Contacts of the helix formed by residues 206 - 219 (chain A) in PDB entry 3C5H
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 VAL 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A VAL 2.8 13.3 + - - +
168A ARG* 3.3 44.4 - - + +
205A GLY* 1.3 71.9 - - - +
207A GLU* 1.3 67.3 + - + +
208A ARG* 3.6 16.8 - - + +
209A TYR* 3.1 33.8 + - + +
210A ILE* 2.9 25.0 + - - +
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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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205A GLY 4.1 2.0 + - - -
206A VAL* 1.3 74.3 - - + +
208A ARG* 1.3 60.3 + - + +
210A ILE* 3.8 10.5 - - - +
211A ARG* 2.9 32.4 + - - +
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Residues in contact with ARG 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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206A VAL* 3.2 12.3 - - + +
207A GLU* 1.3 83.7 - - + +
209A TYR* 1.3 66.5 + - + +
211A ARG* 3.8 5.1 - - - +
212A ASP* 3.0 48.5 + - - +
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Residues in contact with TYR 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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166A VAL* 3.5 27.1 - - + +
167A SER 3.6 17.5 - - - -
168A ARG* 4.7 2.9 - - - -
174A PHE* 3.5 72.3 + + + +
175A ASP* 5.7 0.7 - - - -
206A VAL* 3.1 28.6 + - + +
208A ARG* 1.3 86.6 - - + +
210A ILE* 1.3 65.4 + - - +
212A ASP* 3.2 1.5 + - - -
213A ALA* 2.9 22.2 + - - +
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Residues in contact with ILE 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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166A VAL* 3.8 22.2 - - + -
199A LEU* 3.9 11.9 - - + -
202A CYS* 4.9 9.4 - - + +
205A GLY* 4.3 16.2 - - - -
206A VAL 2.9 25.9 + - - +
207A GLU* 3.8 8.3 - - + +
209A TYR* 1.3 76.3 - - - +
211A ARG* 1.3 63.0 + - - +
213A ALA* 3.2 3.1 + - - +
214A HIS* 3.0 37.8 + - + -
227A GLU* 3.4 30.3 - - - +
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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 2.9 19.2 + - - +
208A ARG* 3.8 5.6 - - - +
210A ILE* 1.3 79.0 - - - +
212A ASP* 1.3 63.0 + - - +
214A HIS* 3.3 8.1 + - - +
215A THR* 2.9 38.0 + - - +
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Residues in contact with ASP 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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174A PHE* 3.9 16.6 - - + -
175A ASP* 4.3 13.9 - - - +
178A LEU* 3.8 14.1 - - + +
208A ARG* 3.0 34.1 + - - +
209A TYR* 3.7 4.0 - - - +
211A ARG* 1.3 81.4 - - - +
213A ALA* 1.3 57.3 + - - +
215A THR* 3.3 9.4 + - - -
216A PHE* 3.0 27.0 + - - +
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Residues in contact with ALA 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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164A ILE* 4.2 15.9 - - + +
166A VAL* 4.4 5.8 - - + -
174A PHE* 4.8 1.1 - - + -
178A LEU* 4.6 7.7 - - - +
197A VAL* 5.3 0.5 - - - +
199A LEU* 3.4 34.1 - - + -
209A TYR 2.9 16.7 + - - +
210A ILE 3.6 3.4 - - - +
212A ASP* 1.3 72.3 - - - +
214A HIS* 1.3 65.4 + - - +
216A PHE* 3.3 11.4 + - - +
217A ALA* 3.0 23.0 + - - +
225A VAL* 4.8 1.9 - - - +
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Residues in contact with HIS 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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199A LEU* 4.1 5.1 - - + +
210A ILE* 3.0 40.0 + - + +
211A ARG* 3.6 7.6 - - - +
213A ALA* 1.3 77.6 - - - +
215A THR* 1.3 56.9 + - - +
217A ALA* 3.1 2.4 + - - +
218A LEU* 2.9 45.2 + - + +
225A VAL* 3.6 40.7 - - + +
227A GLU* 2.8 25.4 + - + -
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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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211A ARG* 2.9 22.2 + - - +
212A ASP* 3.5 12.2 + - - -
214A HIS* 1.3 75.3 - - - +
216A PHE* 1.3 62.7 + - - +
218A LEU* 3.4 12.7 + - + +
219A SER* 3.1 21.7 + - - -
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Residues in contact with PHE 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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162A LEU* 4.3 9.2 - - + -
164A ILE* 4.6 5.4 - - + -
178A LEU* 4.1 26.5 - - + -
181A VAL* 3.8 20.4 - - + -
182A SER* 3.8 28.0 - - - -
185A TYR* 3.7 29.4 - + + -
197A VAL* 4.4 10.8 - - + -
212A ASP 3.0 13.8 + - - +
213A ALA 3.5 9.9 - - - +
215A THR* 1.3 77.0 - - - +
217A ALA* 1.3 64.2 + - + +
219A SER* 2.5 27.4 + - - -
220A LYS* 3.5 29.1 - - + +
223A LEU* 4.4 5.2 - - + -
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Residues in contact with ALA 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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197A VAL* 4.4 5.8 - - + -
213A ALA 3.0 12.1 + - - +
214A HIS 3.1 2.6 + - - +
216A PHE* 1.3 77.0 - - + +
218A LEU* 1.3 57.8 + - + +
220A LYS* 3.1 25.6 + - - +
223A LEU* 3.6 42.6 + - + +
225A VAL* 3.3 33.9 - - + -
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Residues in contact with LEU 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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214A HIS* 2.9 34.7 + - + +
215A THR* 3.7 11.0 - - + +
217A ALA* 1.3 73.2 - - + +
219A SER* 1.3 58.0 + - - +
220A LYS 3.1 13.4 + - - +
223A LEU 6.2 0.2 - - - +
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Residues in contact with SER 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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215A THR* 3.1 12.2 + - - -
216A PHE* 2.5 24.5 + - - -
218A LEU* 1.3 76.3 - - - +
220A LYS* 1.3 77.2 + - - +
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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