Contacts of the strand formed by residues 290 - 297 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192I PHE* 4.2 7.9 - + - -
221I LEU* 4.8 5.2 - - + -
275I ILE* 3.9 10.8 - - + -
276I LYS* 3.8 37.9 - - + +
287I GLU 3.7 16.6 - - - +
288I LEU* 3.5 17.3 - - - -
289I SER* 1.3 75.3 - - - +
291I THR* 1.3 67.2 + - - +
292I SER* 3.6 27.8 - - - -
358I ILE* 4.1 9.9 - - + -
359I SER* 3.0 24.3 - - - -
360I MET* 3.1 47.0 + - + +
361I LYS* 5.7 0.2 - - - +
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Residues in contact with THR 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D LYS* 5.7 3.1 + - - -
290I PHE* 1.3 76.8 - - - +
292I SER* 1.3 66.4 + - - +
357I THR* 4.0 25.4 - - + +
358I ILE 3.9 0.7 - - - +
359I SER* 3.1 26.9 + - - +
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Residues in contact with SER 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I LEU 5.0 0.2 + - - -
275I ILE* 2.5 40.0 + - - +
276I LYS* 5.7 0.2 - - - +
290I PHE* 3.6 15.5 - - - -
291I THR* 1.3 83.1 - - - +
293I ALA* 1.3 67.1 + - - +
357I THR* 3.4 2.0 - - - -
358I ILE* 2.9 37.5 + - - +
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Residues in contact with ALA 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D GLU* 4.7 0.5 - - - +
355D TYR* 3.4 30.7 + - + +
273I CYS* 4.4 2.8 - - - -
274I LEU 4.5 2.9 - - - +
275I ILE* 4.4 4.5 - - - +
292I SER* 1.3 79.7 + - - +
294I PHE* 1.3 61.5 + - - +
356I GLY 3.3 9.9 - - - +
357I THR* 4.0 11.1 - - + +
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Residues in contact with PHE 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D TYR* 3.1 11.8 - - - -
223I VAL* 4.1 8.7 - - + -
273I CYS* 3.6 16.4 - - - -
275I ILE* 4.0 10.8 - - + -
293I ALA* 1.3 76.3 - - - +
295I CYS* 1.3 64.0 + - - +
296I LEU* 4.2 20.4 - - + -
307I LEU* 4.0 25.1 - - + -
354I ILE* 4.2 15.0 - - + -
355I TYR* 3.4 9.3 - - - +
356I GLY* 2.7 76.6 + - - +
357I THR 3.4 13.5 - - - -
358I ILE* 3.5 22.9 - - + -
374I VAL* 4.3 5.6 - - + -
375I ASP 3.8 6.3 - - - -
376I LEU* 4.7 4.3 - - + -
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Residues in contact with CYS 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D CYS* 3.4 45.1 - - + -
353D GLU* 4.2 4.2 - - - +
355D TYR* 3.3 7.1 + - + -
271I ASN* 4.6 3.3 + - - +
272I ALA 5.1 0.5 - - - +
273I CYS* 3.3 23.9 - - - +
294I PHE* 1.3 76.9 - - - +
296I LEU* 1.3 68.2 + - - +
297I GLN* 4.2 1.0 + - - -
353I GLU* 4.1 15.0 - - - -
354I ILE 3.2 9.0 - - - -
355I TYR* 3.6 24.9 - - + -
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Residues in contact with LEU 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I VAL* 3.5 22.4 - - + +
224I VAL* 3.8 6.3 - - - +
225I ALA* 3.6 31.2 - - + +
270I THR* 3.9 13.2 - - + +
271I ASN* 3.4 24.2 - - - +
273I CYS* 3.8 11.4 - - + +
294I PHE* 4.2 17.7 - - + -
295I CYS* 1.3 85.2 - - - +
297I GLN* 1.3 62.3 + - - +
298I ILE* 3.7 2.4 + - - +
307I LEU* 4.2 13.5 - - + -
353I GLU* 3.3 5.2 - - - -
354I ILE* 2.8 46.9 + - + +
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Residues in contact with GLN 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D ASN* 4.2 20.6 + - - +
272D ALA 3.3 22.3 + - - +
273D CYS* 4.6 1.0 - - - +
274D LEU 5.5 0.3 + - - -
295D CYS 5.7 0.2 - - - +
270I THR* 3.3 21.4 - - - -
271I ASN* 2.8 25.9 + - - +
295I CYS* 4.2 1.6 - - - -
296I LEU* 1.3 72.9 - - - +
298I ILE* 1.3 69.1 + - - +
299I GLN* 3.3 22.0 + - - +
351I GLY* 4.8 9.4 - - - +
352I GLU 3.9 7.6 - - - +
353I GLU* 3.5 20.7 - - + +
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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