Contacts of the helix formed by residues 229 - 239 (chain R) in PDB entry 5IYB
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 229 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LYS* 5.0 17.6 - - - +
228R MET* 1.3 73.2 - - - +
230R GLU* 1.3 64.2 + - - +
231R GLU* 3.5 2.2 - - - +
232R LYS* 3.0 45.0 + - + +
233R ILE* 2.9 33.4 + - + +
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Residues in contact with GLU 230 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP* 5.6 2.4 - - - +
32A LYS* 4.9 10.6 + - - -
224R THR* 5.0 1.8 - - + -
225R VAL* 3.0 54.6 - - + +
227R SER* 3.1 21.3 - - - +
228R MET 3.1 4.8 - - - +
229R ASP* 1.3 74.9 - - - +
231R GLU* 1.3 56.7 + - - +
233R ILE* 2.6 45.0 + - - +
234R GLU* 3.0 10.0 + - - +
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Residues in contact with GLU 231 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Q ASN* 4.2 8.9 + - - -
105Q TYR* 2.0 70.9 + - + +
109Q HIS* 3.0 18.8 - - + -
224R THR* 4.3 0.4 - - - +
227R SER 4.7 1.0 + - - -
228R MET* 6.6 0.2 - - - -
229R ASP* 4.8 2.0 - - - +
230R GLU* 1.3 77.1 - - - +
232R LYS* 1.3 56.1 + - - +
234R GLU* 3.3 5.5 + - - +
235R GLU* 2.9 28.2 + - + +
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Residues in contact with LYS 232 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229R ASP* 3.0 43.9 + - + +
230R GLU 2.9 0.8 + - - -
231R GLU* 1.3 77.0 - - - +
233R ILE* 1.3 60.9 + - + +
235R GLU* 3.6 15.5 - - - +
236R TYR* 2.9 28.5 + - + +
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Residues in contact with ILE 233 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP* 5.6 6.3 - - - +
112Q ARG* 5.7 4.3 - - - +
229R ASP* 2.9 25.2 + - + +
230R GLU* 2.6 32.7 + - - +
232R LYS* 1.3 69.9 - - + +
234R GLU* 1.3 57.0 + - - +
236R TYR* 3.3 8.8 + - + +
237R LEU* 2.9 32.3 + - + +
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Residues in contact with GLU 234 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Q ASP* 1.7 48.7 - - + +
109Q HIS* 2.6 41.9 + - - +
112Q ARG* 3.6 30.3 + - + +
230R GLU 3.0 8.7 + - - +
231R GLU* 3.5 10.3 - - - +
233R ILE* 1.3 72.9 - - - +
235R GLU* 1.3 65.3 + - - +
237R LEU* 3.3 7.7 + - - +
238R LYS* 3.1 23.5 + - + +
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Residues in contact with GLU 235 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231R GLU* 2.9 15.9 + - + +
232R LYS* 3.6 19.3 - - - +
233R ILE 3.4 0.2 - - - -
234R GLU* 1.3 75.3 - - - +
236R TYR* 1.3 63.1 + - - +
238R LYS* 3.1 20.2 + - + +
239R ARG* 2.7 59.1 + - + +
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Residues in contact with TYR 236 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232R LYS* 2.9 19.4 + - + +
233R ILE* 3.3 10.7 + - + +
235R GLU* 1.3 75.0 + - - +
237R LEU* 1.3 64.7 + - + +
239R ARG* 3.3 31.9 + - + +
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Residues in contact with LEU 237 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Q ARG* 1.5 87.0 - - - +
115Q GLU* 5.2 1.3 - - - +
119Q ARG* 4.9 4.5 - - - +
233R ILE* 2.9 19.0 + - + +
234R GLU 3.3 5.8 + - - +
236R TYR* 1.3 80.5 - - + +
238R LYS* 1.3 59.3 + - - +
239R ARG 3.6 1.0 + - - -
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Residues in contact with LYS 238 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q LYS* 4.0 22.0 - - - +
108Q ASP* 4.4 13.6 + - + +
111Q ARG* 5.6 1.8 - - - +
234R GLU* 3.1 13.4 + - + +
235R GLU* 3.1 15.5 + - + +
237R LEU* 1.3 77.7 - - - +
239R ARG* 1.3 63.0 + - + +
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Residues in contact with ARG 239 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235R GLU* 2.7 55.9 + - + +
236R TYR* 3.3 27.0 + - + +
237R LEU 3.4 1.3 - - - -
238R LYS* 1.3 80.2 - - + +
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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