Contacts of the helix formed by residues 42 - 50 (chain F) in PDB entry 3EBL
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 GLU 42 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ARG* 5.2 1.4 + - - -
42A GLU* 5.6 0.9 - - - +
61E GLU* 5.6 1.7 - - - +
33F ILE 3.8 16.2 - - - +
34F LEU* 2.9 36.6 + - + +
36F ARG* 2.8 41.9 + - + +
41F PHE* 1.3 71.2 - - - +
43F ARG* 1.3 57.3 + - - +
44F ASP 3.5 2.7 - - - -
45F LEU* 3.5 18.8 + - + +
46F GLY* 2.9 24.9 + - - -
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Residues in contact with ARG 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ARG* 5.4 0.2 - - - +
41F PHE* 2.9 44.9 + - + +
42F GLU* 1.3 71.2 - - - +
44F ASP* 1.3 65.5 + - - +
46F GLY* 3.3 1.8 + - - -
47F GLU* 2.9 49.2 + - + +
125F VAL 2.8 24.6 + - - -
126F HIS* 4.7 1.2 - - - +
156F ARG* 3.3 29.9 - - - +
157F ALA 2.6 30.5 + - - -
158F PRO* 4.1 0.6 - - - +
159F GLU* 2.8 36.3 + - + +
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Residues in contact with ASP 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA* 5.9 2.8 - - - +
60E LEU* 4.0 26.1 - - + +
42F GLU 3.5 0.4 - - - -
43F ARG* 1.3 84.1 - - - +
45F LEU* 1.3 57.5 + - - +
47F GLU* 3.5 7.1 + - - +
48F TYR* 3.0 28.8 + - - +
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E LEU* 5.3 4.2 - - + +
61E GLU* 5.0 14.8 - - - +
33F ILE* 4.4 20.6 - - + +
34F LEU* 3.8 16.2 - - + -
42F GLU* 3.5 28.3 + - + +
43F ARG 3.3 0.4 - - - -
44F ASP* 1.3 76.9 - - - +
46F GLY* 1.3 59.4 + - - +
48F TYR* 3.1 13.2 + - + +
49F LEU* 2.9 58.7 + - + +
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Residues in contact with GLY 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 3.6 24.3 - - - +
41F PHE* 4.7 7.2 - - - -
42F GLU 2.9 18.9 + - - -
43F ARG* 3.6 4.3 - - - -
45F LEU* 1.3 70.9 - - - +
47F GLU* 1.3 62.9 + - - +
49F LEU* 3.3 4.4 + - - +
50F ASP* 3.0 25.5 + - - +
52F ARG* 5.5 0.2 - - - -
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Residues in contact with GLU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E VAL* 5.2 1.9 - - - +
43F ARG* 2.9 34.3 + - + +
44F ASP* 3.7 8.7 - - - +
46F GLY* 1.3 75.1 - - - +
48F TYR* 1.3 63.6 + - - +
50F ASP* 3.5 12.5 + - - +
52F ARG* 2.8 50.8 + - - +
156F ARG* 2.9 30.7 + - - -
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Residues in contact with TYR 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E VAL* 3.1 43.4 - - + +
54E PRO 6.1 0.2 - - - -
60E LEU* 3.7 25.1 - - + -
132E THR* 3.7 24.2 + - + +
135E ASP* 2.8 32.2 + - - +
136E SER* 3.0 34.6 + - - -
139E ARG* 3.7 16.1 - - - -
701E PO4 5.9 0.2 - - - -
44F ASP 3.0 18.4 + - - +
45F LEU* 3.1 14.1 + - + +
47F GLU* 1.3 79.4 - - - +
49F LEU* 1.3 75.4 + - + +
50F ASP 3.7 1.9 + - - +
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E ARG* 3.0 26.7 + - - +
132E THR* 4.6 2.0 - - + -
701E PO4 4.1 29.4 - - - +
30F SER* 5.2 12.3 - - - +
33F ILE* 4.9 10.1 - - + -
34F LEU* 4.5 9.9 - - + -
45F LEU* 2.9 48.4 + - + +
46F GLY* 3.7 3.4 - - - +
48F TYR* 1.3 90.2 - - + +
50F ASP* 1.3 65.4 + - - +
501F MPD 2.8 25.5 + - + -
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Residues in contact with ASP 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ARG* 4.1 5.7 - - - +
52E ARG 4.6 6.6 - - - +
53E VAL* 5.3 0.7 - - - +
132E THR* 5.2 0.2 + - - -
27F PHE* 4.8 10.4 - - - -
31F TYR* 4.9 3.3 + - - -
46F GLY 3.0 15.6 + - - +
47F GLU 4.0 6.7 - - - +
48F TYR 3.4 6.1 - - - +
49F LEU* 1.3 80.3 - - - +
51F ARG* 1.3 70.0 + - - +
52F ARG* 2.7 46.9 + - - +
127F SER* 4.2 12.1 + - - -
131F SER* 2.7 26.6 + - - -
501F MPD 3.8 8.5 + - - +
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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