Contacts of the strand formed by residues 273 - 279 (chain B) in PDB entry 5DK3
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 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B VAL* 5.2 1.1 - - + -
266B VAL* 3.8 24.2 - - + -
271B PRO 3.2 15.9 + - - +
272B GLU* 1.3 75.7 - - - +
274B GLN* 1.4 64.4 + - - +
275B PHE* 4.0 24.0 - - + -
289B THR* 5.7 3.1 - - - +
302B VAL* 4.3 18.1 - - + +
323B VAL* 3.4 29.4 - - + -
324B SER 3.6 3.8 - - - +
325B ASN* 3.7 17.5 - - + +
296G PHE* 3.8 7.0 - - - -
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Residues in contact with GLN 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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273B VAL* 1.4 74.8 - - - +
275B PHE* 1.3 67.7 + - - +
276B ASN* 3.4 25.9 + - - +
322B LYS 3.7 0.7 - - - +
323B VAL* 3.5 8.5 - - - +
324B SER* 2.9 37.1 + - - +
295G GLN 5.6 0.9 - - - +
296G PHE* 3.4 49.2 - - + +
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Residues in contact with PHE 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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261B CYS* 3.9 12.3 - - + -
263B VAL* 3.5 27.4 - - + -
273B VAL* 4.0 9.9 - - + -
274B GLN* 1.3 79.9 - - - +
276B ASN* 1.3 68.0 + - - +
277B TRP* 4.4 9.0 + - + +
289B THR* 3.6 26.8 + - + +
302B VAL* 3.6 48.0 - - + -
304B SER* 3.6 32.1 - - - +
321B CYS* 3.7 19.3 - - - -
322B LYS 3.6 1.6 - - - -
323B VAL* 3.8 10.8 - - + -
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Residues in contact with ASN 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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274B GLN* 3.4 27.5 + - - +
275B PHE* 1.3 80.2 - - - +
277B TRP* 1.3 60.9 + - - +
278B TYR* 3.4 30.0 + - + +
283B GLU* 3.0 27.2 + - - +
320B LYS 3.6 1.0 - - - +
321B CYS* 3.5 4.5 - - - -
322B LYS* 2.8 45.0 + - + +
324B SER* 4.9 5.2 + - - -
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Residues in contact with TRP 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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242B LEU* 3.8 13.2 - - + -
259B VAL* 3.7 37.0 - - + -
261B CYS* 3.5 32.3 - - + -
275B PHE* 4.4 12.9 - - + +
276B ASN* 1.3 75.1 - - - +
278B TYR* 1.3 63.5 + - - +
283B GLU* 3.4 8.0 - - - +
284B VAL* 2.9 51.9 + - + +
287B ALA* 3.3 23.2 - - + +
304B SER* 2.8 38.2 + - - -
306B LEU* 3.8 28.9 - - + -
319B TYR* 4.7 5.2 - + + -
320B LYS 3.4 16.8 - - - -
321B CYS* 4.2 7.0 - - + -
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Residues in contact with TYR 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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276B ASN* 3.4 44.7 + - + +
277B TRP* 1.3 71.7 - - - +
279B VAL* 1.3 64.0 + - - +
280B ASP 3.9 0.4 - - - -
281B GLY* 3.9 24.0 - - - -
282B VAL 3.3 7.2 - - - +
283B GLU* 3.5 40.1 + - + -
284B VAL 4.6 0.2 - - - +
318B GLU 3.3 2.8 - - - +
319B TYR* 3.5 3.3 - - - -
320B LYS* 2.8 68.9 + - + +
322B LYS* 4.1 11.9 - - + +
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Residues in contact with VAL 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 TYR* 1.3 75.0 - - - +
280B ASP* 1.3 69.6 + - - +
282B VAL* 3.0 23.7 + - - +
284B VAL* 3.8 30.5 - - + -
306B LEU* 4.2 4.5 - - + -
312B ASP* 4.2 11.2 - - - +
317B LYS* 3.8 36.6 - - + +
318B GLU 3.3 4.7 - - - +
319B TYR* 4.0 26.9 - - + -
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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