Contacts of the strand formed by residues 272 - 282 (chain B) in PDB entry 5D3Y
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 LEU 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B LEU* 4.3 6.5 - - + +
253B LEU* 4.4 14.8 - - + -
271B GLN* 1.3 92.4 + - - +
273B LEU* 1.3 60.4 + - - +
274B LEU 3.6 18.6 - - - +
275B GLN* 3.6 34.1 - - + +
292B PHE* 3.9 17.5 - - + -
293B LEU 3.6 15.5 - - - +
294B PHE* 3.7 28.7 - - + -
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Residues in contact with LEU 273 (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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271B GLN* 3.6 33.4 - - + +
272B LEU* 1.3 73.5 - - - +
274B LEU* 1.3 62.6 + - + +
293B LEU* 2.8 26.9 + - + +
294B PHE 3.7 2.5 - - - -
295B ASP* 3.6 24.0 - - + +
386B ALA* 5.1 6.5 - - + +
390B GLU* 3.6 34.8 - - + +
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Residues in contact with LEU 274 (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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272B LEU* 3.6 5.8 - - - +
273B LEU* 1.3 83.4 - - - +
275B GLN* 1.3 72.7 + - - +
292B PHE* 3.5 1.9 - - - -
293B LEU* 2.7 35.9 + - + +
379B GLU* 5.4 1.1 - - - +
382B LYS* 3.6 35.9 - - + +
383B TRP* 3.3 63.2 - - + +
386B ALA* 3.9 19.3 - - + -
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Residues in contact with GLN 275 (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* 5.6 1.1 - - - +
272B LEU* 3.6 24.2 - - + +
274B LEU* 1.3 87.2 - - - +
276B GLY* 1.3 59.8 + - - +
291B PHE 3.2 11.7 - - - +
292B PHE* 3.3 30.5 - - + -
325B TYR* 4.5 7.3 + - - -
379B GLU* 4.9 2.6 - - - +
383B TRP* 4.0 4.9 - - - -
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Residues in contact with GLY 276 (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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275B GLN* 1.3 76.4 - - - +
277B THR* 1.3 64.2 + - - -
278B LEU* 4.9 0.4 - - - -
290B ALA* 3.6 3.6 - - - +
291B PHE* 2.8 33.6 + - - +
379B GLU* 4.6 10.8 - - - -
383B TRP* 3.7 11.5 - - - -
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Residues in contact with THR 277 (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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276B GLY* 1.3 73.9 - - - -
278B LEU* 1.3 71.7 + - - +
288B GLU* 2.9 37.9 - - + +
289B ARG 3.2 21.5 - - - +
290B ALA* 4.1 7.3 - - + +
303B ARG* 4.1 18.8 + - + +
374B ALA* 5.2 1.7 - - - -
375B LYS* 5.4 2.9 + - - +
379B GLU* 5.4 4.8 + - - +
383B TRP* 5.4 0.2 + - - -
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Residues in contact with LEU 278 (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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277B THR* 1.3 85.0 - - - +
279B LEU* 1.3 66.6 + - - +
280B LYS 3.8 0.3 + - - -
288B GLU* 3.5 5.6 - - - +
289B ARG* 2.9 32.1 + - - +
291B PHE* 3.6 36.5 - - + -
359B TRP* 3.7 28.0 - - + -
372B CYS* 4.0 8.7 - - + -
373B MET 3.6 5.6 - - - +
374B ALA* 3.8 30.7 - - + -
379B GLU* 4.9 2.2 - - + -
383B TRP* 3.7 32.3 - - + +
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Residues in contact with LEU 279 (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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278B LEU* 1.3 74.9 - - - +
280B LYS* 1.3 59.9 + - - +
286B ILE* 4.3 18.6 - - + -
287B GLN 3.8 0.9 - - - -
288B GLU* 4.0 32.8 - - + +
353B TYR* 4.9 8.7 - - - +
371B VAL 3.5 0.5 - - - +
372B CYS* 3.3 5.7 - - - -
373B MET* 2.9 66.5 + - + +
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Residues in contact with LYS 280 (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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279B LEU* 1.3 75.1 - - - +
281B ILE* 1.3 62.7 + - - +
282B SER* 3.6 11.5 + - - -
285B ASN 3.4 1.9 - - - +
286B ILE* 3.4 4.2 - - - -
287B GLN* 2.9 45.1 + - + +
289B ARG* 4.4 10.4 - - + +
291B PHE* 4.0 21.1 - - + -
300B TYR* 3.9 17.5 - - + -
370B PHE* 3.8 37.2 - - + -
371B VAL 3.2 3.6 - - - +
501B 4IP 2.7 61.8 + - - +
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Residues in contact with ILE 281 (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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280B LYS* 1.3 72.7 - - - +
282B SER* 1.3 62.0 + - - +
284B GLY* 4.8 11.7 - - - +
285B ASN 3.2 10.8 - - - +
286B ILE* 4.0 15.7 - - + -
349B HIS 3.7 16.9 - - - +
350B SER* 4.0 35.0 - - - +
351B ASN* 5.0 0.7 - - + -
353B TYR* 4.1 16.4 - - + -
355B VAL* 4.4 0.4 - - + -
370B PHE* 3.2 6.1 - - - +
371B VAL* 2.8 55.3 + - + +
373B MET* 3.8 31.9 - - + -
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Residues in contact with SER 282 (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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280B LYS* 3.6 18.9 + - - -
281B ILE* 1.3 76.1 - - - +
283B ALA* 1.3 70.1 + - - +
284B GLY 3.1 1.8 - - - -
285B ASN* 2.8 26.2 + - - +
287B GLN* 5.5 0.9 + - - -
349B HIS 5.6 0.7 - - - -
368B LYS* 2.8 25.6 + - - -
369B TRP 5.1 1.6 - - - -
370B PHE* 3.8 7.8 - - - +
501B 4IP 2.5 35.5 + - - -
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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