Contacts of the strand formed by residues 245 - 250 (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 VAL 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B LYS* 3.7 31.4 - - - +
217B ILE* 5.1 11.2 - - + -
236B CYS* 4.7 9.0 - - + -
237B LEU 3.7 5.6 - - - +
238B ILE* 4.2 11.7 - - + -
244B SER* 1.3 70.9 - - - +
246B LEU* 1.3 63.1 + - - +
247B GLY* 3.7 24.9 - - - +
248B ARG* 4.7 13.9 - - - +
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Residues in contact with LEU 246 (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* 2.8 25.2 + - + +
239B ASN* 4.4 18.2 - - + +
244B SER* 4.3 13.5 - - - +
245B VAL* 1.3 73.2 - - - +
247B GLY* 1.3 57.3 + - - +
270B ASN 4.3 1.6 - - - +
271B CYS* 3.4 33.5 - - + +
274B LEU* 4.4 12.8 - - + -
278B VAL* 3.9 22.7 - - + -
282B THR* 3.7 30.3 - - + -
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Residues in contact with GLY 247 (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* 3.2 5.8 - - - +
237B LEU 2.9 25.4 + - - -
245B VAL* 3.3 9.1 - - - +
246B LEU* 1.3 83.9 - - - +
248B ARG* 1.3 62.5 + - - -
267B THR* 4.3 6.1 - - - -
270B ASN* 4.5 5.2 - - - -
271B CYS* 3.6 15.3 - - - -
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Residues in contact with ARG 248 (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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217B ILE* 3.5 36.0 + - + +
220B GLU* 2.8 43.6 + - - +
221B GLU* 2.8 23.2 + - - +
235B GLY 3.4 13.2 - - - +
236B CYS* 3.8 9.9 - - + +
245B VAL* 4.7 10.4 - - + +
247B GLY* 1.3 75.5 - - - +
249B GLY* 1.3 54.5 + - - +
267B THR* 4.2 5.2 - - - -
270B ASN* 2.7 31.3 + - - +
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Residues in contact with GLY 249 (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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221B GLU* 3.2 20.8 + - - +
234B GLY* 3.4 0.2 - - - -
235B GLY 2.9 31.2 + - - +
248B ARG* 1.3 77.0 - - - +
250B HIS* 1.3 59.4 + - - -
263B GLY 4.1 2.2 - - - +
266B SER* 4.2 2.5 - - - -
267B THR* 3.5 12.2 + - - -
270B ASN* 3.5 13.2 - - - -
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Residues in contact with HIS 250 (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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221B GLU* 2.8 44.4 + - - +
222B ALA* 4.8 0.2 - - - -
224B LEU* 3.8 22.0 - - + -
225B GLY* 3.4 21.7 - - - -
228B GLU* 2.8 25.4 + - - -
231B VAL 5.2 0.9 - - - +
233B ILE 3.2 15.3 - - - +
234B GLY* 4.0 0.2 - - - -
249B GLY* 1.3 74.8 - - - +
251B ASN* 1.3 86.9 + - - +
252B MET* 3.2 22.5 - - + +
255B GLN* 3.5 2.9 - - - -
263B GLY* 3.8 7.2 - - - -
266B SER* 3.1 19.5 + - - -
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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