Contacts of the helix formed by residues 286 - 292 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B ARG* 1.3 77.5 - - - +
287B TRP* 1.3 59.1 + - - +
288B ASN* 3.2 12.7 + - - +
289B THR* 2.6 45.5 + - - -
290B TYR* 3.0 21.1 + - - -
397B THR* 4.0 2.2 - - - -
398B PHE* 4.2 17.8 - - + -
399B ASP* 3.3 24.5 - - - +
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Residues in contact with TRP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B ASP* 1.3 71.7 - - - +
288B ASN* 1.3 75.6 + - - +
290B TYR* 3.4 2.4 + - + +
291B LYS* 3.1 23.7 + - + +
354B GLU* 2.8 32.1 + - + -
357B GLY* 4.0 17.7 - - - -
358B TYR* 3.7 35.3 - + - -
395B PHE* 3.2 41.7 - + + -
396B SER* 4.5 0.2 - - - -
397B THR* 3.3 35.1 + - + +
399B ASP* 2.8 16.2 + - - +
400B ARG* 3.3 49.0 - - + +
402B ASN* 3.8 8.7 - - - -
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Residues in contact with ASN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B ASP* 3.2 11.4 + - - +
287B TRP* 1.3 87.6 - - - +
289B THR* 1.3 59.4 + - - +
291B LYS* 3.3 13.1 + - - +
292B ALA* 3.1 29.2 + - - +
354B GLU* 5.7 0.4 + - - -
399B ASP* 5.2 2.9 + - - +
400B ARG* 5.5 3.5 - - - +
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ARG* 3.2 38.6 + - + +
286B ASP* 2.6 35.6 + - - -
288B ASN* 1.3 75.0 - - - +
290B TYR* 1.3 57.2 + - - +
292B ALA* 4.5 4.5 - - - +
293B GLU 2.9 31.7 + - - +
294B PHE* 3.5 24.9 - - + -
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Residues in contact with TYR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B PHE* 2.7 34.9 + - - +
285B ARG 3.1 27.1 - - - -
286B ASP 3.0 11.7 + - - +
287B TRP* 3.4 4.0 + - + +
289B THR* 1.3 76.7 - - - +
291B LYS* 1.3 58.1 + - - +
293B GLU 4.2 0.2 - - - -
294B PHE* 3.5 21.3 - + - -
313B TRP* 3.0 43.9 + + - +
316B THR* 2.8 25.7 + - - +
395B PHE* 3.7 19.7 - + + -
397B THR* 3.9 11.0 - - + -
421B GLY 3.2 26.9 + - - -
433B ASN* 3.4 35.9 - - - +
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B TRP* 3.1 21.1 + - + +
288B ASN* 3.5 12.4 - - - +
289B THR 3.1 0.4 - - - -
290B TYR* 1.3 80.0 - - - +
292B ALA* 1.3 62.8 + - - +
315B GLY* 3.3 5.4 - - - -
316B THR* 3.9 8.5 - - - +
317B LYS* 3.3 42.6 + - + +
318B THR* 4.5 0.9 + - - -
354B GLU* 3.1 33.9 + - - +
358B TYR* 3.3 27.1 - - + +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B ASN 3.1 17.5 + - - +
289B THR* 4.0 4.7 - - - +
291B LYS* 1.3 80.4 - - + +
293B GLU* 1.3 72.2 + - - +
315B GLY* 3.6 3.6 - - - -
318B THR* 5.0 4.0 + - - -
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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