Contacts of the strand formed by residues 286 - 290 (chain K) in PDB entry 3STJ
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 286 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249K MET* 3.5 46.4 - - + -
253K ILE* 4.7 3.4 - - + -
257K PHE* 5.4 2.2 - - + -
259K LEU* 3.5 31.9 - - + -
261K VAL* 4.6 11.2 - - + -
263K ARG 5.2 2.2 - - - +
265K ALA 3.2 7.2 - - - +
266K PHE* 3.9 10.1 - - + -
284K GLY 4.3 7.4 - - - +
285K ASP* 1.3 77.6 - - - +
287K ILE* 1.3 68.1 + - - +
288K THR* 3.4 12.4 + - - +
318K LEU* 4.4 0.9 - - - -
319K LEU* 2.9 45.5 + - + +
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Residues in contact with ILE 287 (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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242K LEU* 4.6 2.0 - - + -
244K ILE* 4.6 10.1 - - + -
264K GLY* 3.3 6.6 - - - -
265K ALA* 2.8 43.0 + - + -
267K VAL* 3.7 28.7 - - + -
281K VAL* 5.1 2.0 - - + -
286K ILE* 1.3 70.9 - - - +
288K THR* 1.3 58.0 + - - +
289K SER 3.7 14.6 - - - +
295K LEU* 3.8 15.8 - - + +
301K LEU* 4.3 20.9 - - + -
316K LEU* 3.9 35.2 - - + -
317K GLY 3.5 16.4 - - - +
318K LEU* 4.4 11.4 - - + +
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Residues in contact with THR 288 (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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261K VAL* 3.4 42.3 - - + +
263K ARG 4.3 5.6 - - - +
286K ILE* 3.5 12.8 + - - +
287K ILE* 1.3 73.1 - - - +
289K SER* 1.4 60.9 + - - +
294K PRO* 3.3 7.8 - - + +
295K LEU* 2.8 34.3 + - - +
317K GLY 2.9 9.8 + - - -
318K LEU 4.7 0.9 - - - -
319K LEU* 4.3 10.4 + - - +
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Residues in contact with SER 289 (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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287K ILE* 3.7 8.6 - - - +
288K THR* 1.4 83.9 + - - +
290K LEU* 1.3 61.8 + - - +
292K GLY* 4.3 15.9 + - - -
293K LYS 3.4 9.2 + - - -
294K PRO* 3.7 15.6 - - - +
295K LEU* 4.0 5.2 - - - -
316K LEU* 3.7 5.2 - - - +
317K GLY* 3.0 40.4 + - - +
326K GLU* 5.2 1.1 - - - -
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Residues in contact with LEU 290 (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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289K SER* 1.3 74.7 - - - +
291K ASN* 1.3 70.7 + - - +
292K GLY 3.2 0.4 - - - -
293K LYS* 3.0 31.0 + - - +
295K LEU* 4.2 15.4 - - + +
301K LEU* 4.0 9.0 - - + -
304K ARG* 3.6 42.0 - - + +
305K ILE* 3.8 19.7 - - + -
308K THR* 5.9 0.7 - - - +
314K VAL* 3.7 31.4 - - + -
315K LYS 3.5 2.9 - - - +
316K LEU* 3.8 19.1 - - + -
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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