Contacts of the strand formed by residues 291 - 296 (chain K) in PDB entry 3IXS
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 TYR 291 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237K MET* 5.3 1.8 - - + -
242K SER* 4.8 2.6 + - - -
256K VAL* 6.1 0.2 - - - +
260K SER* 3.1 38.5 + - - +
263K LEU* 3.8 24.1 + - + -
264K ALA* 3.7 24.0 - - - -
267K LEU* 3.3 29.6 - - - +
288K GLU 4.3 3.3 - - - +
289K LYS* 3.3 1.8 - - - -
290K GLN* 1.3 99.7 + - + +
292K THR* 1.3 65.7 + - - +
293K ILE* 4.1 2.9 + - + +
329K TYR* 3.7 27.8 - + + -
330K ALA 3.5 5.2 - - - +
331K PRO* 3.7 35.9 - - + +
332K THR* 3.2 7.7 + - - -
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Residues in contact with THR 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291K TYR* 1.3 72.7 - - - +
293K ILE* 1.3 63.7 + - - +
294K TYR* 3.4 37.1 - - + +
304K VAL* 4.0 24.9 - - + -
329K TYR* 3.3 4.5 - - - +
330K ALA* 2.9 35.5 + - - -
331K PRO 5.5 0.4 - - - -
332K THR* 3.3 24.9 + - - +
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Residues in contact with ILE 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230K PHE* 4.1 21.1 - - + -
256K VAL* 3.5 43.2 - - + +
259K LEU* 3.8 11.9 - - + -
260K SER* 3.6 23.1 - - - +
263K LEU* 4.6 3.4 - - + -
291K TYR 4.5 3.6 - - - +
292K THR* 1.3 81.2 - - - +
294K TYR* 1.3 64.8 + - - +
304K VAL* 3.7 5.0 - - - +
305K LEU* 2.9 47.1 + - + +
327K LEU* 4.1 12.6 - - + -
328K TYR 3.2 9.9 - - - +
329K TYR* 4.4 4.9 - - + -
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Residues in contact with TYR 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233K HIS* 3.8 24.0 - + - -
236K LEU* 3.6 20.0 - - + +
292K THR* 3.4 35.9 - - + +
293K ILE* 1.3 75.4 - - - +
295K ILE* 1.3 63.0 + - - +
302K PHE* 3.8 44.0 - + + -
303K THR 3.1 7.4 - - - +
304K VAL* 3.8 26.0 - - + -
305K LEU* 4.1 3.6 - - - -
327K LEU* 3.5 9.9 - - - +
328K TYR* 2.8 45.3 + - + +
330K ALA* 4.1 10.7 - - + +
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Residues in contact with ILE 295 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294K TYR* 1.3 73.6 - - - +
296K ALA* 1.3 76.3 + - - +
297K THR* 3.4 9.2 + - + +
301K GLN 3.6 0.2 - - - +
302K PHE* 4.4 2.0 - - - -
303K THR* 2.9 33.5 + - - +
305K LEU* 4.1 8.6 - - + +
314K VAL* 3.6 19.1 - - + -
318K TYR* 3.5 46.9 - - + +
319K TRP* 4.0 24.9 - - + -
325K MET* 4.6 0.9 - - + -
326K GLU 3.9 7.6 - - - +
327K LEU* 3.4 24.5 - - + -
328K TYR* 5.1 0.2 - - - -
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Residues in contact with ALA 296 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294K TYR 4.3 0.4 - - - -
295K ILE* 1.3 79.4 - - - +
297K THR* 1.3 63.6 + - - +
300K GLY* 6.1 1.8 - - - -
301K GLN 3.3 6.3 - - - +
302K PHE* 3.8 25.6 - - + -
319K TRP* 4.8 9.5 - - + -
326K GLU 5.1 2.0 + - - -
328K TYR* 3.9 23.9 - - + +
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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