Contacts of the helix formed by residues 346 - 351 (chain D) in PDB entry 2EWY
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 GLY 346 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ASP 3.5 11.0 - - - -
244D THR* 3.0 16.2 - - - -
246D LEU 3.4 11.1 + - - -
247D LEU* 4.3 3.2 - - - +
344D VAL 3.0 10.1 + - - -
345D ILE* 1.3 76.8 - - - +
347D ALA* 1.3 66.7 + - - -
348D THR 3.4 2.5 - - - -
349D VAL* 3.0 5.2 + - - +
350D MET* 2.9 23.1 + - - +
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Residues in contact with ALA 347 (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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26D SER* 4.3 20.9 - - - +
30D TYR* 5.2 1.1 - - + -
170D MET* 3.7 24.9 - - + +
241D ASP 4.3 1.6 + - - -
242D SER 4.9 6.0 + - - +
244D THR 2.8 12.2 + - - +
245D THR* 3.1 18.3 + - - +
346D GLY* 1.3 68.0 - - - -
348D THR* 1.3 68.1 + - - +
349D VAL 2.8 0.2 + - - -
350D MET* 4.9 0.4 - - - -
351D GLU* 2.7 31.0 + - - +
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Residues in contact with THR 348 (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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245D THR 3.1 5.9 + - - +
246D LEU* 3.0 36.3 - - + -
247D LEU* 3.0 19.0 - - - +
313D ILE* 4.2 4.2 - - - +
317D LEU* 3.8 31.0 + - - +
318D TYR* 4.5 7.6 - - - +
320D GLN* 3.2 29.4 - - - +
335D GLY 3.1 15.3 + - - +
347D ALA* 1.3 71.5 - - - +
349D VAL* 1.3 61.8 + - - +
351D GLU* 4.3 8.5 + - - +
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Residues in contact with VAL 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D LEU* 3.8 35.7 - - + -
298D ILE* 4.6 7.9 - - + -
311D ILE* 4.3 20.4 - - + -
313D ILE* 4.1 21.2 - - + +
345D ILE* 3.4 32.3 - - + -
346D GLY 3.0 4.6 + - - +
347D ALA 2.8 0.8 + - - -
348D THR* 1.3 79.7 + - - +
350D MET* 1.3 66.3 + - - +
351D GLU 3.1 2.0 - - - -
352D GLY 3.1 10.6 + - - -
353D PHE* 3.2 21.6 - - + -
366D PHE* 5.5 2.2 - - + -
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Residues in contact with MET 350 (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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168D MET* 4.1 20.0 - - + +
170D MET* 2.9 34.3 + - + +
240D VAL* 3.9 19.3 - - + -
241D ASP 4.1 3.1 - - - -
242D SER* 3.6 42.0 - - - -
345D ILE* 4.2 11.4 - - + +
346D GLY 2.9 12.1 + - - +
349D VAL* 1.3 72.6 - - + +
351D GLU* 1.3 57.7 + - - +
352D GLY 2.8 11.3 + - - -
353D PHE* 2.9 26.2 + - - +
355D VAL* 4.0 33.6 - - + +
357D PHE* 4.5 4.3 - - + -
366D PHE* 5.8 1.8 - - + -
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Residues in contact with GLU 351 (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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26D SER* 2.9 37.0 + - - -
30D TYR* 2.6 30.1 + - - +
170D MET* 3.3 30.6 - - + +
171D CYS* 5.2 0.5 - - - -
172D GLY* 3.3 32.8 + - - +
317D LEU* 4.7 13.2 - - + +
320D GLN* 4.9 2.1 + - - -
347D ALA* 2.7 19.2 + - - +
348D THR* 4.3 9.3 - - - +
349D VAL 3.1 0.8 - - - -
350D MET* 1.3 76.7 - - - +
352D GLY* 1.3 57.0 + - - +
369D SER* 5.0 0.3 - - - -
372D ALA* 3.7 13.7 - - - +
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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