Contacts of the helix formed by residues 284 - 294 (chain A) in PDB entry 5JQE
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 ASN 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LYS 3.1 36.2 + - - +
19A LEU* 4.1 16.4 - - + -
45A ILE* 5.5 2.8 - - - +
70A ASP* 4.2 10.7 - - - +
282A SER* 3.2 4.8 + - - -
283A PRO* 1.3 87.2 + - - +
285A LYS* 1.3 54.0 + - - +
286A GLU* 3.0 8.4 + - - +
287A LEU* 2.8 30.9 + - - +
288A ALA* 2.7 35.2 + - - +
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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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89A ALA* 4.3 16.9 - - + +
278A ILE* 4.0 22.0 - - + +
279A ASN 4.0 14.4 - - - +
280A ALA 4.0 17.5 - - - +
282A SER* 3.4 24.3 + - - +
283A PRO 3.5 2.3 + - - +
284A ASN* 1.3 73.0 - - - +
286A GLU* 1.3 70.8 + - - +
287A LEU 3.3 0.3 + - - -
288A ALA* 3.4 2.8 + - - +
289A LYS* 3.3 28.3 + - + +
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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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283A PRO 3.0 24.2 - - - +
284A ASN* 4.3 6.4 + - - -
285A LYS* 1.3 87.6 - - + +
287A LEU* 1.3 59.2 + - + +
289A LYS* 3.9 16.5 + - - +
290A GLU* 4.5 3.3 + - - +
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Residues in contact with LEU 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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19A LEU* 4.0 14.1 - - + -
39A PHE* 3.9 31.9 - - + -
43A THR* 4.1 5.2 - - + -
45A ILE* 3.7 46.2 - - + -
284A ASN* 2.8 24.5 + - - +
286A GLU* 1.3 73.1 - - + +
288A ALA* 1.3 65.5 + - - +
289A LYS 3.1 2.8 + - - -
290A GLU* 3.6 5.8 + - + +
291A PHE* 3.4 19.2 + - - +
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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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19A LEU* 3.7 27.2 - - + +
70A ASP* 5.3 1.6 - - + -
71A ILE* 4.0 17.2 - - + +
278A ILE* 4.2 16.2 - - + -
284A ASN 2.7 19.6 + - - +
285A LYS* 3.4 8.9 + - - +
287A LEU* 1.3 71.7 - - - +
289A LYS* 1.3 61.8 + - - +
291A PHE* 3.6 2.5 + - - +
292A LEU* 3.1 29.7 + - - +
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Residues in contact with LYS 289 (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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91A ILE* 5.5 1.6 - - + -
92A THR* 3.2 46.6 + - + +
118A TYR* 3.8 16.6 - - - +
278A ILE* 4.2 11.9 - - + -
285A LYS* 3.3 17.2 + - + +
286A GLU* 4.0 10.8 - - - +
287A LEU 3.1 0.8 - - - -
288A ALA* 1.3 77.0 - - - +
290A GLU* 1.3 53.0 + - - +
292A LEU* 2.9 8.9 + - - +
293A GLU* 2.7 57.1 + - - +
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Residues in contact with GLU 290 (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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39A PHE* 4.7 5.7 - - + -
286A GLU 4.5 3.9 + - - +
287A LEU* 3.6 7.9 + - + +
289A LYS* 1.3 75.8 - - - +
291A PHE* 1.3 64.5 + - - +
293A GLU* 3.9 6.7 - - - +
294A ASN* 3.1 40.5 + - + +
295A TYR* 3.4 27.8 + - + -
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Residues in contact with PHE 291 (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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19A LEU* 3.9 14.6 - - + -
21A ILE* 3.5 32.5 - - + -
32A LEU* 4.2 17.0 - - + -
35A VAL* 4.2 14.6 - - + -
36A GLY* 4.0 26.0 - - - -
39A PHE* 3.8 36.6 - + + -
47A VAL* 4.6 4.3 - - + -
71A ILE* 3.7 20.2 - - + -
73A PHE* 5.3 0.4 - + - -
287A LEU 3.4 13.5 + - - +
288A ALA 3.7 6.3 - - - +
289A LYS 3.2 0.6 - - - -
290A GLU* 1.3 78.5 - - - +
292A LEU* 1.3 68.9 + - + +
295A TYR* 3.4 6.8 - - + +
296A LEU* 2.9 31.4 + - + -
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Residues in contact with LEU 292 (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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71A ILE* 4.0 17.9 - - + -
73A PHE* 4.0 4.9 - - + -
118A TYR* 3.8 37.9 - - + -
120A ILE* 5.1 0.4 - - + -
276A ALA* 3.6 24.2 - - + +
278A ILE* 4.2 12.6 - - + -
288A ALA 3.1 20.8 + - - +
289A LYS 2.9 4.9 + - - +
291A PHE* 1.3 86.9 - - + +
293A GLU* 1.3 60.5 + - - +
296A LEU* 3.6 28.3 - - + -
297A LEU* 2.9 38.2 + - + +
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Residues in contact with GLU 293 (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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92A THR 4.2 0.3 - - - +
93A PRO* 3.5 15.6 - - - +
94A ASP* 4.5 4.4 + - - +
97A PHE* 3.5 44.5 - - + +
100A LYS* 5.2 1.6 + - - +
118A TYR* 3.0 37.6 + - + +
289A LYS* 2.7 39.6 + - - +
290A GLU* 4.4 0.9 - - - -
292A LEU* 1.3 75.1 - - - +
294A ASN* 1.3 78.4 + - - +
295A TYR 3.9 0.2 + - - -
297A LEU* 3.9 17.3 - - - +
298A THR* 4.6 2.3 - - - +
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Residues in contact with ASN 294 (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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97A PHE* 5.8 0.4 - - - -
100A LYS* 4.4 16.2 - - - +
290A GLU* 3.1 35.1 + - + +
293A GLU* 1.3 92.9 + - - +
295A TYR* 1.3 77.2 + - + +
298A THR* 4.4 14.4 - - - +
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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