* 3.1 11.4 + - + +
176D LEU* 2.9 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 5.6 1.8 - - + -
128B GLU* 5.4 0.2 - - - +
142D LYS* 4.6 6.1 - - + +
145D LEU* 3.7 46.2 - - + +
146D GLU* 3.9 27.6 - - + +
149D TYR* 4.1 10.3 - - + -
169D VAL* 3.0 27.8 + - + +
170D SER* 3.6 11.4 - - - +
171D ASN 3.3 0.2 - - - -
172D ILE* 1.3 76.0 - - - +
174D ASN* 1.3 60.6 + - - +
176D LEU* 3.3 7.9 + - - +
177D ILE* 2.9 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY 5.7 0.8 + - - -
124B ARG* 3.1 34.3 - - - +
127B SER* 6.2 0.2 - - - -
170D SER* 3.2 20.6 + - - +
171D ASN* 3.5 18.0 + - - +
172D ILE 3.2 0.2 - - - -
173D ILE* 1.3 80.3 - - - +
175D LYS* 1.3 57.1 + - + +
177D ILE* 3.4 14.8 + - - +
178D GLU* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU* 4.3 24.5 - - + -
171D ASN* 3.1 16.0 + - + +
172D ILE* 3.1 12.0 + - + +
174D ASN* 1.3 72.3 - - + +
176D LEU* 1.3 66.9 + - - +
178D GLU* 3.2 9.4 - - - +
179D PHE* 3.0 44.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D ILE* 5.5 0.2 - - + -
123D LEU* 3.9 19.7 - - + +
126D SER* 3.9 25.1 - - - +
130D LEU* 4.7 7.2 - - + -
138D ALA* 3.8 22.2 - - + +
141D ALA* 3.9 11.0 - - + -
142D LYS* 3.5 37.5 - - + +
145D LEU* 4.0 17.7 - - + -
172D ILE 2.9 10.7 + - - +
173D ILE* 3.5 9.6 - - - +
175D LYS* 1.3 73.0 - - - +
177D ILE* 1.3 65.2 + - - +
179D PHE* 3.1 6.3 + - + +
180D ILE* 2.8 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG* 5.6 1.8 - - + +
127B SER* 3.8 28.5 - - - +
128B GLU* 3.5 33.4 - - + +
131B ILE* 3.8 21.7 - - + +
142D LYS* 4.0 20.4 - - + -
173D ILE* 2.9 35.6 + - + +
174D ASN* 3.6 15.7 - - - +
175D LYS 3.4 0.2 - - - -
176D LEU* 1.3 75.7 - - - +
178D GLU* 1.3 57.4 + - - +
180D ILE* 3.2 9.6 + - - +
181D ILE* 2.9 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PHE* 3.9 28.5 - - + -
174D ASN 3.0 13.6 + - - +
175D LYS* 3.2 13.5 - - - +
177D ILE* 1.3 78.8 - - - +
179D PHE* 1.3 69.6 + - + +
181D ILE* 3.2 11.8 + - + +
182D TRP* 3.0 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU* 3.7 25.1 - - + -
127D SER* 3.5 25.6 - - - -
130D LEU* 3.6 26.9 - - + -
175D LYS* 3.0 37.4 + - + -
176D LEU* 3.1 7.2 + - + +
178D GLU* 1.3 84.1 - - + +
180D ILE* 1.3 57.6 + - - +
182D TRP* 3.4 17.9 + + - +
183D LYS* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 4.6 17.0 - - + -
130D LEU* 5.3 0.9 - - + -
135D ILE* 3.7 11.2 - - + +
138D ALA* 3.7 43.1 - - + +
139D LYS* 4.0 35.7 - - + +
142D LYS* 4.1 22.9 - - + -
176D LEU* 2.8 23.9 + - + +
177D ILE* 3.5 8.1 - - - +
179D PHE* 1.3 73.9 - - - +
181D ILE* 1.3 60.3 + - - +
183D LYS* 3.4 1.0 + - - -
184D SER* 2.5 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B SER* 3.4 31.2 - - - +
130B LEU* 3.8 26.5 - - + +
131B ILE* 3.3 30.5 - - + +
179B PHE* 5.3 13.0 - - + -
182B TRP* 3.1 48.0 - - + -
177D ILE* 2.9 21.7 + - + +
178D GLU* 3.5 11.4 - - + +
180D ILE* 1.3 76.6 - - - +
182D TRP* 1.3 68.3 + - + +
184D SER* 3.3 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 2.9 37.7 + - + -
179B PHE* 4.5 12.8 - + - -
182B TRP* 3.1 65.8 + + + -
178D GLU* 3.0 42.5 + - + +
179D PHE* 3.5 19.2 - + - +
181D ILE* 1.3 79.3 - - + +
183D LYS* 1.3 62.9 - - + +
184D SER 3.3 7.4 + - - +
178E GLU* 4.2 16.8 - - - -
182E TRP* 4.4 13.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D LEU* 3.0 52.5 + - + -
131D ILE* 4.8 3.6 + - - +
133D GLY* 3.6 19.6 - - - +
135D ILE* 3.7 26.4 - - + +
179D PHE* 3.0 16.0 + - + +
180D ILE 3.8 0.2 - - - +
181D ILE 3.3 0.2 - - - -
182D TRP* 1.3 77.3 - - + +
184D SER* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 5.6 4.6 + - - -
182B TRP* 3.6 20.1 - - - -
135D ILE* 3.7 12.3 - - - +
139D LYS* 5.1 4.0 + - - -
180D ILE* 2.5 28.5 + - - +
181D ILE* 3.6 9.4 - - - -
182D TRP 3.2 9.4 - - - +
183D LYS* 1.3 81.4 - - - +
----------------------------------------------------------
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