Contacts of the strand formed by residues 225 - 229 (chain B) in PDB entry 3DRB
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 PHE 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 4.1 12.1 - - + -
169B LEU* 4.2 16.2 - - + -
218B TRP* 3.7 25.1 - + - -
219B HIS* 3.3 2.6 - - - -
220B ASN* 3.1 40.8 + - + +
223B LYS 3.5 0.2 - - - -
224B THR* 1.3 79.4 - - - +
226B LEU* 1.3 61.8 + - - +
227B VAL* 4.7 3.6 - - + -
237B VAL* 3.6 32.8 - - + -
238B ILE 3.2 14.8 - - - -
239B SER* 4.4 8.7 - - - -
252B ARG* 4.3 17.0 - - + -
253B PHE* 4.3 10.8 - - - -
256B GLY* 3.5 34.8 - - - -
260B ILE* 3.9 15.9 - - + -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B PHE* 3.8 39.9 - - + +
217B ILE* 4.0 15.9 - - + -
218B TRP* 3.2 11.2 - - - +
219B HIS* 3.5 18.8 - - + +
223B LYS* 3.7 17.5 - - + +
224B THR 4.0 2.5 - - - -
225B PHE* 1.3 92.9 - - - +
227B VAL* 1.3 67.4 + - - +
228B TRP* 4.3 0.7 - - + -
237B VAL* 4.6 0.3 - - - +
238B ILE* 2.8 52.6 + - + +
240B MET* 4.0 18.4 - - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 4.2 19.3 - - + -
217B ILE* 3.5 2.8 - - - -
218B TRP* 2.7 60.7 + - + +
225B PHE* 4.7 3.4 - - + -
226B LEU* 1.3 79.7 - - - +
228B TRP* 1.3 75.3 + - - +
229B VAL* 3.7 7.7 + - + +
235B LEU* 4.4 19.3 - - + -
236B ARG 3.3 7.6 - - - +
237B VAL* 4.5 8.5 - - + -
260B ILE* 4.0 26.2 - - + -
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Residues in contact with TRP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG* 4.0 16.4 - - - -
191B HIS 5.4 1.6 - - - -
192B PHE 2.9 27.6 + - - -
193B LEU 3.8 2.5 - - - -
194B PHE* 3.4 58.3 - + + +
216B GLY 3.8 3.8 - - - -
217B ILE* 3.7 21.5 - - + +
226B LEU* 5.2 0.4 - - + +
227B VAL* 1.3 75.7 - - - +
229B VAL* 1.3 60.6 + - - +
230B ASN 4.0 0.3 + - - -
231B GLU* 3.9 12.6 - - + -
233B ASP 4.8 0.7 - - - +
234B HIS 3.7 0.3 - - - +
235B LEU* 3.3 8.5 - - - -
236B ARG* 2.9 55.7 + - + +
238B ILE* 3.5 22.2 - - + +
400B ADP 3.8 24.2 - + - -
500B MG 3.7 19.3 - - - -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ILE* 5.0 0.9 - - + -
155B GLU* 4.0 18.6 - - + +
158B ALA* 4.1 21.8 - - + -
162B LEU* 4.9 4.0 - - + -
173B TYR* 3.7 33.4 - - + +
194B PHE* 4.5 1.8 - - - -
214B ALA 4.2 0.2 - - - +
215B ARG* 3.4 3.6 - - - +
216B GLY 2.8 31.3 + - - +
218B TRP* 5.3 0.4 - - + +
227B VAL* 4.1 16.6 - - + +
228B TRP* 1.3 76.7 - - - +
230B ASN* 1.3 90.0 + - - +
231B GLU 3.4 1.6 + - - -
234B HIS 3.6 7.0 - - - +
235B LEU* 5.5 0.4 - - + -
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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