Contacts of the helix formed by residues 214 - 222 (chain A) in PDB entry 2WQN
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 ASN 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A MET* 3.3 16.4 - - - -
206A GLU* 4.4 2.9 - - - +
212A GLY 4.5 6.4 + - - +
213A TYR* 1.3 85.8 - - - +
215A PHE* 1.3 69.8 + - + +
216A LYS* 3.2 20.1 + - - +
217A SER* 3.0 29.0 + - - -
279A PRO* 5.4 5.6 - - - +
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Residues in contact with PHE 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 HIS* 3.6 43.1 - + + +
156A ARG* 3.2 62.6 - - + -
157A VAL 3.9 15.7 - - - -
158A MET* 3.6 28.0 - - + -
214A ASN* 1.3 81.8 - - + +
216A LYS* 1.3 66.5 + - + +
218A ASP* 3.0 21.5 + - - +
219A ILE* 3.3 6.2 + - - +
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Residues in contact with LYS 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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214A ASN* 3.2 13.4 + - - +
215A PHE* 1.3 79.6 - - + +
217A SER* 1.3 56.7 + - - +
219A ILE* 3.1 9.8 + - + +
220A TRP 3.0 18.4 + - - -
279A PRO* 3.3 41.3 + - + +
280A GLU* 4.3 9.3 + - - +
282A ARG* 2.9 47.7 + - + +
283A PRO 3.7 14.3 - - - +
284A ASP* 3.1 29.2 + - - +
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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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204A SER* 4.2 8.2 - - - -
206A GLU* 2.8 32.7 + - - +
213A TYR* 3.6 29.0 + - - -
214A ASN* 3.0 31.3 + - - -
216A LYS* 1.3 74.5 - - - +
218A ASP* 1.3 62.7 + - - +
220A TRP* 3.2 7.1 + - - +
221A SER* 3.2 23.2 + - - -
282A ARG* 4.0 1.3 - - - +
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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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149A LEU* 3.6 4.8 - - + +
153A HIS* 2.9 27.2 + - + +
158A MET* 3.7 3.7 - - - +
159A HIS 2.8 24.5 + - - -
160A ARG 3.1 10.0 + - - -
162A ILE* 3.6 24.4 - - + +
213A TYR* 2.4 41.0 + - - -
214A ASN 3.5 1.2 + - - -
215A PHE 3.0 11.7 + - - +
217A SER* 1.3 77.9 - - - +
219A ILE* 1.3 59.4 + - - +
221A SER* 3.3 1.3 + - - +
222A LEU* 2.9 29.4 + - - +
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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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149A LEU* 4.5 3.1 - - + -
153A HIS* 4.4 8.7 - - + -
215A PHE 3.6 11.7 - - - +
216A LYS* 3.1 18.3 + - + +
218A ASP* 1.3 76.5 - - - +
220A TRP* 1.3 63.9 + - - +
222A LEU* 3.3 8.4 + - + +
223A GLY 3.0 18.0 + - - -
274A CYS* 3.7 34.5 - - + +
282A ARG* 4.1 8.3 - - + -
283A PRO* 3.4 23.8 - - + +
284A ASP* 4.0 1.1 - - - +
285A VAL* 3.6 42.8 - - + +
288A VAL* 4.7 4.0 - - + -
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Residues in contact with TRP 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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202A TYR* 4.6 2.4 - - + -
203A MET 3.5 9.8 + - - +
204A SER* 3.4 31.1 - - - +
205A PRO* 3.9 10.1 - - + -
216A LYS 3.0 5.7 + - - -
217A SER 3.2 8.3 + - - +
219A ILE* 1.3 76.7 - - - +
221A SER* 1.3 72.9 + - - +
223A GLY 3.1 2.4 + - - -
224A CYS* 3.1 36.7 + - - -
236A PHE* 3.6 28.0 - + - -
250A ILE* 3.5 46.0 - - + -
274A CYS 3.5 11.8 + - - -
275A ILE* 2.9 45.7 - - + +
276A ASN 4.0 4.5 - - - -
282A ARG* 3.8 30.1 - - - +
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Residues in contact with SER 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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162A ILE* 3.6 40.2 + - - -
202A TYR* 3.7 26.0 + - - +
204A SER* 5.8 0.2 - - - -
213A TYR* 4.1 9.8 + - - -
217A SER 3.2 10.1 + - - -
218A ASP* 3.6 5.8 - - - -
220A TRP* 1.3 83.9 - - - +
222A LEU* 1.3 63.2 + - - +
224A CYS* 3.2 4.4 + - - +
225A LEU* 2.9 23.6 + - - +
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Residues in contact with LEU 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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142A PHE* 3.7 24.2 - - + -
145A LEU* 3.7 39.3 - - + +
146A CYS* 4.2 8.5 - - - -
149A LEU* 3.9 26.9 - - + -
162A ILE* 4.3 8.9 - - + +
218A ASP 2.9 13.1 + - - +
219A ILE* 3.4 16.2 - - + +
221A SER* 1.3 77.5 - - - +
223A GLY* 1.3 56.0 + - - +
225A LEU* 3.4 5.8 + - - +
226A LEU 3.1 21.5 + - - -
274A CYS* 5.4 2.0 - - - -
285A VAL* 4.6 6.1 - - + -
288A VAL* 3.9 29.8 - - + -
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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