Contacts of the helix formed by residues 219 - 226 (chain A) in PDB entry 6B3I
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 ASP 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A PHE* 5.8 1.0 - - - +
212A TYR* 4.1 0.6 - - - -
213A GLN* 3.4 16.4 + - - +
218A LYS* 1.3 79.2 - - - +
220A ILE* 1.3 71.2 + - - +
221A GLU* 2.9 38.8 + - + +
222A GLU* 3.1 24.7 + - + +
223A ALA* 3.2 11.3 + - - +
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Residues in contact with ILE 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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178A LEU* 4.3 17.9 - - + -
193A PHE* 4.6 13.0 - - + -
197A LEU* 5.7 0.9 - - + -
209A PHE* 3.6 48.1 + - + -
212A TYR* 4.0 43.3 - - + +
218A LYS 3.9 1.2 + - - -
219A ASP* 1.3 83.8 + - - +
221A GLU* 1.3 63.8 + - - +
223A ALA* 3.4 4.7 + - + -
224A ILE* 3.1 32.3 + - + +
240A VAL* 3.7 21.5 - - + -
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Residues in contact with GLU 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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219A ASP* 2.9 18.8 + - - +
220A ILE* 1.3 75.4 - - - +
222A GLU* 1.3 64.6 + - - +
224A ILE* 3.1 2.8 + - - +
225A GLU* 3.0 39.4 + - - +
237A LEU* 4.0 21.8 - - + +
240A VAL* 3.9 23.1 - - + +
241A ARG* 3.4 33.2 - - - +
244A GLN* 5.8 2.4 - - - +
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Residues in contact with GLU 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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218A LYS* 3.9 33.5 - - + +
219A ASP* 3.1 21.4 + - + +
221A GLU* 1.3 78.6 - - - +
223A ALA* 1.3 61.6 + - - +
225A GLU* 3.7 15.8 + - - +
226A GLU* 3.2 29.7 + - - +
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Residues in contact with ALA 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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193A PHE* 5.6 2.7 - - + -
212A TYR* 3.3 33.7 - - + +
218A LYS* 5.0 5.1 - - + +
219A ASP 3.2 9.6 + - - +
220A ILE* 3.6 13.2 - - + +
221A GLU 3.2 0.2 - - - -
222A GLU* 1.3 77.4 - - - +
224A ILE* 1.3 63.1 + - + +
226A GLU* 3.7 10.3 + - - +
227A GLU* 3.3 42.2 + - - +
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Residues in contact with ILE 224 (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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193A PHE* 4.2 20.2 - - + -
197A LEU* 4.6 5.6 - - + -
220A ILE* 3.1 22.7 + - + +
221A GLU 3.1 6.5 + - - +
223A ALA* 1.3 76.6 - - - +
225A GLU* 1.3 65.2 + - - +
227A GLU* 5.0 1.6 - - - -
228A THR* 2.8 48.0 + - - +
233A GLN* 4.1 4.2 - - + +
236A TYR* 3.7 33.0 - - + -
237A LEU* 3.7 23.6 - - + -
240A VAL* 3.7 28.9 - - + -
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Residues in contact with GLU 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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221A GLU* 3.0 30.6 + - - +
222A GLU* 4.1 11.4 - - - +
223A ALA 3.4 0.4 - - - -
224A ILE* 1.3 75.8 - - - +
226A GLU* 1.3 57.4 + - + +
227A GLU 3.6 0.2 - - - -
228A THR 4.0 4.4 - - - +
233A GLN* 3.7 23.3 - - - +
237A LEU* 4.1 25.3 - - + +
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Residues in contact with GLU 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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218A LYS* 3.6 32.0 - - - +
222A GLU* 3.2 26.5 - - - +
223A ALA* 3.7 9.9 - - - +
224A ILE 3.1 0.2 - - - -
225A GLU* 1.3 77.8 - - + +
227A GLU* 1.3 68.8 + - + +
228A THR 3.9 0.7 - - - -
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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