Contacts of the strand formed by residues 182 - 186 (chain B) in PDB entry 1WSQ
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 182 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 4.0 1.2 - - - +
134B VAL* 3.1 44.7 + - + +
154B ILE* 4.2 11.2 - - + -
158B THR* 3.3 30.5 - - + +
178B LYS 3.7 13.5 - - - +
179B VAL* 3.2 12.4 + - + +
180B GLU 3.5 0.9 - - - -
181B ASN* 1.3 79.1 - - - +
183B LEU* 1.3 68.0 + - - +
190B TYR* 4.0 20.4 - - + -
191B VAL 3.6 7.0 - - - +
192B LEU* 3.7 32.5 - - + +
251B LEU* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 4.1 6.5 - - + -
129B CYS* 3.9 17.9 - - + -
132B GLY 3.4 12.8 - - - +
133B GLN* 4.2 4.9 - - - -
134B VAL* 4.6 0.9 - - - +
180B GLU 4.9 0.9 - - - +
182B ILE* 1.3 81.1 - - - +
184B LEU* 1.3 61.9 + - - +
190B TYR* 3.3 10.4 - - - +
191B VAL* 2.9 40.8 + - + +
193B CYS* 4.0 18.4 - - - -
404B KSA 3.4 79.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 5.4 4.7 - - + -
129B CYS* 3.6 7.6 - - - +
131B GLY* 3.0 49.9 + - - +
132B GLY 2.9 16.9 + - - +
133B GLN 5.6 0.2 - - - +
134B VAL* 4.9 1.5 - - + +
137B LEU* 3.9 30.3 - - + -
183B LEU* 1.3 72.9 - - - +
185B HIS* 1.3 58.2 + - - +
186B ASP* 3.3 31.9 - - - +
187B ARG* 4.4 3.1 - - - +
188B GLY 4.3 4.7 - - - +
189B HIS 4.0 3.1 - - - +
190B TYR* 3.4 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY 5.7 0.2 - - - +
127B ASP* 3.5 28.1 + - - -
128B PHE 4.4 9.1 + - - -
129B CYS* 4.3 14.5 - - - +
130B ARG* 4.3 8.5 + - - +
131B GLY 4.1 9.2 + - - -
183B LEU 3.8 2.2 + - - -
184B LEU* 1.3 75.4 - - - +
186B ASP* 1.3 86.5 + - - +
189B HIS* 3.0 40.3 + + + +
191B VAL* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLY* 5.6 1.3 - - - -
184B LEU* 3.3 15.8 - - - +
185B HIS* 1.3 99.0 + - - +
187B ARG* 1.3 70.1 + - - +
188B GLY 3.2 0.3 + - - -
189B HIS* 2.9 32.1 + - - +
----------------------------------------------------------
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