Contacts of the strand formed by residues 226 - 230 (chain E) in PDB entry 1UCY
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 GLY 226 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E CYS* 3.1 23.4 - - - -
183E ALA 3.2 14.8 + - - -
189E ASP* 4.1 12.4 + - - -
215E TRP 3.7 2.2 - - - -
216E GLY* 4.6 0.2 - - - -
225E TYR* 1.3 72.6 - - - +
227E PHE* 1.3 61.6 + - - -
228E TYR* 3.4 9.4 - - - -
16F OPR 3.6 27.8 - - - -
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Residues in contact with PHE 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E CYS* 3.7 26.0 - - + -
171E SER* 4.2 8.7 - - - -
172E THR* 4.1 4.5 - - + -
176E ILE* 3.5 35.4 - - + -
180E MET* 4.1 12.3 - - + -
181E PHE 3.4 13.9 - - - -
182E CYS* 3.6 19.7 - - + -
213E VAL* 4.4 0.2 - - - -
214E SER* 3.1 21.7 + - - -
215E TRP* 2.6 71.2 + + + +
217E GLU* 5.8 0.2 - - - -
225E TYR 3.0 30.3 - - - -
226E GLY* 1.3 70.8 - - - -
228E TYR* 1.3 69.6 + - - +
16F OPR 4.9 1.6 + - - -
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Residues in contact with TYR 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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160E LEU* 3.2 24.3 - - + +
180E MET* 3.1 5.8 - - - -
181E PHE* 2.8 65.0 + + + +
183E ALA* 4.0 17.3 - - + -
189E ASP* 4.4 4.0 + - - -
190E ALA* 4.1 14.0 - - + +
199E PHE* 3.9 27.1 - + + -
212E ILE 3.1 20.9 - - - +
213E VAL* 3.6 30.3 - - + -
214E SER* 3.9 3.8 - - - -
226E GLY* 3.4 25.5 - - - -
227E PHE* 1.3 77.8 - - - +
229E THR* 1.3 66.0 + - - +
16F OPR 5.2 1.1 - - - -
138H VAL* 3.6 7.4 - - + +
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Residues in contact with THR 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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179E ASN 3.6 7.9 - - - +
180E MET* 4.4 1.8 - - - +
181E PHE* 3.9 1.7 - - - -
210E MET 3.8 0.2 - - - +
211E GLY* 3.2 25.1 - - - -
212E ILE* 2.9 25.9 + - + +
214E SER* 3.9 8.5 + - - -
228E TYR* 1.3 74.3 - - - +
230E HIS* 1.3 61.3 + - - +
231E VAL 3.3 1.4 + - - -
234E LEU* 3.2 36.3 - - + -
101H ARG* 5.0 0.4 - - - +
102H ASP* 2.7 44.6 + - - +
103H ILE* 4.2 4.7 - - + -
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Residues in contact with HIS 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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165E ARG* 4.2 5.8 - - - -
178E ASP 3.3 7.0 - - - +
179E ASN* 2.7 29.9 + - - +
180E MET* 3.7 3.8 - - - +
181E PHE* 4.0 22.4 - + + +
210E MET 5.0 1.0 + - - -
228E TYR 3.5 0.2 + - - -
229E THR* 1.3 74.1 - - - +
231E VAL* 1.3 62.7 + - - +
232E PHE* 3.9 12.9 + + + -
233E ARG* 3.0 68.2 + - + +
234E LEU* 3.1 13.9 + - - +
130H LEU* 3.9 29.2 - - + +
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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