Contacts of the strand formed by residues 155 - 161 (chain B) in PDB entry 1AR4
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 ILE 155 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.1 4.2 - - - -
131B TRP* 2.8 59.5 + - + +
133B PRO* 4.3 4.9 - - + -
153B GLY* 3.7 17.0 - - - +
154B SER* 1.3 73.0 - - - +
156B PRO* 1.3 77.3 - - + +
157B LEU* 3.4 4.0 + - + +
194B ARG* 5.0 2.2 - - + +
198B ALA* 3.9 23.3 - - + +
201B ALA* 5.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 4.8 13.0 - - + -
77B VAL* 4.0 21.8 - - + -
129B LEU 4.0 4.3 - - - +
130B VAL* 4.1 6.7 - - + -
143B PHE* 5.8 0.4 - - + -
154B SER 3.5 9.6 - - - +
155B ILE* 1.3 90.5 - - + +
157B LEU* 1.3 65.0 - - - +
159B GLN* 3.4 32.8 - - + +
194B ARG* 3.7 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 4.7 0.9 - - - -
81B ASN* 3.2 18.2 - - - +
96B LEU* 5.3 1.6 - - + -
129B LEU* 2.8 17.9 + - + +
130B VAL 4.1 4.5 - - - -
131B TRP* 3.9 16.2 - - + +
138B ILE* 4.3 17.5 - - + -
155B ILE* 3.8 13.7 - - + +
156B PRO* 1.3 81.6 - - - +
158B LEU* 1.3 62.0 + - - +
191B VAL* 3.7 22.3 - - + +
194B ARG* 3.4 46.2 - - + +
195B PHE* 3.8 28.9 - - + +
198B ALA* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ASN* 3.4 15.3 - - + +
110B MET* 5.0 0.7 - - + -
114B PHE* 3.9 10.7 - - + -
128B SER* 3.5 0.9 - - - -
129B LEU* 2.8 52.5 + - + +
157B LEU* 1.3 80.2 - - - +
159B GLN* 1.3 67.7 + - - +
182B TRP* 3.7 30.3 - - + -
183B TRP* 4.3 10.3 - - + -
186B VAL* 3.7 22.9 - - + -
188B TRP* 3.7 29.8 - - + -
191B VAL* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 5.8 0.2 - - - +
74B ASN* 3.4 46.3 + - - +
77B VAL* 4.4 9.6 - - + +
78B PHE* 3.1 20.7 - - + -
81B ASN* 2.8 17.5 + - - +
114B PHE* 4.5 1.3 - - - -
126B TRP* 3.9 14.2 - - + -
127B ALA 3.5 6.1 - - - +
128B SER* 3.1 22.0 + - - +
143B PHE* 3.2 20.5 - - - -
156B PRO* 3.4 27.1 - - + +
158B LEU* 1.3 81.4 - - - +
160B LEU* 1.3 59.6 + - - +
182B TRP* 3.5 13.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 3.9 1.6 - - + -
114B PHE* 3.7 19.9 - - + -
118B ALA* 3.9 18.2 - - + -
126B TRP* 3.3 6.8 - - - -
127B ALA* 3.0 28.9 + - + +
159B GLN* 1.3 74.4 - - - +
161B ASP* 1.3 62.2 + - - +
162B MET* 3.3 11.5 + - + +
178B TYR* 3.5 31.4 - - + +
179B VAL* 3.8 35.2 - - + -
182B TRP* 3.6 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS* 2.8 8.7 + - - -
75B HIS* 3.2 1.6 + - - -
78B PHE* 3.6 24.8 - - + -
126B TRP* 3.5 28.2 - - + -
160B LEU* 1.3 71.0 - - - +
162B MET* 1.3 59.5 + - - +
163B TRP* 3.1 30.1 + - - -
166B ALA* 3.7 13.7 - - + +
178B TYR* 2.9 29.3 + - - -
202B MN 1.9 36.0 + - - -
----------------------------------------------------------
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