Contacts of the strand formed by residues 166 - 168 (chain B) in PDB entry 4WLU
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 166 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 3.6 18.8 - - + +
139B VAL* 5.4 0.2 - - + -
148B ILE* 3.9 29.8 - - + +
151B THR* 4.0 18.8 - - + -
152B ALA* 4.2 10.5 - - + +
155B PHE* 4.2 23.1 - - + -
161B TYR* 4.0 33.2 - - + -
162B ASN 4.0 9.4 + - - +
163B PRO* 4.0 8.9 + - + +
164B ASN 3.7 0.8 - - - -
165B LYS* 1.3 82.1 - - + +
167B PHE* 1.3 64.1 + - - +
277B PHE 4.3 0.2 - - - +
278B VAL* 3.5 23.7 - - - +
279B LYS 5.0 0.7 + - - -
287B TYR* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B MET* 4.1 7.0 - - + -
137B ILE 2.8 14.9 + - - +
138B CYS* 3.5 5.2 - - + -
139B VAL 2.8 27.5 + - - -
148B ILE* 3.4 6.7 - - - +
164B ASN 3.4 18.6 - - - -
165B LYS* 3.6 24.5 - - - -
166B ILE* 1.3 74.6 - - - +
168B GLY* 1.3 59.3 + - - +
169B VAL 3.6 0.7 + - - +
258B PHE* 3.6 31.6 - + + -
262B LEU* 4.0 31.2 - - + -
276B SER* 3.5 16.8 - - - +
277B PHE 4.1 0.7 - - - -
278B VAL* 3.8 9.0 - - + -
292B LEU* 4.4 1.3 - - + -
294B LEU* 4.0 13.7 - - + -
298B GLY 4.2 1.1 - - - -
299B ILE* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL 3.8 4.3 - - - -
144B VAL* 3.9 10.5 - - - -
148B ILE* 3.3 20.6 - - - +
167B PHE* 1.3 70.7 - - - +
169B VAL* 1.3 58.5 + - - -
170B THR* 3.1 7.1 + - - +
276B SER* 2.7 19.1 + - - -
277B PHE* 2.8 35.3 + - - -
----------------------------------------------------------
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