Contacts of the strand formed by residues 273 - 279 (chain O) in PDB entry 5DST
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 CYS 273 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297J GLN* 5.0 0.4 - - - -
353J GLU* 3.5 27.8 - - - +
222O TYR* 3.3 5.7 - - - -
223O VAL* 3.0 37.7 + - + +
272O ALA* 1.3 75.5 - - - +
274O LEU* 1.3 76.8 + - - +
275O ILE 3.4 0.3 + - - -
293O ALA 4.5 0.4 - - - -
294O PHE* 3.6 15.5 - - - -
295O CYS 3.5 36.3 - - - +
296O LEU* 3.8 9.6 - - + -
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Residues in contact with LEU 274 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349J ARG* 5.9 0.9 - - - +
350J ARG 6.0 0.4 - - - +
351J GLY* 4.5 26.1 + - - +
352J GLU* 5.9 4.3 - - + -
353J GLU* 5.4 0.4 - - - +
220O ALA* 3.8 10.8 - - + -
221O LEU 3.7 13.9 - - - +
222O TYR* 3.6 36.1 - - + +
273O CYS* 1.3 81.2 - - - +
275O ILE* 1.3 63.7 + - - +
276O LYS 3.8 21.8 - - - +
277O GLU* 3.6 30.5 - - + +
293O ALA 4.4 4.0 - - - +
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Residues in contact with ILE 275 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221O LEU* 2.8 52.8 + - + +
222O TYR* 4.2 3.1 - - - +
223O VAL* 3.5 36.6 - - + -
273O CYS 3.7 0.4 - - - +
274O LEU* 1.3 80.9 - - - +
276O LYS* 1.3 64.1 + - - +
290O PHE* 3.7 7.7 - - + -
292O SER* 2.6 33.6 + - - +
293O ALA 4.2 3.8 - - - +
294O PHE* 3.9 16.4 - - + -
309O THR* 4.6 3.6 - - + -
358O ILE* 3.9 36.8 - - + -
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Residues in contact with LYS 276 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191O LEU* 5.3 0.5 - - - +
192O PHE* 3.9 21.5 - - + -
219O ALA 4.0 0.5 - - - +
220O ALA* 3.4 4.0 - - - -
221O LEU* 2.9 43.7 + - + +
274O LEU* 3.8 6.3 - - - +
275O ILE* 1.3 80.5 - - - +
277O GLU* 1.3 75.5 + - - +
278O VAL* 4.1 9.7 - - + +
283O VAL* 5.7 3.4 - - - -
287O GLU* 2.8 39.0 + - - +
288O LEU* 4.7 7.0 - - - -
290O PHE* 3.8 37.3 - - + +
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Residues in contact with GLU 277 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349J ARG* 3.4 35.7 + - - -
381J GLN* 4.0 10.0 - - - +
218O ARG* 3.3 36.7 + - - +
219O ALA 3.7 2.9 - - - +
220O ALA* 4.6 2.0 - - + +
274O LEU* 3.6 28.2 - - + +
276O LYS* 1.3 87.2 - - - +
278O VAL* 1.3 70.0 + - - +
279O ASP 4.2 1.2 + - - +
283O VAL* 4.8 2.9 - - - +
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Residues in contact with VAL 278 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186O TRP* 5.3 0.9 - - + -
191O LEU* 4.9 1.1 - - + -
192O PHE* 4.0 29.6 - - + -
197O LEU* 4.2 11.7 - - + -
218O ARG* 3.5 10.5 - - - +
219O ALA* 2.9 45.6 + - + +
276O LYS* 4.1 13.0 - - + +
277O GLU* 1.3 83.5 - - - +
279O ASP* 1.3 60.4 + - - +
280O ILE* 3.5 17.8 + - + -
283O VAL* 3.8 29.4 - - + -
288O LEU* 4.9 1.8 - - + -
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Residues in contact with ASP 279 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217O ASP 3.6 6.0 - - - +
218O ARG* 4.9 8.2 - - + +
277O GLU* 4.2 1.2 + - - +
278O VAL* 1.3 69.8 - - - +
280O ILE* 1.3 67.5 + - - +
281O TYR* 3.0 28.3 - - - +
282O THR* 2.9 42.4 + - - +
283O VAL* 3.1 17.7 + - + +
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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