Contacts of the helix formed by residues 228 - 236 (chain L) in PDB entry 5DST
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 228 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226L ILE* 3.9 18.7 - - + +
227L GLU* 1.3 74.7 - - - +
229L ARG* 1.3 62.2 + - - +
230L GLN 3.2 3.3 + - - -
231L TYR* 3.4 23.4 + - - +
232L LYS* 2.8 28.2 + - - +
267L GLN* 2.7 24.5 + - - +
305L HIS* 3.2 20.6 + - + +
306L ALA* 5.4 0.2 - - + -
339L VAL* 4.8 3.5 - - - +
341L TYR* 2.7 30.9 + - + -
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Residues in contact with ARG 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J HIS* 4.8 23.5 + - - -
227L GLU* 3.2 16.7 + - + +
228L ASP* 1.3 77.0 - - - +
230L GLN* 1.3 78.9 + - + +
232L LYS* 3.6 2.2 - - - +
233L ASP* 2.8 51.0 + - - +
237L HIS* 5.5 0.3 - - - -
305L HIS* 3.1 33.5 + - + +
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Residues in contact with GLN 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227L GLU* 4.5 1.3 + - - +
228L ASP 3.2 1.0 - - - -
229L ARG* 1.3 103.4 + - - +
231L TYR* 1.3 64.1 + - - +
233L ASP* 3.2 10.5 - - - +
234L PHE* 3.1 19.6 + - + +
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Residues in contact with TYR 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L ASP* 3.4 24.7 + - - +
230L GLN* 1.3 81.5 - - - +
232L LYS* 1.3 56.7 + - - +
234L PHE* 3.1 25.7 + + + +
235L LYS* 2.9 66.5 + - + +
259L LEU* 3.5 15.5 - - + -
261L ASP* 3.1 24.3 + - + -
341L TYR* 3.5 15.5 - - - -
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Residues in contact with LYS 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L ASP 2.8 20.8 + - - +
229L ARG 3.6 4.0 - - - +
231L TYR* 1.3 77.6 - - - +
233L ASP* 1.3 62.7 + - - +
236L ILE* 3.0 41.4 + - + -
237L HIS* 3.2 30.3 + - + +
255L MET* 3.8 3.4 - - - -
305L HIS* 4.2 24.4 + - + -
341L TYR* 3.6 35.5 + - + -
342L LEU 2.9 27.6 + - - +
343L GLU 3.0 18.8 + - - -
344L ASP* 4.4 6.5 - - - +
345L TYR* 4.8 3.4 - - - +
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Residues in contact with ASP 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229L ARG* 2.8 28.9 + - - +
230L GLN* 3.2 13.7 - - - +
232L LYS* 1.3 76.7 - - - +
234L PHE* 1.3 58.2 + - - +
237L HIS* 3.7 25.1 - - - +
238L TRP* 2.8 32.4 + - - +
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Residues in contact with PHE 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K LYS* 2.8 59.9 + - + -
230L GLN* 3.1 8.6 + - + +
231L TYR* 3.1 37.9 + + + +
233L ASP* 1.3 79.0 - - - +
235L LYS* 1.3 75.0 + - + +
238L TRP* 3.4 18.1 - + - +
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Residues in contact with LYS 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K PHE* 6.2 0.4 - - - -
87K GLU* 2.9 34.5 + - - +
91K LYS* 4.4 0.6 - - - +
231L TYR* 2.9 58.5 + - + +
234L PHE* 1.3 94.3 - - + +
236L ILE* 1.3 70.2 + - + +
238L TRP* 4.9 0.9 - - - -
239L TRP* 3.4 19.6 + - - -
254L ALA* 4.9 3.8 - - - +
259L LEU* 3.9 22.8 - - + +
341L TYR* 4.6 3.4 - - + -
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Residues in contact with ILE 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L LYS* 3.0 43.4 + - + +
234L PHE 3.7 0.4 - - - -
235L LYS* 1.3 82.6 - - + +
237L HIS* 1.3 79.5 + - + +
238L TRP 3.2 1.6 - - - -
239L TRP* 3.4 15.0 + - + +
251L ARG* 3.1 33.7 - - + +
254L ALA* 4.9 9.4 - - + -
255L MET* 3.7 33.0 - - + +
259L LEU* 5.9 0.7 - - + -
341L TYR* 3.9 32.5 - - + -
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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