Contacts of the helix formed by residues 159 - 173 (chain A) in PDB entry 1B3U
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 SER 159 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL 3.8 0.8 + - - -
158A SER* 1.3 73.0 - - - +
160A ALA* 1.3 63.3 + - - +
162A LYS* 3.3 17.3 + - - +
163A ALA* 3.2 22.2 + - - +
166A ARG* 5.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER* 3.2 8.2 + - - +
159A SER* 1.3 80.3 - - - +
161A VAL* 1.3 62.2 + - + +
163A ALA* 3.5 8.9 + - - +
164A GLU* 3.3 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU* 3.6 23.3 - - + +
128A VAL* 4.0 31.0 - - + -
157A VAL* 3.8 22.2 - - + -
158A SER* 3.1 22.8 + - - +
160A ALA* 1.3 75.0 - - + +
162A LYS* 1.3 66.7 + - - +
164A GLU* 3.0 22.9 + - + +
165A LEU* 2.9 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 2.9 73.3 + - + +
155A PRO* 3.0 21.3 + - - +
157A VAL* 3.3 19.3 - - + +
158A SER 2.9 17.4 + - - +
159A SER* 3.3 15.7 + - - +
161A VAL* 1.3 76.7 - - - +
163A ALA* 1.3 61.9 + - - +
165A LEU* 3.1 5.2 + - - +
166A ARG* 2.9 31.9 + - - +
194A VAL 5.5 0.2 + - - -
196A GLU* 4.4 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER 3.2 9.1 + - - +
160A ALA* 3.6 11.7 - - - +
161A VAL 3.2 0.4 - - - -
162A LYS* 1.3 79.0 - - - +
164A GLU* 1.3 63.5 + - + +
166A ARG* 3.5 28.9 + - - +
167A GLN* 3.3 21.1 + - - +
170A ARG* 5.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 3.1 35.6 + - - +
160A ALA* 3.3 14.8 - - - +
161A VAL* 3.0 31.3 + - + +
163A ALA* 1.3 78.2 - - + +
165A LEU* 1.3 62.7 + - + +
167A GLN* 3.2 6.8 + - - +
168A TYR* 3.1 32.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.6 18.4 - - + -
131A VAL* 4.8 9.4 - - + -
132A LYS* 5.9 2.0 - - + +
150A PHE* 3.5 34.1 - - + +
153A CYS* 4.0 22.0 - - - -
154A TYR* 3.7 42.8 - - + +
157A VAL* 4.2 14.8 - - + -
161A VAL* 2.9 18.4 + - + +
162A LYS 3.1 7.2 + - - +
164A GLU* 1.3 74.7 - - + +
166A ARG* 1.3 66.3 + - - +
168A TYR* 3.0 15.1 + - + +
169A PHE* 3.0 11.6 + - - +
191A PHE* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 2.8 39.4 + - + -
159A SER 5.2 1.2 + - - -
162A LYS* 2.9 26.7 + - - +
163A ALA* 3.5 30.9 - - - +
165A LEU* 1.3 76.2 - - - +
167A GLN* 1.3 62.5 + - - +
169A PHE* 3.4 3.3 + - - +
170A ARG* 3.1 27.7 + - - +
191A PHE* 4.3 16.8 - - + -
195A LEU* 4.0 21.8 - - + -
196A GLU* 4.2 0.6 + - - -
199A ASN* 3.7 19.8 + - - +
203A GLU* 2.9 40.7 + - + +
207A MET* 5.1 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA 3.3 10.1 + - - +
164A GLU* 3.2 11.8 + - - +
165A LEU 3.1 0.4 - - - -
166A ARG* 1.3 80.0 - - - +
168A TYR* 1.3 68.2 + - + +
170A ARG* 2.7 43.4 + - - +
171A ASN* 2.8 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 5.6 0.9 - - + -
132A LYS* 3.3 63.8 - - + +
135A ALA* 4.0 20.3 - - + +
136A GLY* 5.6 1.8 - - - -
150A PHE* 3.9 16.8 - + + -
164A GLU* 3.1 29.2 + - + +
165A LEU* 3.0 11.5 + - + +
167A GLN* 1.3 81.7 - - + +
169A PHE* 1.3 62.3 + - - +
171A ASN* 3.4 17.2 + - + +
172A LEU* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A CYS* 4.1 23.3 - - + -
150A PHE* 3.7 30.9 - + + -
165A LEU 3.0 9.0 + - - +
166A ARG 3.7 5.4 - - - +
168A TYR* 1.3 75.3 - - - +
170A ARG* 1.3 66.2 + - - +
172A LEU* 3.2 7.0 + - + +
173A CYS* 3.0 41.0 + - - -
184A ALA* 3.5 27.4 - - + -
187A LYS* 4.2 7.6 - - + -
188A LEU* 3.9 29.4 - - + -
191A PHE* 3.6 37.2 - + + -
207A MET* 4.0 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA 5.2 1.0 + - - -
166A ARG* 3.1 14.0 + - - +
167A GLN* 2.7 54.8 + - - +
169A PHE* 1.3 77.4 - - - +
171A ASN* 1.3 63.5 + - - +
173A CYS* 3.1 14.5 + - - +
174A SER* 3.2 13.8 + - - -
203A GLU* 3.3 40.8 + - - +
207A MET* 4.0 31.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLN* 2.8 41.8 + - - +
168A TYR* 3.6 21.5 - - + +
169A PHE 3.3 0.2 - - - -
170A ARG* 1.3 73.7 - - - +
172A LEU* 1.3 65.8 + - + +
174A SER* 3.2 11.0 + - - -
175A ASP* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ALA* 4.1 23.6 - - + +
143A ARG* 4.0 23.1 - - + +
146A ALA* 4.5 0.2 - - + -
147A CYS* 3.9 26.9 - - - +
150A PHE* 3.6 37.9 - - + -
168A TYR 3.2 10.0 + - - +
169A PHE* 3.5 10.8 - - + +
170A ARG 3.2 0.4 - - - -
171A ASN* 1.3 76.4 - - - +
173A CYS* 1.3 59.6 + - - +
175A ASP* 2.9 30.0 + - - +
180A VAL* 3.8 26.1 - - + +
181A ARG* 4.2 5.2 - - - +
184A ALA* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 3.0 42.3 + - - +
170A ARG* 3.1 13.7 + - - +
172A LEU* 1.3 75.5 - - - +
174A SER* 1.3 56.9 + - - +
175A ASP 3.5 0.2 - - - -
181A ARG* 3.3 19.4 - - - +
184A ALA* 3.8 16.4 - - - +
188A LEU* 5.0 0.9 - - - -
207A MET* 4.1 20.2 - - + +
211A LEU* 3.8 36.4 - - + +
----------------------------------------------------------
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