Contacts of the helix formed by residues 45 - 57 (chain A) in PDB entry 3F40
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 GLY 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLU 3.5 11.2 - - - -
33A ASN* 4.4 4.9 - - - -
34A PHE* 2.7 22.8 + - - +
43A ARG 5.1 0.3 - - - -
44A GLU* 1.3 79.5 + - - +
46A SER* 1.3 67.5 + - - -
47A GLU* 3.1 4.0 - - - -
48A ARG 3.5 1.5 + - - -
49A TYR* 3.2 21.8 + - - +
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Residues in contact with SER 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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27A LYS* 3.5 26.2 + - - -
30A LEU* 3.8 26.3 + - - -
31A ASN 3.4 20.2 + - - -
32A GLU* 3.0 21.0 + - - +
34A PHE* 4.0 8.3 + - - -
45A GLY* 1.3 72.3 - - - -
47A GLU* 1.3 59.7 + - - +
50A MSE 2.9 34.7 + - - +
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Residues in contact with GLU 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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27A LYS* 4.0 15.7 - - - +
32A GLU 4.7 0.2 + - - -
45A GLY* 3.1 1.7 - - - -
46A SER* 1.3 83.0 + - - +
48A ARG* 1.3 63.6 + - - +
50A MSE 3.9 1.5 - - - +
51A ASN* 2.9 44.4 + - - +
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Residues in contact with ARG 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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43A ARG* 3.3 44.3 - - + +
44A GLU 3.7 21.5 + - - +
45A GLY 3.5 1.4 + - - +
46A SER 3.3 0.2 - - - -
47A GLU* 1.3 82.0 - - - +
49A TYR* 1.3 62.8 + - - +
51A ASN* 3.3 11.0 + - - +
52A ASP* 3.1 32.3 + - - -
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Residues in contact with TYR 49 (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 PHE* 4.6 13.0 - + - -
18A LEU* 5.9 0.4 - - + +
30A LEU* 4.5 8.7 - - + -
34A PHE* 3.4 33.9 - + + -
36A PHE* 3.3 53.1 - + + -
43A ARG* 4.4 14.6 - - + +
45A GLY 3.2 14.5 + - - +
46A SER 4.1 2.0 - - - +
48A ARG* 1.3 79.1 - - - +
50A MSE 1.3 60.6 + - - +
52A ASP* 3.2 9.8 + - + +
53A MSE 2.8 69.6 + - + +
60A TYR* 4.6 4.2 + - - -
101A LEU* 3.7 10.8 - - + +
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Residues in contact with MSE 50 (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 PHE* 4.1 15.5 - - - -
18A LEU* 4.1 1.6 - - + -
23A PHE* 3.5 48.3 - - + +
26A ALA* 3.8 11.9 - - + -
27A LYS* 3.7 33.7 - - + -
30A LEU* 3.9 21.1 - - + -
46A SER 2.9 21.6 + - - +
47A GLU 4.1 1.6 - - - +
49A TYR* 1.3 74.7 - - - +
51A ASN* 1.3 66.6 + - - +
53A MSE 3.6 20.0 - - + +
54A GLU* 2.9 24.9 + - - +
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Residues in contact with ASN 51 (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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47A GLU* 2.9 37.7 + - - +
48A ARG* 3.7 11.2 - - - +
50A MSE 1.3 79.0 - - - +
52A ASP* 1.3 65.3 + - - +
54A GLU* 3.4 6.2 + - - +
55A LYS* 3.3 26.3 + - - +
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Residues in contact with ASP 52 (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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43A ARG* 2.9 37.7 + - - +
48A ARG* 3.1 25.6 + - - +
49A TYR* 3.2 11.3 + - + +
51A ASN* 1.3 79.9 - - - +
53A MSE 1.3 64.3 + - + +
55A LYS* 3.0 7.3 + - - +
56A MSE 2.8 38.4 + - + +
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Residues in contact with MSE 53 (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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18A LEU* 4.2 20.2 - - + -
23A PHE* 3.6 9.6 - - + -
49A TYR* 2.8 67.2 + - + +
50A MSE 3.2 26.4 + - + +
52A ASP* 1.3 80.0 - - + +
54A GLU* 1.3 57.0 + - - +
56A MSE 4.4 6.1 - - + +
57A LYS* 2.9 26.3 + - - -
58A PHE* 3.7 35.8 + - + -
60A TYR* 3.7 18.8 - - - -
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Residues in contact with GLU 54 (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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23A PHE* 3.6 36.7 - - + -
50A MSE 2.9 16.5 + - - +
51A ASN* 3.8 7.2 - - - +
52A ASP 3.2 0.2 - - - -
53A MSE 1.3 77.7 - - - +
55A LYS* 1.3 57.2 + - + +
57A LYS* 2.7 41.1 + - - +
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Residues in contact with LYS 55 (chain A).
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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51A ASN 3.3 13.4 + - - +
52A ASP* 3.0 9.5 + - - +
54A GLU* 1.3 80.6 - - + +
56A MSE 1.3 79.2 + - + +
57A LYS* 4.1 8.1 + - - +
81A ASN* 5.4 0.9 + - - -
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Residues in contact with MSE 56 (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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52A ASP* 2.8 29.1 + - + +
53A MSE 4.0 7.9 - - + +
55A LYS* 1.3 86.3 - - + +
57A LYS* 1.3 72.8 + - - +
58A PHE* 3.3 45.9 + - + +
81A ASN* 3.8 38.8 + - - +
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Residues in contact with LYS 57 (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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21A GLU* 3.7 26.7 - - - +
23A PHE* 4.3 15.9 - - + -
53A MSE 2.9 14.7 + - - -
54A GLU* 2.7 36.4 + - - +
55A LYS* 4.1 7.1 + - - +
56A MSE 1.3 81.2 - - - +
58A PHE* 1.3 62.6 + - - +
59A LYS* 3.0 28.1 + - - +
79A ASN 4.6 1.7 - - - +
81A ASN 5.9 0.2 + - - -
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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