Contacts of the helix formed by residues 35 - 43 (chain F) in PDB entry 2GZJ
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 PRO 35 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F LYS 3.4 8.5 - - - +
18F VAL* 3.9 22.4 - - + -
22F TRP* 3.4 45.5 - - + +
33F PRO 3.5 1.7 - - - +
34F ILE* 1.3 92.4 - - + +
36F ASP* 1.3 66.4 + - - +
37F ARG* 4.2 7.2 - - + +
38F ILE* 3.0 34.6 + - + +
39F ALA* 3.0 10.6 + - - +
57F VAL* 6.2 0.9 - - + -
67F LEU* 4.3 10.5 - - + -
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Residues in contact with ASP 36 (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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14F LYS 3.3 21.9 - - - +
15F GLY 4.2 1.3 - - - +
16F LYS* 2.9 28.1 + - - +
17F PRO* 3.5 27.8 - - + +
18F VAL* 4.8 1.6 + - - +
34F ILE 3.4 1.2 + - - -
35F PRO* 1.3 71.3 - - - +
37F ARG* 1.3 84.1 + - - +
39F ALA* 3.3 2.4 + - - +
40F ASP* 2.9 39.6 + - - +
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Residues in contact with ARG 37 (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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18F VAL* 5.8 5.4 - - - +
35F PRO* 3.1 6.5 - - + -
36F ASP* 1.3 93.3 + - - +
38F ILE* 1.3 59.4 + - - +
40F ASP* 3.6 9.3 - - - +
41F LYS* 2.9 41.6 + - - +
64F ASP* 2.8 46.9 + - - +
65F PRO* 5.2 3.6 - - - +
66F GLU* 3.3 28.6 - - - +
67F LEU* 4.9 13.7 - - + -
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Residues in contact with ILE 38 (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 ILE* 4.3 13.9 - - + -
35F PRO* 3.0 20.5 + - + +
37F ARG* 1.3 73.9 - - - +
39F ALA* 1.3 66.9 + - - +
41F LYS* 2.9 17.6 + - + +
42F LEU* 3.0 35.0 + - + +
57F VAL* 4.6 12.8 - - + +
60F GLU* 3.3 41.3 - - + +
61F VAL* 3.7 9.6 - - + +
64F ASP* 4.9 2.7 - - + +
67F LEU* 3.6 33.2 - - + -
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Residues in contact with ALA 39 (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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13F GLY 3.7 16.6 - - - +
14F LYS 3.4 28.9 - - - +
15F GLY* 4.1 3.4 - - - +
34F ILE* 4.3 2.4 - - + +
35F PRO 3.0 10.5 + - - +
36F ASP 3.6 2.5 - - - +
38F ILE* 1.3 76.3 - - - +
40F ASP* 1.3 63.1 + - - +
43F ARG* 2.9 32.9 + - - +
116F MET* 3.6 21.8 - - + -
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Residues in contact with ASP 40 (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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14F LYS 5.1 1.0 - - - +
36F ASP* 2.9 26.3 + - - +
37F ARG* 3.6 12.3 - - - +
38F ILE 3.1 0.2 - - - -
39F ALA* 1.3 76.9 - - - +
41F LYS* 1.3 67.1 + - + +
43F ARG* 2.9 38.7 + - - +
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Residues in contact with LYS 41 (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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37F ARG* 2.9 39.9 + - - +
38F ILE* 2.9 12.3 + - + +
40F ASP* 1.3 84.6 + - + +
42F LEU* 1.3 61.6 + - - +
43F ARG 3.7 1.8 - - - +
45F LYS* 3.7 22.0 + - - +
60F GLU* 3.6 34.1 - - + +
64F ASP* 4.7 7.6 + - - -
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Residues in contact with LEU 42 (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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11F ALA* 3.4 15.3 - - + +
38F ILE* 3.0 30.8 + - + +
39F ALA 3.2 0.2 + - - -
41F LYS* 1.3 81.3 - - - +
43F ARG* 1.3 67.9 + - - +
44F ASP 3.3 0.5 + - - -
45F LYS* 3.1 32.9 + - + +
47F PHE* 4.3 3.6 - - + -
53F PHE* 3.9 15.7 - - + -
56F ALA* 4.0 17.3 - - + -
57F VAL* 3.8 36.8 - - + +
60F GLU* 3.7 25.4 - - + +
116F MET* 4.1 13.5 - - + -
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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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11F ALA 3.5 5.4 - - - -
12F THR* 4.1 5.2 - - - +
13F GLY 3.0 42.5 + - - +
14F LYS* 3.9 16.8 + - - +
39F ALA* 2.9 26.9 + - - +
40F ASP* 2.9 42.3 + - - +
41F LYS 3.7 3.0 - - - +
42F LEU* 1.3 79.3 - - - +
44F ASP* 1.3 76.7 + - - +
45F LYS* 3.2 5.9 + - - +
116F MET* 3.8 8.0 - - + +
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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