Contacts of the strand formed by residues 172 - 179 (chain B) in PDB entry 1WNT
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 172 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 4.5 11.2 - - + +
122B LEU* 4.0 29.2 - - + -
123B ILE* 4.1 12.3 - - + -
127B VAL 4.4 1.6 - - - +
128B PRO 4.1 2.2 - - - -
129B GLY* 3.3 33.7 - - - +
130B ALA* 3.6 4.0 - - - +
131B ILE* 4.2 14.4 - - + -
164B ALA 4.8 1.2 - - - +
167B LEU* 3.4 34.4 + - + +
168B GLY* 4.2 6.1 + - - -
170B HIS* 3.0 34.7 - - + +
171B LYS* 1.3 80.6 - - - +
173B ARG* 1.3 74.3 + - - +
174B VAL* 4.7 1.4 - - - +
231B THR* 4.6 1.0 + - - -
206C LEU* 4.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY 3.0 13.8 + - - +
130B ALA* 3.3 11.7 - - + +
131B ILE* 2.7 31.2 + - - -
171B LYS 5.0 2.2 - - - +
172B ILE* 1.3 78.4 - - - +
174B VAL* 1.3 65.0 + - - +
175B ASN* 3.3 13.6 + - - +
222B LEU* 2.5 27.0 + - - +
223B LEU 3.4 8.3 + - - -
224B SER 2.9 22.2 + - - -
225B ASP* 4.8 7.1 + - - +
227B SER* 2.9 27.3 + - - -
228B GLY* 4.1 19.2 - - - -
230B THR* 2.7 34.2 + - - -
231B THR* 3.5 13.7 - - - +
206C LEU* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 3.3 19.3 - - + +
133B ASN* 3.9 4.9 - - - +
160B THR* 3.6 17.2 - - + +
163B MET* 3.3 44.6 - - + +
164B ALA* 3.3 25.8 - - - +
167B LEU* 3.9 11.9 - - + -
172B ILE 4.7 2.0 - - - +
173B ARG* 1.3 79.6 - - - +
175B ASN* 1.3 57.9 + - - +
231B THR* 2.9 8.3 + - - -
232B GLY* 2.5 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE 2.9 10.0 + - - +
132B VAL* 3.2 7.5 - - - -
133B ASN* 2.8 24.6 + - - +
160B THR* 3.6 7.8 - - - +
173B ARG* 3.3 13.0 + - - +
174B VAL* 1.3 75.4 + - - +
176B ALA* 1.3 62.5 + - - +
222B LEU* 3.3 32.0 - - + +
230B THR* 2.8 21.4 - - - +
231B THR* 3.0 20.2 - - - +
232B GLY 3.1 0.2 - - - +
233B SER* 2.7 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 5.2 0.7 - - - -
133B ASN* 3.0 19.1 - - + +
135B SER* 4.0 18.2 - - - -
157B ASP* 4.0 6.7 - - - +
160B THR* 3.8 19.0 - - + +
175B ASN* 1.3 76.2 - - - +
177B VAL* 1.3 59.6 + - - +
178B ASN* 3.6 3.6 - - - +
222B LEU* 5.4 2.3 - - - +
233B SER* 2.7 19.0 + - - +
234B THR* 4.7 1.6 - - + -
235B LEU* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 3.7 26.2 - - + -
133B ASN 3.2 3.9 + - - +
134B VAL* 3.8 10.4 - - + -
135B SER 3.0 21.8 + - - -
176B ALA* 1.3 74.2 - - - +
178B ASN* 1.3 63.4 + - - +
179B PRO* 3.3 13.5 - - + +
215B VAL* 4.6 11.4 - - + +
218B ALA* 4.3 12.6 - - + -
219B ILE* 4.0 16.4 - - + +
222B LEU* 5.8 2.7 - - + -
235B LEU* 3.3 10.5 - - + +
237B VAL* 3.3 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 3.2 10.8 + - - -
136B SER* 3.1 28.9 + - - +
137B GLN 4.0 1.9 + - - -
139B SER* 3.2 14.5 + - - -
157B ASP* 3.2 15.6 + - - -
176B ALA 3.5 1.9 - - - +
177B VAL* 1.3 80.4 + - - +
179B PRO* 1.3 67.1 - - - +
234B THR* 3.3 26.6 - - - -
235B LEU 2.9 9.8 + - - +
236B PRO* 3.5 0.3 - - - +
237B VAL 3.1 17.5 + - - -
238B GLU* 3.5 11.4 - - - +
242B TRP* 3.3 23.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 5.3 1.1 - - + -
134B VAL* 5.1 7.4 - - + -
135B SER 3.9 11.9 - - - +
136B SER* 4.0 0.3 + - - -
137B GLN* 3.2 20.5 + - - +
177B VAL* 3.3 14.8 - - + +
178B ASN* 1.3 87.9 - - - +
180B THR* 1.3 67.8 + - - +
182B VAL* 4.5 4.9 - - + -
210B ALA* 4.6 0.9 - - + -
215B VAL* 3.7 32.3 - - + -
237B VAL* 2.9 21.7 - - + +
1245B NAP 3.7 22.4 - - + -
----------------------------------------------------------
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