Contacts of the helix formed by residues 236 - 244 (chain T) in PDB entry 2P8Z
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 ASP 236 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230T ALA* 4.6 0.7 - - - -
235T VAL* 1.3 77.3 - - - +
237T LYS* 1.3 61.6 + - - +
238T ALA* 3.2 12.0 + - + +
239T LYS* 2.7 34.0 + - - +
240T MET* 3.1 8.3 + - - +
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Residues in contact with LYS 237 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84T GLU* 2.1 43.0 + - - -
88T GLU* 4.1 3.6 - - - +
223T ARG* 3.4 16.9 - - - +
226T ALA* 3.8 22.9 - - + +
227T THR* 2.6 35.8 + - - +
230T ALA* 3.6 9.9 - - + +
236T ASP* 1.3 70.4 - - - +
238T ALA* 1.3 61.5 + - - +
240T MET* 3.5 9.0 - - - -
241T MET* 2.8 50.9 + - + +
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Residues in contact with ALA 238 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236T ASP* 3.1 11.7 + - + +
237T LYS* 1.3 82.3 - - - +
239T LYS* 1.3 62.0 + - - +
241T MET* 3.7 11.5 - - - +
242T ASP* 3.0 28.1 + - - +
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Residues in contact with LYS 239 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235T VAL* 3.3 25.6 - - + -
236T ASP* 2.7 19.3 + - - +
238T ALA* 1.3 79.2 - - - +
240T MET* 1.3 60.9 + - - +
242T ASP* 3.4 11.2 + - + +
243T ARG* 3.2 65.7 + - - +
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Residues in contact with MET 240 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226T ALA* 4.0 11.7 - - + -
229T TYR* 3.5 22.2 - - + +
230T ALA* 3.9 21.3 - - - +
233T PHE* 3.4 42.6 - - + -
235T VAL* 4.3 12.3 - - + -
236T ASP 3.1 9.8 + - - +
237T LYS* 3.1 14.0 + - - +
239T LYS* 1.3 75.3 - - - +
241T MET* 1.3 60.5 + - - +
243T ARG* 3.1 14.3 + - - +
244T LEU* 2.9 43.3 + - + +
257T TRP* 4.4 22.0 - - + -
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Residues in contact with MET 241 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88T GLU* 5.0 3.8 - - - +
205T ALA* 4.6 18.0 - - - +
222T ILE* 3.5 32.8 - - + +
223T ARG* 3.4 40.8 - - + +
226T ALA* 3.6 25.3 - - + +
237T LYS* 2.8 45.5 + - + +
238T ALA* 3.7 12.3 - - - +
240T MET* 1.3 70.9 - - - +
242T ASP* 1.3 67.4 + - - +
243T ARG 3.6 0.2 + - - -
244T LEU 3.6 2.8 + - - -
245T TRP* 4.0 7.6 + - - +
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Residues in contact with ASP 242 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205T ALA* 5.4 10.7 - - - +
238T ALA* 3.0 18.2 + - - +
239T LYS* 3.4 15.1 + - + +
240T MET 3.2 0.8 - - - -
241T MET* 1.3 82.3 - - - +
243T ARG* 1.3 59.2 + - + +
245T TRP* 3.3 20.6 + - - +
248T SER* 3.9 5.0 + - - -
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Residues in contact with ARG 243 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233T PHE* 5.9 0.2 - - - -
235T VAL* 4.1 23.0 - - - +
239T LYS* 3.3 49.4 - - - +
240T MET* 3.1 16.8 + - - +
242T ASP* 1.3 78.0 - - + +
244T LEU* 1.3 56.0 + - - +
245T TRP 3.3 3.6 - - - -
248T SER* 3.1 22.0 - - - +
257T TRP* 3.1 73.5 - - + +
272T ALA* 3.0 26.4 - - - +
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Residues in contact with LEU 244 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222T ILE* 3.5 19.8 - - + +
225T PHE* 4.0 16.8 - - + -
226T ALA* 3.8 30.3 - - - +
229T TYR* 4.0 11.7 - - + -
240T MET* 2.9 29.6 + - + +
241T MET 3.6 0.8 + - - -
242T ASP 3.3 1.0 - - - -
243T ARG* 1.3 80.8 - - - +
245T TRP* 1.3 58.6 + - - +
257T TRP* 5.1 1.8 - - + -
272T ALA* 4.1 10.5 - - + +
273T PHE* 3.2 33.0 - - - +
276T PHE* 4.0 33.4 - - + -
277T ILE* 4.1 8.7 - - + -
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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