Contacts of the helix formed by residues 211 - 224 (chain D) 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 GLU 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182D VAL* 4.0 6.0 - - - +
183D MET* 5.1 11.3 - - - +
209D PHE 5.3 1.8 - - - +
210D ALA* 1.3 78.4 - - - +
212D VAL* 1.3 74.9 + - - +
213D GLU* 3.1 8.9 + - + +
214D HIS* 3.0 42.5 + - + +
215D VAL* 3.3 9.2 - - - +
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Residues in contact with VAL 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLY* 4.3 7.0 - - - +
19D ILE* 3.9 22.9 - - + +
22D GLY* 4.4 10.3 - - - -
182D VAL* 3.8 22.2 - - + +
183D MET 6.1 0.2 - - - -
184D THR* 3.9 18.4 - - + -
211D GLU* 1.3 83.0 + - - +
213D GLU* 1.3 57.4 + - - +
215D VAL* 3.4 6.1 + - - +
216D VAL* 2.8 50.4 + - + +
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Residues in contact with GLU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASP 6.2 0.2 - - - -
226A ARG* 3.2 27.4 + - - +
211D GLU* 3.1 8.1 - - + +
212D VAL* 1.3 76.8 - - - +
214D HIS* 1.3 63.6 + - + +
216D VAL* 2.9 9.7 + - + +
217D ASN* 2.5 64.1 + - - +
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Residues in contact with HIS 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASP 5.0 4.4 + - - -
226A ARG 4.4 11.5 + - - +
227A SER* 6.5 0.2 - - - -
228A GLY* 4.2 27.6 + - - -
229A MET* 3.8 15.7 + - + +
208D LYS* 4.7 14.2 - - - -
210D ALA* 4.0 6.5 - - - -
211D GLU* 3.0 46.6 - - + +
213D GLU* 1.3 84.0 + - + +
215D VAL* 1.3 64.2 + - - +
217D ASN* 3.2 3.6 + - - +
218D ALA* 3.0 22.5 + - - +
237D VAL* 3.8 21.2 - - + +
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Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 3.3 43.3 - - + -
134D VAL* 5.6 2.5 - - + -
177D VAL* 4.7 8.0 - - + +
179D PRO* 4.0 29.4 - - + -
182D VAL* 4.2 14.1 - - + -
210D ALA* 4.5 4.0 - - + -
211D GLU 3.3 16.6 - - - +
212D VAL* 3.4 4.7 - - - +
213D GLU 3.3 0.4 - - - -
214D HIS* 1.3 77.2 - - + +
216D VAL* 1.3 61.3 + - - +
218D ALA* 3.3 6.9 + - - +
219D ILE* 3.0 35.0 + - + +
237D VAL* 4.7 7.0 - - + -
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE 4.2 1.1 - - - +
22D GLY 4.1 2.5 - - - +
23D THR* 3.5 33.2 - - - +
26D ALA* 3.7 30.5 - - + -
212D VAL* 2.8 45.8 + - + +
213D GLU* 3.3 9.2 - - + +
215D VAL* 1.3 80.9 - - + +
217D ASN* 1.3 59.7 + - - +
219D ILE* 3.2 7.3 + - - +
220D LEU* 2.9 37.3 + - + +
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Residues in contact with ASN 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.0 31.7 - - + +
221A PHE* 4.1 2.8 - - - -
225A ASP 5.0 0.7 - - - +
226A ARG* 3.2 53.4 + - + +
213D GLU* 2.5 48.0 + - - +
214D HIS* 3.6 2.2 + - - +
216D VAL* 1.3 76.0 - - - +
218D ALA* 1.3 60.5 + - - +
220D LEU* 4.7 3.4 - - - +
221D PHE* 3.1 24.6 + - - +
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Residues in contact with ALA 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A PHE* 4.2 10.5 - - + -
226A ARG 5.2 0.2 + - - -
230A THR* 5.7 0.2 - - - +
177D VAL* 4.5 9.6 - - + -
214D HIS 3.0 12.8 + - - +
215D VAL 3.8 6.1 - - - +
