Contacts of the helix formed by residues 276 - 288 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C PHE* 4.0 22.8 - - + -
78C GLU* 5.5 0.9 - - - +
81C LYS* 5.1 3.7 + - - +
94C LEU* 3.9 10.9 - - - +
100C ASN* 3.0 10.6 + - - +
135C ARG* 3.0 26.7 + - - -
167C ARG* 3.1 31.0 + - - +
274C VAL* 3.3 11.2 + - + +
275C PHE* 1.3 74.4 - - - +
277C ALA* 1.3 80.9 + - - +
278C GLU* 3.1 7.0 + - - +
279C GLU* 3.4 2.5 + - - +
280C ILE* 3.1 25.1 + - - +
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Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ASN* 3.3 26.0 + - + +
104C ALA* 4.9 0.7 - - - +
135C ARG* 3.7 19.5 - - + +
139C LEU* 4.0 17.8 - - + +
168C PHE* 4.0 17.9 - - + -
276C ASP* 1.3 82.0 + - - +
278C GLU* 1.3 62.8 + - - +
280C ILE* 3.8 3.4 - - - +
281C TYR* 3.0 26.2 + - - +
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Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C LEU* 4.6 8.1 - - + -
167C ARG* 3.0 38.6 + - - -
168C PHE* 3.6 25.3 - - + -
276C ASP* 4.1 4.2 - - - +
277C ALA* 1.3 77.1 + - - +
279C GLU* 1.3 60.8 + - - +
281C TYR* 3.4 7.2 + - - +
282C LYS* 3.0 26.0 + - - +
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Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C VAL 3.6 25.1 - - - +
275C PHE* 4.0 32.7 - - + -
276C ASP 3.4 5.6 + - - +
278C GLU* 1.3 79.2 + - - +
280C ILE* 1.3 64.0 + - - +
282C LYS* 3.4 30.9 + - - +
283C LEU* 3.3 20.8 + - - +
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Residues in contact with ILE 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C MET* 4.2 16.4 - - + -
94C LEU 3.9 7.2 - - - +
100C ASN* 3.7 26.2 - - + +
101C THR* 4.1 9.0 - - + -
104C ALA* 3.8 9.9 - - + -
259C LEU* 3.6 23.6 - - + +
263C CYS* 4.1 14.4 - - - -
275C PHE* 3.6 35.2 - - + +
276C ASP 3.1 18.9 + - - +
277C ALA* 3.8 4.5 - - - +
279C GLU* 1.3 76.7 - - - +
281C TYR* 1.3 59.2 + - - +
283C LEU* 3.2 4.5 + - - +
284C ALA* 2.9 25.3 + - - +
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Residues in contact with TYR 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ALA* 3.7 19.5 - - - -
107C VAL* 3.7 12.6 - - + +
108C ALA* 3.5 29.8 - - + -
111C VAL* 3.5 17.3 - - - +
139C LEU* 3.7 37.5 - - + -
143C GLU* 2.7 41.2 + - + +
277C ALA 3.0 17.8 + - - +
278C GLU* 3.6 5.2 - - - +
280C ILE* 1.3 75.3 - - - +
282C LYS* 1.3 67.5 + - - +
284C ALA* 3.1 0.8 + - - -
285C LYS* 3.0 41.0 + - + +
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Residues in contact with LYS 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C GLU 3.0 14.6 + - - +
279C GLU* 3.6 33.2 + - - +
280C ILE 3.3 0.2 - - - -
281C TYR* 1.3 80.9 - - - +
283C LEU* 1.3 61.7 + - - +
285C LYS* 3.4 15.4 + - - +
286C GLU* 3.5 30.1 + - + +
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C LEU* 3.9 7.6 - - + -
262C ALA* 3.9 16.4 - - + +
263C CYS* 3.9 38.8 - - - +
266C LYS* 4.1 27.6 - - + -
275C PHE* 4.6 4.5 - - + -
279C GLU 3.3 8.8 + - - +
280C ILE* 3.2 8.8 + - - +
281C TYR 3.1 0.6 - - - -
282C LYS* 1.3 77.5 - - - +
284C ALA* 1.3 67.2 + - - +
286C GLU* 3.1 35.7 + - + +
287C MET* 3.2 27.7 + - + +
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Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ALA 3.7 23.6 - - - +
105C ALA* 4.5 2.2 - - - +
108C ALA* 3.8 7.0 - - + -
255C LEU* 4.7 4.4 - - + +
259C LEU* 3.6 25.9 - - + +
280C ILE 2.9 14.4 + - - +
281C TYR* 3.5 11.7 - - - +
283C LEU* 1.3 77.0 - - - +
285C LYS* 1.3 56.8 + - - +
287C MET* 3.1 3.9 + - - +
288C ALA* 2.9 32.7 + - - +
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Residues in contact with LYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ALA* 4.3 8.3 - - + -
111C VAL* 4.6 13.6 - - - +
112C LYS* 6.1 0.3 - - - +
116C GLY* 4.7 6.6 + - - -
143C GLU* 2.8 33.6 + - - +
281C TYR* 3.0 45.0 + - + +
282C LYS* 3.7 10.1 - - - +
283C LEU 3.2 0.2 - - - -
284C ALA* 1.3 76.1 - - - +
286C GLU* 1.3 62.6 + - + +
287C MET 3.4 0.3 + - - -
288C ALA* 3.9 10.1 + - - +
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Residues in contact with GLU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C LYS* 5.1 6.3 + - - -
282C LYS* 3.5 33.4 + - + +
283C LEU* 3.1 29.3 + - + +
285C LYS* 1.3 77.5 - - + +
287C MET* 1.3 60.5 + - + +
288C ALA 5.1 0.9 - - - +
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Residues in contact with MET 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C LEU* 4.1 15.3 - - + +
258C LYS* 3.6 39.3 - - + +
259C LEU* 4.0 13.5 - - - +
262C ALA* 3.7 24.9 - - + -
283C LEU* 3.4 32.3 - - + +
284C ALA* 3.1 4.9 + - - +
286C GLU* 1.3 80.9 - - + +
288C ALA* 1.3 66.6 + - - +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ALA* 4.2 22.9 - - + +
109C LEU* 4.0 19.8 - - + +
112C LYS* 2.8 45.4 + - + +
237C LYS* 4.9 7.6 + - - -
255C LEU* 4.0 22.7 - - + +
284C ALA 2.9 18.7 + - - +
285C LYS* 3.9 8.2 + - - +
286C GLU 3.7 1.9 - - - +
287C MET* 1.3 79.9 - - - +
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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