Contacts of the helix formed by residues 219 - 228 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C PHE* 5.6 4.2 - - - +
212C TYR* 4.1 2.6 - - - -
213C GLN* 3.3 19.6 + - - +
218C LYS* 1.3 77.0 - - - +
220C ILE* 1.3 72.4 + - - +
221C GLU* 2.9 42.4 + - + +
222C GLU* 3.0 23.7 + - + +
223C ALA 3.3 8.8 + - - -
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Residues in contact with ILE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LEU* 4.3 11.0 - - + -
193C PHE* 4.3 21.8 - - + -
197C LEU* 5.7 1.3 - - + -
209C PHE* 3.7 39.5 + - + -
212C TYR* 4.0 44.7 - - + +
218C LYS 4.0 1.0 + - - -
219C ASP* 1.3 81.8 + - - +
221C GLU* 1.3 64.6 + - - +
223C ALA* 3.4 3.3 + - + -
224C ILE* 3.1 39.9 + - + +
240C VAL* 3.6 27.8 - - + -
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Residues in contact with GLU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ASP* 2.9 18.6 + - + +
220C ILE* 1.3 78.1 - - + +
222C GLU* 1.3 60.2 + - - +
224C ILE* 3.5 2.7 + - - +
225C GLU* 3.1 35.2 + - - +
237C LEU* 3.9 21.1 - - + +
240C VAL* 3.9 22.8 - - + +
241C ARG* 4.0 30.3 + - - +
244C GLN* 5.7 4.2 - - - +
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Residues in contact with GLU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C LYS* 3.5 38.8 - - + +
219C ASP* 3.0 18.6 + - + +
221C GLU* 1.3 77.4 - - - +
223C ALA* 1.3 63.8 + - - +
225C GLU* 3.4 13.6 + - - +
226C GLU* 3.2 49.0 + - + +
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C PHE* 5.7 1.8 - - + -
212C TYR* 3.2 35.2 - - + +
218C LYS* 5.0 7.8 - - + +
219C ASP 3.3 3.8 + - - +
220C ILE* 3.9 9.9 - - + +
222C GLU* 1.3 79.1 - - - +
224C ILE* 1.3 63.2 + - + +
226C GLU* 3.3 8.6 + - - -
227C GLU* 3.0 47.0 + - - +
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Residues in contact with ILE 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C PHE* 4.0 22.0 - - + -
197C LEU* 4.5 6.3 - - + -
220C ILE* 3.1 24.5 + - + +
221C GLU* 3.8 4.7 - - - +
222C GLU 3.3 0.2 - - - -
223C ALA* 1.3 77.9 - - - +
225C GLU* 1.3 57.5 + - - +
227C GLU* 5.0 2.9 - - - -
228C THR* 2.6 49.4 + - - +
233C GLN* 4.1 3.4 - - + -
236C TYR* 3.7 31.4 - - + +
237C LEU* 3.7 23.1 - - + -
240C VAL* 3.7 30.3 - - + -
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Residues in contact with GLU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C GLU* 3.1 22.9 + - - +
222C GLU* 3.8 12.9 - - - +
223C ALA 3.3 0.4 - - - -
224C ILE* 1.3 76.5 - - - +
226C GLU* 1.3 61.0 + - + +
227C GLU 3.5 0.2 - - - -
228C THR 3.4 3.3 - - - +
233C GLN* 3.4 24.1 + - - +
237C LEU* 4.0 26.8 - - + +
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Residues in contact with GLU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C LYS* 2.9 27.3 + - - +
222C GLU* 3.2 42.9 + - + +
223C ALA* 3.3 6.1 + - - +
224C ILE 3.2 0.6 - - - -
225C GLU* 1.3 81.0 - - + +
227C GLU* 1.3 64.6 + - + +
228C THR 3.7 0.7 - - - -
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Residues in contact with GLU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LEU 4.6 0.9 - - - +
179C TYR* 5.3 2.4 - - - +
182C GLY* 3.3 40.6 - - - +
183C GLU* 4.3 6.4 - - - +
189C ASP* 4.5 11.6 - - - +
190C GLU* 5.2 2.6 - - - +
193C PHE* 3.7 22.3 - - + -
212C TYR* 4.6 3.6 + - - -
223C ALA* 3.0 32.8 + - - +
224C ILE* 4.5 0.9 - - - +
226C GLU* 1.3 84.8 - - + +
228C THR* 1.3 68.5 + - + +
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Residues in contact with THR 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ASP* 5.6 1.1 - - - +
190C GLU* 4.6 11.4 - - + +
193C PHE* 6.0 4.9 - - + -
224C ILE* 2.6 35.5 + - + +
225C GLU 3.4 7.6 - - - +
226C GLU 4.7 0.5 - - - -
227C GLU* 1.3 85.9 + - + +
229C SER* 1.3 61.3 + - - +
232C LEU* 4.5 11.9 - - + -
233C GLN* 2.7 39.9 + - - +
236C TYR* 3.9 27.1 - - + -
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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