Contacts of the strand formed by residues 288 - 292 (chain D) in PDB entry 4RYD
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D HIS 3.2 17.0 + - - +
249D ILE* 3.5 12.5 - - + -
250D TYR* 2.8 30.1 + - - +
282D ARG* 3.7 27.8 - - - +
286D GLY 3.9 0.2 - - - +
287D SER* 1.3 73.0 - - - +
289D PHE* 1.3 61.3 + - - +
290D VAL* 4.1 11.0 - - + -
315D LEU* 3.7 22.9 - - + -
378D ILE* 4.0 23.8 - - + -
382D LEU* 4.8 3.8 - - + -
389D THR 4.5 0.4 - - - +
390D TRP* 3.7 25.1 - - + +
393D MET* 4.1 18.8 - - + -
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Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D LEU* 3.7 42.0 - - + -
250D TYR* 3.7 34.3 - + + -
273D ALA 4.3 1.3 - - - -
274D PHE* 3.6 44.2 - + + -
277D GLY* 4.3 9.0 - - - -
278D VAL* 4.2 7.6 - - + -
287D SER* 3.7 27.5 + - - -
288D ILE* 1.3 72.8 - - - +
290D VAL* 1.3 56.5 + - - +
291D TRP* 4.8 3.8 - + + -
313D TYR 3.7 21.4 + - - +
314D THR* 3.2 15.6 - - + -
315D LEU* 2.8 35.4 + - - +
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Residues in contact with VAL 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ILE* 3.9 18.6 - - + -
250D TYR 2.8 15.6 + - - +
251D SER* 3.6 5.5 - - - -
252D ALA* 2.9 29.3 + - - +
288D ILE* 4.1 4.7 - - + -
289D PHE* 1.3 75.2 - - - +
291D TRP* 1.3 64.5 + - - +
315D LEU* 3.7 6.3 - - + +
317D ILE* 4.0 20.9 - - + -
371D ALA* 3.4 30.2 - - + +
374D ALA* 4.0 6.3 - - + -
375D ALA* 4.1 5.6 - - + +
378D ILE* 3.8 25.8 - - + -
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Residues in contact with TRP 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D LEU* 3.9 13.5 - - + -
250D TYR* 6.5 0.4 - - + -
252D ALA* 3.6 28.0 - - + -
254D TRP* 2.8 50.5 + + - -
255D GLY* 4.5 0.4 - - - -
274D PHE* 3.5 24.7 - + - -
289D PHE* 4.0 5.6 + + + -
290D VAL* 1.3 77.9 - - - +
292D ALA* 1.3 81.2 + - - +
308D TYR* 3.4 43.7 - + + +
309D THR* 3.7 20.0 - - + -
314D THR* 3.7 29.2 - - + +
315D LEU 3.0 9.1 + - - +
316D SER* 3.5 2.5 - - - -
317D ILE* 2.8 31.4 + - - +
371D ALA* 3.9 4.5 - - - -
5K 00S 4.0 2.3 + - - -
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Residues in contact with ALA 292 (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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252D ALA 3.1 15.3 + - - +
253D SER* 3.9 7.9 - - - -
291D TRP* 1.3 78.5 - - - +
293D SER* 1.3 58.4 + - - +
294D GLY 3.3 0.2 - - - -
309D THR* 3.4 0.4 - - - +
317D ILE 3.9 3.6 - - - -
367D THR* 3.3 29.6 - - - +
371D ALA* 3.7 11.3 - - + +
5K 00S 2.9 44.2 + - + -
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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
------------------------------------------------------------
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