Contacts of the helix formed by residues 162 - 179 (chain B) in PDB entry 4BT9
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 ASP 162 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 5.7 2.9 - - - +
122B ASP* 4.8 5.1 - - - +
157B ALA* 3.0 19.7 + - + +
160B GLU* 3.2 9.6 - - + +
161B ALA* 1.3 74.7 - - - +
163B TYR* 1.3 53.3 + - - +
164B TYR* 3.6 8.8 + - - +
165B HIS* 2.6 46.9 + - - +
166B THR* 2.7 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR* 3.9 28.7 + + - -
161B ALA* 3.4 40.5 + - + +
162B ASP* 1.3 73.5 + - - +
164B TYR* 1.3 60.7 + - - +
166B THR* 3.6 5.9 - - - -
167B GLU* 2.8 32.1 + - - +
196B TYR* 3.4 29.8 + + - -
197B ALA* 3.8 26.1 - - + +
200B GLN* 3.6 31.2 - - + -
201B GLN* 3.7 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASP* 5.5 0.2 - - - -
125B ASN* 4.3 15.0 + - - -
162B ASP* 3.6 7.9 - - - +
163B TYR* 1.3 80.0 - - - +
165B HIS* 1.3 84.0 + + - +
167B GLU* 3.4 4.7 + - - +
168B LEU* 3.2 58.1 + - + +
201B GLN* 3.4 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 4.2 15.6 + - + +
121B GLN* 3.7 42.1 + - + +
122B ASP* 3.3 41.3 - - + -
126B LEU 5.5 0.2 + - - -
157B ALA* 4.0 13.2 - - + -
162B ASP* 2.6 38.4 + - - +
164B TYR* 1.3 98.5 - + + +
166B THR* 1.3 65.9 - - - +
168B LEU* 4.0 8.1 - - + -
169B TRP* 3.0 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLY* 3.8 18.4 - - - +
157B ALA* 3.8 1.2 - - - +
158B TYR* 3.1 38.7 + - + -
162B ASP 2.7 23.4 + - - -
163B TYR* 3.6 11.0 - - - -
165B HIS* 1.3 77.4 - - - +
167B GLU* 1.3 57.5 + - - +
170B MET* 2.9 53.8 + - + +
193B TYR 4.5 4.7 - - - +
197B ALA* 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TYR 2.8 17.8 + - - +
164B TYR* 3.6 5.2 - - - +
166B THR* 1.3 77.1 - - - +
168B LEU* 1.3 67.7 + - + +
171B GLU* 2.9 44.2 + - - +
194B LEU* 3.8 18.4 - - + -
197B ALA* 4.6 5.4 - - + -
198B VAL* 3.8 16.1 - - + +
201B GLN* 3.8 25.3 + - - +
206B LYS* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLN* 4.3 10.1 - - - +
126B LEU 5.2 4.0 - - - +
127B ASP* 5.7 2.7 - - - -
128B THR* 4.0 21.6 - - + +
164B TYR* 3.2 50.6 + - + +
165B HIS* 3.8 19.5 - - + +
166B THR 3.4 0.2 - - - -
167B GLU* 1.3 83.4 - - + +
169B TRP* 1.3 65.0 + - + +
171B GLU* 3.9 7.8 - - - +
172B GLN* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.2 1.1 - - + +
118B LEU* 3.8 18.9 - - + +
121B GLN* 2.9 41.2 + - - +
128B THR* 3.9 29.6 - - + -
131B ILE* 3.9 20.6 - - + -
132B SER* 5.4 0.9 - - - -
145B LEU* 3.6 32.3 - - + -
150B CYS* 3.4 53.3 - - + +
153B LEU* 3.9 24.9 - - + +
154B GLY* 3.6 9.6 - - - +
165B HIS* 3.0 28.8 + - + +
168B LEU* 1.3 74.5 - - + +
170B MET* 1.3 62.0 + - - +
172B GLN* 3.3 4.6 + - + +
173B ALA* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE* 3.4 55.9 - - + +
154B GLY* 3.9 5.6 - - - +
155B LYS* 3.8 18.2 - - + +
166B THR* 2.9 33.6 + - + +
169B TRP* 1.3 73.0 - - - +
