Contacts of the helix formed by residues 214 - 226 (chain A) in PDB entry 3G26
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 THR 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ALA* 5.9 0.2 - - - -
190A ILE* 3.6 4.9 - - - -
213A THR* 1.3 90.5 - - - +
215A PRO* 1.3 76.2 - - - +
216A GLY 3.6 1.3 + - - -
217A GLU* 3.1 36.4 + - - +
218A ILE* 3.2 15.1 + - - +
4892A MLA 2.8 29.0 + - - +
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Residues in contact with PRO 215 (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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172A ILE* 4.5 9.4 - - + -
186A ALA* 4.1 24.0 - - + +
189A ILE* 3.6 42.0 - - + -
190A ILE* 3.6 16.4 - - + -
193A PHE* 3.7 9.5 - - + -
214A THR* 1.3 87.4 - - - +
216A GLY* 1.3 57.2 + - - +
218A ILE* 3.1 3.8 + - - +
219A ILE* 2.8 35.5 + - + +
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Residues in contact with GLY 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 THR* 3.2 3.0 + - - -
215A PRO* 1.3 80.6 - - - +
217A GLU* 1.3 58.2 + - - +
219A ILE* 3.4 10.8 + - - +
220A LYS* 3.0 34.7 + - - +
4892A MLA 3.3 17.5 - - - -
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Residues in contact with GLU 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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211A THR 3.8 4.2 - - - +
212A LEU* 3.4 33.7 - - + +
213A THR* 2.8 33.6 + - - -
214A THR* 3.1 30.8 + - - +
216A GLY* 1.3 76.0 - - - +
218A ILE* 1.3 57.7 + - - +
220A LYS* 3.5 11.9 + - - +
221A TYR* 3.0 28.2 + - - +
4892A MLA 3.2 18.5 + - + +
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Residues in contact with ILE 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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164A PHE* 4.9 0.9 - - + -
190A ILE* 4.0 15.3 - - + -
193A PHE* 3.9 22.9 - - + -
194A ARG* 4.5 13.7 - - - +
205A ILE* 4.0 35.4 - - + -
208A ALA* 4.1 19.5 - - + -
212A LEU* 3.9 33.2 - - + +
214A THR 3.2 11.8 + - - +
215A PRO 3.1 8.3 + - - +
217A GLU* 1.3 73.8 - - - +
219A ILE* 1.3 64.9 + - - +
221A TYR* 3.2 5.6 + - + +
222A VAL* 2.9 24.6 + - + +
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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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164A PHE* 4.1 15.0 - - + -
165A VAL* 4.6 10.1 - - + -
168A ALA* 4.3 7.6 - - + -
169A ASN* 5.6 2.9 - - - +
172A ILE* 4.1 16.2 - - + -
193A PHE* 3.8 27.6 - - + -
215A PRO 2.8 25.3 + - - +
216A GLY* 3.7 9.4 - - - +
218A ILE* 1.3 76.8 - - - +
220A LYS* 1.3 60.1 + - + +
222A VAL* 3.4 0.3 + - - -
223A LEU* 2.9 54.3 + - + +
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Residues in contact with LYS 220 (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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216A GLY 3.0 20.5 + - - +
217A GLU* 3.9 14.1 - - - +
219A ILE* 1.3 79.7 - - + +
221A TYR* 1.3 64.1 + - - +
223A LEU* 4.6 3.1 - - - +
224A ASP* 2.9 45.8 + - - +
4892A MLA 2.9 35.6 + - - +
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Residues in contact with TYR 221 (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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204A LEU* 3.5 26.2 - - + -
205A ILE* 4.9 2.2 - - + -
207A THR* 2.6 30.6 + - - -
208A ALA* 3.5 17.5 - - + -
209A PRO* 3.8 16.6 - - + -
212A LEU* 3.7 22.0 - - + -
217A GLU 3.0 15.8 + - - +
218A ILE* 3.2 11.6 + - + +
220A LYS* 1.3 77.3 - - - +
222A VAL* 1.3 73.5 + - + +
225A ARG* 2.9 79.3 + - - +
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Residues in contact with VAL 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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164A PHE* 3.7 28.3 - - + -
201A ILE* 4.0 22.2 - - + -
204A LEU* 4.1 18.6 - - + +
205A ILE* 3.6 34.5 - - + -
218A ILE* 2.9 20.5 + - + +
219A ILE 3.9 2.5 - - - +
221A TYR* 1.3 78.0 - - + +
223A LEU* 1.3 67.2 + - - +
225A ARG* 3.0 13.7 + - - +
226A GLN* 3.2 24.2 + - - +
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Residues in contact with LEU 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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164A PHE* 3.8 25.4 - - + -
165A VAL* 4.0 28.0 - - + +
219A ILE* 2.9 41.4 + - + +
220A LYS* 4.3 2.5 - - - +
222A VAL* 1.3 73.9 - - - +
224A ASP* 1.3 67.6 + - - +
226A GLN* 3.1 38.3 + - - +
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Residues in contact with ASP 224 (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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220A LYS* 2.9 39.0 + - - +
223A LEU* 1.3 78.7 - - - +
225A ARG* 1.3 75.1 + - - +
226A GLN* 3.5 2.8 - - - +
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Residues in contact with ARG 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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204A LEU* 4.2 22.4 - - + +
221A TYR* 2.9 80.9 + - - +
222A VAL 3.0 6.6 + - - +
224A ASP* 1.3 91.6 + - - +
226A GLN* 1.3 66.2 + - - +
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Residues in contact with GLN 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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163A SER* 5.8 3.2 - - - -
164A PHE* 4.8 11.4 + - - +
165A VAL* 5.5 0.7 + - - +
201A ILE* 4.3 18.1 - - + +
204A LEU* 5.4 2.7 - - + -
222A VAL* 3.4 21.6 - - + +
223A LEU* 3.1 41.2 + - - +
224A ASP 4.5 3.1 - - - +
225A ARG* 1.3 84.6 - - - +
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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