Contacts of the strand formed by residues 234 - 239 (chain B) in PDB entry 1YSD
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 234 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ALA 3.5 18.2 - - - -
221B GLU* 3.8 6.3 - - - -
222B ALA* 3.7 5.8 - - - +
233B ILE* 1.3 77.0 - - - +
235B GLY* 1.3 57.8 + - - -
249B GLY 3.4 10.3 - - - -
250B HIS* 4.0 0.7 - - - -
263B GLY* 4.9 5.1 - - - -
267B THR* 4.8 0.7 - - - -
286B THR* 3.4 6.4 + - - -
287B THR* 3.1 32.3 + - - +
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Residues in contact with GLY 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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218B ALA* 3.6 14.8 - - - +
221B GLU* 3.8 3.8 - - - +
234B GLY* 1.3 75.0 - - - -
236B CYS* 1.3 63.6 + - - +
248B ARG* 3.4 2.6 - - - +
249B GLY 2.9 29.0 + - - +
263B GLY 5.6 0.4 - - - -
264B GLU* 6.0 0.9 - - - -
267B THR* 3.3 13.1 + - - -
284B LEU* 5.1 0.2 - - - -
285B TYR 2.9 15.7 - - - -
286B THR* 4.3 0.4 - - - -
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Residues in contact with CYS 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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214B GLY* 3.4 30.1 - - - -
217B ILE* 3.6 26.7 - - + -
235B GLY* 1.3 75.6 - - - +
237B LEU* 1.3 60.7 + - - +
238B ILE* 4.0 11.4 - - - -
245B VAL* 4.7 4.0 - - + -
247B GLY 3.2 15.9 - - - +
248B ARG* 3.8 1.1 - - + -
267B THR* 3.4 9.2 - - - +
284B LEU* 3.3 2.6 - - - +
285B TYR* 2.8 44.3 + - - -
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Residues in contact with LEU 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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236B CYS* 1.3 74.2 - - - +
238B ILE* 1.3 62.3 + - - +
245B VAL* 3.7 2.9 - - - +
246B LEU* 2.8 45.0 + - + +
247B GLY 2.9 7.5 + - - +
267B THR* 3.8 6.0 - - + +
268B LEU* 4.2 7.6 - - + -
271B CYS* 3.8 29.8 - - + -
274B LEU* 4.9 0.2 - - + -
279B TYR* 4.1 25.4 - - + -
282B THR* 3.4 24.9 - - - +
283B THR 3.5 17.9 - - - +
284B LEU* 3.8 15.9 - - + +
303B ILE* 4.0 11.0 - - + -
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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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210B TRP* 4.0 19.1 - - + +
213B LYS* 4.4 15.7 - - + -
214B GLY* 3.6 23.6 - - - +
217B ILE* 5.7 0.2 - - + -
236B CYS* 4.0 10.1 - - - -
237B LEU* 1.3 78.5 - - - +
239B ASN* 1.3 76.5 + - - +
240B ASN* 3.3 3.8 + - - +
243B GLY* 3.7 17.5 - - - -
244B SER 3.3 10.3 - - - +
245B VAL* 4.2 11.9 - - + -
282B THR* 3.2 6.7 - - - -
283B THR* 3.0 30.3 + - - -
285B TYR* 3.6 28.7 - - + +
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Residues in contact with ASN 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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237B LEU 4.3 0.2 + - - -
238B ILE* 1.3 71.0 - - - +
240B ASN* 1.3 59.0 + - - +
241B LYS* 2.9 37.4 + - - +
242B ASP* 3.4 21.4 + - - +
243B GLY* 2.8 32.4 + - - -
244B SER* 2.8 19.1 + - - +
246B LEU* 4.4 14.7 - - + +
278B VAL* 4.6 18.7 + - - +
281B ASP* 3.5 12.2 - - - +
282B THR* 4.1 7.0 - - - -
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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