Contacts of the strand formed by residues 290 - 297 (chain K) 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 PHE 290 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192K PHE* 4.2 6.7 - + - -
221K LEU* 5.0 5.4 - - + -
275K ILE* 3.9 12.3 - - + -
276K LYS* 3.8 39.3 - - + +
287K GLU 3.6 15.7 - - - +
288K LEU* 3.4 17.5 - - - -
289K SER* 1.3 75.1 - - - +
291K THR* 1.3 67.7 + - - +
292K SER* 3.7 26.7 - - - -
358K ILE* 4.3 7.9 - - + -
359K SER* 3.1 24.0 - - - -
360K MET* 3.1 45.5 + - + +
361K LYS* 5.7 0.2 - - - +
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Residues in contact with THR 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379F LYS* 5.6 3.3 + - - -
290K PHE* 1.3 75.1 - - - +
292K SER* 1.3 68.5 + - - +
357K THR* 4.0 26.0 - - + +
358K ILE 3.8 0.9 - - - -
359K SER* 3.1 26.4 + - - +
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Residues in contact with SER 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274K LEU 5.0 0.2 + - - -
275K ILE* 2.6 39.4 + - - -
290K PHE* 3.7 11.9 - - - -
291K THR* 1.3 83.4 - - - +
293K ALA* 1.3 65.1 + - - +
357K THR* 4.2 2.5 - - - -
358K ILE* 2.9 38.9 + - - +
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Residues in contact with ALA 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353F GLU* 4.6 1.0 - - - +
355F TYR* 3.2 31.4 + - + -
273K CYS* 4.4 0.2 - - - -
274K LEU 4.4 5.5 - - - +
275K ILE* 4.3 4.9 - - - +
292K SER* 1.3 80.2 + - - +
294K PHE* 1.3 62.3 + - - +
356K GLY 3.4 10.1 - - - +
357K THR* 4.2 10.9 - - + +
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Residues in contact with PHE 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F TYR* 2.8 14.1 + - - -
223K VAL* 4.0 9.4 - - + -
273K CYS* 3.6 15.3 - - - -
275K ILE* 3.9 12.1 - - + -
293K ALA* 1.3 75.4 - - - +
295K CYS* 1.3 62.8 + - - +
296K LEU* 4.2 23.6 - - + -
307K LEU* 4.1 21.8 - - + -
354K ILE* 4.2 18.2 - - + -
355K TYR* 3.5 5.0 - - - -
356K GLY* 2.9 72.6 + - - +
357K THR 3.5 12.8 - - - -
358K ILE* 3.5 24.0 - - + -
374K VAL* 4.4 4.9 - - + -
375K ASP 3.8 5.2 - - - -
376K LEU* 4.7 4.5 - - + -
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Residues in contact with CYS 295 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295F CYS* 3.4 44.0 - - + -
297F GLN* 5.6 0.3 - - - +
353F GLU* 4.0 3.5 - - - +
355F TYR* 3.2 6.6 + - + -
271K ASN* 4.4 4.9 + - - +
273K CYS* 3.5 21.0 - - - +
294K PHE* 1.3 77.4 - - - +
296K LEU* 1.3 66.8 + - - +
297K GLN* 4.2 1.2 + - - -
353K GLU* 4.1 16.8 - - - -
354K ILE 3.2 10.3 - - - -
355K TYR* 3.6 25.8 - - + -
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Residues in contact with LEU 296 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223K VAL* 3.5 22.7 - - + +
224K VAL* 3.9 6.5 - - - +
225K ALA* 3.7 30.1 - - + +
270K THR* 3.8 12.6 - - + +
271K ASN* 3.3 24.7 - - - +
273K CYS* 3.9 11.4 - - + +
294K PHE* 4.2 19.3 - - + -
295K CYS* 1.3 84.0 - - - +
297K GLN* 1.3 64.3 + - - +
298K ILE* 3.6 2.4 + - - +
307K LEU* 4.1 14.4 - - + -
353K GLU* 3.4 3.3 - - - -
354K ILE* 2.9 39.8 + - + +
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Residues in contact with GLN 297 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271F ASN* 4.2 17.1 + - - +
272F ALA 3.2 25.9 + - - +
273F CYS* 4.4 1.4 - - - +
274F LEU 5.2 0.7 + - - -
295F CYS 5.6 0.3 - - - +
270K THR* 3.2 15.0 - - - -
271K ASN* 2.8 25.1 + - - +
295K CYS* 4.2 1.4 - - - -
296K LEU* 1.3 73.3 - - - +
298K ILE* 1.3 69.4 + - - +
299K GLN* 3.1 29.6 + - - +
351K GLY* 4.8 9.3 - - - +
352K GLU 4.0 7.0 - - - +
353K GLU* 3.5 22.9 - - + +
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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