Contacts of the helix formed by residues 239 - 247 (chain D) in PDB entry 1Y8Q
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 SER 239 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D GLN* 5.5 0.7 + - - -
200D GLU* 2.7 29.1 + - - -
238D ILE* 1.3 77.1 - - - +
240D THR* 1.3 67.1 + - - +
241D LYS 3.2 1.4 + - - -
242D GLU* 2.7 43.1 + - - -
243D TRP* 3.1 13.7 + - - +
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Residues in contact with THR 240 (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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192D LEU* 5.2 4.7 - - + -
195D GLN* 4.4 21.7 + - + +
196D LEU* 3.5 27.6 - - + -
205D GLU* 3.4 20.5 + - - -
206D VAL* 5.3 4.8 - - + +
207D SER* 4.1 12.0 + - - +
238D ILE 3.9 1.6 + - - -
239D SER* 1.3 74.5 + - - +
241D LYS* 1.3 57.3 + - - +
243D TRP* 3.6 17.4 + - + -
244D ALA* 3.0 27.4 + - - +
257D LYS* 5.5 5.0 - - - +
258D LEU* 5.4 6.3 - - + -
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Residues in contact with LYS 241 (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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195D GLN 3.2 10.9 + - - +
196D LEU 3.3 22.2 - - - +
197D PHE 3.8 18.5 + - - -
198D GLY 3.8 7.6 - - - +
200D GLU* 3.0 45.5 + - + +
239D SER* 3.2 2.2 + - - -
240D THR* 1.3 80.2 - - - +
242D GLU* 1.3 61.5 + - + +
244D ALA* 3.8 5.4 - - - +
245D LYS* 3.4 24.6 + - - +
249D TYR* 3.5 14.5 + - - +
333D LEU* 4.6 3.6 - - - +
339D GLY* 6.3 0.8 - - - -
340D ALA 4.6 10.6 + - - -
341D GLU* 5.2 5.6 - - - -
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Residues in contact with GLU 242 (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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200D GLU* 5.9 1.1 - - - +
238D ILE* 3.1 18.5 + - - +
239D SER* 2.7 45.1 + - - +
241D LYS* 1.3 76.2 - - + +
243D TRP* 1.3 65.6 + - - +
245D LYS* 3.3 6.5 + - - +
246D SER* 3.0 22.0 + - - -
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Residues in contact with TRP 243 (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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238D ILE 5.4 4.2 - - - +
239D SER 3.1 10.1 + - - +
240D THR* 3.9 19.3 - - + -
242D GLU* 1.3 78.9 - - - +
244D ALA* 1.3 71.9 + - + +
246D SER* 2.4 32.1 + - - -
247D THR* 3.3 22.4 + - + +
253D LYS* 3.7 20.7 - - + +
254D LEU* 3.4 35.0 - - + -
257D LYS* 3.2 57.0 - - + -
258D LEU* 5.1 3.1 - - + -
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Residues in contact with ALA 244 (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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196D LEU* 4.4 8.5 - - + -
240D THR 3.0 20.0 + - - +
241D LYS* 3.8 6.7 - - - +
242D GLU 3.2 0.2 - - - -
243D TRP* 1.3 83.9 - - + +
245D LYS* 1.3 51.7 + - - +
247D THR* 2.9 11.6 + - - -
249D TYR* 2.7 57.5 + - + -
254D LEU* 4.0 19.1 - - + -
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Residues in contact with LYS 245 (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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241D LYS* 3.4 15.5 + - + +
242D GLU* 3.3 5.0 + - - +
243D TRP 3.2 0.2 - - - -
244D ALA* 1.3 75.6 - - - +
246D SER* 1.3 61.4 + - - +
247D THR 3.0 2.0 - - - -
248D GLY* 2.9 25.4 + - - +
249D TYR* 3.5 35.1 - - + +
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Residues in contact with SER 246 (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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242D GLU 3.0 13.9 + - - -
243D TRP* 2.4 35.5 + - - -
245D LYS* 1.3 77.0 - - - +
247D THR* 1.3 60.5 + - - +
248D GLY 3.3 0.7 - - - -
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Residues in contact with THR 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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243D TRP* 3.5 34.2 + - + +
244D ALA* 2.9 16.8 + - - -
246D SER* 1.3 82.3 - - - +
248D GLY* 1.3 61.4 + - - +
250D ASP* 3.5 33.5 + - - +
253D LYS* 4.1 26.0 + - + +
254D LEU* 5.1 2.1 - - - +
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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