Contacts of the helix formed by residues 163 - 184 (chain o) in PDB entry 5JPQ
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 LYS 163 (chain o).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9352 U 5.6 0.2 - - - -
10452 C 2.1 98.7 + - - +
10462 G 3.6 34.9 + - - +
10472 G 5.6 0.6 + - - -
161o TYR* 5.4 0.2 - - - +
162o ALA* 1.3 74.0 - - - +
164o SER* 1.3 53.7 + - - +
165o SER* 2.6 10.8 + - - +
166o GLN* 2.4 52.4 + - - +
167o VAL 3.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8752 G 3.2 21.3 + - - -
8762 G 4.3 16.1 + - - -
9352 U 4.4 19.0 + - - +
9362 G 5.4 3.5 + - - -
10452 C 4.7 4.5 - - - -
162o ALA 3.1 5.8 + - - -
163o LYS* 1.3 69.0 - - - +
165o SER* 1.3 60.4 + - - +
167o VAL* 3.3 11.5 + - - +
168o ARG* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8742 C 2.4 48.0 + - - +
8752 G 2.3 23.7 + - - -
10452 C 3.7 1.4 + - - -
10462 G 3.0 21.0 + - - -
163o LYS* 2.6 14.9 + - - +
164o SER* 1.3 72.3 + - - +
166o GLN* 1.3 64.3 + - - +
168o ARG* 3.3 1.2 - - - +
169o ALA* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10462 G 5.3 1.1 - - - +
10662 C 4.0 2.9 + - - +
10672 C 3.2 5.6 + - - -
161o TYR 5.1 0.2 + - - -
162o ALA* 3.7 11.6 - - + +
163o LYS* 2.4 64.3 + - + +
165o SER* 1.3 73.5 - - - +
167o VAL* 1.3 68.6 + - - +
169o ALA* 2.9 20.2 - - - +
170o ILE* 3.1 14.2 + - - +
210o ILE* 3.4 22.1 - - + +
211o PHE* 3.0 28.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122o THR* 4.1 22.2 - - + -
123o LEU 5.5 0.9 - - - +
124o ILE* 3.3 33.9 - - + +
162o ALA* 3.4 24.7 - - + +
163o LYS 3.2 0.8 + - - -
164o SER* 3.4 15.5 - - - +
166o GLN* 1.3 76.4 - - - +
168o ARG* 1.3 55.4 + - - +
170o ILE* 2.6 35.0 + - - +
171o ARG* 3.2 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8742 C 1.5 30.1 + - - -
8752 G 0.9 209.5 + - - +
8762 G 3.4 13.1 + - - -
8772 G 5.5 0.2 + - - -
164o SER 3.2 8.2 + - - +
165o SER* 3.1 5.3 - - - +
167o VAL* 1.3 79.2 - - - +
169o ALA* 1.3 60.6 + - - +
171o ARG* 3.5 26.0 - - + +
172o ARG* 2.8 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165o SER 3.2 13.0 - - - +
166o GLN* 2.9 20.4 + - - +
167o VAL 2.9 0.4 - - - -
168o ARG* 1.3 83.9 - - - +
170o ILE* 1.3 58.5 + - - +
172o ARG* 3.7 7.3 - - - +
173o LYS* 3.3 17.5 + - - +
210o ILE* 3.2 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124o ILE* 3.7 29.4 - - + -
144o ALA* 5.5 0.4 - - + -
166o GLN* 3.2 16.2 - - + +
167o VAL* 2.6 12.5 + - - +
169o ALA* 1.3 70.5 - - - +
171o ARG* 1.3 55.5 + - - +
173o LYS* 2.9 5.2 + - + -
174o ILE* 2.5 54.9 + - + +
207o THR* 3.3 28.7 - - + +
210o ILE* 3.6 25.6 - - + -
211o PHE* 4.4 4.9 - - + +
213o LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8762 G 6.1 3.4 - - - -
9462 U 5.4 5.3 + - - -
123o LEU 5.5 1.8 + - - -
124o ILE* 4.1 11.7 - - + +
125o GLU* 3.1 32.0 + - - +
126o ALA* 4.1 18.2 - - + +
167o VAL* 3.2 31.7 + - - +
168o ARG* 3.1 24.3 + - + +
170o ILE* 1.3 78.7 - - - +
172o ARG* 1.3 68.1 + - - +
174o ILE* 4.4 1.3 - - - +
175o ASN* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168o ARG 2.8 21.1 + - - +
169o ALA* 3.7 7.6 - - - +
171o ARG* 1.3 74.0 - - - +
173o LYS* 1.3 58.1 - - + +
175o ASN* 4.6 1.9 - - - +
176o THR* 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10562 U 5.5 0.2 + - - -
10642 G 3.1 26.3 + - - -
10652 A 3.6 5.7 + - - -
169o ALA 3.3 9.1 + - - +
170o ILE* 2.9 12.6 + - + +
172o ARG* 1.3 79.9 - - + +
174o ILE* 1.3 65.6 + - + +
176o THR* 3.5 4.0 + - - +
177o PHE* 3.0 23.2 + - - +
206o GLU* 2.9 61.1 + - + +
207o THR* 5.5 0.9 - - - +
