Contacts of the strand formed by residues 225 - 230 (chain E) in PDB entry 3ZXR
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 GLN 225 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135E GLU* 4.3 3.4 + - - +
136E PHE 3.3 12.3 - - - +
137E TYR* 3.4 34.6 + - + -
218E HIS* 3.1 14.5 + - - -
219E GLU* 2.8 38.3 + - + +
220E VAL 3.5 2.1 + - - -
221E GLY* 2.8 41.0 + - - +
224E GLY* 1.3 78.0 - - - +
226E ALA* 1.3 64.3 + - - +
271E ASN* 3.8 7.8 - - - +
272E GLY 2.9 27.1 + - - -
273E SER* 3.0 20.2 + - - +
505E P3S 4.2 3.0 + - - -
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Residues in contact with ALA 226 (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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135E GLU* 3.4 8.0 - - - +
136E PHE* 2.7 62.8 + - + -
138E ILE* 4.2 4.7 - - + -
199E ARG* 3.7 26.0 - - - +
217E HIS 3.5 4.9 - - - -
219E GLU* 3.8 5.9 - - - +
224E GLY 4.2 4.7 - - - +
225E GLN* 1.3 77.1 - - - +
227E GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 227 (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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133E GLU* 2.9 15.4 - - + +
134E ALA 5.1 1.6 - - - +
135E GLU* 3.1 15.3 - - + +
136E PHE* 4.5 3.4 - - - -
216E GLY* 3.2 2.6 - - - -
217E HIS* 2.8 61.8 + - + +
219E GLU* 2.9 5.7 - - + +
226E ALA* 1.3 76.8 - - - +
228E ILE* 1.3 68.2 + - - +
229E ASN* 3.1 26.4 + - - +
502E MG 2.0 31.5 - - - -
504E MG 2.2 24.9 - - - -
505E P3S 3.5 0.9 - - - -
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Residues in contact with ILE 228 (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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132E ALA 5.0 1.0 - - - +
134E ALA 4.7 5.0 + - - +
136E PHE* 4.4 6.5 - - + -
199E ARG* 4.1 19.1 - - + +
202E MET* 3.7 36.6 - - + -
203E LEU* 3.7 10.3 - - + +
206E LEU* 3.7 22.4 - - + -
213E LEU* 3.7 15.0 - - + -
215E LYS 3.3 8.1 - - - +
216E GLY* 3.9 10.5 - - - -
217E HIS 4.9 0.2 - - - +
227E GLU* 1.3 80.5 - - - +
229E ASN* 1.3 73.0 + - - +
230E TYR* 4.3 2.8 + - + -
245E TYR* 3.2 36.1 + - + +
249E ILE* 4.1 10.5 - - + -
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Residues in contact with ASN 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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132E ALA 4.3 3.1 + - - -
133E GLU* 3.9 15.5 - - - +
213E LEU* 3.5 9.7 - - - +
214E GLU* 2.9 31.3 + - + -
215E LYS* 2.7 48.0 + - - +
227E GLU* 3.1 31.7 + - - +
228E ILE* 1.3 82.9 + - - +
230E TYR* 1.3 60.4 + - - +
501E IQ1 3.9 29.3 - - + +
504E MG 4.2 2.1 - - - -
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Residues in contact with TYR 230 (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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132E ALA* 4.7 20.3 + - + +
134E ALA 6.3 0.4 - - - -
206E LEU* 5.5 0.9 - - + -
211E PHE* 3.8 23.3 - + + -
212E ILE 3.2 15.0 - - - +
213E LEU* 4.4 6.3 - - + -
214E GLU* 4.3 5.4 - - - +
228E ILE* 4.7 3.4 - - + -
229E ASN* 1.3 76.6 - - - +
231E GLN* 1.3 79.4 + - - +
232E PHE* 4.5 0.8 - - - -
238E ALA* 4.4 4.1 + - + -
241E ASP* 3.7 27.3 - - + +
242E MET* 3.3 43.7 + - + +
245E TYR* 3.5 43.3 - + + -
501E IQ1 3.4 17.5 - - - +
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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