Contacts of the strand formed by residues 288 - 293 (chain G) in PDB entry 1P8J
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 ILE 288 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248G HIS 3.2 12.4 + - - +
249G ILE* 3.5 5.7 - - + +
250G TYR* 2.8 30.7 + - - +
282G ARG* 3.8 24.5 - - - +
286G GLY 4.0 0.4 - - - +
287G SER* 1.3 77.9 - - - +
289G PHE* 1.3 62.1 + - - +
290G VAL* 4.2 8.5 - - + -
315G LEU* 3.7 24.7 - - + -
378G ILE* 4.1 19.1 - - + -
382G LEU* 4.1 16.4 - - + -
389G THR 5.2 0.7 - - - +
390G TRP* 4.4 12.6 - - - -
393G MET* 3.7 36.3 - - + -
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Residues in contact with PHE 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G LEU* 3.6 40.8 - - + -
250G TYR* 3.7 29.6 - + + -
273G ALA 4.5 3.8 - - - -
274G PHE* 3.7 42.6 - + + -
277G GLY* 4.4 8.3 - - - -
278G VAL* 4.4 4.5 - - + -
287G SER* 3.6 30.0 + - - -
288G ILE* 1.3 74.3 - - - +
290G VAL* 1.3 56.1 + - - +
291G TRP* 4.5 4.9 - + + -
313G TYR* 3.5 23.8 + - + +
314G THR* 3.2 16.8 - - + -
315G LEU* 2.8 34.3 + - - +
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Residues in contact with VAL 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G ILE* 4.0 22.0 - - + -
250G TYR 2.8 13.6 + - - +
251G SER* 3.5 4.6 + - - +
252G ALA* 2.8 29.3 + - - +
288G ILE* 4.2 5.2 - - + -
289G PHE* 1.3 75.5 - - - +
291G TRP* 1.3 64.1 + - - +
315G LEU* 3.7 5.8 - - + +
317G ILE* 4.0 22.0 - - + -
371G ALA* 3.4 30.2 - - - +
374G ALA* 4.0 5.2 - - + -
375G ALA* 4.2 5.4 - - + -
378G ILE* 3.7 27.1 - - + -
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Residues in contact with TRP 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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152G LEU* 5.5 0.2 - - + -
240G LEU* 3.9 13.0 - - + -
250G TYR* 6.5 0.2 - - + -
252G ALA* 3.5 35.6 + - + -
254G TRP* 2.6 47.2 + + - -
274G PHE* 3.5 25.6 - + - -
289G PHE* 4.0 7.2 + + + -
290G VAL* 1.3 76.9 - - - +
292G ALA* 1.3 78.7 + - - +
308G TYR* 3.5 43.2 - + + +
309G THR* 3.8 17.5 - - + -
314G THR* 3.7 28.7 - - + +
315G LEU 2.9 11.5 + - - +
316G SER* 3.5 2.0 - - - -
317G ILE* 2.8 35.7 + - - +
371G ALA* 3.9 5.4 - - - -
805Q AR7 4.1 0.4 + - - -
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Residues in contact with ALA 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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252G ALA 3.2 7.1 + - - -
253G SER* 3.8 24.5 - - - +
291G TRP* 1.3 72.7 - - - +
293G SER* 1.3 60.4 + - - +
309G THR* 3.3 5.8 - - - +
317G ILE 3.9 5.2 - - - -
367G THR* 3.4 34.3 - - - +
368G SER 4.2 0.9 - - - +
371G ALA* 3.7 8.2 - - + +
805Q AR7 2.8 31.2 + - - -
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Residues in contact with SER 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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291G TRP 3.6 1.0 + - - -
292G ALA* 1.3 72.5 - - - +
294G GLY* 1.3 58.9 + - - +
303G CYS* 3.4 27.6 - - - +
306G ASP* 4.5 1.4 - - - +
309G THR* 3.6 12.5 + - - +
316G SER* 3.3 17.3 - - - -
317G ILE 3.0 19.0 + - - -
318G SER* 2.9 28.3 + - - -
331G GLU* 3.8 10.8 + - - +
336G THR* 4.2 6.5 - - - -
367G THR* 3.9 7.4 - - - +
805Q AR7 3.8 3.9 + - - -
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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