Contacts of the strand formed by residues 226 - 232 (chain B) in PDB entry 1RY7
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 TYR 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B PHE* 3.5 33.0 - + + -
188B TRP* 4.8 3.8 - - + -
189B LEU 3.7 14.6 - - - -
190B LYS* 3.5 19.5 - - + -
195B PHE* 3.5 28.7 - + - -
213B LEU* 3.8 20.4 - - + -
215B MET* 3.3 33.6 - - + -
222B ASP* 3.2 28.0 + - - +
224B GLY 2.7 23.9 + - - -
225B ASN* 1.3 67.7 - - - +
227B THR* 1.3 58.2 + - - +
228B CYS 4.4 0.2 + - - -
239B GLN 4.2 0.5 - - - +
240B THR* 3.2 0.4 - - - -
241B TYR* 2.2 56.9 + - + +
243B LEU* 3.7 13.2 - - + -
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Residues in contact with THR 227 (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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187B SER 3.6 0.7 - - - +
188B TRP* 3.0 30.9 - - - -
189B LEU* 3.2 31.7 + - + +
192B GLY* 5.8 0.2 - - - -
225B ASN 4.3 1.2 + - - -
226B TYR* 1.3 72.4 - - - +
228B CYS* 1.3 73.5 + - - +
229B VAL* 4.4 6.5 - - + -
238B ARG* 4.3 16.6 - - + +
239B GLN 3.4 10.5 - - - +
240B THR* 2.3 43.0 + - - +
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Residues in contact with CYS 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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153B TRP* 3.8 10.1 - - + -
176B CYS* 3.0 46.0 - - - -
186B ILE* 4.9 3.4 - - + -
187B SER 3.3 4.5 - - - +
188B TRP* 3.4 17.2 - - + -
227B THR* 1.3 75.0 - - - +
229B VAL* 1.3 62.8 + - - +
230B VAL* 5.4 0.4 - - + -
238B ARG* 2.8 27.3 - - - +
239B GLN* 3.0 41.6 + - - -
241B TYR* 5.4 3.8 - - - -
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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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185B SER 3.1 5.7 - - - +
186B ILE* 3.2 1.5 - - - +
187B SER* 2.5 59.3 + - - +
189B LEU* 4.6 11.4 - - + -
227B THR* 4.4 7.0 - - + +
228B CYS* 1.3 78.5 - - - +
230B VAL* 1.3 64.9 + - - +
231B GLU* 3.8 7.1 + - + +
236B SER* 4.2 14.1 - - - +
237B ILE 3.7 2.0 - - - -
238B ARG* 3.0 50.9 - - + +
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Residues in contact with VAL 230 (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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151B PRO* 3.4 29.6 - - + +
153B TRP* 3.2 39.0 - - + -
176B CYS* 5.5 0.9 - - - -
178B ALA* 4.1 11.7 - - + -
184B PRO* 3.5 20.4 - - + -
185B SER 3.1 7.4 - - - +
186B ILE* 5.3 1.6 - - + -
211B TRP* 4.2 8.5 - - + -
228B CYS* 5.2 2.0 - - + -
229B VAL* 1.3 74.5 - - - +
231B GLU* 1.3 58.6 + - - +
236B SER* 2.8 4.9 + - - -
237B ILE* 2.6 47.6 + - + +
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Residues in contact with GLU 231 (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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184B PRO* 3.7 1.1 - - - +
185B SER* 3.2 34.9 + - - +
229B VAL* 3.8 9.7 + - + +
230B VAL* 1.3 73.0 - - - +
232B ASN* 1.3 61.9 + - - +
236B SER* 3.1 18.8 - - - +
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Residues in contact with ASN 232 (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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150B ALA 3.5 19.9 + - - -
151B PRO* 3.5 16.5 - - + +
181B ASN 3.8 7.2 + - - +
182B PRO* 2.9 42.4 + - - +
183B THR 4.2 1.4 + - - -
184B PRO* 3.7 19.0 - - + +
231B GLU* 1.3 74.6 + - - +
233B LYS* 1.3 71.5 + - - +
234B PHE 2.9 5.2 + - - +
235B GLY* 2.5 28.8 + - - +
236B SER* 4.3 0.9 - - - -
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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