216D VAL 3.3 0.2 - - - -
217D ASN* 1.3 74.5 - - - +
219D ILE* 1.3 61.0 + - - +
221D PHE* 3.5 5.5 - - - +
222D LEU* 2.9 36.7 + - + +
235D LEU* 4.2 18.4 - - + -
237D VAL* 4.1 21.8 - - + -
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Residues in contact with ILE 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 4.0 10.3 - - + -
23D THR* 3.5 29.8 - - + +
81D VAL* 3.6 34.5 - - + -
132D VAL* 3.8 22.1 - - + +
134D VAL* 4.0 22.0 - - + -
177D VAL* 4.2 11.2 - - + +
215D VAL* 3.0 26.9 + - + +
216D VAL* 3.5 7.2 - - - +
218D ALA* 1.3 75.1 - - - +
220D LEU* 1.3 60.9 + - + +
222D LEU* 3.1 4.7 + - - +
223D LEU* 2.9 32.4 + - + +
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.3 8.1 - - + -
3D LEU* 3.6 19.5 - - + +
5D LEU* 4.3 14.7 - - + +
23D THR* 4.8 3.6 - - + +
26D ALA* 4.1 29.2 - - + +
27D LEU* 4.1 27.6 - - + -
30D THR* 4.8 5.6 - - - +
216D VAL* 2.9 31.3 + - + +
217D ASN* 4.1 6.1 - - - +
219D ILE* 1.3 81.7 - - + +
221D PHE* 1.3 57.2 + - - +
223D LEU* 3.0 8.5 + - + +
224D SER* 2.8 35.5 + - - -
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Residues in contact with PHE 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.9 3.1 - - - -
217A ASN 4.1 6.3 - - - -
218A ALA* 4.2 16.4 - - + -
221A PHE* 3.3 62.1 - + + -
235A LEU* 4.7 12.1 - - + -
1D MET* 4.4 9.2 - - - -
3D LEU* 3.8 11.6 - - + +
217D ASN 3.1 17.8 + - - +
218D ALA 3.5 3.6 - - - +
220D LEU* 1.3 77.9 - - - +
222D LEU* 1.3 65.4 + - + +
224D SER* 3.4 12.5 + - - +
226D ARG* 4.3 22.9 - - + -
227D SER* 2.8 38.5 + - - -
235D LEU* 4.3 13.7 - - + -
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Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LEU* 6.1 0.2 - - + -
130D ALA* 4.4 3.3 - - - +
131D ILE 5.6 0.7 - - - +
132D VAL* 3.7 20.2 - - + +
173D ARG* 3.3 23.7 + - - -
175D ASN* 3.9 32.9 - - + +
176D ALA 3.8 25.6 - - - +
177D VAL* 4.8 5.4 - - + -
218D ALA 2.9 24.8 + - - +
219D ILE* 3.1 4.7 + - - +
221D PHE* 1.3 82.4 - - + +
223D LEU* 1.3 61.0 + - - +
227D SER* 3.5 10.9 + - - +
230D THR* 4.4 14.1 - - + -
233D SER* 4.8 1.6 - - - +
235D LEU* 4.2 27.8 - - + -
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Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.0 11.7 - - + -
8D ARG* 3.7 12.6 + - - -
10D VAL* 4.6 0.9 - - + -
27D LEU* 4.6 13.5 - - + -
79D LEU* 3.3 37.5 - - + +
80D LEU 3.7 18.8 - - - +
81D VAL* 3.4 26.7 - - + -
130D ALA* 3.8 24.6 - - - +
132D VAL* 4.0 9.0 - - + -
173D ARG* 3.9 4.9 + - - -
219D ILE* 2.9 21.2 + - + +
220D LEU* 3.5 16.8 - - + +
222D LEU* 1.3 75.6 - - - +
224D SER* 1.3 67.0 + - - +
225D ASP* 4.0 0.9 - - - +
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Residues in contact with SER 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.2 42.8 + - - +
5D LEU* 3.8 10.0 - - - +
173D ARG* 2.7 24.8 + - - -
220D LEU 2.8 12.7 + - - -
221D PHE 3.4 4.2 + - - -
223D LEU* 1.3 78.6 - - - +
225D ASP* 1.3 52.9 + - - +
226D ARG* 2.6 33.5 + - - +
227D SER* 3.3 10.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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