209o ASN* 3.7 4.0 - - - +
210o ILE* 4.3 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126o ALA* 4.0 4.7 - - + -
142o THR* 3.6 27.1 - - + +
144o ALA* 5.1 11.7 - - + -
170o ILE* 2.5 40.8 + - + +
171o ARG* 2.9 4.0 + - - +
173o LYS* 1.3 70.6 - - + +
175o ASN* 1.3 81.6 + - - +
177o PHE* 2.9 18.1 + - - +
178o ILE* 3.1 27.7 + - + +
203o ILE* 3.5 45.5 - - + -
206o GLU* 6.5 2.0 - - + -
207o THR* 4.6 1.1 - - - +
213o LEU* 5.2 0.4 - - + -
216o ILE* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 175 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126o ALA* 2.8 34.1 - - - +
127o ARG 2.6 23.6 + - - +
128o VAL* 3.1 33.2 - - + +
171o ARG* 2.9 20.3 + - - +
172o ARG* 4.6 1.8 - - - +
174o ILE* 1.3 73.7 - - - +
176o THR* 1.3 63.9 + - - +
178o ILE* 2.9 14.5 + - - +
179o THR* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172o ARG* 3.0 25.0 + - - +
173o LYS* 3.8 5.4 - - - +
174o ILE 3.3 0.6 - - - -
175o ASN* 1.3 78.8 - - - +
177o PHE* 1.3 55.9 + - - +
179o THR* 3.8 5.6 + - - -
180o ASN* 2.5 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173o LYS 3.0 12.4 + - - +
174o ILE* 2.9 10.8 + - - +
176o THR* 1.3 78.2 - - - +
178o ILE* 1.3 73.4 + - + +
180o ASN* 3.5 7.7 + - - +
181o GLU* 3.1 41.4 + - + +
199o TYR* 3.6 39.0 - + - -
202o LYS* 4.0 34.3 - - + -
203o ILE* 4.3 20.6 - - + -
206o GLU* 5.4 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128o VAL* 4.1 17.3 - - + -
130o CYS* 3.6 21.6 - - - -
140o VAL* 4.2 12.8 - - + -
142o THR* 4.2 7.9 - - + +
174o ILE* 3.1 36.6 - - + +
175o ASN* 2.9 4.7 + - - +
177o PHE* 1.3 86.9 - - + +
179o THR* 1.3 64.2 + - - +
180o ASN 3.1 2.5 - - - -
181o GLU* 3.1 7.7 + - + +
182o ALA 3.0 19.6 + - - -
190o PHE* 3.9 20.2 - - + -
194o LEU* 5.5 2.0 - - + -
199o TYR* 5.0 6.7 - - + -
203o ILE* 5.1 5.2 - - + -
218o ILE* 6.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128o VAL* 3.5 16.6 - - - +
129o ASP 4.2 15.7 + - - +
130o CYS* 4.0 12.9 - - - -
131o LYS* 4.5 9.3 - - + +
175o ASN 3.0 15.4 + - - -
176o THR* 3.8 6.4 + - - -
177o PHE 3.5 0.2 - - - -
178o ILE* 1.3 76.7 - - - +
180o ASN* 1.3 64.2 + - - +
182o ALA* 4.1 2.1 - - - +
183o ALA* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176o THR* 2.5 35.3 + - - +
177o PHE* 3.5 8.5 + - - +
178o ILE 3.1 0.4 - - - -
179o THR* 1.3 79.9 - - - +
181o GLU* 1.3 66.6 + - - +
182o ALA 3.2 0.6 + - - -
183o ALA* 3.5 14.0 + - - +
184o LYS* 3.5 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177o PHE* 3.1 33.4 + - + +
178o ILE* 3.1 15.4 + - + +
180o ASN* 1.3 79.2 - - - +
182o ALA* 1.3 59.5 + - - +
184o LYS* 3.5 12.0 + - - +
185o LEU* 3.4 37.5 - - + +
190o PHE* 4.8 2.5 - - + -
199o TYR* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130o CYS* 3.3 25.1 - - + -
131o LYS 3.2 9.2 - - - +
132o THR* 3.3 20.8 - - + +
178o ILE 3.0 8.1 + - - +
179o THR 4.1 0.9 - - - +
181o GLU* 1.3 73.1 - - - +
183o ALA* 1.3 58.3 + - - +
184o LYS 2.8 11.6 + - - -
185o LEU* 2.9 12.5 + - - +
190o PHE* 3.0 37.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131o LYS* 2.9 20.2 + - + +
132o THR* 4.6 0.4 - - - +
133o ASN* 3.0 18.6 + - - +
179o THR* 3.3 17.2 + - + +
180o ASN* 3.5 9.6 + - - +
182o ALA* 1.3 75.4 - - - +
184o LYS* 1.3 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133o ASN* 3.4 7.6 - - - +
180o ASN 3.5 13.3 + - - +
181o GLU* 4.0 10.5 - - - +
182o ALA 2.8 1.4 + - - -
183o ALA* 1.3 80.6 - - - +
185o LEU* 1.3 73.6 + - + +
----------------------------------------------------------
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