Contacts of the helix formed by residues 199 - 221 (chain A) in PDB entry 1WVA
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 SER 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.4 31.9 - - - +
197A TYR* 3.8 11.4 - - - -
198A PHE* 1.3 79.0 - - - +
200A MET* 1.3 65.6 + - - +
201A THR* 3.2 19.2 + - - -
202A GLU* 2.7 34.3 + - - -
203A VAL* 3.1 9.8 + - - +
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Residues in contact with MET 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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178A GLY* 3.6 26.2 - - - +
179A LEU 2.9 20.0 + - - +
180A ARG* 3.8 23.8 - - + +
199A SER* 1.3 72.3 - - - +
201A THR* 1.3 56.3 + - - +
203A VAL* 3.2 17.1 + - + +
204A ASP* 2.8 48.9 + - - +
250A GLY 3.2 27.8 - - - +
251A GLY 3.8 15.3 - - - +
252A LEU* 3.9 19.7 - - + +
256A GLU* 4.6 2.7 - - - +
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 3.0 13.0 + - - -
200A MET* 1.3 78.2 - - - +
202A GLU* 1.3 63.0 + - - +
204A ASP* 3.4 10.9 + - - +
205A ARG* 3.0 48.2 + - - +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 3.8 19.6 - - - +
198A PHE* 3.9 32.8 - - + -
199A SER* 2.7 41.1 + - - +
201A THR* 1.3 78.1 - - - +
203A VAL* 1.3 59.3 + - - +
204A ASP 3.1 1.6 - - - -
205A ARG* 2.7 35.3 + - + +
206A LEU* 2.7 41.0 + - + +
211A VAL* 4.4 1.3 - - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 4.8 4.5 - - + -
178A GLY 4.7 2.5 - - - +
198A PHE* 4.0 13.2 - - + +
199A SER 3.1 16.7 + - - +
200A MET* 3.6 25.8 - - + +
202A GLU* 1.3 75.4 - - - +
204A ASP* 1.3 59.0 + - - +
207A GLY* 2.9 25.6 + - - -
208A ILE* 4.3 18.4 - - + +
211A VAL* 3.9 16.6 - - + +
252A LEU* 4.3 10.8 - - + -
256A GLU* 3.5 29.7 - - - +
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Residues in contact with ASP 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A MET* 2.8 40.6 + - - +
201A THR* 3.4 9.6 - - - +
203A VAL* 1.3 81.6 - - - +
205A ARG* 1.3 62.0 + - - +
207A GLY* 4.3 2.6 + - - -
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Residues in contact with ARG 205 (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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201A THR* 3.0 29.2 + - - +
202A GLU* 2.7 44.3 + - - +
204A ASP* 1.3 80.7 - - - +
206A LEU* 1.3 81.8 + - + +
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Residues in contact with LEU 206 (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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198A PHE* 3.6 26.2 - - + -
202A GLU* 2.7 22.2 + - + +
205A ARG* 1.3 94.9 - - + +
207A GLY* 1.3 66.8 + - - +
210A LYS* 3.4 27.0 + - + +
211A VAL* 4.0 6.7 - - + +
214A GLU* 3.2 36.8 - - - +
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Residues in contact with GLY 207 (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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203A VAL 2.9 19.0 + - - -
204A ASP 4.3 2.4 + - - -
205A ARG 3.6 1.6 - - - -
206A LEU* 1.3 83.6 - - - +
208A ILE* 1.3 66.4 + - - -
209A GLY 3.1 4.0 + - - -
211A VAL* 3.2 17.2 + - - +
256A GLU* 5.9 0.2 - - - -
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Residues in contact with ILE 208 (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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177A ILE* 4.7 1.8 - - + -
203A VAL* 4.1 18.0 + - + +
207A GLY* 1.3 71.0 - - - -
209A GLY* 1.3 65.0 + - - +
211A VAL* 3.8 20.6 - - + -
212A MET* 3.1 19.4 + - + -
252A LEU* 4.6 4.3 - - + -
256A GLU* 4.0 42.6 + - + +
259A TYR* 3.6 35.6 - - + -
260A ILE* 3.8 26.7 - - + -
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Residues in contact with GLY 209 (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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207A GLY 3.1 2.0 + - - -
208A ILE* 1.3 84.9 - - - +
210A LYS* 1.3 60.1 + - - +
212A MET* 3.6 2.3 + - - +
213A GLU* 3.3 21.3 + - - +
259A TYR* 3.7 23.7 + - - -
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Residues in contact with LYS 210 (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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206A LEU* 3.4 35.0 + - + +
207A GLY 3.3 2.0 + - - -
209A GLY* 1.3 73.9 - - - +
211A VAL* 1.3 60.5 + - - +
213A GLU* 3.1 25.9 + - - +
214A GLU* 2.7 75.5 + - - +
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Residues in contact with VAL 211 (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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177A ILE* 4.4 13.2 - - + -
198A PHE* 3.8 34.5 - - + -
202A GLU 4.1 0.4 - - - +
203A VAL* 3.9 27.1 - - + +
206A LEU* 4.0 15.3 - - + -
207A GLY 3.2 16.6 + - - +
208A ILE* 3.6 24.2 - - + +
209A GLY 3.3 0.2 - - - -
210A LYS* 1.3 76.3 - - - +
212A MET* 1.3 55.7 + - - +
