Contacts of the strand formed by residues 290 - 295 (chain Y) in PDB entry 1IRA
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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226Y LEU* 3.6 19.7 - - + -
240Y TRP* 3.4 21.0 - + + -
241Y LYS 3.7 4.3 - - - -
242Y TRP* 3.4 41.1 - + + -
247Y ILE* 5.2 0.2 - - + -
254Y LEU* 4.4 11.2 - - + -
276Y LEU* 3.4 28.0 - - + -
278Y ILE* 3.8 17.5 - - + -
285Y PHE* 4.0 22.4 - + + -
288Y HIS 4.7 1.6 - - - -
289Y PRO* 1.3 70.8 - - - +
291Y THR* 1.3 59.7 + - - +
304Y TYR* 3.0 4.0 - - - -
305Y ILE* 2.9 33.6 + - + +
307Y LEU* 3.7 32.8 - - + -
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Residues in contact with THR 291 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240Y TRP* 3.3 6.0 - - - -
241Y LYS* 2.7 46.9 + - - +
243Y ASN 5.9 0.3 + - - -
289Y PRO* 3.8 12.0 + - - +
290Y PHE* 1.3 76.0 - - - +
292Y CYS* 1.3 64.4 + - - +
293Y PHE* 3.6 32.5 - - + -
302Y ALA* 4.2 7.9 - - + -
303Y ALA 3.5 15.9 - - - +
304Y TYR* 4.0 10.1 - - + +
402Y NAG 5.7 3.8 - - - +
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Residues in contact with CYS 292 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Y ILE* 3.2 21.1 - - + +
211Y PRO* 4.4 2.7 - - + -
228Y CYS* 2.0 53.4 - - + -
230Y VAL* 4.6 3.1 - - - -
238Y ALA* 5.1 1.3 - - - -
239Y TYR 3.4 17.0 - - - -
240Y TRP* 3.8 15.8 - - + -
274Y THR* 5.2 0.7 - - - -
291Y THR* 1.3 73.0 - - - +
293Y PHE* 1.3 67.9 + - - +
302Y ALA* 3.4 4.5 - - - +
303Y ALA 2.8 23.2 + - - +
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Residues in contact with PHE 293 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237Y ILE 4.0 0.4 - - - -
238Y ALA* 3.1 4.2 - - - +
239Y TYR* 2.8 69.2 + - + +
241Y LYS* 3.5 44.0 - - + -
291Y THR* 3.6 28.5 - - + -
292Y CYS* 1.3 78.9 - - - +
294Y ALA* 1.3 60.1 + - - +
295Y LYS* 5.9 2.0 - - + -
300Y ILE* 4.4 26.5 - - + -
301Y ASP 3.4 10.5 - - - -
302Y ALA* 3.7 15.3 - - + -
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Residues in contact with ALA 294 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206Y PRO* 3.6 24.8 - - + +
208Y ILE* 4.1 11.4 - - + -
230Y VAL* 3.9 27.4 - - + -
236Y ASP* 6.0 0.4 - - + -
237Y ILE 2.9 8.7 - - - +
238Y ALA* 4.6 1.1 - - + -
293Y PHE* 1.3 76.1 - - - +
295Y LYS* 1.3 63.7 + - - +
300Y ILE* 3.2 1.6 - - - +
301Y ASP* 2.8 33.1 + - + +
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Residues in contact with LYS 295 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X ILE 3.5 25.1 + - - +
52X GLU* 4.5 10.9 - - - +
53X PRO* 4.6 7.0 - - + -
90X GLU* 5.6 1.8 + - - -
206Y PRO* 3.6 6.4 - - - +
236Y ASP* 3.8 3.1 - - - +
237Y ILE* 2.8 57.0 + - + +
239Y TYR* 3.5 34.5 + - + +
293Y PHE* 5.9 2.0 - - + -
294Y ALA* 1.3 76.7 - - - +
296Y ASN* 1.3 69.1 - - - +
299Y GLY 3.5 6.5 - - - -
300Y ILE* 3.4 29.6 - - + -
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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