Contacts of the helix formed by residues 171 - 183 (chain B) in PDB entry 1PJS
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 THR 171 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE 3.5 0.6 - - - -
170B ALA* 1.3 79.6 - - - +
172B MET* 1.3 66.1 + - - +
173B GLY* 3.7 6.6 + - - -
174B GLU* 2.7 62.7 + - + +
175B ARG* 3.1 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ALA 4.3 0.2 + - - -
171B THR* 1.3 72.3 + - - +
173B GLY* 1.3 63.0 + - - +
175B ARG* 2.9 44.7 + - - +
176B ARG* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B THR* 3.0 8.2 + - - -
172B MET* 1.3 77.8 - - - +
174B GLU* 1.3 59.8 + - - +
176B ARG* 3.6 7.5 + - - +
177B ARG* 3.3 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN 5.0 1.2 - - - +
169B PHE* 3.8 32.1 - - + -
170B ALA* 4.0 6.1 + - - +
171B THR* 2.7 49.7 + - + +
173B GLY* 1.3 70.9 - - - -
175B ARG* 1.3 63.3 + - - +
176B ARG 3.2 0.2 - - - -
177B ARG* 3.3 24.8 + - - +
178B PHE* 3.1 20.1 + - - +
212B LEU* 3.9 15.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
165B VAL* 3.8 14.1 - - + -
166B LYS* 3.7 42.7 + - - +
169B PHE* 2.9 40.3 + - + +
170B ALA* 4.4 13.2 + - - +
171B THR 3.1 7.0 + - - +
172B MET* 2.9 51.3 - - - +
174B GLU* 1.3 73.4 - - - +
176B ARG* 1.3 64.5 + - - +
178B PHE* 3.3 8.3 - - - +
179B TRP* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 5.2 11.9 - - + -
137A ARG* 5.7 5.3 - - - +
138A LEU* 3.4 27.5 - - + +
141A GLU* 3.2 33.3 + - - -
172B MET 3.0 15.9 + - - +
173B GLY* 3.8 7.9 - - - +
174B GLU 3.2 0.2 - - - -
175B ARG* 1.3 73.6 - - - +
177B ARG* 1.3 67.4 + - + +
178B PHE 3.0 1.6 - - - -
179B TRP* 2.9 11.7 + - - +
180B GLU* 2.9 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLY 3.3 14.4 + - - +
174B GLU* 3.3 22.2 + - - +
176B ARG* 1.3 80.3 - - + +
178B PHE* 1.3 62.2 + - - +
180B GLU* 3.3 23.6 + - - +
181B LYS* 3.1 22.9 + - - +
212B LEU* 3.0 42.8 - - + +
213B ASP* 2.7 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.8 2.0 - - + -
165B VAL* 3.5 25.1 - - + -
169B PHE* 3.3 28.0 - + + -
174B GLU 3.1 12.7 + - - +
175B ARG* 3.3 13.7 - - - +
176B ARG 3.0 0.8 - - - -
177B ARG* 1.3 77.3 - - - +
179B TRP* 1.3 69.5 + + - +
181B LYS* 2.9 17.1 + - + +
182B PHE* 2.8 55.5 + + + +
207B LEU* 3.7 34.8 - - + -
208B PHE* 3.7 33.7 - + - -
212B LEU* 4.4 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.6 43.9 - - + +
138A LEU* 4.7 0.7 - - - -
158B ALA* 3.6 35.9 - - + -
161B LEU* 4.4 2.7 - - + -
162B ARG* 4.1 24.0 - - + -
165B VAL* 3.9 30.8 - - + +
175B ARG* 3.0 25.4 + - + +
176B ARG* 2.9 7.2 + - - +
178B PHE* 1.3 92.8 - + - +
180B GLU* 1.3 57.8 + - - +
182B PHE* 3.6 35.7 - + - -
183B PHE* 2.8 47.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.1 24.2 - - + -
505A PGE 5.1 2.5 - - - +
176B ARG* 2.9 56.9 + - - +
177B ARG* 3.3 29.9 - - - +
179B TRP* 1.3 76.6 - - - +
181B LYS* 1.3 58.0 + - - +
183B PHE* 4.4 2.0 - - - +
184B VAL* 3.2 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 6.1 0.2 - - - -
177B ARG 3.1 11.9 + - - +
178B PHE* 2.9 14.5 + - + +
180B GLU* 1.3 77.2 - - - +
182B PHE* 1.3 64.1 + - - +
184B VAL* 3.4 19.5 - - + +
185B ASN* 3.4 12.4 + - - +
207B LEU* 3.7 32.7 + - + -
210B GLU* 2.8 29.8 + - - +
211B PRO 3.7 6.5 + - - -
212B LEU* 3.1 41.4 + - - +
214B HIS 3.6 7.4 + - - +
215B ARG* 4.2 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 3.2 45.8 - - + +
157B TYR* 3.9 8.7 - + - -
158B ALA* 3.8 16.8 - - + -
161B LEU* 3.5 27.6 - - + -
178B PHE* 2.8 29.0 + + + +
179B TRP* 3.6 28.5 - + - +
181B LYS* 1.3 79.2 - - - +
183B PHE* 1.3 74.8 + + - +
185B ASN* 3.3 21.6 + - - +
188B LEU* 3.5 17.2 - - + +
207B LEU* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER* 3.5 22.4 - - - -
134A VAL* 4.3 2.9 - - + -
135A LEU* 3.5 55.4 - - + -
138A LEU* 4.6 4.5 - - + -
505A PGE 3.9 23.2 - - - +
148B PRO* 5.8 2.1 - - - +
151B LEU* 3.9 19.9 - - + +
154B VAL* 3.8 24.8 - - + +
155B ALA* 3.9 1.8 - - - -
158B ALA* 4.2 5.2 - - + -
179B TRP* 2.8 55.8 + + + +
180B GLU* 4.6 1.6 - - - +
182B PHE* 1.3 92.3 - + - +
184B VAL* 1.3 62.2 + - - +
185B ASN 3.4 0.4 - - - -
186B ASP* 5.6 0.3 - - - +
----------------------------------------------------------
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