214A GLU* 3.3 1.7 + - - +
215A THR* 2.6 45.7 + - + +
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Residues in contact with MET 212 (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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177A ILE* 3.9 21.3 - - + -
208A ILE* 3.1 20.5 + - + +
209A GLY 4.1 0.4 - - - +
211A VAL* 1.3 74.5 - - - +
213A GLU* 1.3 64.8 + - - +
215A THR* 3.7 5.8 + - - +
216A LEU* 3.2 34.5 + - + +
259A TYR* 3.6 30.3 - - + +
260A ILE* 3.4 50.3 - - + +
263A GLU* 3.9 15.3 - - + +
264A ILE* 3.5 26.5 - - + -
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Residues in contact with GLU 213 (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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209A GLY 3.3 15.9 + - - +
210A LYS* 3.1 37.7 + - - +
211A VAL 3.3 0.6 - - - -
212A MET* 1.3 78.5 - - - +
214A GLU* 1.3 58.6 + - + +
216A LEU* 4.1 3.3 - - - +
217A SER* 3.0 30.3 + - - -
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Residues in contact with GLU 214 (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 LYS* 4.6 8.9 + - - -
198A PHE* 3.6 23.3 - - + -
206A LEU* 3.2 33.8 - - - +
210A LYS* 2.7 48.0 + - - +
211A VAL 3.8 0.2 - - - +
213A GLU* 1.3 79.1 - - + +
215A THR* 1.3 59.9 + - - +
217A SER* 3.1 7.2 + - - +
218A TYR* 2.9 30.0 + - - +
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Residues in contact with THR 215 (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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121A ILE* 4.8 6.1 - - - +
175A VAL* 3.7 18.2 - - + -
177A ILE* 3.8 23.9 - - + +
198A PHE* 3.1 31.6 - - + -
211A VAL* 2.6 27.5 + - + +
212A MET* 3.7 11.8 + - - +
214A GLU* 1.3 76.5 - - - +
216A LEU* 1.3 65.7 + - - +
218A TYR* 3.5 5.3 + - - +
219A LEU* 3.1 35.1 + - - +
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Residues in contact with LEU 216 (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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121A ILE* 5.5 4.9 - - + -
212A MET* 3.2 27.8 + - + +
213A GLU* 4.1 3.8 - - - +
215A THR* 1.3 84.6 + - - +
217A SER* 1.3 56.5 + - - +
218A TYR 3.2 0.2 - - - -
219A LEU* 4.8 1.6 - - + -
220A LEU* 2.6 53.8 + - + +
227A ILE* 5.5 6.7 - - + -
263A GLU* 4.0 19.3 - - + +
264A ILE* 3.8 22.2 - - + -
267A THR* 3.5 31.6 - - + -
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Residues in contact with SER 217 (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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213A GLU* 3.0 20.3 + - - -
214A GLU* 3.1 14.0 + - - +
216A LEU* 1.3 77.1 - - - +
218A TYR* 1.3 61.6 + - - +
220A LEU 4.8 0.4 - - - -
221A GLY* 2.9 32.9 + - - +
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Residues in contact with TYR 218 (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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171A ALA 4.4 1.0 + - - -
172A LYS* 3.5 40.5 + - + +
174A ILE 4.2 3.8 - - - -
175A VAL* 3.5 23.6 - - + -
194A GLY 4.4 6.2 + - - -
196A LYS* 3.5 50.7 + - + +
214A GLU 2.9 15.6 + - - +
215A THR* 3.6 6.1 - - - +
217A SER* 1.3 84.5 + - - +
219A LEU* 1.3 62.9 + - + +
221A GLY* 4.6 1.4 + - - -
225A ARG* 5.7 0.2 + - - -
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Residues in contact with LEU 219 (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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119A GLY* 4.2 2.5 - - - -
120A VAL 4.0 1.6 - - - +
121A ILE* 3.3 37.7 - - + -
172A LYS 4.7 0.4 - - - +
173A ASP* 3.4 23.3 - - - +
174A ILE 4.1 0.4 - - - +
175A VAL* 3.4 30.3 - - + -
215A THR 3.1 17.4 + - - +
216A LEU* 4.2 3.4 - - + +
218A TYR* 1.3 84.1 - - + +
220A LEU* 1.3 65.2 + - + +
221A GLY 3.4 3.0 + - - -
222A ARG 5.3 0.5 + - - -
223A LYS 3.7 6.8 + - - +
225A ARG* 2.9 54.3 + - - +
227A ILE* 4.7 5.6 - - + -
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Residues in contact with LEU 220 (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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216A LEU* 2.6 46.4 + - + +
217A SER* 3.9 1.1 - - - -
219A LEU* 1.3 80.8 - - + +
221A GLY* 1.3 65.7 + - - +
223A LYS 3.7 10.5 - - - +
224A LYS* 3.8 21.2 + - + -
225A ARG* 3.9 15.5 - - + +
227A ILE* 3.9 25.1 - - + -
267A THR* 4.0 17.0 - - + +
269A LEU* 3.6 33.7 - - + -
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Residues in contact with GLY 221 (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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217A SER* 2.9 22.9 + - - -
218A TYR 4.4 1.5 + - - -
219A LEU 3.4 3.2 - - - -
220A LEU* 1.3 80.0 - - - +
222A ARG* 1.3 68.6 + - - +
224A LYS* 3.8 9.7 + - - -
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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