Contacts of the helix formed by residues 276 - 288 (chain A) in PDB entry 1LUA
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 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLU* 5.0 1.4 - - - +
77A PHE* 4.3 17.6 - - + -
78A GLU* 5.6 1.0 - - - +
81A LYS* 5.5 2.0 + - - +
94A LEU* 3.8 15.5 - - - +
100A ASN* 2.9 23.6 + - - +
135A ARG* 3.1 19.0 + - - -
167A ARG* 3.0 31.0 + - - +
274A VAL* 3.7 7.5 + - + -
275A PHE* 1.3 72.6 - - - +
277A ALA* 1.3 82.1 + - - +
278A GLU* 3.2 6.3 + - - +
279A GLU* 3.3 3.0 + - - +
280A ILE* 3.1 21.8 + - - +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 3.3 24.9 - - - +
104A ALA* 5.2 1.0 - - - +
135A ARG* 3.6 20.6 - - + +
139A LEU* 4.0 17.7 - - + +
168A PHE* 4.0 16.4 - - + -
276A ASP* 1.3 81.6 + - - +
278A GLU* 1.3 62.7 + - - +
280A ILE* 4.0 3.2 - - - +
281A TYR* 3.0 27.9 + - - +
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.8 6.1 - - + -
167A ARG* 2.8 43.8 + - - -
168A PHE* 3.6 17.3 - - + -
276A ASP* 4.1 4.5 - - - +
277A ALA* 1.3 76.7 + - - +
279A GLU* 1.3 64.9 + - + +
281A TYR* 3.5 6.4 + - - +
282A LYS* 3.1 22.5 + - - +
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LYS* 5.9 1.6 - - - -
274A VAL 3.4 27.8 - - - +
275A PHE* 4.1 29.3 - - + -
276A ASP 3.3 3.0 + - - +
278A GLU* 1.3 80.0 + - + +
280A ILE* 1.3 65.8 + - - +
282A LYS* 3.3 34.6 + - - +
283A LEU* 3.2 21.0 + - - +
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A MET* 4.3 15.5 - - + -
94A LEU 3.8 8.5 - - - +
100A ASN* 3.7 25.8 - - + +
101A THR* 4.0 13.9 - - + -
104A ALA* 3.8 10.3 - - + -
259A LEU* 3.8 26.0 - - + +
263A CYS* 4.1 15.5 - - - -
275A PHE* 3.8 29.6 - - + +
276A ASP 3.1 17.9 + - - +
277A ALA* 4.0 3.8 - - - +
279A GLU* 1.3 75.6 - - - +
281A TYR* 1.3 58.7 + - - +
283A LEU* 3.3 5.7 + - - +
284A ALA* 2.9 24.9 + - - +
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA* 3.7 21.1 - - + -
107A VAL* 3.7 12.4 + - + +
108A ALA* 3.6 29.1 - - + -
111A VAL* 3.7 15.8 - - - +
139A LEU* 3.8 34.8 - - + -
143A GLU* 2.6 42.4 + - + +
277A ALA 3.0 18.9 + - - +
278A GLU* 3.8 4.0 - - - +
280A ILE* 1.3 76.4 - - - +
282A LYS* 1.3 65.4 + - - +
284A ALA* 3.1 1.7 + - - +
285A LYS* 3.0 43.6 + - + +
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLU 3.1 13.7 + - - +
279A GLU* 3.3 38.3 + - - +
281A TYR* 1.3 80.4 - - - +
283A LEU* 1.3 59.9 + - - +
285A LYS* 3.5 14.9 + - - +
286A GLU* 3.6 30.4 + - - +
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU* 3.9 8.7 - - + -
262A ALA* 4.2 11.9 - - + +
263A CYS* 3.9 39.7 - - - +
266A LYS* 4.5 26.9 - - + +
275A PHE* 4.8 6.1 - - + -
279A GLU 3.2 9.1 + - - +
280A ILE* 3.6 8.7 - - - +
281A TYR 3.2 0.2 - - - -
282A LYS* 1.3 78.0 - - - +
284A ALA* 1.3 66.6 + - - +
286A GLU* 3.1 30.2 + - + +
287A MET* 3.2 27.4 + - + +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA 3.6 24.2 - - - +
105A ALA* 4.5 1.8 - - - +
108A ALA* 3.9 6.5 - - + +
255A LEU* 4.7 4.9 - - + +
259A LEU* 3.8 24.8 - - + +
280A ILE 2.9 13.7 + - - +
281A TYR* 3.1 12.3 + - - +
283A LEU* 1.3 77.6 - - - +
285A LYS* 1.3 57.5 + - - +
287A MET* 3.1 3.6 + - - +
288A ALA* 2.9 32.2 + - - +
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA* 4.3 9.6 - - + +
111A VAL* 4.5 13.7 - - - +
116A GLY 4.8 5.5 + - - -
143A GLU* 2.8 26.1 + - - -
281A TYR* 3.0 51.1 + - + +
282A LYS* 3.8 10.5 - - - +
283A LEU 3.2 0.2 - - - -
284A ALA* 1.3 76.8 - - - +
286A GLU* 1.3 60.1 + - + +
287A MET 3.5 0.3 + - - -
288A ALA* 4.0 10.2 + - - +
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LYS* 4.8 9.6 + - - -
282A LYS* 3.7 34.4 + - - +
283A LEU* 3.1 28.3 + - + +
285A LYS* 1.3 78.2 - - + +
287A MET* 1.3 59.5 + - + +
288A ALA* 5.4 0.6 - - - +
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Residues in contact with MET 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 4.0 16.0 - - + +
258A LYS* 3.6 37.9 - - + +
259A LEU* 4.1 14.8 - - - +
262A ALA* 3.7 23.8 - - + -
283A LEU* 3.4 31.0 - - + +
284A ALA* 3.1 5.2 + - - +
286A GLU* 1.3 83.7 - - + +
288A ALA* 1.3 66.0 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA* 4.1 23.8 - - + +
109A LEU* 4.1 18.9 - - + +
112A LYS* 3.0 43.1 + - + +
237A LYS* 5.2 5.7 + - - -
255A LEU* 4.0 23.4 - - + +
284A ALA 2.9 19.7 + - - +
285A LYS* 4.0 8.9 + - - +
286A GLU 3.8 0.9 - - - +
287A MET* 1.3 77.1 - - - +
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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