Contacts of the helix formed by residues 228 - 236 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226E ILE* 3.9 17.2 - - + +
227E GLU* 1.3 76.7 - - - +
229E ARG* 1.3 67.4 + - - +
230E GLN 3.3 3.1 - - - -
231E TYR* 3.2 25.4 + - - +
232E LYS* 3.0 18.0 + - - +
267E GLN* 3.1 19.0 + - - +
305E HIS* 3.3 19.9 + - + +
306E ALA* 5.3 0.4 - - + -
339E VAL* 4.7 3.8 - - - +
341E TYR* 2.7 31.9 + - + -
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Residues in contact with ARG 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E GLU* 3.0 17.7 + - - +
228E ASP* 1.3 76.1 - - - +
230E GLN* 1.3 86.2 + - - +
232E LYS* 3.9 2.2 - - - +
233E ASP* 3.0 38.5 + - - +
237E HIS* 5.6 0.2 - - - -
303E TYR* 6.5 0.7 - - - -
305E HIS* 3.1 35.1 + - + +
105G HIS* 4.6 25.6 + - - -
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Residues in contact with GLN 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E GLU* 4.5 1.5 + - - +
228E ASP 3.3 0.8 - - - -
229E ARG* 1.3 105.9 + - - +
231E TYR* 1.3 65.0 + - - +
233E ASP* 3.3 7.0 + - - +
234E PHE* 3.2 17.7 + - - +
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Residues in contact with TYR 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E ASP* 3.2 26.5 + - - +
229E ARG 3.4 0.2 - - - -
230E GLN* 1.3 81.3 - - - +
232E LYS* 1.3 56.3 + - - +
234E PHE* 3.2 25.0 + + + +
235E LYS* 2.9 66.8 + - + +
259E LEU* 3.6 15.2 - - + +
261E ASP* 3.1 25.6 + - + -
341E TYR* 3.5 14.8 - - - -
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Residues in contact with LYS 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E ASP 3.0 20.2 + - - +
229E ARG 3.9 3.4 - - - +
231E TYR* 1.3 73.8 - - - +
233E ASP* 1.3 67.2 + - - +
236E ILE* 2.9 47.8 + - + -
237E HIS* 3.1 26.8 + - + +
255E MET* 3.9 4.7 - - - -
305E HIS* 4.1 24.0 + - + -
341E TYR* 3.5 36.0 + - + -
342E LEU 2.8 28.4 + - - +
343E GLU 3.1 16.0 + - - -
344E ASP* 4.5 6.3 - - - +
345E TYR* 4.8 2.4 - - - +
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Residues in contact with ASP 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E ARG* 3.0 26.9 + - - +
230E GLN* 3.3 11.9 - - - +
232E LYS* 1.3 77.7 - - - +
234E PHE* 1.3 59.0 + - - +
237E HIS* 3.7 27.0 - - - +
238E TRP* 2.9 31.4 + - - +
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Residues in contact with PHE 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E GLN* 3.2 8.6 + - + +
231E TYR* 3.2 36.6 + + + +
233E ASP* 1.3 79.5 - - - +
235E LYS* 1.3 74.5 + - + +
238E TRP* 3.3 19.5 - + - +
91F LYS* 2.8 59.2 + - + -
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Residues in contact with LYS 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E TYR* 2.9 55.8 + - + +
234E PHE* 1.3 94.4 - - + +
236E ILE* 1.3 68.6 + - + +
238E TRP* 4.9 0.4 - - - -
239E TRP* 3.4 19.5 + - - -
254E ALA* 5.0 3.5 - - - +
259E LEU* 3.9 24.2 - - + +
341E TYR* 4.6 3.6 - - + +
83F PHE* 5.8 1.0 - - + -
87F GLU* 3.0 36.3 + - - +
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Residues in contact with ILE 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E LYS* 2.9 48.2 + - + +
234E PHE 3.7 0.2 - - - -
235E LYS* 1.3 83.2 - - + +
237E HIS* 1.3 80.8 + - + +
238E TRP 3.1 1.9 + - - -
239E TRP* 3.3 14.5 + - + -
251E ARG* 3.2 30.3 - - + +
254E ALA* 5.0 4.0 - - + -
255E MET* 3.6 41.7 - - + +
259E LEU* 5.9 1.1 - - + -
341E TYR* 3.9 26.9 - - + -
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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