Contacts of the helix formed by residues 212 - 226 (chain A) in PDB entry 2WJW
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ASP* 3.3 16.1 + - + +
155A ASP* 3.2 38.1 - - - +
156A ARG* 5.2 8.3 - - + +
211A CYS* 1.3 77.2 - - - +
213A ARG* 1.3 68.7 + - - +
214A ASP* 3.2 5.4 - - + +
215A LYS* 2.9 23.1 + - + +
216A VAL* 3.4 6.6 + - - +
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A GLU* 5.5 1.4 + - - -
211A CYS 3.7 2.0 + - - +
212A GLU* 1.3 71.2 - - - +
214A ASP* 1.3 67.9 + - - +
216A VAL* 3.0 28.4 + - - +
217A ASN* 3.6 9.6 - - - +
239A ASN* 5.0 11.9 - - - +
244A ASP* 6.3 1.9 - - - +
247A LEU* 4.7 17.9 - - + +
294A LYS* 3.4 41.6 - - - +
295A TYR* 6.5 0.9 - - - -
296A THR* 5.6 1.6 + - - -
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Residues in contact with ASP 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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212A GLU* 3.0 4.9 + - + +
213A ARG* 1.3 82.6 - - - +
215A LYS* 1.3 62.2 + - + +
216A VAL 3.1 0.3 + - - -
217A ASN* 3.2 16.1 + - - +
218A ASP* 2.9 35.0 + - - +
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Residues in contact with LYS 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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153A ASP* 3.3 35.0 - - - +
155A ASP* 4.3 8.0 + - - +
180A VAL* 3.2 28.5 - - + +
181A GLY* 4.3 2.0 - - - -
183A ILE* 4.0 26.6 + - + +
185A ASN* 4.9 7.3 + - - -
192A TYR* 4.7 8.1 - - - +
211A CYS* 4.0 14.1 - - + -
212A GLU* 2.9 16.2 + - + +
214A ASP* 1.3 76.0 - - + +
216A VAL* 1.3 62.6 + - - +
218A ASP* 3.8 15.2 + - - +
219A ILE* 3.0 36.0 + - + +
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Residues in contact with VAL 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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209A LEU* 3.9 29.2 - - + +
211A CYS* 4.3 17.5 - - - +
212A GLU 3.8 9.9 - - - +
213A ARG* 3.0 21.2 + - - +
215A LYS* 1.3 75.6 - - - +
217A ASN* 1.3 67.2 + - - +
219A ILE* 3.1 3.8 + - - +
220A VAL* 2.9 39.8 + - + +
237A ILE* 4.5 17.0 - - + -
239A ASN* 5.7 2.9 - - - +
247A LEU* 4.6 15.0 - - + -
250A ILE* 4.4 8.1 - - + -
252A PHE* 5.4 2.2 - - + -
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Residues in contact with ASN 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 ARG 3.6 14.1 + - - +
214A ASP* 3.2 15.8 + - - +
216A VAL* 1.3 76.2 - - - +
218A ASP* 1.3 61.1 + - - +
220A VAL* 3.9 1.7 - - - +
221A ASP* 2.8 35.8 + - - +
246A ASP* 5.1 8.7 + - - -
247A LEU* 4.8 5.9 - - - +
250A ILE* 3.2 34.8 - - + +
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Residues in contact with ASP 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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188A LYS* 5.4 8.7 - - + +
192A TYR* 3.6 29.9 + - + +
214A ASP* 2.9 26.2 + - - +
215A LYS* 3.8 12.3 + - - +
217A ASN* 1.3 80.5 - - - +
219A ILE* 1.3 59.6 + - - +
221A ASP* 4.4 4.9 - - - +
222A GLN* 3.7 18.5 + - - +
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Residues in contact with ILE 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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151A LEU* 4.1 27.1 - - + -
180A VAL* 4.1 20.2 - - + -
192A TYR* 4.0 21.3 - - + +
195A LEU* 5.3 0.7 - - + -
196A PHE* 3.6 17.2 - - + -
209A LEU* 4.1 27.8 - - + -
