Contacts of the helix formed by residues 266 - 275 (chain D) in PDB entry 2E52
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 266 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D ASN 4.5 1.6 - - - +
262D PHE* 3.7 28.1 - - + -
263D THR* 2.4 66.5 + - - +
265D GLU* 1.3 75.9 - - - +
267D ALA* 1.3 53.3 + - - -
269D GLU* 3.5 8.3 - - - +
270D ALA* 2.9 28.7 + - - +
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Residues in contact with ALA 267 (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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264C ARG 4.3 0.2 - - - +
267C ALA* 3.6 16.4 - - + +
268C ILE* 3.6 31.2 - - + +
271C LEU* 4.6 3.5 - - - +
262D PHE* 3.9 14.4 - - + -
263D THR 2.9 3.0 + - - -
264D ARG 3.3 19.1 - - - +
265D GLU 2.9 0.2 - - - -
266D GLU* 1.3 77.5 - - - +
268D ILE* 1.3 61.0 - - - +
270D ALA* 3.8 1.3 - - - +
271D LEU* 3.0 28.1 + - - +
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Residues in contact with ILE 268 (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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259C ILE* 4.0 22.7 - - + +
260C LYS* 3.8 22.4 - - + +
262C PHE* 3.5 24.0 - - + +
267C ALA* 3.8 14.1 - - + -
264D ARG* 3.4 37.7 - - - +
265D GLU* 3.4 9.4 - - - +
267D ALA* 1.3 73.1 - - - +
269D GLU* 1.3 66.8 + - - +
270D ALA 3.2 0.2 + - - -
271D LEU* 3.3 3.6 + - - +
272D LEU* 2.9 43.0 + - + +
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Residues in contact with GLU 269 (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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265D GLU 2.9 19.3 + - - +
266D GLU* 3.5 10.0 - - - +
268D ILE* 1.3 77.6 - - - +
270D ALA* 1.3 58.5 + - - +
272D LEU* 3.9 7.0 - - - +
273D LYS* 2.9 53.8 + - - +
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Residues in contact with ALA 270 (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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271C LEU* 3.8 26.6 - - + +
262D PHE* 3.8 13.0 - - + -
266D GLU 2.9 20.1 + - - +
267D ALA 3.8 2.2 - - - +
268D ILE 3.2 0.4 - - - -
269D GLU* 1.3 77.9 - - - +
271D LEU* 1.3 55.6 + - - +
273D LYS* 3.4 7.5 + - - +
274D ASP* 2.8 35.5 + - - +
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Residues in contact with LEU 271 (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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259C ILE* 3.8 19.5 - - + -
262C PHE* 3.6 34.5 - - + -
267C ALA* 4.4 6.1 - - - +
270C ALA* 3.9 17.5 - - + +
271C LEU* 4.0 33.3 - - + +
274C ASP* 5.1 1.3 - - + -
267D ALA 3.0 18.1 + - - +
268D ILE* 3.3 5.4 + - - +
270D ALA* 1.3 76.5 - - - +
272D LEU* 1.3 56.2 + - - +
274D ASP* 3.3 7.2 + - - +
275D ILE* 2.8 55.3 + - + +
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Residues in contact with LEU 272 (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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256C ILE* 4.3 16.2 - - + +
259C ILE* 3.6 30.7 - - + -
260C LYS* 3.9 26.2 - - + +
268D ILE* 2.9 38.7 + - + +
269D GLU* 3.9 6.1 - - - +
271D LEU* 1.3 68.4 - - - +
273D LYS* 1.3 60.8 + - - +
276D ASN* 2.8 28.6 + - - -
277D MET* 3.8 28.2 - - + +
278D SER* 5.6 1.2 + - - -
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Residues in contact with LYS 273 (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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54D LYS* 3.5 25.4 - - - +
269D GLU* 2.9 40.1 + - - +
270D ALA* 3.6 7.0 - - - +
272D LEU* 1.3 76.0 - - - +
274D ASP* 1.3 62.4 + - - +
276D ASN* 3.7 16.8 - - - +
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Residues in contact with ASP 274 (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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271C LEU* 3.9 13.5 - - + +
274C ASP* 2.5 37.8 - - - +
275C ILE* 3.1 27.3 - - + +
270D ALA 2.8 21.5 + - - +
271D LEU* 3.3 9.6 + - - +
273D LYS* 1.3 72.9 - - - +
275D ILE* 1.3 67.7 + - - +
276D ASN* 3.6 5.0 + - - +
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Residues in contact with ILE 275 (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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54C LYS* 5.3 7.9 - - - +
252C TRP* 3.6 24.0 - - + -
259C ILE* 3.6 28.7 - - + -
274C ASP* 5.1 8.5 - - - +
271D LEU* 2.8 42.1 + - + +
274D ASP* 1.3 75.4 - - - +
276D ASN* 1.3 71.1 + - - +
277D MET* 3.4 23.6 - - + +
280D LYS* 3.3 17.6 + - - -
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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