Contacts of the helix formed by residues 346 - 351 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ASP 3.5 10.3 - - - -
244C THR* 3.0 17.3 - - - -
246C LEU 3.4 10.0 + - - -
247C LEU* 4.3 3.2 - - - +
344C VAL 3.0 10.1 + - - -
345C ILE* 1.3 76.5 - - - +
347C ALA* 1.3 66.2 + - - -
348C THR 3.4 2.9 - - - -
349C VAL* 3.0 5.0 + - - +
350C MET* 2.9 22.8 + - - +
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Residues in contact with ALA 347 (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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26C SER* 4.3 21.3 - - - +
30C TYR* 5.2 1.1 - - + -
170C MET* 3.7 25.1 - - + +
241C ASP 4.3 1.6 + - - -
242C SER 4.9 6.2 + - - +
244C THR 2.8 12.8 + - - +
245C THR* 3.1 17.9 + - - +
346C GLY* 1.3 67.8 - - - -
348C THR* 1.3 67.6 + - - +
350C MET* 4.9 0.2 - - - -
351C GLU* 2.7 31.5 + - - +
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Residues in contact with THR 348 (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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26C SER* 4.6 0.2 + - - -
245C THR 3.1 5.9 + - - +
246C LEU* 3.0 35.9 - - + -
247C LEU* 3.0 19.2 - - - +
313C ILE* 4.2 3.1 - - - +
317C LEU* 3.8 32.4 + - - +
318C TYR* 4.5 7.8 - - - +
320C GLN* 3.2 28.5 - - - +
335C GLY 3.1 14.9 + - - +
347C ALA* 1.3 72.0 - - - +
349C VAL* 1.3 62.3 + - - +
351C GLU* 4.3 8.3 + - - +
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Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C LEU* 3.8 34.8 - - + -
298C ILE* 4.6 7.6 - - + -
311C ILE* 4.3 20.6 - - + -
313C ILE* 4.1 21.2 - - + +
345C ILE* 3.4 31.9 - - + -
346C GLY 3.0 4.6 + - - +
347C ALA 2.8 0.8 + - - -
348C THR* 1.3 81.0 + - - +
350C MET* 1.3 66.2 + - + +
351C GLU 3.1 2.0 - - - -
352C GLY* 3.1 10.4 + - - -
353C PHE* 3.2 22.0 - - + -
366C PHE* 5.5 1.8 - - + -
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Residues in contact with MET 350 (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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168C MET* 4.1 20.0 - - + +
170C MET* 2.9 36.4 + - + +
240C VAL* 3.9 18.2 - - + -
241C ASP 4.1 3.1 - - - -
242C SER* 3.6 42.2 - - - -
345C ILE* 4.2 12.8 - - + +
346C GLY 2.9 13.2 + - - +
349C VAL* 1.3 72.0 - - - +
351C GLU* 1.3 56.6 + - - +
352C GLY 2.8 12.2 + - - -
353C PHE* 2.9 26.1 + - - +
355C VAL* 4.0 31.6 - - + -
357C PHE* 4.5 4.9 - - + -
366C PHE* 5.8 1.6 - - + -
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Residues in contact with GLU 351 (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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26C SER* 2.9 38.8 + - - -
30C TYR* 2.6 29.5 + - - +
170C MET* 3.3 30.9 - - + +
171C CYS* 5.2 0.7 - - - -
172C GLY* 3.3 32.7 + - - +
317C LEU* 4.7 12.9 - - + +
320C GLN* 4.9 2.1 + - - -
347C ALA 2.7 18.7 + - - +
348C THR* 4.3 9.6 - - - +
349C VAL 3.1 0.4 - - - -
350C MET* 1.3 76.5 - - - +
352C GLY* 1.3 58.0 + - - +
353C PHE 3.5 0.2 - - - -
369C SER* 5.0 0.7 - - - -
372C ALA* 3.7 12.6 - - - +
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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