Contacts of the helix formed by residues 286 - 292 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285E ARG* 1.3 77.2 - - - +
287E TRP* 1.3 59.8 + - - +
288E ASN* 3.2 13.0 + - - +
289E THR* 2.6 45.5 + - - -
290E TYR* 3.0 22.0 + - - +
397E THR* 4.0 2.2 - - - -
398E PHE* 4.2 17.1 - - + -
399E ASP* 3.3 24.5 - - - +
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Residues in contact with TRP 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ASP* 1.3 69.9 - - - +
288E ASN* 1.3 77.3 + - - +
290E TYR* 3.4 2.4 + - + +
291E LYS* 3.1 23.5 + - + +
354E GLU* 2.8 33.2 + - + -
357E GLY* 4.0 17.3 - - - -
358E TYR* 3.7 34.6 - + - -
395E PHE* 3.3 41.5 - + + -
396E SER* 4.5 0.2 - - - -
397E THR* 3.3 34.9 + - + +
399E ASP* 2.8 16.4 + - - +
400E ARG* 3.3 48.4 - - + +
402E ASN* 3.8 8.7 - - - -
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Residues in contact with ASN 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E ASP* 3.2 11.9 + - - +
287E TRP* 1.3 88.7 - - - +
289E THR* 1.3 59.0 + - - +
291E LYS* 3.3 13.0 + - - +
292E ALA* 3.1 29.5 + - - +
354E GLU* 5.7 0.4 + - - -
399E ASP* 5.2 2.1 + - - +
400E ARG* 5.5 3.1 - - - +
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Residues in contact with THR 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E ARG* 3.2 39.5 + - + +
286E ASP* 2.6 35.3 + - - -
288E ASN* 1.3 71.5 - - - +
290E TYR* 1.3 60.3 + - - +
292E ALA* 4.6 3.6 - - - -
293E GLU 2.9 30.7 + - - +
294E PHE* 3.5 25.3 - - + -
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Residues in contact with TYR 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E PHE* 2.7 34.3 + - - +
285E ARG 3.2 26.9 - - - -
286E ASP 3.0 10.9 + - - +
287E TRP* 3.4 4.2 + - + +
289E THR* 1.3 77.7 - - - +
291E LYS* 1.3 58.4 + - - +
294E PHE* 3.5 20.4 - + - -
313E TRP* 3.0 44.9 + + - +
315E GLY* 3.7 0.7 - - - -
316E THR* 2.8 24.6 + - - +
395E PHE* 3.7 19.3 - + + -
397E THR* 3.9 10.8 - - + -
421E GLY 3.2 27.3 + - - -
433E ASN* 3.4 35.9 - - - +
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Residues in contact with LYS 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287E TRP* 3.1 21.3 + - + +
288E ASN* 3.5 11.6 - - - +
289E THR 3.1 0.2 - - - -
290E TYR* 1.3 78.9 - - - +
292E ALA* 1.3 61.8 + - - +
315E GLY* 3.3 5.5 - - - -
316E THR* 3.9 8.7 - - - +
317E LYS* 3.3 40.1 + - + +
318E THR* 4.5 0.7 + - - -
354E GLU* 3.1 33.8 + - - +
358E TYR* 3.4 28.0 - - + +
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Residues in contact with ALA 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E ASN 3.1 17.8 + - - +
289E THR* 4.0 4.5 - - - +
291E LYS* 1.3 80.2 - - + +
293E GLU* 1.3 71.7 + - - +
315E GLY* 3.6 3.4 + - - -
318E 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