Contacts of the strand formed by residues 246 - 250 (chain D) in PDB entry 5WYF
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 LEU 246 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ALA* 3.8 26.7 - - - -
129D TYR* 3.9 29.2 - - + -
130D THR* 3.9 8.3 - - + -
212D ALA 3.0 19.2 + - - +
213D CYS* 3.0 9.9 - - + +
214D VAL 2.9 26.2 + - - -
240D CYS* 4.4 1.0 - - - -
244D GLY 3.7 4.2 + - - +
245D ILE* 1.3 75.9 - - - +
247D PHE* 1.3 60.0 + - - +
248D ALA* 5.8 0.2 - - + -
274D ASP* 3.6 25.6 - - + +
275D LEU* 4.0 9.6 - - + -
297D VAL* 4.0 26.2 - - + -
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Residues in contact with PHE 247 (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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214D VAL* 4.0 4.3 - - + -
216D ILE* 4.0 15.7 - - + -
233D MET* 3.7 26.5 - - - -
236D VAL* 4.0 20.2 - - + -
237D TYR* 3.6 44.4 - + + +
240D CYS* 4.2 21.5 - - + -
245D ILE 3.6 1.2 + - - -
246D LEU* 1.3 70.9 - - - +
248D ALA* 1.3 58.7 + - - +
249D ILE* 3.7 19.3 - - + -
265D ILE* 4.4 1.1 - - + -
271D ILE* 3.4 27.1 - - + -
273D PRO* 3.8 8.8 - - + +
274D ASP* 2.9 45.8 + - - +
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Residues in contact with ALA 248 (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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122D ILE* 3.9 20.4 - - + -
213D CYS* 4.3 7.9 - - + -
214D VAL 2.9 17.0 + - - +
215D LEU* 3.7 16.6 - - + -
216D ILE* 3.0 26.7 + - - +
246D LEU* 5.8 0.2 - - + -
247D PHE* 1.3 75.7 - - - +
249D ILE* 1.3 66.8 - - - +
275D LEU* 3.3 17.5 - - + +
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Residues in contact with ILE 249 (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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122D ILE* 4.1 2.3 - - - +
215D LEU* 3.8 4.3 - - - -
216D ILE* 3.2 12.8 - - + +
218D PRO* 4.2 8.3 - - + -
247D PHE* 3.7 26.5 - - + -
248D ALA* 1.3 79.0 - - - +
250D ASP* 1.3 58.9 + - - +
251D GLU* 3.6 21.1 - - + +
265D ILE* 3.5 44.9 - - + -
273D PRO* 3.6 21.1 - - + -
275D LEU 3.1 6.1 + - - -
276D MET* 3.2 22.4 - - + +
277D SER* 3.2 20.6 + - - -
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Residues in contact with ASP 250 (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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119D ASN* 2.7 27.7 + - - +
143D HIS* 2.9 30.5 + - + +
215D LEU* 3.9 2.6 - - + +
216D ILE 3.1 7.6 + - - +
217D GLU* 4.0 10.2 - - + +
218D PRO* 3.5 18.2 - - - +
219D ILE 5.6 0.2 - - - +
249D ILE* 1.3 72.1 - - - +
251D GLU* 1.3 59.2 + - - +
252D VAL* 2.9 26.4 + - - +
254D GLN* 5.3 5.2 + - - +
277D SER* 3.3 14.8 - - - +
1001D ILP 2.9 21.8 + - - +
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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