Contacts of the helix formed by residues 206 - 220 (chain A) in PDB entry 3D0O
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 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A ARG 3.3 0.6 + - - -
205A PRO* 1.3 77.2 - - + +
207A GLY* 1.3 64.5 + - - +
208A LYS 3.2 3.4 - - - +
209A ALA* 3.0 28.8 + - + +
210A GLN* 3.1 13.8 + - + +
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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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201A LEU 3.0 26.7 - - - +
202A GLU* 4.4 2.7 + - - -
204A ARG 3.0 14.3 + - - -
205A PRO 3.0 0.9 - - - -
206A GLU* 1.3 77.6 - - - +
208A LYS* 1.3 57.9 + - - +
210A GLN* 3.1 11.8 + - - +
211A ILE* 2.9 36.0 + - - +
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Residues in contact with LYS 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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202A GLU* 2.8 40.6 + - - +
206A GLU* 3.2 1.2 - - - -
207A GLY* 1.3 76.1 - - - +
209A ALA* 1.3 62.0 + - - +
211A ILE* 3.6 9.6 + - + +
212A GLU* 3.1 23.0 + - - +
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Residues in contact with ALA 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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206A GLU* 3.0 28.2 + - + +
208A LYS* 1.3 79.1 - - - +
210A GLN* 1.3 58.0 + - + +
212A GLU* 3.4 7.9 + - - +
213A GLN* 2.9 36.9 + - + +
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Residues in contact with GLN 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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163A ALA* 5.7 0.5 - - - +
201A LEU* 4.0 9.7 - - + +
204A ARG* 3.3 50.1 + - - +
205A PRO* 3.3 23.2 + - - +
206A GLU* 3.1 11.8 + - + +
207A GLY* 3.1 7.9 + - - +
209A ALA* 1.3 74.3 - - + +
211A ILE* 1.3 61.7 + - - +
213A GLN* 3.1 6.0 + - - +
214A ILE* 2.9 38.7 + - + +
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Residues in contact with ILE 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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187A TRP* 3.7 37.2 - - + +
198A LYS* 3.8 26.0 - - + +
201A LEU* 3.6 27.3 - - + +
202A GLU* 3.3 38.4 - - + +
207A GLY 2.9 19.1 + - - +
208A LYS* 3.6 12.3 - - + +
210A GLN* 1.3 75.1 - - - +
212A GLU* 1.3 65.8 + - - +
214A ILE* 3.4 1.1 + - - +
215A PHE* 3.3 18.5 + - - +
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Residues in contact with GLU 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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208A LYS 3.1 17.8 + - - +
209A ALA* 3.7 8.5 - - - +
211A ILE* 1.3 78.2 - - - +
213A GLN* 1.3 69.8 + - - +
215A PHE* 3.1 6.8 + - + +
216A VAL* 2.9 45.0 + - + +
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Residues in contact with GLN 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 ALA* 2.9 23.2 + - + +
210A GLN* 3.8 5.4 - - - +
212A GLU* 1.3 96.0 - - - +
214A ILE* 1.3 65.9 + - - +
216A VAL* 4.0 22.6 - - - +
217A GLN* 2.9 46.4 + - - +
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Residues in contact with ILE 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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156A PHE* 3.9 29.8 - - + -
159A LEU* 3.7 29.3 - - + +
160A LEU* 4.0 15.9 - - + -
163A ALA* 4.2 19.3 - - + -
187A TRP* 4.3 2.5 - - + -
201A LEU* 3.7 33.7 - - + -
210A GLN* 2.9 22.9 + - + +
211A ILE 3.8 4.0 - - - +
213A GLN* 1.3 76.1 - - - +
215A PHE* 1.3 63.2 + - - +
217A GLN* 3.5 3.5 + - - -
218A THR* 3.0 26.7 + - - -
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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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156A PHE* 5.2 2.5 - + + -
175A ILE* 4.0 11.2 - - + -
183A GLU* 3.4 50.3 - - + -
185A PRO* 3.6 47.1 - - + -
187A TRP* 4.9 5.2 - - + +
211A ILE 3.3 8.7 + - - +
212A GLU* 3.1 10.2 + - + +
214A ILE* 1.3 79.1 - - - +
216A VAL* 1.3 65.2 + - + +
218A THR* 3.1 5.8 + - - -
219A ARG* 2.8 55.3 + - + +
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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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212A GLU* 2.9 37.3 + - + +
213A GLN* 3.9 25.4 - - - +
215A PHE* 1.3 78.1 - - + +
217A GLN* 1.3 61.2 + - + +
219A ARG* 3.8 25.3 - - - +
220A ASP* 2.9 48.1 + - + +
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Residues in contact with GLN 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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159A LEU* 3.7 35.5 - - + +
213A GLN* 2.9 41.3 + - - +
214A ILE* 5.5 0.7 - - - -
216A VAL* 1.3 79.6 - - + +
218A THR* 1.3 61.3 + - - +
220A ASP 4.0 0.2 - - - -
221A ALA* 3.2 24.3 + - - +
224A ASP* 4.7 13.6 - - - +
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Residues in contact with THR 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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152A ASP* 3.5 29.3 - - - +
155A ARG* 4.0 15.1 + - + -
156A PHE* 3.5 18.6 - - - +
159A LEU* 3.4 15.2 - - - +
175A ILE* 3.9 16.2 - - + -
183A GLU* 3.7 15.5 - - - +
214A ILE 3.0 14.1 + - - -
215A PHE* 3.1 13.2 + - + -
217A GLN* 1.3 75.3 - - - +
219A ARG* 1.3 65.4 + - - +
220A ASP 3.3 0.5 + - - -
221A ALA* 3.4 15.2 + - - +
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Residues in contact with ARG 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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152A ASP* 5.5 0.9 - - - +
155A ARG* 5.8 0.9 + - - -
180A GLY 4.5 8.4 - - - +
181A ASP* 4.2 20.0 - - - +
183A GLU* 3.5 31.7 - - + +
215A PHE* 2.8 42.3 + - + +
216A VAL* 3.9 27.2 - - - +
218A THR* 1.3 74.4 - - - +
220A ASP* 1.3 94.2 + - - +
221A ALA 3.6 0.7 + - - -
222A ALA* 5.0 1.7 + - - +
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Residues in contact with ASP 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 VAL* 2.9 24.0 + - + +
217A GLN 4.0 0.9 - - - -
219A ARG* 1.3 122.0 + - - +
221A ALA* 1.3 65.5 + - - +
222A ALA 3.4 2.5 - - - -
223A TYR* 3.3 17.9 + - + +
224A ASP* 3.0 33.3 + - - +
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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