Contacts of the helix formed by residues 181 - 201 (chain B) in PDB entry 5WN1
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 ARG 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B TYR* 3.6 5.9 + - - -
154B GLU* 3.1 37.5 + - - -
156B ARG* 3.5 14.6 - - - +
173B PRO* 3.6 15.5 - - + +
174B ASN 3.6 17.4 + - - +
175B ALA* 2.8 14.7 + - - +
176B GLY* 5.2 2.0 - - - -
180B VAL* 1.3 90.4 - - + +
182B LEU* 1.3 65.1 + - - +
183B GLU 3.2 2.9 - - - -
184B TYR* 3.1 37.4 + - + +
185B ARG* 2.9 21.8 + - - +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ALA* 3.4 22.7 + - + -
179B LEU* 3.1 46.6 + - + +
180B VAL 3.5 0.6 - - - -
181B ARG* 1.3 76.3 - - - +
183B GLU* 1.3 61.9 + - - +
185B ARG* 3.3 5.4 - - + +
186B GLN* 3.2 38.3 + - + +
233B THR* 3.8 20.4 - - + +
235B GLN* 3.0 31.9 - - + +
236B GLU* 4.0 10.3 - - + +
402B NA 4.2 3.6 - - - -
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL 5.3 2.0 + - - +
181B ARG 3.2 1.0 - - - -
182B LEU* 1.3 77.2 - - - +
184B TYR* 1.3 71.2 + - + +
186B GLN* 3.3 16.6 + - - +
187B ARG* 3.2 34.7 + - - +
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Residues in contact with TYR 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLU* 3.6 30.6 + - + -
151B HIS* 3.1 42.9 + + - -
154B GLU* 4.7 9.3 + - - -
156B ARG* 5.8 0.5 + - - -
173B PRO* 3.8 20.9 - - + -
181B ARG* 3.1 58.7 + - - +
183B GLU* 1.3 83.1 - - + +
185B ARG* 1.3 66.6 + - - +
187B ARG* 3.2 13.1 + - - +
188B TRP* 2.9 26.5 + - + +
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Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 3.5 16.3 - - - +
173B PRO* 3.2 31.0 + - + +
174B ASN 5.3 0.2 - - - +
175B ALA* 4.4 6.0 - - + +
181B ARG 2.9 12.7 + - - +
182B LEU* 3.3 15.0 - - + +
184B TYR* 1.3 79.3 - - - +
186B GLN* 1.3 58.7 + - + +
188B TRP* 3.2 8.8 + - - +
189B ASP* 2.8 55.1 + - - +
211B LEU 2.9 22.0 + - - -
212B ASN* 3.1 18.6 + - - +
213B VAL* 3.5 15.8 - - - +
236B GLU* 2.9 43.7 + - + +
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Residues in contact with GLN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 3.2 32.5 + - + +
183B GLU* 3.7 17.4 - - - +
184B TYR 3.2 0.4 - - - -
185B ARG* 1.3 75.0 - - + +
187B ARG* 1.3 66.1 + - + +
189B ASP* 3.2 9.9 + - - +
190B GLU* 3.2 23.6 + - - +
235B GLN* 3.5 39.8 - - + +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLU* 2.7 38.5 + - - +
151B HIS* 3.8 12.2 + - + +
183B GLU* 3.2 26.0 - - - +
184B TYR* 3.2 15.2 + - - +
186B GLN* 1.3 79.4 - - + +
188B TRP* 1.3 62.4 + - - +
190B GLU* 3.5 8.3 + - - +
191B ALA* 3.1 22.7 + - - +
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Residues in contact with TRP 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 4.5 10.3 - - + -
151B HIS* 3.6 56.0 - + + -
156B ARG* 4.1 21.1 - - + -
157B VAL* 3.8 26.0 - - + -
170B ALA* 5.1 0.7 - - + -
171B TYR 4.9 0.4 - - - -
172B VAL* 3.6 27.6 - - + +
173B PRO* 3.5 38.4 - - + +
184B TYR* 2.9 20.5 + - + +
185B ARG* 3.4 8.1 - - - +
187B ARG* 1.3 76.0 - - - +
189B ASP* 1.3 73.1 + - - +
191B ALA* 3.2 1.0 + - - +
192B PHE* 2.7 67.7 + + + +
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 4.5 1.6 - - - +
185B ARG* 2.8 54.7 + - - +
186B GLN* 3.2 10.4 + - - +
188B TRP* 1.3 84.2 + - - +
190B GLU* 1.3 57.2 + - - +
192B PHE* 3.8 4.4 - - - +
193B ARG* 2.8 41.9 + - - +
235B GLN 4.7 1.6 - - - +
236B GLU* 4.7 8.8 - - - +
239B GLY* 4.3 22.2 - - - -
240B PHE 5.2 0.2 + - - -
243B LEU* 5.4 0.3 - - - +
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLN 3.2 9.2 + - - +
187B ARG* 3.8 10.2 - - - +
189B ASP* 1.3 78.3 - - - +
191B ALA* 1.3 57.7 + - - +
193B ARG* 3.5 33.8 + - - +
194B LYS* 2.9 31.0 + - + +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 4.2 7.8 - - + +
