Contacts of the strand formed by residues 290 - 297 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G PHE* 4.2 9.0 - + - -
221G LEU* 4.7 6.5 - - + -
275G ILE* 3.8 12.8 - - + -
276G LYS* 4.0 38.1 - - + +
287G GLU 3.7 13.5 - - - +
288G LEU* 3.6 20.2 - - - -
289G SER* 1.3 75.1 - - - +
291G THR* 1.3 66.1 + - - +
292G SER* 3.6 28.7 - - - -
358G ILE* 4.1 9.6 - - + -
359G SER* 3.0 5.2 - - - -
360G MET* 3.0 69.2 + - + +
361G LYS* 5.6 0.2 - - - +
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Residues in contact with THR 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B LYS* 5.3 6.2 + - - -
290G PHE* 1.3 75.6 - - - +
292G SER* 1.3 67.4 + - - +
357G THR* 4.0 26.0 - - + +
358G ILE 3.8 1.1 - - - +
359G SER* 3.2 25.3 + - - +
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Residues in contact with SER 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G LEU 4.9 0.2 + - - -
275G ILE* 2.5 42.8 + - - +
290G PHE* 3.6 14.4 - - - -
291G THR* 1.3 83.3 - - - +
293G ALA* 1.3 65.3 + - - +
357G THR* 4.3 2.5 - - - -
358G ILE* 3.0 35.2 + - - +
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Residues in contact with ALA 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B GLU* 4.6 0.9 - - - +
355B TYR* 3.4 31.6 + - + -
273G CYS* 4.4 2.4 - - - -
274G LEU 4.5 2.8 - - - +
275G ILE* 4.1 4.9 - - - +
292G SER* 1.3 81.9 + - - +
294G PHE* 1.3 62.1 + - - +
356G GLY 3.4 10.1 - - - +
357G THR* 4.2 10.5 - - + +
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Residues in contact with PHE 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B TYR* 3.0 13.3 - - - -
223G VAL* 4.1 7.2 - - + -
273G CYS* 3.4 15.9 - - - -
275G ILE* 3.9 11.4 - - + -
293G ALA* 1.3 77.1 - - - +
295G CYS* 1.3 62.2 + - - +
296G LEU* 4.2 24.2 - - + -
307G LEU* 4.0 22.4 - - + -
354G ILE* 4.2 18.4 - - + -
355G TYR* 3.4 4.7 - - - -
356G GLY* 2.8 76.4 + - - +
357G THR 3.4 12.8 - - - -
358G ILE* 3.5 21.5 - - + -
374G VAL* 4.4 6.1 - - + -
375G ASP 3.9 5.6 - - - -
376G LEU* 4.7 5.2 - - + -
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Residues in contact with CYS 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B CYS* 3.4 45.1 - - + -
353B GLU* 4.1 3.3 - - - +
355B TYR* 3.2 7.4 + - + -
271G ASN* 4.4 3.8 + - - +
272G ALA 5.2 0.3 - - - +
273G CYS* 3.3 22.8 - - - +
294G PHE* 1.3 75.1 - - - +
296G LEU* 1.3 67.5 + - - +
297G GLN* 4.4 0.8 + - - -
353G GLU* 4.1 15.3 - - - -
354G ILE 3.2 9.9 - - - -
355G TYR* 3.6 27.1 - - + -
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Residues in contact with LEU 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G VAL* 3.5 21.3 - - + +
224G VAL* 3.8 6.5 - - - +
225G ALA* 3.8 29.4 - - + +
270G THR* 3.8 14.1 - - + +
271G ASN* 3.4 24.5 - - - +
273G CYS* 3.8 11.7 - - + +
294G PHE* 4.2 17.7 - - + -
295G CYS* 1.3 83.3 - - - +
297G GLN* 1.3 62.7 + - - +
298G ILE* 3.6 2.9 + - - +
307G LEU* 4.1 14.4 - - + -
353G GLU* 3.3 4.8 - - - -
354G ILE* 2.9 44.2 + - + +
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Residues in contact with GLN 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ASN* 4.4 17.1 + - - +
272B ALA 3.2 24.7 + - - +
273B CYS* 4.3 1.7 - - - +
274B LEU 5.1 0.5 + - - -
295B CYS 5.5 0.7 - - - +
270G THR* 3.2 15.3 - - - -
271G ASN* 2.9 20.8 + - - +
295G CYS* 4.3 1.2 - - - -
296G LEU* 1.3 72.0 - - - +
298G ILE* 1.3 65.7 + - - +
299G GLN* 2.8 39.9 + - - +
351G GLY* 4.8 9.3 - - - +
352G GLU 3.9 8.3 - - - +
353G GLU* 3.5 23.3 - - + +
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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