171B GLU* 1.3 60.9 + - - +
173B ALA* 3.2 4.7 + - - +
174B LEU* 2.8 31.5 + - - +
190B VAL* 3.7 12.7 - - + +
193B TYR* 3.7 28.0 - - + -
194B LEU* 3.9 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 2.9 33.3 + - - +
168B LEU* 3.9 7.6 - - - +
170B MET* 1.3 76.4 - - - +
172B GLN* 1.3 58.4 + - - +
174B LEU* 3.8 8.3 - - + +
175B ARG* 2.9 28.8 + - - +
194B LEU* 4.0 21.4 - - + +
206B LYS* 2.6 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B THR* 4.1 19.2 + - - +
129B ASP* 4.7 10.1 + - - +
143B SER* 5.8 1.8 + - - -
150B CYS* 3.7 20.9 - - - -
168B LEU 3.2 14.5 + - - +
169B TRP* 3.6 14.6 - - + +
170B MET 3.2 0.8 - - - -
171B GLU* 1.3 77.3 - - - +
173B ALA* 1.3 63.6 + - - +
175B ARG* 3.4 20.5 + - - +
176B GLN* 3.0 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.5 28.9 - - - +
150B CYS* 3.7 9.6 - - + +
151B PHE* 4.0 8.3 - - + +
169B TRP 3.0 14.2 + - - +
170B MET* 3.5 9.9 - - - +
172B GLN* 1.3 77.0 - - - +
174B LEU* 1.3 61.3 + - - +
176B GLN* 3.2 3.8 + - - +
177B LEU* 3.0 28.4 + - - +
185B ILE* 4.2 12.3 - - + -
190B VAL* 4.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B MET 2.8 19.8 + - - +
171B GLU* 3.8 7.0 - - + +
173B ALA* 1.3 74.0 - - - +
175B ARG* 1.3 57.6 + - - +
177B LEU* 3.2 7.9 + - + +
178B ASP* 2.9 54.9 + - - +
187B LYS* 4.5 21.3 - - + -
190B VAL* 4.3 10.5 - - + +
191B LEU* 4.1 32.8 - - + -
194B LEU* 4.2 14.1 - - + -
210B LEU* 4.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLU 2.9 18.8 + - - +
172B GLN* 3.5 23.1 - - - +
173B ALA 3.2 0.2 - - - -
174B LEU* 1.3 77.6 - - - +
176B GLN* 1.3 62.2 + - - +
178B ASP* 3.2 10.2 + - - +
179B GLU* 3.0 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER* 4.4 8.5 + - - -
145B LEU 3.1 27.1 + - - +
147B ALA* 3.4 13.6 - - + +
150B CYS* 3.8 7.4 - - - -
172B GLN* 3.0 46.7 + - - +
173B ALA 3.2 4.0 + - - +
175B ARG* 1.3 75.5 - - - +
177B LEU* 1.3 62.3 + - - +
179B GLU* 3.2 24.7 + - - +
180B GLY 3.4 0.3 + - - -
181B GLU* 2.8 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.8 10.3 - - + -
173B ALA 3.0 17.2 + - - +
174B LEU* 3.6 11.0 - - - +
175B ARG 3.2 0.2 - - - -
176B GLN* 1.3 77.6 - - - +
178B ASP* 1.3 56.9 + - - +
180B GLY* 2.8 22.2 + - - -
181B GLU 3.9 11.6 + - - +
183B SER* 3.5 32.1 - - - -
185B ILE* 3.6 33.0 - - + +
187B LYS* 3.6 47.6 + - + -
190B VAL* 4.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 2.9 37.8 + - - +
175B ARG* 3.2 9.7 + - - +
177B LEU* 1.3 75.8 - - - +
179B GLU* 1.3 58.6 + - + +
180B GLY* 3.0 3.9 + - - -
187B LYS* 3.3 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 3.0 41.2 + - + +
176B GLN* 3.6 20.8 - - - +
177B LEU 3.1 0.8 - - - -
178B ASP* 1.3 76.2 - - + +
180B GLY* 1.3 59.2 + - - +
181B GLU 3.5 1.7 + - - +
----------------------------------------------------------
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