Contacts of the helix formed by residues 169 - 185 (chain B) in PDB entry 4J1O
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 PRO 169 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 1.3 89.8 - - + +
170B VAL* 1.3 65.4 + - - +
171B GLU* 3.1 29.6 - - + +
172B ILE* 3.0 35.0 + - + +
173B ASP 3.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ILE* 5.5 0.9 - - + -
168B ARG 3.3 3.5 + - - +
169B PRO* 1.3 71.4 - - - +
171B GLU* 1.3 67.8 + - - +
173B ASP* 3.0 24.1 + - + +
174B ILE* 2.9 32.3 + - + +
199B LEU* 4.9 8.3 - - + -
203B ASP* 3.7 52.2 + - + +
206B ARG* 3.5 35.0 - - - +
207B LEU* 4.8 4.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
169B PRO* 3.2 28.7 - - + +
170B VAL* 1.3 81.2 + - - +
172B ILE* 1.3 64.9 + - + +
174B ILE* 3.4 7.3 + - - +
175B GLU* 3.0 29.0 + - - +
206B ARG* 3.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PRO* 4.0 19.9 - - + +
168B ARG* 3.6 35.7 - - + +
169B PRO* 3.0 33.1 + - + +
171B GLU* 1.3 84.5 - - + +
173B ASP* 1.3 60.9 + - - +
175B GLU* 3.4 10.6 + - - +
176B THR* 2.9 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ILE* 3.3 33.0 - - + +
166B GLY* 3.1 26.1 + - - -
168B ARG* 2.8 42.1 + - - +
169B PRO 4.4 0.9 - - - -
170B VAL* 3.0 30.0 + - + +
172B ILE* 1.3 79.1 - - - +
174B ILE* 1.3 56.8 + - + +
176B THR* 3.2 3.0 + - - -
177B VAL* 3.0 34.3 + - + +
199B LEU* 4.3 2.9 - - - +
207B LEU* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 2.9 26.7 + - + +
171B GLU* 3.8 7.0 - - - +
173B ASP* 1.3 74.3 - - - +
175B GLU* 1.3 65.1 + - - +
177B VAL* 3.3 7.3 + - - +
178B ARG* 2.9 35.9 + - + +
206B ARG* 3.7 32.5 - - + +
207B LEU* 3.9 29.2 - - + -
210B GLU* 3.5 28.3 - - + +
211B CYS* 4.1 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PRO* 3.6 21.9 - - + +
144B ASP* 4.6 0.3 - - - +
171B GLU 3.0 17.0 + - - +
172B ILE* 3.7 11.1 - - - +
174B ILE* 1.3 75.8 - - - +
176B THR* 1.3 57.3 + - - +
178B ARG* 3.4 7.5 + - + +
179B LYS* 2.4 67.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY 4.2 0.9 + - - -
143B PRO* 3.5 25.5 - - + +
146B ILE* 3.8 28.9 - - + -
163B ILE* 3.8 26.5 - - + -
164B LYS 5.5 0.7 - - - +
165B ILE* 5.3 0.7 - - + -
168B ARG* 3.4 18.4 + - - +
172B ILE 2.9 15.8 + - - -
173B ASP* 3.4 9.6 - - - -
175B GLU* 1.3 77.2 - - - +
177B VAL* 1.3 56.4 + - - +
179B LYS* 3.3 1.6 + - - +
180B VAL* 2.9 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 5.0 6.1 - - + -
165B ILE* 4.6 6.3 - - + -
173B ASP* 3.0 22.1 + - + +
174B ILE* 3.7 5.8 - - - +
176B THR* 1.3 74.5 - - - +
178B ARG* 1.3 57.9 + - + +
180B VAL* 3.4 6.1 + - - +
181B TRP* 2.9 28.6 + - - +
191B LEU* 4.7 4.9 - - + +
193B VAL* 3.8 32.8 - - + -
207B LEU* 4.4 11.4 - - + -
211B CYS* 5.0 2.0 - - - -
214B ILE* 4.0 18.6 - - + -
216B PHE* 3.9 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 2.9 32.4 + - + +
175B GLU* 3.8 6.5 - - - +
177B VAL* 1.3 77.0 - - - +
179B LYS* 1.3 59.1 + - + +
181B TRP* 3.4 3.1 + - - +
182B GLU* 3.0 28.1 + - - +
210B GLU* 2.7 35.2 + - - +
211B CYS* 3.8 11.3 - - - -
213B GLU* 2.6 29.7 + - - -
214B ILE* 3.9 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PRO* 3.8 17.5 - - + +
144B ASP* 2.9 43.0 + - - +
147B ALA* 3.5 23.2 - - + +
175B GLU* 2.4 48.2 + - + +
176B THR 4.0 1.8 - - - +
178B ARG* 1.3 75.4 - - + +
180B VAL* 1.3 66.9 + - - +
182B GLU* 3.4 16.0 + - - +
183B ARG* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 3.9 23.1 - - + +
147B ALA* 3.9 24.5 - - - +
150B ALA* 3.9 17.3 - - + -
161B LEU* 4.7 0.7 - - + -
163B ILE* 4.1 22.9 - - + -
176B THR* 2.9 23.4 + - + +
177B VAL* 3.8 6.7 - - - +
179B LYS* 1.3 76.6 - - - +
181B TRP* 1.3 63.5 + - - +
183B ARG* 3.0 12.2 + - - -
184B ILE* 3.0 31.5 + - + +
191B LEU* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL 2.9 18.1 + - - +
178B ARG 3.7 4.3 - - - +
180B VAL* 1.3 77.4 - - - +
182B GLU* 1.3 65.0 + - - +
184B ILE* 3.9 25.1 - - + -
185B ARG* 2.9 84.5 + - + +
186B GLY 4.8 3.6 - - - -
189B THR 4.7 9.6 - - - -
191B LEU* 4.5 7.6 - - + -
213B GLU* 4.0 15.5 + - + +
214B ILE* 3.8 32.5 - - + -
215B PRO* 3.4 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ARG 3.0 15.1 + - - +
179B LYS* 3.6 20.7 - - - +
181B TRP* 1.3 78.1 - - - +
183B ARG* 1.3 65.6 + - + +
185B ARG* 3.7 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASP 5.1 1.6 + - - -
147B ALA* 3.5 28.7 - - + +
148B ARG* 3.7 27.7 + - - +
151B ALA* 3.6 30.2 - - + +
179B LYS 3.4 11.6 + - - +
180B VAL 3.0 7.3 + - - +
182B GLU* 1.3 87.3 - - + +
184B ILE* 1.3 61.6 + - + +
185B ARG 3.6 1.7 - - - +
187B THR* 4.6 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ALA* 4.3 13.9 - - + +
151B ALA* 4.6 3.1 - - - +
154B VAL* 3.8 24.0 - - + -
161B LEU* 4.1 17.7 - - + -
180B VAL* 3.0 31.3 + - + +
181B TRP* 3.9 22.5 - - + -
183B ARG* 1.3 81.2 - - + +
185B ARG* 1.3 69.2 + - - +
186B GLY 3.4 0.2 + - - -
187B THR* 2.5 36.2 + - - +
188B GLY 4.5 0.9 + - - -
189B THR* 4.3 23.3 + - + +
191B LEU* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B TRP* 2.9 67.3 + - + +
182B GLU* 3.7 19.9 - - - +
183B ARG 4.8 1.9 - - - +
184B ILE* 1.3 79.3 - - - +
186B GLY* 1.3 59.8 - - - +
187B THR* 3.5 4.3 + - - +
213B GLU* 6.2 1.8 - - - +
----------------------------------------------------------
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