Contacts of the strand formed by residues 291 - 300 (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 ALA 291 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B GLY 3.0 24.1 + - - -
259B TYR* 3.1 26.1 + - + +
261B PRO* 4.1 14.9 - - + +
290B LEU* 1.3 76.6 - - - +
292B SER* 1.3 66.7 + - - +
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Residues in contact with SER 292 (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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256B VAL 3.3 11.2 - - - -
257B SER* 3.6 15.9 - - - -
258B GLY 4.3 0.2 - - - -
259B TYR* 3.2 16.2 + - - -
291B ALA* 1.3 83.8 - - - +
293B THR* 1.3 65.8 + - - +
294B GLN* 5.9 1.2 - - - +
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Residues in contact with THR 293 (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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255B LEU* 4.1 0.2 - - - -
256B VAL* 2.7 40.2 + - - +
259B TYR* 4.0 12.3 - - - -
264B ILE* 5.8 4.9 - - - -
266B ILE* 5.1 7.0 - - - -
280B SER* 6.3 2.7 - - - -
292B SER* 1.3 76.9 + - - +
294B GLN* 1.3 73.2 + - - +
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Residues in contact with GLN 294 (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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253B LEU* 4.1 18.2 - - + -
254B CYS 3.2 9.4 - - - +
255B LEU* 4.0 19.5 - - + -
266B ILE* 4.2 5.0 - - - +
292B SER* 5.9 1.3 - - - +
293B THR* 1.3 82.4 - - - +
295B SER* 1.3 63.6 + - - +
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Residues in contact with SER 295 (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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253B LEU* 4.3 0.9 - - - -
254B CYS* 3.1 28.2 + - - +
266B ILE* 3.5 27.1 - - - +
268B TRP* 3.3 31.9 + - - -
276B ASP* 4.8 0.9 + - - -
278B ASP* 3.6 28.5 - - - +
294B GLN* 1.3 75.3 - - - +
296B GLU* 1.3 59.3 + - - +
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Residues in contact with GLU 296 (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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252B GLN* 4.4 25.1 - - - +
253B LEU* 3.2 25.1 - - + +
268B TRP* 4.3 2.3 + - - -
276B ASP* 5.1 4.7 - - - +
294B GLN* 5.5 0.2 - - - +
295B SER* 1.3 75.7 + - - +
297B LEU* 1.3 61.8 + - - +
298B THR* 5.0 1.8 + - - -
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Residues in contact with LEU 297 (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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251B ILE 3.9 0.3 - - - +
252B GLN* 3.6 1.3 - - - +
253B LEU* 2.6 47.6 + - + +
268B TRP* 3.6 58.8 - - + -
269B LEU 6.0 0.2 - - - +
270B GLU 6.3 0.2 - - - +
275B MET* 4.6 13.7 - - + -
276B ASP* 4.5 13.7 - - + +
295B SER 4.0 0.8 + - - -
296B GLU* 1.3 75.4 - - - +
298B THR* 1.3 69.0 + - - +
299B LEU* 4.7 4.7 - - + -
310B TYR* 4.1 26.0 - - + -
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Residues in contact with THR 298 (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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250B THR* 3.1 33.7 - - + -
251B ILE 3.6 2.7 - - - +
252B GLN* 3.5 34.4 + - + +
296B GLU 5.0 1.7 + - - -
297B LEU* 1.3 83.4 - - - +
299B LEU* 1.3 71.3 + - - +
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Residues in contact with LEU 299 (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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250B THR* 3.1 10.0 - - - +
251B ILE* 2.9 35.6 + - + +
253B LEU* 3.5 34.1 - - + -
270B GLU* 4.3 0.4 - - - +
297B LEU* 4.7 5.8 - - + -
298B THR* 1.3 83.8 - - - +
300B SER* 1.3 68.8 + - - +
303B HIS* 3.8 13.7 - - + -
304B TRP* 3.8 19.7 - - + -
310B TYR* 3.2 51.8 - - + +
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Residues in contact with SER 300 (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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249B PRO 4.5 2.5 - - - -
250B THR* 4.9 3.1 - - - -
299B LEU* 1.3 76.2 - - - +
301B GLN* 1.3 66.2 + - - +
302B LYS* 3.9 6.3 - - - -
303B HIS* 3.4 31.9 + - - +
304B TRP* 3.0 21.8 + - - +
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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