Contacts of the helix formed by residues 286 - 292 (chain K) in PDB entry 1LWU
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 ASP 286 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285K ARG* 1.3 77.3 - - - +
287K TRP* 1.3 63.5 + - - +
288K ASN* 3.2 12.7 + - - +
289K THR* 2.6 45.6 + - - -
290K TYR* 3.0 18.4 + - - +
397K THR* 4.1 2.2 - - - -
398K PHE* 4.2 17.7 - - + -
399K ASP* 3.3 23.8 - - - +
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Residues in contact with TRP 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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286K ASP* 1.3 69.5 - - - +
288K ASN* 1.3 78.3 + - - +
290K TYR* 3.3 2.6 + - + +
291K LYS* 3.1 26.5 + - + +
354K GLU* 2.8 32.5 + - + -
357K GLY* 3.9 17.7 - - - -
358K TYR* 3.7 36.2 - + - -
395K PHE* 3.2 41.5 - + + -
397K THR* 3.4 36.2 + - + +
399K ASP* 2.8 15.2 + - - +
400K ARG* 3.3 49.4 - - + +
402K ASN* 3.8 8.7 - - - -
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Residues in contact with ASN 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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286K ASP* 3.2 12.2 + - - +
287K TRP* 1.3 90.3 - - - +
289K THR* 1.3 64.9 + - - +
291K LYS* 3.4 11.5 + - - +
292K ALA* 3.1 24.8 + - - +
354K GLU* 5.7 0.2 + - - -
399K ASP* 5.6 2.3 - - - +
400K ARG* 5.5 3.4 - - - +
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Residues in contact with THR 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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285K ARG* 3.2 39.0 + - + +
286K ASP* 2.6 33.7 + - - -
288K ASN* 1.3 72.5 - - - +
290K TYR* 1.3 58.4 + - - +
292K ALA* 3.4 3.9 + - - +
293K GLU 2.9 31.5 + - - +
294K PHE* 3.5 25.7 - - + -
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Residues in contact with TYR 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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283K PHE* 2.8 32.7 + - - +
285K ARG 3.2 26.7 - - - -
286K ASP 3.0 11.1 + - - +
287K TRP* 3.3 4.2 + - + +
289K THR* 1.3 76.0 - - - +
291K LYS* 1.3 57.8 + - - +
293K GLU 4.2 0.2 - - - -
294K PHE* 3.5 20.9 - + - -
313K TRP* 3.0 46.1 + + - +
315K GLY* 3.7 0.5 - - - -
316K THR* 2.8 25.7 + - - +
395K PHE* 3.8 18.6 - + + -
397K THR* 3.9 10.1 - - + -
421K GLY* 3.1 27.9 + - - -
433K ASN* 3.4 36.1 - - - +
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Residues in contact with LYS 291 (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 TRP* 3.1 21.2 + - + +
288K ASN* 3.5 11.8 - - - +
290K TYR* 1.3 79.5 - - - +
292K ALA* 1.3 62.1 + - + +
315K GLY* 3.3 5.4 - - - -
316K THR* 3.9 8.5 - - - +
317K LYS* 3.3 40.4 + - + +
318K THR* 4.5 0.9 + - - -
354K GLU* 3.1 34.4 + - - +
358K TYR* 3.4 28.0 - - + +
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Residues in contact with ALA 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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288K ASN 3.1 14.1 + - - +
289K THR* 3.4 4.9 + - - +
291K LYS* 1.3 83.4 - - + +
293K GLU* 1.3 70.6 - - - +
315K GLY* 3.6 3.4 - - - -
318K THR* 5.1 3.8 + - - -
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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