Contacts of the helix formed by residues 212 - 217 (chain D) in PDB entry 2BKU
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 ILE 212 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D CYS* 6.3 1.6 - - - -
177D SER* 5.7 4.0 - - - +
180D ILE* 6.4 2.2 - - + -
181D LEU* 3.7 37.7 - - + +
205D LEU* 3.9 11.9 - - + -
208D SER* 3.4 26.9 - - - +
209D LEU* 3.5 16.4 - - + +
211D PHE* 1.3 79.8 - - + +
213D LYS* 1.3 64.3 + - - -
214D ASN 3.1 3.1 - - - -
215D ASN* 2.7 35.7 + - + +
216D MET* 2.8 21.8 + - + +
225D LEU* 3.7 20.2 - - + -
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Residues in contact with LYS 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B GLN* 4.5 22.9 - - - +
169D GLN* 3.2 33.0 - - - +
210D ILE* 3.0 27.8 + - + +
211D PHE* 3.6 7.4 + - - +
212D ILE* 1.3 75.9 - - - +
214D ASN* 1.3 88.8 + - - +
216D MET* 3.2 3.0 + - - +
217D GLU* 3.0 34.8 + - - +
255D TYR* 3.2 28.6 + - + +
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Residues in contact with ASN 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LYS* 4.9 6.5 + - - +
313B GLN* 5.5 0.9 - - - +
169D GLN* 5.7 2.2 + - - -
211D PHE 5.6 1.0 + - - -
212D ILE 3.1 0.8 - - - -
213D LYS* 1.3 104.8 - - - +
215D ASN* 1.3 64.3 + - - +
217D GLU* 3.6 23.1 + - - +
218D ARG* 3.5 32.2 + - - +
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Residues in contact with ASN 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D SER* 4.9 12.1 + - - -
178D ASN* 4.5 16.6 + - - +
181D LEU* 4.6 21.0 - - + +
211D PHE 4.7 1.8 + - - -
212D ILE* 2.7 44.0 + - + +
214D ASN* 1.3 73.5 - - - +
216D MET* 1.3 64.1 + - - +
217D GLU 3.1 2.6 + - - -
218D ARG* 3.3 30.6 + - - +
221D GLU* 3.0 35.0 - - + +
222D ARG 3.9 2.9 + - - -
225D LEU* 6.1 2.5 - - + -
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Residues in contact with MET 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LEU* 5.0 3.1 - - + -
212D ILE* 2.8 28.8 + - + +
213D LYS 3.2 8.7 + - - +
215D ASN* 1.3 76.3 - - - +
217D GLU* 1.3 50.6 + - - +
218D ARG 3.3 1.3 + - - -
222D ARG* 2.7 66.4 + - + +
225D LEU* 4.0 28.3 - - - -
226D MET* 5.1 1.8 - - - -
251D ILE* 3.9 18.2 - - + -
255D TYR* 3.4 63.0 - - + -
258D PHE* 4.1 3.7 - - - -
259D MET* 4.7 1.8 - - + -
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Residues in contact with GLU 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LYS* 3.3 44.5 + - + +
264B GLU* 5.6 0.3 - - - +
313B GLN* 2.9 39.0 + - - +
314B SER 5.0 0.3 - - - +
315B TYR* 4.1 16.9 - - + -
213D LYS* 3.0 21.2 + - - +
214D ASN* 3.9 15.1 - - - +
215D ASN 3.1 1.0 - - - -
216D MET* 1.3 75.9 - - + +
218D ARG* 1.3 67.7 + - - +
222D ARG* 3.8 7.2 - - - +
255D TYR* 5.4 2.4 - - + -
258D PHE* 3.8 25.0 - - + -
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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