211A CYS* 4.2 13.2 - - - -
215A LYS* 3.0 23.1 + - + +
216A VAL 3.1 3.3 + - - +
218A ASP* 1.3 77.4 - - - +
220A VAL* 1.3 66.4 + - + +
221A ASP 3.3 0.2 - - - -
222A GLN* 3.2 15.9 + - - +
223A VAL* 3.3 15.3 + - + +
235A TYR* 5.6 3.4 - - + -
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Residues in contact with VAL 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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209A LEU* 4.3 12.1 - - + -
216A VAL* 2.9 30.9 + - + +
217A ASN* 3.9 2.7 - - - +
219A ILE* 1.3 75.8 - - - +
221A ASP* 1.3 63.2 + - - +
223A VAL* 3.0 20.6 + - + +
224A ILE* 3.3 11.9 + - + +
235A TYR* 4.7 13.7 - - + +
250A ILE* 3.7 28.7 - - + -
251A GLN 4.2 9.0 - - - +
252A PHE* 3.8 35.0 - - + -
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Residues in contact with ASP 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 ASN 2.8 18.8 + - - +
218A ASP* 4.4 5.4 - - - +
220A VAL* 1.3 77.9 - - - +
222A GLN* 1.3 53.5 + - - +
224A ILE* 3.1 16.5 - - - +
225A THR* 2.7 47.8 + - - -
250A ILE* 5.7 1.1 - - - +
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Residues in contact with GLN 222 (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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188A LYS* 4.9 8.5 + - - -
189A ASP* 3.9 19.2 + - - +
192A TYR* 3.6 34.9 - - + +
193A ARG* 4.6 8.1 - - - +
196A PHE* 3.3 28.8 - - + -
218A ASP 3.7 12.9 + - - +
219A ILE* 3.2 11.1 + - - +
220A VAL 3.1 0.6 - - - -
221A ASP* 1.3 79.1 - - - +
223A VAL* 1.3 60.4 + - - +
225A THR* 4.0 14.1 + - - +
226A ILE* 3.1 32.8 + - + +
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Residues in contact with VAL 223 (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 PHE* 3.4 22.4 - - + -
200A GLU* 4.7 2.8 - - - +
219A ILE* 3.3 18.8 - - + +
220A VAL* 3.0 9.3 + - + +
222A GLN* 1.3 76.9 - - - +
224A ILE* 1.3 64.0 + - - +
225A THR 3.6 0.2 + - - -
226A ILE* 3.6 21.1 - - - +
227A GLY* 3.7 3.5 + - - -
228A LYS 4.2 1.3 + - - +
230A VAL* 4.0 15.2 - - + +
233A TYR* 3.5 34.5 - - + +
235A TYR* 3.2 32.5 - - + +
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Residues in contact with ILE 224 (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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220A VAL* 3.3 9.8 + - + +
221A ASP* 3.1 30.7 - - - +
223A VAL* 1.3 76.6 - - - +
225A THR* 1.3 70.3 + - - +
227A GLY* 3.1 14.6 + - - -
230A VAL* 4.2 23.7 - - + +
251A GLN* 4.7 28.0 - - + +
253A GLY* 6.2 0.7 - - - -
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Residues in contact with THR 225 (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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221A ASP* 2.7 37.6 + - - -
222A GLN* 4.0 18.9 + - - +
223A VAL 3.3 0.2 - - - -
224A ILE* 1.3 83.2 - - - +
226A ILE* 1.3 59.9 + - + +
227A GLY 2.8 6.9 + - - -
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Residues in contact with ILE 226 (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* 6.3 3.4 - - - -
196A PHE* 5.2 9.2 - - + -
200A GLU* 4.0 17.3 - - + +
222A GLN* 3.1 24.7 - - + +
223A VAL* 3.6 8.9 - - - +
225A THR* 1.3 77.6 - - + +
227A GLY* 1.3 65.5 + - - +
228A LYS* 2.8 32.1 + - + +
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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