Contacts of the strand formed by residues 273 - 279 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222J TYR* 3.2 6.9 - - - -
223J VAL* 3.0 35.9 + - + +
272J ALA* 1.3 75.8 - - - +
274J LEU* 1.3 76.4 + - - +
275J ILE* 3.6 0.6 + - - -
293J ALA 4.4 0.7 - - - -
294J PHE* 3.7 13.7 - - - -
295J CYS 3.4 34.5 - - - +
296J LEU* 3.8 10.5 - - + -
297O GLN* 4.7 1.8 - - - +
353O GLU* 3.3 29.8 - - - +
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Residues in contact with LEU 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J ARG* 6.0 0.2 - - - +
220J ALA* 3.9 10.1 - - + -
221J LEU 3.6 15.5 - - - +
222J TYR* 3.5 35.6 - - + +
272J ALA 4.3 0.2 - - - -
273J CYS* 1.3 82.5 - - - +
275J ILE* 1.3 63.3 + - - +
276J LYS 3.6 21.1 - - - +
277J GLU* 3.6 29.4 - - + +
293J ALA 4.5 3.6 - - - +
297O GLN* 5.6 0.4 + - - -
349O ARG* 6.1 0.2 - - - +
350O ARG 5.8 1.3 - - - +
351O GLY* 4.5 27.0 + - - +
352O GLU* 6.0 4.0 - - + -
353O GLU* 5.3 0.9 - - - +
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Residues in contact with ILE 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221J LEU* 2.9 48.0 + - + +
222J TYR* 4.1 4.9 - - - +
223J VAL* 3.5 35.7 - - + -
273J CYS 4.0 0.4 - - - +
274J LEU* 1.3 78.5 - - - +
276J LYS* 1.3 66.9 + - - +
290J PHE* 3.9 6.5 - - + -
292J SER* 2.5 34.2 + - - +
293J ALA 4.4 4.3 - - - +
294J PHE* 3.9 16.4 - - + -
309J THR* 4.6 2.7 - - + -
358J ILE* 4.0 35.0 - - + -
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Residues in contact with LYS 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191J LEU* 5.5 0.5 - - - +
192J PHE* 3.9 22.0 - - + -
219J ALA 4.6 0.2 - - - -
220J ALA* 3.3 3.5 - - - -
221J LEU* 2.8 46.1 + - + -
274J LEU* 3.6 5.9 - - - +
275J ILE* 1.3 82.2 - - - +
277J GLU* 1.3 74.8 + - - +
278J VAL* 4.2 8.6 - - + +
283J VAL* 5.7 3.1 - - - -
287J GLU* 2.8 40.1 + - - +
288J LEU* 4.8 6.7 - - - -
290J PHE* 3.7 37.1 - - + +
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Residues in contact with GLU 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J ARG* 3.2 35.6 + - - +
219J ALA 3.6 3.4 - - - +
220J ALA* 4.5 1.8 - - + +
274J LEU* 3.6 26.5 - - + +
276J LYS* 1.3 86.2 - - - +
278J VAL* 1.3 72.6 + - - +
279J ASP 4.2 1.0 + - - +
283J VAL* 4.9 2.6 - - - +
349O ARG* 3.5 35.3 + - - -
381O GLN* 4.2 8.5 - - - +
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Residues in contact with VAL 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J TRP* 5.3 0.7 - - + -
191J LEU* 4.9 2.0 - - + -
192J PHE* 4.0 29.8 - - + -
197J LEU* 4.2 11.4 - - + -
218J ARG* 3.5 10.6 - - - +
219J ALA* 2.9 45.2 + - + +
276J LYS* 4.2 11.0 - - + -
277J GLU* 1.3 83.3 - - - +
279J ASP* 1.3 59.0 + - - +
280J ILE* 3.5 18.6 + - + -
283J VAL* 3.9 28.9 - - + -
288J LEU* 4.9 2.2 - - + -
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Residues in contact with ASP 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217J ASP 3.9 5.6 - - - +
218J ARG* 5.1 7.2 - - + +
277J GLU* 4.2 1.2 - - - +
278J VAL* 1.3 70.9 - - - +
280J ILE* 1.3 60.5 + - - +
281J TYR* 3.0 29.3 - - - +
282J THR* 2.8 51.7 + - - +
283J VAL* 3.1 16.8 + - + +
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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