Contacts of the strand formed by residues 178 - 184 (chain A) in PDB entry 1WS6
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 ASN 178 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 2.6 31.3 + - - +
38A PRO* 3.9 23.6 - - + +
41A LEU* 4.9 5.4 - - + -
134A TYR* 2.5 33.7 + - - +
160A GLN* 3.9 14.1 + - + +
161A HIS 3.5 4.5 - - - +
163A LYS* 4.2 1.6 - - - -
174A VAL* 3.6 2.9 - - - +
175A TYR* 2.7 43.4 + - - +
177A GLU* 1.3 87.7 + - - +
179A ALA* 1.3 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 5.2 0.9 - - - -
159A LEU 3.6 0.9 - - - +
160A GLN* 3.4 4.9 - - - +
161A HIS* 2.8 53.9 + - + -
163A LYS* 3.8 17.5 - - + +
172A ARG* 4.4 8.7 - - + +
173A ARG 3.3 11.2 - - - +
174A VAL* 4.2 10.5 - - + -
175A TYR* 5.3 0.2 - - - -
178A ASN* 1.3 76.2 - - - +
180A LEU* 1.3 66.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.5 34.8 - - + +
45A LEU* 4.2 29.8 - - + -
129A PHE* 4.1 8.3 - - + -
158A VAL* 3.8 16.2 - - + -
159A LEU 3.2 3.6 - - - +
160A GLN* 3.5 35.4 - - + +
161A HIS* 4.5 0.2 - - - -
172A ARG* 3.2 6.0 - - - +
173A ARG* 2.9 39.4 + - + +
175A TYR* 4.2 10.8 - - + +
179A ALA* 1.3 73.7 - - - +
181A THR* 1.3 61.8 + - - +
182A LEU* 3.5 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR 3.5 2.1 - - - +
158A VAL* 3.4 3.6 - - - -
159A LEU* 2.8 47.0 + - + +
161A HIS* 3.1 23.2 + - - -
167A LEU* 4.4 22.2 + - + +
169A LEU* 4.7 0.2 - - + -
170A GLY 4.1 21.3 + - - +
171A GLU 3.7 2.9 - - - -
172A ARG* 4.3 10.7 + - - +
180A LEU* 1.3 74.4 + - - +
182A LEU* 1.3 62.9 + - - +
183A VAL* 4.0 19.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.9 7.0 - - + -
48A TYR* 4.0 33.0 - - + -
156A LEU* 4.2 18.2 - - + -
157A TYR 3.5 2.9 - - - -
158A VAL* 4.3 14.8 - - + -
170A GLY* 3.5 4.2 - - - -
171A GLU* 3.0 34.5 + - + +
173A ARG* 3.9 30.7 - - - +
180A LEU* 3.5 27.4 - - + +
181A THR* 1.3 78.3 - - - +
183A VAL* 1.3 61.5 + - - +
184A GLU* 4.1 3.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 4.4 19.7 - - + -
156A LEU* 3.3 6.7 - - - +
157A TYR* 2.8 50.4 + - + +
159A LEU* 4.4 6.7 - - + -
169A LEU* 3.7 44.6 - - + +
170A GLY* 4.8 0.7 - - - -
181A THR* 4.0 12.6 - - + -
182A LEU* 1.3 76.9 - - - +
184A GLU* 1.3 71.8 + - - +
185A VAL* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 2.8 42.7 + - - +
155A GLY 3.8 0.4 - - - -
156A LEU* 3.5 15.3 - - + -
169A LEU 5.6 0.2 + - - -
182A LEU* 4.1 3.5 + - + +
183A VAL* 1.3 82.7 - - - +
185A VAL* 1.3 67.1 + - - +
----------------------------------------------------------
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