Contacts of the helix formed by residues 171 - 188 (chain A) in PDB entry 3J8B
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 GLU 171 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASN 2.9 9.1 + - - +
168A SER* 3.7 15.9 + - - +
169A ARG 3.4 2.4 - - - -
170A VAL* 1.3 77.0 - - - +
172A ARG* 1.3 58.7 + - - +
174A TYR* 3.7 5.8 - - - +
175A HIS* 2.9 31.2 + - - +
218A ILE* 6.2 3.4 - - + -
225A SER* 5.9 8.5 - - - -
228A MET* 5.4 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ARG 5.1 1.2 + - - +
170A VAL 3.4 0.4 - - - -
171A GLU* 1.3 77.8 - - - +
173A LEU* 1.3 63.5 + - - +
175A HIS* 3.3 7.5 + - - +
176A ASP* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.9 34.3 - - + +
90A VAL* 5.7 4.0 - - + -
91A ARG* 6.2 1.8 - - + -
164A LEU* 5.4 2.9 - - + -
169A ARG 5.9 0.2 - - - +
170A VAL* 3.4 9.4 + - + +
171A GLU 3.3 0.2 - - - -
172A ARG* 1.3 76.3 - - - +
174A TYR* 1.3 64.9 + - - +
176A ASP* 3.2 8.8 + - - +
177A ILE* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 5.8 2.9 - - - +
164A LEU* 3.7 32.2 - - + +
165A ARG* 5.5 2.2 - - - -
166A ASN 6.0 0.2 - - - +
170A VAL 2.8 19.9 + - - +
171A GLU* 3.7 6.1 - - - +
173A LEU* 1.3 76.3 - - - +
175A HIS* 1.3 60.9 + - - +
176A ASP 3.3 0.2 + - - -
177A ILE* 3.3 7.2 + - - +
178A ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU 2.9 19.7 + - - +
172A ARG* 3.6 7.4 - - - +
173A LEU 3.3 0.2 - - - -
174A TYR* 1.3 74.6 - - - +
176A ASP* 1.3 61.9 + - - +
178A ALA* 3.4 9.0 + - - +
179A GLN* 3.3 20.3 + - - +
228A MET* 4.3 27.1 - - + +
232A THR* 5.8 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ARG 3.1 12.4 + - - +
173A LEU* 3.4 12.3 - - - +
174A TYR 3.1 0.2 - - - -
175A HIS* 1.3 74.9 - - - +
177A ILE* 1.3 64.2 + - - +
179A GLN* 3.2 8.7 + - - +
180A GLN* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 5.7 9.0 - - + -
157A TYR* 5.6 5.8 - - + +
160A CYS* 5.2 15.5 - - + -
161A LEU* 5.5 9.4 - - + +
173A LEU 3.1 9.7 + - - +
174A TYR* 3.9 8.5 - - - +
176A ASP* 1.3 75.9 - - - +
178A ALA* 1.3 61.4 + - - +
180A GLN* 3.2 8.7 + - - +
181A ALA* 2.7 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 6.3 2.2 - - - +
174A TYR 3.1 12.5 + - - +
175A HIS* 3.5 13.2 - - - +
176A ASP 3.2 0.4 - - - -
177A ILE* 1.3 76.9 - - - +
179A GLN* 1.3 62.6 + - - +
181A ALA* 3.1 7.8 + - - +
182A PHE* 2.9 24.8 + - - +
232A THR* 4.8 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A HIS 3.3 8.3 + - - +
176A ASP* 3.2 11.7 + - - +
178A ALA* 1.3 78.7 - - - +
180A GLN* 1.3 61.0 + - - +
182A PHE* 3.4 6.2 + - - +
183A LYS* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 6.4 1.6 - - + -
176A ASP 3.1 13.2 + - - +
177A ILE* 3.5 12.1 - - - +
179A GLN* 1.3 77.3 - - - +
181A ALA* 1.3 62.7 + - - +
183A LYS* 3.3 8.1 + - - +
184A PHE* 3.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 4.3 25.4 - - + -
161A LEU* 6.6 0.2 - - + -
177A ILE 2.7 16.9 + - - +
178A ALA* 3.1 8.7 + - - +
180A GLN* 1.3 78.4 - - - +
182A PHE* 1.3 60.1 + - - +
184A PHE* 3.3 9.5 + - - +
185A CYS* 3.2 19.9 + - - +
197A LEU* 6.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ALA 2.9 15.4 + - - +
179A GLN* 3.9 6.3 - - - +
181A ALA* 1.3 72.7 - - - +
183A LYS* 1.3 66.3 + - - +
184A PHE 3.1 1.6 - - - -
185A CYS* 3.2 8.2 + - - +
186A LEU* 3.1 22.5 + - - +
235A VAL* 5.3 14.4 - - + +
236A GLN* 5.8 2.5 - - - +
239A SER* 4.8 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLN 3.0 17.8 + - - +
180A GLN* 3.7 8.1 - - - +
181A ALA 3.3 0.2 - - - -
182A PHE* 1.3 76.2 - - - +
184A PHE* 1.3 57.5 + - - +
186A LEU* 3.4 6.4 + - - +
187A GLN* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLN 3.1 13.7 + - - +
181A ALA* 3.3 13.9 - - - +
182A PHE 3.1 0.2 - - - -
183A LYS* 1.3 77.7 - - - +
185A CYS* 1.3 60.9 - - - +
187A GLN* 3.3 4.8 + - - +
188A TYR* 3.0 28.6 + - - +
190A ARG* 5.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA 3.2 10.0 + - - +
182A PHE* 3.2 10.7 + - - +
184A PHE* 1.3 80.6 - - - +
186A LEU* 1.3 57.4 + - - +
189A THR* 3.0 9.9 + - - -
190A ARG* 2.9 39.9 + - + +
193A GLU* 6.0 0.2 - - + -
194A PHE* 3.9 31.6 - - + +
239A SER* 6.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE 3.1 15.4 + - - +
183A LYS* 3.8 6.5 - - - +
184A PHE 3.3 0.2 - - - -
185A CYS* 1.3 77.9 - - - +
187A GLN* 1.3 62.5 + - - +
188A TYR 3.4 0.9 + - - -
189A THR* 3.6 7.7 + - - +
239A SER* 4.9 16.3 - - - +
242A SER* 5.8 6.7 - - - -
243A MET* 6.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS 2.9 18.8 + - - +
184A PHE* 3.8 5.2 - - - +
186A LEU* 1.3 78.9 - - - +
188A TYR* 1.3 58.2 + - + +
189A THR 3.5 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 6.1 5.2 - - + -
184A PHE 3.0 14.1 + - - +
187A GLN* 1.3 77.9 - - + +
189A THR* 1.3 71.2 + - - +
190A ARG* 3.0 11.7 + - + +
----------------------------------------------------------
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