Contacts of the helix formed by residues 181 - 201 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 3.4 20.9 + - - -
154A GLU* 2.9 30.9 + - - -
156A ARG* 3.7 2.2 - - - +
173A PRO* 3.7 18.8 - - - +
174A ASN 3.7 17.7 + - - +
175A ALA* 2.9 15.8 + - - +
176A GLY* 5.1 2.7 - - - -
180A VAL* 1.3 90.0 - - + +
182A LEU* 1.3 63.0 + - - +
183A GLU 3.1 3.4 - - - -
184A TYR* 2.9 39.7 + - + +
185A ARG* 2.8 20.8 + - + +
9D G 4.6 13.5 + - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA* 3.2 18.9 + - + -
179A LEU* 3.1 45.5 + - + +
181A ARG* 1.3 75.9 - - - +
183A GLU* 1.3 62.4 + - - +
185A ARG* 3.3 5.8 + - + -
186A GLN* 3.1 34.4 + - + +
233A THR* 4.1 8.3 - - + +
235A GLN* 3.9 31.4 - - + +
236A GLU* 3.9 28.3 - - + -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU 4.6 1.2 + - - -
180A VAL 5.2 2.4 - - - +
181A ARG* 3.1 1.0 - - - -
182A LEU* 1.3 80.0 - - - +
184A TYR* 1.3 62.5 + - - +
186A GLN* 3.4 14.7 + - - +
187A ARG* 3.4 25.7 + - - +
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 3.8 21.5 + - + -
151A HIS* 3.0 50.1 + + - +
154A GLU* 4.7 8.7 + - - -
156A ARG* 5.7 0.9 + - - -
173A PRO* 3.6 29.6 - - + -
181A ARG* 2.9 49.5 + - + +
183A GLU* 1.3 79.6 - - - +
185A ARG* 1.3 58.5 + - + +
187A ARG* 2.9 16.3 + - + +
188A TRP* 2.8 30.3 + - + -
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.5 15.8 - - - +
173A PRO* 2.9 31.7 + - - +
174A ASN* 4.3 3.2 - - - +
175A ALA* 4.4 4.9 - - + +
181A ARG* 2.8 17.2 + - + +
182A LEU* 3.3 15.2 + - + +
184A TYR* 1.3 76.4 - - + +
186A GLN* 1.3 57.7 + - + +
188A TRP* 3.1 8.5 + - - +
189A ASP* 2.7 53.2 + - - +
211A LEU 3.0 14.1 + - - -
212A ASN* 2.8 32.1 + - - +
213A VAL* 3.5 15.8 - - - +
236A GLU* 3.1 39.4 + - + +
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Residues in contact with GLN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 3.1 37.6 + - + +
183A GLU* 3.7 13.2 + - - +
184A TYR 3.2 0.2 - - - -
185A ARG* 1.3 73.6 - - + +
187A ARG* 1.3 66.1 + - + +
189A ASP* 3.3 9.8 + - + +
190A GLU* 3.0 24.8 + - - +
235A GLN* 3.2 45.5 - - + +
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Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 2.6 51.6 + - - +
151A HIS* 3.6 12.8 + - + +
183A GLU* 3.4 16.6 + - - +
184A TYR* 2.9 18.5 + - - +
186A GLN* 1.3 79.2 - - + +
188A TRP* 1.3 60.4 + - - +
190A GLU* 3.6 7.6 + - - +
191A ALA* 3.1 17.0 + - - +
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Residues in contact with TRP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 4.7 7.0 - - + -
151A HIS* 3.8 52.2 - + + +
156A ARG* 4.2 19.5 - - + -
157A VAL* 3.5 31.9 - - + -
170A ALA* 5.4 0.7 - - + -
171A TYR 5.3 0.4 - - - -
172A VAL* 3.6 28.6 - - + +
173A PRO* 3.5 32.5 - - + -
184A TYR* 2.8 22.0 + - + +
185A ARG* 3.1 7.8 + - - +
187A ARG* 1.3 69.7 - - - +
189A ASP* 1.3 79.0 + - - +
191A ALA* 3.1 2.1 + - - +
192A PHE* 2.8 67.7 + + + +
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Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL* 4.4 1.2 - - - +
185A ARG* 2.7 54.0 + - - +
186A GLN* 3.3 10.4 + - + +
188A TRP* 1.3 84.1 - - - +
190A GLU* 1.3 58.4 + - - +
192A PHE* 3.9 2.3 - - - +
193A ARG* 2.9 40.3 + - - +
235A GLN 4.5 2.1 - - - +
236A GLU* 4.4 10.4 - - - +
239A GLY* 4.2 25.8 - - - +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLN 3.0 17.0 + - - +
187A ARG* 3.9 7.1 - - - +
189A ASP* 1.3 79.2 - - - +
191A ALA* 1.3 66.7 + - - +
193A ARG* 3.5 24.6 + - - +
194A LYS* 3.0 55.2 + - - +
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 3.8 9.7 - - + +
148A ASP* 4.0 11.0 - - + +
151A HIS* 3.5 36.8 - - + +
187A ARG 3.1 5.3 + - - +
188A TRP 3.1 2.9 + - - +
190A GLU* 1.3 85.1 + - - +
192A PHE* 1.3 62.1 + - - +
194A LYS* 3.4 6.8 + - - +
195A PHE* 3.1 22.3 + - - +
