Contacts of the helix formed by residues 39 - 48 (chain A) in PDB entry 2JY8
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.3 0.3 - - - +
30A THR* 4.4 7.8 - - - +
33A LEU* 4.3 1.7 - - - +
34A GLN* 3.5 21.0 + - - +
38A TYR* 1.3 99.1 - - + +
40A ILE* 1.3 63.8 + - - +
41A GLY* 3.5 18.0 + - - +
42A ALA* 3.6 18.1 + - + +
43A ALA 3.8 1.6 + - - -
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Residues in contact with ILE 40 (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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14A LEU* 5.1 0.2 - - + -
24A ASP* 2.7 40.2 - - + +
29A LEU* 3.2 28.3 - - + -
30A THR* 3.5 27.4 - - + +
33A LEU* 3.3 39.6 - - + +
34A GLN* 3.7 4.0 - - - +
39A ASP* 1.3 71.1 - - - +
41A GLY* 1.3 60.7 + - - +
42A ALA 2.9 2.7 - - - -
43A ALA* 2.4 15.8 + - + -
44A LEU* 2.4 51.0 + - + +
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Residues in contact with GLY 41 (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 ASP* 3.2 14.6 + - - -
40A ILE* 1.3 83.7 - - - +
42A ALA* 1.3 55.4 + - - +
44A LEU* 3.3 11.1 - - - +
45A ASP* 2.9 36.5 + - - +
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Residues in contact with ALA 42 (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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10A LEU* 3.2 20.5 - - + +
38A TYR* 6.2 2.5 - - + -
39A ASP* 3.6 12.0 + - + +
40A ILE 2.9 0.2 - - - -
41A GLY* 1.3 76.8 - - - +
43A ALA* 1.3 63.5 + - - +
45A ASP* 3.5 14.9 - - - +
46A THR* 4.0 5.2 + - - -
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Residues in contact with ALA 43 (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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10A LEU* 3.0 36.1 - - + +
14A LEU* 3.0 13.2 - - + +
33A LEU* 3.3 27.1 - - + -
40A ILE* 2.4 20.3 + - + +
42A ALA* 1.3 66.0 - - - +
44A LEU* 1.3 53.6 + - - +
45A ASP 2.9 3.8 - - - -
46A THR* 2.6 42.4 + - - +
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Residues in contact with LEU 44 (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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14A LEU* 4.0 0.2 - - - +
23A SER* 3.2 17.7 - - - -
24A ASP* 3.2 30.3 - - - +
25A GLU* 4.8 3.1 - - + -
40A ILE* 2.4 41.3 + - + +
41A GLY* 3.3 20.9 - - - +
43A ALA* 1.3 69.1 - - - +
45A ASP* 1.3 77.4 + - - +
46A THR 2.9 5.4 + - - -
47A ILE* 3.0 27.0 + - + +
49A TYR* 2.9 49.0 - - + +
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Residues in contact with ASP 45 (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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41A GLY 2.9 22.2 + - - +
42A ALA* 3.5 12.3 - - - +
43A ALA 2.8 0.8 + - - -
44A LEU* 1.3 84.0 - - - +
46A THR* 1.3 57.3 + - - +
47A ILE 3.5 0.2 - - - -
48A GLN 3.4 6.9 - - - +
49A TYR* 2.9 62.6 - - - +
50A SER* 4.3 1.6 - - - -
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Residues in contact with THR 46 (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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7A ASP* 5.4 0.3 + - - -
10A LEU* 6.3 0.2 - - - -
11A ILE* 3.2 42.2 - - + +
14A LEU* 2.9 22.0 - - + -
18A LEU* 5.0 4.5 - - + +
42A ALA 4.5 4.5 - - - -
43A ALA* 2.6 28.8 + - - +
45A ASP* 1.3 71.5 - - - +
47A ILE* 1.3 59.3 + - - +
48A GLN* 2.9 10.1 + - - +
50A SER* 5.7 2.4 - - - -
51A LYS 5.7 0.9 - - - +
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Residues in contact with ILE 47 (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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14A LEU* 3.5 29.2 - - + -
17A MET* 4.2 9.4 - - + -
18A LEU* 3.2 41.3 - - + +
21A GLY* 4.8 5.9 - - - +
22A PHE 3.2 36.8 - - - +
23A SER* 3.2 21.8 - - - +
24A ASP 4.7 0.9 - - - +
29A LEU* 4.8 2.7 - - + -
44A LEU* 3.0 23.8 + - + +
46A THR* 1.3 75.6 - - - +
48A GLN* 1.3 61.6 + - - +
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Residues in contact with GLN 48 (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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22A PHE* 5.1 5.1 - - - -
23A SER* 2.5 34.9 + - - +
25A GLU* 3.7 11.1 + - - +
44A LEU 3.8 0.6 + - - -
45A ASP 3.4 2.9 - - - +
46A THR 2.9 4.4 - - - +
47A ILE* 1.3 82.9 - - + +
49A TYR* 1.3 94.4 + - + +
50A SER* 2.4 32.5 + - - -
51A LYS 3.9 4.1 + - - +
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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