Contacts of the strand formed by residues 273 - 279 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222D TYR* 3.3 6.1 - - - -
223D VAL* 2.9 37.7 + - + +
272D ALA* 1.3 75.4 - - - +
274D LEU* 1.3 76.9 + - - +
275D ILE 3.6 0.2 + - - -
293D ALA 4.4 0.4 - - - -
294D PHE* 3.7 13.0 - - - -
295D CYS 3.3 34.8 - - - +
296D LEU* 3.9 9.2 - - + +
297I GLN* 4.6 0.2 - - - -
353I GLU* 3.1 33.9 - - - +
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Residues in contact with LEU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D ALA* 3.9 10.1 - - + -
221D LEU 3.7 14.4 - - - +
222D TYR* 3.6 34.4 - - + +
273D CYS* 1.3 88.8 - - - +
275D ILE* 1.3 61.4 + - - +
276D LYS* 3.9 20.4 - - - +
277D GLU* 3.8 31.0 - - + +
292D SER* 5.0 0.2 + - - -
293D ALA 4.4 3.8 - - - +
297I GLN* 5.5 0.4 + - - -
350I ARG 6.0 0.2 - - - +
351I GLY* 4.3 27.5 + - - +
352I GLU* 5.2 5.6 - - + +
353I GLU* 4.6 3.9 + - - +
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Residues in contact with ILE 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU* 2.8 49.7 + - + +
222D TYR 4.2 3.6 - - - +
223D VAL* 3.5 35.2 - - + -
273D CYS 4.0 0.2 - - - +
274D LEU* 1.3 80.0 - - - +
276D LYS* 1.3 65.5 + - - +
290D PHE* 3.8 6.9 - - + -
292D SER* 2.8 35.2 + - - +
293D ALA 4.3 4.5 - - - +
294D PHE* 3.9 16.4 - - + -
309D THR* 4.6 1.8 - - + -
358D ILE* 3.9 35.2 - - + -
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Residues in contact with LYS 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D LEU* 5.3 0.3 - - - +
192D PHE* 3.9 23.8 - - + -
219D ALA 4.0 0.5 - - - +
220D ALA* 3.2 4.0 - - - -
221D LEU* 2.8 44.8 + - + +
274D LEU* 3.8 6.6 - - - +
275D ILE* 1.3 81.1 - - - +
277D GLU* 1.3 74.3 + - - +
278D VAL* 4.2 7.6 - - + +
283D VAL* 5.7 3.1 - - - -
287D GLU* 2.8 40.4 + - - +
288D LEU* 4.7 7.2 - - - -
290D PHE* 3.8 35.7 - - + +
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Residues in contact with GLU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D ARG* 3.5 34.4 + - - +
219D ALA 3.6 2.9 - - - +
220D ALA* 4.4 2.0 - - + +
274D LEU* 3.8 27.4 - - + +
276D LYS* 1.3 86.8 - - - +
278D VAL* 1.3 68.8 + - - +
279D ASP 4.2 0.6 + - - +
283D VAL* 4.9 2.6 - - - +
349I ARG* 3.3 38.8 + - - -
352I GLU* 5.2 1.4 - - - +
381I GLN* 4.3 8.0 - - - +
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Residues in contact with VAL 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D TRP* 5.3 1.1 - - + -
191D LEU* 4.8 0.4 - - + -
192D PHE* 3.9 30.3 - - + -
197D LEU* 4.2 11.7 - - + -
218D ARG* 3.5 7.8 - - - +
219D ALA* 2.8 43.2 + - + +
276D LYS* 4.2 12.1 - - + +
277D GLU* 1.3 84.4 - - - +
279D ASP* 1.3 60.0 + - - +
280D ILE* 3.4 21.6 + - + -
283D VAL* 3.8 28.9 - - + -
288D LEU* 4.9 1.8 - - + -
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Residues in contact with ASP 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D ASP 3.9 4.7 - - - +
218D ARG* 5.2 6.7 - - + +
277D GLU* 4.2 0.8 - - - +
278D VAL* 1.3 73.1 - - - +
280D ILE* 1.3 57.3 + - - +
281D TYR* 3.0 30.7 - - - +
282D THR* 2.8 52.8 + - - +
283D VAL* 3.0 17.1 + - + +
381I GLN* 6.0 1.8 - - - +
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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