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Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 3.5 34.0 - - + +
157A VAL* 4.2 7.6 - - + -
168A VAL* 4.2 7.0 - - + -
170A ALA* 3.8 27.4 - - + -
172A VAL* 4.4 8.3 - - + -
188A TRP* 2.8 51.3 + + + +
189A ASP* 3.9 3.4 - - - +
191A ALA* 1.3 70.2 - - - +
193A ARG* 1.3 66.4 + - - +
195A PHE* 3.4 3.4 + + - +
196A LEU* 3.0 65.6 + - + +
207A LEU* 4.1 18.2 - - + -
211A LEU* 5.0 1.1 - - + -
243A LEU* 5.4 7.0 - - + -
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Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP* 2.9 21.1 + - - +
190A GLU* 3.8 39.6 + - - +
191A ALA 3.4 0.2 - - - -
192A PHE* 1.3 76.9 - - - +
194A LYS* 1.3 75.2 + - - +
196A LEU* 3.3 2.1 + - - +
197A LYS* 3.1 22.8 + - + +
239A GLY* 5.0 4.2 + - - -
242A GLU* 3.1 41.5 + - - +
243A LEU* 3.7 31.2 - - + +
246A ALA* 3.8 28.7 - - + -
247A VAL* 4.3 3.9 - - + +
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLU* 3.0 49.2 + - - +
191A ALA* 3.8 6.3 - - - +
192A PHE 3.3 0.2 - - - -
193A ARG* 1.3 86.3 - - + +
195A PHE* 1.3 66.2 + - - +
197A LYS* 2.9 18.6 + - - +
198A GLY* 3.1 10.2 + - - -
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Residues in contact with PHE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A SER* 5.5 1.8 - - - -
145A GLY 3.8 14.1 - - - -
146A ILE* 3.1 55.4 - - + +
147A GLY* 4.5 1.6 - - - -
157A VAL* 5.0 0.9 - - + -
159A VAL* 4.1 15.9 - - + -
168A VAL* 5.0 0.9 - - + -
191A ALA 3.1 14.7 + - - +
192A PHE* 3.7 5.2 - + - +
194A LYS* 1.3 79.4 - - - +
196A LEU* 1.3 78.4 + - + +
198A GLY* 3.3 3.6 + - - +
199A LEU* 3.2 50.4 + - + +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A VAL* 3.9 28.9 - - + -
192A PHE* 3.0 59.8 + - + +
193A ARG 3.8 3.4 - - - +
195A PHE* 1.3 81.8 - - + +
197A LYS* 1.3 58.6 + - - +
199A LEU* 3.1 9.1 + - + +
200A ALA* 2.8 30.1 + - - +
205A LEU* 4.8 11.8 - - + +
207A LEU* 3.8 14.1 - - + -
243A LEU* 3.8 20.9 - - + -
247A VAL* 4.3 12.1 - - + -
249A LEU* 4.9 5.6 - - + -
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Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ARG* 3.1 13.9 + - + +
194A LYS* 2.9 12.4 + - - +
196A LEU* 1.3 75.9 - - - +
198A GLY* 1.3 63.7 + - - +
200A ALA* 3.3 1.2 + - - +
201A SER* 3.0 26.9 + - - -
246A ALA* 3.2 30.7 + - + +
247A VAL* 3.9 28.5 + - - +
248A PRO* 5.7 0.8 - - - +
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Residues in contact with GLY 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LYS 3.1 12.0 + - - -
195A PHE* 3.7 4.3 - - - -
197A LYS* 1.3 77.2 - - - +
199A LEU* 1.3 59.5 + - - +
201A SER* 2.8 22.7 + - - -
202A ARG* 3.7 5.5 + - - +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LYS* 5.7 5.2 - - - +
159A VAL* 4.2 11.4 - - + -
166A VAL* 4.3 19.0 - - + +
168A VAL* 3.5 32.1 - - + -
195A PHE* 3.2 40.6 + - + +
196A LEU* 3.1 11.7 + - + +
198A GLY* 1.3 76.0 - - - +
200A ALA* 1.3 58.4 + - - +
202A ARG* 2.8 24.3 + - - +
203A LYS 3.3 11.3 + - - +
205A LEU* 3.8 13.9 - - + -
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU 2.8 18.9 + - - +
197A LYS 4.0 1.8 - - - +
199A LEU* 1.3 73.1 - - - +
201A SER* 1.3 60.8 + - - +
202A ARG 3.2 0.2 - - - -
203A LYS 3.4 20.2 + - - +
204A PRO* 5.1 0.5 - - - +
205A LEU* 4.1 11.4 - - + +
247A VAL* 3.6 29.2 - - + +
248A PRO 5.4 0.4 - - - +
249A LEU* 5.1 0.2 - - + -
288A SER* 4.1 18.2 + - - +
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LYS* 3.0 16.1 + - - -
198A GLY* 2.8 22.7 + - - -
199A LEU 3.1 0.2 - - - -
200A ALA* 1.3 77.3 - - - +
202A ARG* 1.3 58.3 + - - +
247A VAL 5.8 0.2 + - - -
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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
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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