Contacts of the strand formed by residues 264 - 270 (chain B) in PDB entry 2Y7Q
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 ILE 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B PRO* 6.2 0.2 - - + -
256B VAL* 5.5 3.8 - - + -
259B TYR* 4.2 28.9 + - + +
262B GLY 3.8 2.6 + - - -
263B THR* 1.3 74.4 - - - +
265B GLN* 1.3 63.2 + - - +
266B ILE* 5.5 3.6 - - + -
279B LEU* 3.6 1.8 - - - +
280B SER* 2.9 33.7 + - - +
293B THR* 5.8 4.9 - - - -
314B VAL* 4.5 11.7 - - + -
315B THR 3.8 4.0 - - - -
316B TYR* 4.5 12.6 - - + -
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Residues in contact with GLN 265 (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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264B ILE* 1.3 75.6 - - - +
266B ILE* 1.3 62.7 + - - +
267B THR* 3.8 16.6 + - - +
277B VAL* 4.0 22.9 - - - +
278B ASP 3.1 10.8 - - - +
279B LEU* 3.8 20.2 - - + +
313B GLN 3.4 1.0 - - - +
314B VAL* 3.5 2.0 - - - -
315B THR* 3.0 53.0 + - - +
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Residues in contact with ILE 266 (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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254B CYS* 4.5 1.3 - - - -
256B VAL* 3.6 30.5 - - + -
264B ILE* 5.5 3.4 - - + -
265B GLN* 1.3 75.9 - - - +
267B THR* 1.3 65.5 + - - +
268B TRP* 3.9 11.8 + - - +
276B ASP 4.5 0.3 - - - -
277B VAL* 3.5 3.4 - - - -
278B ASP* 2.7 38.3 + - + +
293B THR* 5.1 5.8 - - - -
294B GLN* 4.2 7.9 - - - +
295B SER* 3.5 40.2 - - - +
312B CYS* 3.5 28.5 - - - -
313B GLN 3.7 4.7 - - - +
314B VAL* 4.4 6.3 - - + -
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Residues in contact with THR 267 (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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265B GLN* 3.8 20.6 + - - -
266B ILE* 1.3 73.9 - - - +
268B TRP* 1.3 64.8 + - - +
269B LEU* 4.5 5.2 - - + -
274B VAL* 3.9 26.2 - - + -
276B ASP 3.6 9.4 - - - +
277B VAL* 4.0 11.9 - - + +
311B THR 3.5 1.2 - - - +
312B CYS* 3.7 1.7 - - - -
313B GLN* 2.7 66.6 + - - +
315B THR* 4.2 3.5 + - - -
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Residues in contact with TRP 268 (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 ILE* 4.3 14.4 - - + -
253B LEU* 4.0 28.5 - - + -
254B CYS* 3.5 17.3 - - + -
266B ILE* 4.3 7.3 - - + +
267B THR* 1.3 75.0 - - - +
269B LEU* 1.3 61.5 + - - +
270B GLU 4.1 0.2 - - - -
274B VAL* 3.4 6.2 - - - +
275B MET* 2.8 27.3 + - + -
276B ASP* 2.9 33.1 + - + +
295B SER* 3.3 46.5 + - - -
296B GLU 4.3 0.9 - - - -
297B LEU* 3.6 51.6 - - + +
310B TYR* 4.6 4.7 - - + -
311B THR 3.4 19.7 - - - -
312B CYS* 3.9 26.0 - - + -
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Residues in contact with LEU 269 (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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267B THR* 4.5 6.5 - - + -
268B TRP* 1.3 76.1 - - - +
270B GLU* 1.3 60.6 + - - +
271B ASP 3.2 7.4 + - - -
272B GLY* 4.2 19.7 - - - +
273B GLN 3.3 4.0 - - - +
274B VAL* 3.8 36.3 - - + +
309B THR 3.4 1.7 - - - +
310B TYR* 3.4 3.0 - - - -
311B THR* 2.8 55.9 + - + +
313B GLN* 3.2 40.2 - - + +
322B GLU* 5.1 0.2 - - - +
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Residues in contact with GLU 270 (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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269B LEU* 1.3 68.4 - - - +
271B ASP* 1.3 76.3 + - + +
272B GLY 3.1 0.4 - - - -
273B GLN* 2.8 26.4 + - + +
275B MET* 3.4 32.7 - - + +
299B LEU* 4.3 1.0 - - - +
303B HIS* 2.9 25.4 + - - -
308B ARG* 3.4 19.9 + - + -
310B TYR* 2.8 47.9 + - + -
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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