Contacts of the helix formed by residues 201 - 213 (chain A) in PDB entry 3CNO
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A PHE* 3.8 2.0 - - - -
199A GLU 4.0 0.8 + - - -
200A SER* 1.3 78.0 - - - +
202A PHE* 1.3 64.0 + - - +
203A SER* 3.7 7.7 + - - -
204A GLU* 3.2 36.1 + - - +
205A PHE* 3.0 23.9 + - - +
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Residues in contact with PHE 202 (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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182A GLN* 5.0 9.9 - - + -
185A PHE* 3.8 23.3 - - + -
186A GLU* 3.9 38.8 - - + +
189A PHE* 3.5 29.7 - + + -
201A SER* 1.3 72.7 - - - +
203A SER* 1.3 71.2 + - - +
205A PHE* 3.8 0.2 - - - +
206A PHE* 3.1 58.7 + + + +
224A ILE* 5.1 8.7 - - + -
228A LEU* 3.7 30.1 - - + -
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Residues in contact with SER 203 (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 SER* 3.3 7.2 + - - -
202A PHE* 1.3 83.7 - - - +
204A GLU* 1.3 66.2 + - - +
206A PHE* 3.4 1.8 + - - +
207A GLU* 2.9 28.7 + - - +
224A ILE* 5.3 1.2 - - - +
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Residues in contact with GLU 204 (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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200A SER* 3.4 23.9 - - - -
201A SER* 3.2 30.6 + - - +
203A SER* 1.3 77.5 - - - +
205A PHE* 1.3 63.6 + - - +
207A GLU* 3.9 6.7 - - - +
208A ASP* 3.1 25.9 + - - +
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Residues in contact with PHE 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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189A PHE* 3.5 26.9 - + + -
192A PHE* 4.3 3.1 - + - -
198A ILE* 3.5 33.7 - - + -
200A SER* 4.4 12.1 - - - +
201A SER 3.0 15.2 + - - +
202A PHE 3.8 1.8 - - - +
204A GLU* 1.3 80.7 - - - +
206A PHE* 1.3 75.3 + + - +
208A ASP* 3.4 7.0 + - + +
209A PHE* 2.9 33.6 + + + +
212A LYS* 6.0 3.8 - - - -
231A PHE* 3.6 43.7 - + - -
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Residues in contact with PHE 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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189A PHE* 3.8 15.7 - + + -
202A PHE* 3.1 62.5 + + + +
203A SER* 4.4 1.6 - - - +
205A PHE* 1.3 85.3 - + - +
207A GLU* 1.3 67.1 + - - +
209A PHE* 3.8 5.5 - - + +
210A ALA* 2.9 25.5 + - - +
224A ILE* 3.7 23.6 - - + +
227A ALA* 4.0 16.3 - - + +
228A LEU* 3.5 24.5 - - + -
231A PHE* 3.6 47.3 - + + -
232A PHE* 3.9 8.5 - + - -
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Residues in contact with GLU 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 SER 2.9 19.9 + - - +
204A GLU* 3.9 6.7 - - - +
206A PHE* 1.3 77.2 - - - +
208A ASP* 1.3 57.3 + - - +
210A ALA* 3.4 2.4 + - - +
211A ARG* 2.8 64.5 + - - +
222A PRO* 3.7 20.2 - - + -
224A ILE* 3.7 14.1 - - + +
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Residues in contact with ASP 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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204A GLU 3.1 21.0 + - - +
205A PHE* 3.5 6.3 - - + +
207A GLU* 1.3 77.1 - - - +
209A PHE* 1.3 51.8 + - - +
211A ARG* 3.2 12.9 + - - +
212A LYS* 2.8 63.1 + - - +
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Residues in contact with PHE 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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205A PHE* 2.9 25.4 + + + +
206A PHE* 3.8 11.2 - + + +
207A GLU 3.3 0.4 - - - -
208A ASP* 1.3 76.0 - - - +
210A ALA* 1.3 60.8 + - - +
212A LYS* 3.5 22.3 + - - +
213A ARG* 3.1 66.7 + - + +
215A LEU* 4.6 1.6 - - + -
227A ALA* 3.5 36.3 - - + -
230A LEU* 4.1 15.3 - - + -
231A PHE* 3.6 37.9 - + + -
234A GLU* 3.8 18.2 - - - -
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Residues in contact with ALA 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 PHE 2.9 17.5 + - - +
207A GLU 3.6 4.3 - - - +
209A PHE* 1.3 76.6 - - - +
211A ARG* 1.3 61.9 + - - +
214A GLY 3.2 2.3 + - - -
215A LEU* 2.7 55.8 + - - +
216A LEU* 5.1 0.9 - - - -
222A PRO* 3.8 15.0 - - + -
223A ASP 3.8 18.4 - - - +
224A ILE* 4.4 0.9 - - + -
227A ALA* 4.0 6.0 - - + +
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Residues in contact with ARG 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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207A GLU* 2.8 47.2 + - - +
208A ASP* 3.4 15.5 - - - +
210A ALA* 1.3 73.0 - - - +
212A LYS* 1.3 62.1 + - + +
214A GLY* 2.8 23.0 + - - -
216A LEU* 4.8 13.9 - - + +
220A GLY 4.5 9.9 + - - -
222A PRO* 3.7 25.3 - - + +
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Residues in contact with LYS 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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205A PHE* 6.0 3.8 - - - -
208A ASP* 2.8 48.4 + - - +
209A PHE* 3.9 28.3 - - - +
211A ARG* 1.3 72.1 - - + +
213A ARG* 1.3 73.4 + - + +
214A GLY 3.3 0.7 + - - -
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Residues in contact with ARG 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 PHE* 3.1 47.0 + - + +
211A ARG 3.1 1.0 - - - -
212A LYS* 1.3 90.8 - - + +
214A GLY* 1.3 62.9 + - - +
215A LEU* 3.2 25.4 + - + +
230A LEU* 4.0 15.8 - - + +
234A GLU* 2.9 41.7 + - - -
239A LYS 5.7 2.2 + - - -
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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
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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