148B ASP* 4.2 9.9 - - + +
151B HIS* 3.5 37.0 - - + +
187B ARG 3.1 10.1 + - - +
188B TRP 3.8 1.6 - - - +
190B GLU* 1.3 75.2 - - - +
192B PHE* 1.3 64.5 + - - +
194B LYS* 3.3 12.5 + - - +
195B PHE* 2.9 24.1 + - - +
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 4.1 23.4 - - + +
157B VAL* 4.2 17.0 - - + -
168B VAL* 4.4 5.4 - - + -
170B ALA* 3.6 22.4 - - + -
172B VAL* 4.1 17.3 - - + -
188B TRP* 2.7 47.3 + + + +
189B ASP* 3.8 5.4 - - - +
191B ALA* 1.3 71.3 - - - +
193B ARG* 1.3 57.5 + - - +
195B PHE* 3.1 6.1 + + - +
196B LEU* 2.8 66.1 + - + +
207B LEU* 3.9 19.7 - - + -
211B LEU* 4.6 2.2 - - + -
243B LEU* 5.1 7.6 - - + -
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Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ASP* 2.8 18.6 + - - +
190B GLU* 3.5 42.9 + - - +
192B PHE* 1.3 74.7 - - - +
194B LYS* 1.3 66.0 + - - +
195B PHE 3.1 0.2 + - - -
196B LEU* 3.1 2.8 + - - +
197B LYS* 2.9 25.2 + - + +
239B GLY* 4.8 9.7 + - - -
242B GLU* 3.0 41.6 + - - +
243B LEU* 3.6 31.2 - - + +
246B ALA* 4.1 27.4 - - + -
247B VAL* 4.4 3.2 - - + +
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASP* 5.3 6.7 + - - -
190B GLU* 2.9 20.5 + - + +
191B ALA* 3.7 10.1 - - - +
193B ARG* 1.3 76.9 - - - +
195B PHE* 1.3 61.9 + - - +
197B LYS* 3.4 9.2 + - - +
198B GLY* 3.2 19.1 + - - -
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Residues in contact with PHE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER* 5.7 0.7 - - - -
145B GLY 4.2 0.9 - - - -
146B ILE* 3.2 58.1 - - + +
157B VAL* 4.9 2.5 - - + -
159B VAL* 3.8 31.0 - - + -
168B VAL* 4.7 5.4 - - + -
191B ALA 2.9 17.9 + - - +
192B PHE* 3.5 5.8 - + - +
194B LYS* 1.3 75.9 - - - +
196B LEU* 1.3 85.0 + - + +
198B GLY* 3.6 1.3 + - - -
199B LEU* 3.1 39.5 + - + +
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 4.0 32.1 - - + -
192B PHE* 2.8 61.7 + - + +
193B ARG 3.9 2.5 - - - +
195B PHE* 1.3 79.1 - - + +
197B LYS* 1.3 58.2 + - - +
199B LEU* 3.6 3.8 - - + +
200B ALA* 2.8 31.9 + - - +
205B LEU* 3.8 25.8 - - + +
207B LEU* 3.9 16.6 - - + -
243B LEU* 4.0 13.2 - - + -
247B VAL* 4.0 12.5 - - + +
249B LEU* 5.1 1.8 - - + -
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Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ARG* 2.9 18.2 + - + +
194B LYS* 3.8 9.2 - - - +
195B PHE 3.2 0.2 - - - -
196B LEU* 1.3 75.0 - - - +
198B GLY* 1.3 68.0 + - - +
200B ALA* 3.4 2.3 + - - +
201B SER* 3.1 23.5 + - - -
246B ALA* 3.2 40.4 + - - +
247B VAL* 4.3 18.1 + - + +
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B LYS 3.2 11.6 + - - -
195B PHE* 3.6 2.7 + - - -
197B LYS* 1.3 79.2 - - - +
199B LEU* 1.3 60.8 + - - +
201B SER* 2.7 23.6 + - - -
202B ARG* 3.8 6.2 + - - +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B VAL* 4.4 11.4 - - + -
166B VAL* 3.6 45.5 - - + -
168B VAL* 4.8 7.4 - - + -
195B PHE* 3.1 35.0 + - + +
196B LEU* 3.6 6.7 - - - +
197B LYS 3.2 0.2 - - - -
198B GLY* 1.3 74.8 - - - +
200B ALA* 1.3 61.2 + - - +
202B ARG* 2.9 24.7 + - + +
203B LYS 3.3 7.7 + - - +
205B LEU* 4.0 21.8 - - + -
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU 2.8 21.2 + - - +
197B LYS 3.9 3.4 - - - +
199B LEU* 1.3 73.8 - - - +
201B SER* 1.3 60.8 + - - +
203B LYS 3.2 21.2 + - - +
204B PRO* 5.1 0.5 - - - +
205B LEU* 4.3 12.1 - - + -
247B VAL* 3.6 29.6 - - + +
248B PRO 5.4 0.2 - - - +
288B SER* 4.4 12.6 + - - +
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Residues in contact with SER 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LYS* 3.1 13.7 + - - -
198B GLY* 2.7 23.4 + - - -
199B LEU 3.1 0.2 - - - -
200B ALA* 1.3 78.7 - - - +
202B ARG* 1.3 56.2 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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