Contacts of the helix formed by residues 30 - 39 (chain J) in PDB entry 5IYB
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 THR 30 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25J LEU* 5.7 0.4 - - - +
28J GLU* 3.3 43.9 + - + +
29J TYR* 1.3 77.7 - - - +
31J GLU* 1.3 55.7 + - - +
32J GLY 3.2 2.5 - - - -
33J ASP* 2.8 33.1 + - + +
34J ALA* 2.6 37.3 + - + +
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Residues in contact with GLU 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994B GLY 4.0 17.2 - - - +
995B GLU* 4.8 11.1 - - - +
21J TYR* 2.8 26.8 + - + +
25J LEU* 3.7 30.0 - - + +
29J TYR* 5.5 10.1 - - + -
30J THR* 1.3 74.9 - - - +
32J GLY* 1.3 61.9 - - - +
34J ALA* 3.6 7.3 - - - +
35J LEU* 3.1 25.9 + - + +
50J LEU* 3.3 18.0 - - + +
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Residues in contact with GLY 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993B LYS 3.6 24.3 + - - -
994B GLY* 4.9 2.6 + - - -
30J THR 3.2 0.6 - - - -
31J GLU* 1.3 78.3 - - - +
33J ASP* 1.3 61.1 + - - +
35J LEU* 3.5 4.9 + - - +
36J ASP* 3.3 19.6 + - - +
46J ARG* 4.0 11.9 + - - -
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Residues in contact with ASP 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J GLU* 4.3 7.3 - - - +
30J THR* 2.8 37.5 + - + +
32J GLY* 1.3 70.7 - - - +
34J ALA* 1.3 58.5 + - - +
36J ASP* 3.1 10.8 + - - +
37J ALA* 2.9 33.5 + - - +
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Residues in contact with ALA 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J TYR* 5.0 2.5 - - + -
24J LEU* 3.8 25.5 - - + +
25J LEU* 3.5 32.8 - - + -
28J GLU* 5.1 3.1 - - - +
30J THR* 2.6 21.4 + - + +
31J GLU* 3.6 4.0 - - - +
32J GLY 3.3 0.2 - - - -
33J ASP* 1.3 73.1 - - - +
35J LEU* 1.3 61.7 + - - +
37J ALA* 3.5 2.1 + - - +
38J LEU* 3.1 30.0 + - + +
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Residues in contact with LEU 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994B GLY* 4.4 13.0 - - - -
21J TYR* 4.2 11.4 - - + -
31J GLU* 3.1 19.3 + - + +
32J GLY 3.6 7.6 - - - +
34J ALA* 1.3 76.6 - - - +
36J ASP* 1.3 61.2 + - - +
38J LEU* 3.4 10.0 + - + +
39J GLY 3.2 15.8 + - - -
40J LEU* 3.4 39.8 + - + +
46J ARG* 3.7 38.4 - - + +
49J LEU* 4.1 22.4 - - + -
50J LEU* 4.4 22.4 - - + +
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Residues in contact with ASP 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J GLY 3.3 9.8 + - - +
33J ASP* 3.1 17.1 + - - +
35J LEU* 1.3 76.1 - - - +
37J ALA* 1.3 65.2 + - - +
39J GLY* 3.0 15.5 + - - +
40J LEU 5.2 2.5 - - - +
41J LYS* 3.5 40.6 + - - +
46J ARG* 4.2 12.7 + - - +
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Residues in contact with ALA 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J LEU* 4.4 14.6 - - + -
33J ASP* 2.9 19.9 + - - +
34J ALA 3.9 4.0 - - - +
36J ASP* 1.3 76.3 - - - +
38J LEU* 1.3 62.4 + - - +
39J GLY* 3.4 1.6 + - - -
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Residues in contact with LEU 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C TYR* 5.7 0.3 - - - -
17J LYS* 3.1 52.0 + - + +
20J ALA* 3.9 22.7 - - + +
21J TYR* 3.4 41.1 - - + +
24J LEU* 4.9 6.5 - - + -
34J ALA* 3.1 19.6 + - + +
35J LEU* 3.4 16.6 - - + +
36J ASP 3.2 0.2 - - - -
37J ALA* 1.3 76.3 - - - +
39J GLY* 1.3 57.8 + - - +
40J LEU* 3.7 10.3 - - + -
49J LEU* 4.6 4.0 - - + -
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Residues in contact with GLY 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J LYS* 4.6 11.1 + - - +
17J LYS* 5.0 5.5 - - - -
35J LEU 3.2 1.2 + - - -
36J ASP 3.0 16.2 + - - -
37J ALA 3.2 1.5 - - - -
38J LEU* 1.3 78.2 - - - +
40J LEU* 1.3 61.0 + - - +
41J LYS* 2.9 28.5 + - - +
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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