Contacts of the strand formed by residues 232 - 241 (chain B) in PDB entry 2YVC
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 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B TYR* 3.7 9.9 - - - +
229B GLU* 3.0 25.3 + - + +
230B HIS 3.5 0.6 - - - -
231B ASP* 1.3 87.4 - - - +
233B LYS* 1.3 57.4 + - - +
234B LEU* 3.2 14.7 + - - +
235B THR* 2.9 46.1 + - - +
237B LYS* 4.5 9.9 + - - -
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Residues in contact with LYS 233 (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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199B GLU* 5.4 0.3 - - - +
200B MET* 3.8 23.8 - - + +
205B TYR* 2.8 58.4 + - + +
217B TRP* 3.5 54.2 - - + +
228B TYR* 3.2 21.1 - - - -
230B HIS 5.4 0.4 - - - +
231B ASP 4.1 1.1 - - - -
232B ASP* 1.3 71.5 - - - +
234B LEU* 1.3 63.5 + - + +
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Residues in contact with LEU 234 (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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116B TYR* 3.7 38.8 - - + -
199B GLU* 3.1 50.8 - - + +
200B MET* 3.7 31.6 - - + -
228B TYR* 4.2 1.6 - - - -
232B ASP* 3.1 9.3 - - - +
233B LYS* 1.3 83.3 - - + +
235B THR* 1.3 64.4 + - - +
236B PRO* 3.1 10.6 - - - +
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Residues in contact with THR 235 (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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199B GLU* 4.8 1.6 - - - -
228B TYR* 3.6 14.8 - - - -
229B GLU 4.4 0.3 + - - -
232B ASP* 2.9 32.5 + - - +
234B LEU* 1.3 77.7 - - - +
236B PRO* 1.3 79.1 - - + +
237B LYS* 3.7 17.8 + - + +
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Residues in contact with PRO 236 (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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199B GLU* 4.5 7.0 - - + +
226B ASN* 4.0 23.6 - - + +
227B ILE 4.0 1.8 - - - +
228B TYR* 3.8 28.0 - - + +
234B LEU 3.1 10.1 - - - +
235B THR* 1.3 94.9 - - + +
237B LYS* 1.3 61.7 + - - +
238B ILE 4.9 2.9 - - - +
239B GLY* 5.7 0.4 - - - +
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Residues in contact with LYS 237 (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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227B ILE* 2.8 19.5 + - + +
228B TYR 5.3 0.2 - - - -
229B GLU* 3.3 47.2 - - + +
232B ASP* 4.5 10.1 + - - -
235B THR* 4.3 14.4 - - + +
236B PRO* 1.3 79.8 - - - +
238B ILE* 1.3 75.0 + - + +
239B GLY 4.3 0.6 + - - -
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Residues in contact with ILE 238 (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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226B ASN* 3.2 10.9 - - - +
227B ILE* 3.2 40.4 + - + -
236B PRO* 5.3 1.6 - - - -
237B LYS* 1.3 97.0 - - + +
239B GLY* 1.3 66.9 + - - +
240B PHE* 3.7 28.5 - - + -
267B PHE* 5.3 8.5 - - + -
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Residues in contact with GLY 239 (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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226B ASN* 3.5 12.8 - - - -
236B PRO* 5.7 0.9 - - - +
237B LYS 4.3 0.8 + - - -
238B ILE* 1.3 79.7 - - - +
240B PHE* 1.3 72.8 + - - -
241B PRO* 3.6 10.3 - - - +
244B GLU* 4.7 4.7 - - - +
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Residues in contact with PHE 240 (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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224B GLY* 3.4 2.3 - - - -
225B LEU* 2.8 50.5 + - + +
227B ILE* 3.9 24.5 - - + -
238B ILE* 3.7 31.6 - - + -
239B GLY* 1.3 81.6 - - - -
241B PRO* 1.3 72.1 - - - +
244B GLU* 5.3 3.4 - - + -
245B ILE* 3.7 24.2 - - + +
257B ILE* 4.0 24.2 - - + -
259B PRO* 5.4 9.4 - - + -
267B PHE* 3.6 34.1 - + + -
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Residues in contact with PRO 241 (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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223B LEU* 3.6 11.0 - - + +
224B GLY* 4.6 0.2 - - - -
239B GLY* 3.6 6.7 - - - -
240B PHE* 1.3 94.9 - - - +
242B TRP* 1.3 64.0 + - - +
243B SER* 4.0 16.4 - - - +
244B GLU* 3.2 41.0 + - + +
245B ILE* 3.2 10.0 - - - +
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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