Contacts of the helix formed by residues 159 - 173 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASP* 3.8 29.0 - - - -
391A ASN* 2.9 31.7 + - - +
392A GLU* 4.3 11.2 - - - +
431A GLY 5.1 1.2 + - - -
432A GLN* 2.8 27.3 + - - +
158B SER* 1.3 72.5 - - - +
160B ALA* 1.3 60.1 + - - +
162B LYS* 3.4 15.1 + - - +
163B ALA* 3.2 22.3 + - - +
166B ARG* 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASN* 3.8 22.2 + - - +
392A GLU* 5.3 6.3 - - - +
396A ILE* 5.7 6.1 - - + +
436A GLU* 4.6 6.5 - - - +
158B SER* 3.2 8.8 + - - +
159B SER* 1.3 83.0 + - - +
161B VAL* 1.3 62.6 + - + +
163B ALA* 3.6 13.2 + - - +
164B GLU* 3.6 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLU* 4.6 2.9 - - - +
124B GLU* 3.7 27.4 - - + +
128B VAL* 3.9 33.9 - - + -
157B VAL* 3.9 21.1 - - + -
158B SER* 3.2 18.8 + - - +
160B ALA* 1.3 77.6 - - + +
162B LYS* 1.3 66.9 + - - +
163B ALA 3.1 0.7 - - - -
164B GLU* 3.1 17.7 + - + +
165B LEU* 3.0 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLY 5.0 7.7 + - - -
154B TYR* 3.3 61.4 - - + +
155B PRO* 4.2 12.4 + - - +
157B VAL* 3.3 20.2 + - + +
158B SER 3.0 17.4 + - - +
159B SER* 3.6 14.6 - - - +
160B ALA 3.3 0.2 - - - -
161B VAL* 1.3 78.0 - - - +
163B ALA* 1.3 59.8 + - - +
165B LEU* 3.3 1.8 + - - -
166B ARG* 3.0 32.3 + - - +
196B GLU* 3.1 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU* 4.1 17.0 - - + +
159B SER 3.2 10.2 + - - +
160B ALA* 3.7 10.8 - - - +
161B VAL 3.1 0.4 - - - -
162B LYS* 1.3 81.2 - - - +
164B GLU* 1.3 61.1 + - + +
166B ARG* 3.3 29.0 + - - +
167B GLN* 3.1 21.8 + - - +
170B ARG* 5.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 5.3 1.0 - - - +
132B LYS* 2.8 38.5 + - - +
160B ALA* 3.6 17.1 + - - +
161B VAL* 3.1 19.4 + - + +
163B ALA* 1.3 76.2 - - + +
165B LEU* 1.3 65.5 + - + +
167B GLN* 3.0 7.5 + - - +
168B TYR* 2.9 33.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 4.5 16.6 - - + -
131B VAL* 4.3 15.0 - - + -
132B LYS* 5.4 4.0 - - + +
150B PHE* 3.3 37.4 - - + +
153B CYS* 3.9 27.8 - - - -
154B TYR* 4.0 32.1 - - + -
157B VAL* 4.3 12.1 - - + -
161B VAL* 3.0 23.9 + - + +
162B LYS 3.6 6.3 - - - +
164B GLU* 1.3 75.4 - - - +
166B ARG* 1.3 64.2 + - - +
168B TYR* 3.3 2.5 + - + +
169B PHE* 2.9 21.5 + - - +
191B PHE* 4.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU* 2.8 32.7 + - - -
154B TYR* 2.9 36.6 + - + -
162B LYS* 3.0 30.7 + - - +
163B ALA* 3.6 20.7 - - - +
165B LEU* 1.3 77.1 - - - +
167B GLN* 1.3 56.5 + - - +
169B PHE* 3.6 2.8 + - - +
170B ARG* 3.1 32.1 + - - +
191B PHE* 4.2 16.2 - - + -
195B LEU* 4.1 18.2 - - - -
196B GLU* 4.5 0.4 + - - -
199B ASN* 3.8 22.8 + - - +
203B GLU* 3.0 43.5 + - - +
207B MET* 4.2 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA 3.1 12.3 + - - +
164B GLU* 3.0 12.8 + - - +
166B ARG* 1.3 75.6 - - - +
168B TYR* 1.3 70.4 + - + +
170B ARG* 2.8 43.2 + - - +
171B ASN* 2.7 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL* 5.8 0.7 - - + -
132B LYS* 3.2 62.4 + - + +
135B ALA* 3.8 21.3 - - + +
136B GLY* 5.2 3.6 - - - -
150B PHE* 3.9 16.2 - - + -
164B GLU* 2.9 28.0 + - + +
165B LEU* 3.8 5.4 - - + +
167B GLN* 1.3 82.3 - - + +
169B PHE* 1.3 63.0 + - - +
171B ASN* 3.2 20.6 + - + +
172B LEU* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B CYS* 4.0 24.9 - - + -
150B PHE* 3.6 32.7 - + + -
165B LEU 2.9 17.2 + - - +
166B ARG 3.9 3.1 - - - +
168B TYR* 1.3 78.2 - - - +
170B ARG* 1.3 61.3 + - - +
172B LEU* 3.4 6.8 + - + +
173B CYS* 3.2 33.8 + - - -
184B ALA* 3.7 24.9 - - + -
187B LYS* 4.0 16.6 - - + -
188B LEU* 3.7 24.5 - - + -
191B PHE* 3.8 33.4 - + + -
207B MET* 3.9 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA 5.2 0.8 + - - -
166B ARG* 3.1 12.8 + - - +
167B GLN* 2.8 50.0 + - - +
169B PHE* 1.3 78.7 - - - +
171B ASN* 1.3 62.8 + - - +
173B CYS* 3.5 4.2 + - - +
174B SER* 3.4 25.7 + - - +
203B GLU* 3.0 39.3 + - - +
206B PRO* 6.5 0.7 - - - -
207B MET* 3.9 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLN* 2.7 45.2 + - - +
168B TYR* 3.2 28.6 + - + +
170B ARG* 1.3 78.5 - - - +
172B LEU* 1.3 63.0 + - + +
174B SER* 3.3 7.3 + - - -
175B ASP* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 3.8 31.6 - - + +
143B ARG* 3.9 22.9 - - + +
146B ALA* 4.5 4.0 - - + -
147B CYS* 4.1 23.1 - - - -
150B PHE* 3.7 37.2 - - + -
168B TYR 3.2 9.7 + - - +
169B PHE* 3.8 9.9 - - + +
170B ARG 3.3 0.4 - - - -
171B ASN* 1.3 74.1 - - + +
173B CYS* 1.3 64.8 + - - +
174B SER 3.0 2.2 - - - -
175B ASP* 3.1 21.9 + - - +
180B VAL* 3.8 18.7 - - + +
181B ARG* 4.0 6.8 - - - -
184B ALA* 4.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 3.2 41.7 + - - -
170B ARG* 3.8 9.9 - - + +
171B ASN 3.4 0.2 - - - -
172B LEU* 1.3 78.1 - - - +
174B SER* 1.3 60.8 + - - +
175B ASP 3.4 0.2 - - - -
181B ARG* 3.3 20.6 - - - +
184B ALA* 3.9 15.9 - - - -
188B LEU* 4.6 1.6 - - - -
207B MET* 4.0 21.1 - - + +
211B LEU* 3.8 35.0 - - + +
----------------------------------------------------------
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