Contacts of the helix formed by residues 52 - 62 (chain E) in PDB entry 3F6W
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 52 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50E ARG 3.4 3.4 + - - -
51E LEU* 1.3 75.6 - - - +
53E VAL* 1.3 61.8 + - + +
54E ILE* 3.1 13.1 + - - +
55E GLU* 2.8 54.2 + - - +
56E PHE* 2.8 26.6 + - - +
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Residues in contact with VAL 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ASP* 1.3 75.0 - - + +
54E ILE* 1.3 75.8 + - + +
56E PHE* 3.3 10.7 + - + +
57E MSE 2.9 43.0 + - + +
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Residues in contact with ILE 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ASP* 3.1 8.8 + - - +
53E VAL* 1.3 89.6 - - + +
55E GLU* 1.3 68.7 + - + +
57E MSE 3.0 13.7 + - + +
58E ASP* 2.9 36.4 + - - +
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Residues in contact with GLU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ARG* 4.5 19.8 + - - +
40E PHE* 4.8 6.2 - - + -
49E ARG* 2.8 45.1 + - - -
50E ARG 3.4 1.4 - - - +
51E LEU* 3.5 14.9 - - + +
52E ASP* 2.8 48.5 + - - +
54E ILE* 1.3 76.1 - - + +
56E PHE* 1.3 53.6 + - - +
58E ASP* 3.1 10.0 + - - +
59E PHE* 2.7 36.2 + - - +
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Residues in contact with PHE 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LEU* 3.7 30.5 - - + -
16E LEU* 3.9 24.2 - - + -
51E LEU* 3.8 17.2 - - + +
52E ASP 2.8 14.2 + - - +
53E VAL* 3.3 16.2 - - + +
55E GLU* 1.3 76.7 - - - +
57E MSE 1.3 66.2 + - - +
59E PHE* 3.2 4.6 + - - +
60E CYS* 2.9 55.7 + - - -
67E PRO* 4.1 11.2 - - + -
70E LEU* 3.9 11.2 - - + -
71E LEU* 3.7 41.5 - - + -
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Residues in contact with MSE 57 (chain E).
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* 2.9 38.7 + - + +
54E ILE* 3.0 15.7 + - + +
56E PHE* 1.3 86.9 - - - +
58E ASP* 1.3 65.3 + - - +
60E CYS* 3.5 4.1 + - - +
61E ARG* 3.3 38.6 + - - +
67E PRO* 3.8 21.8 - - + -
68E TYR* 3.3 40.2 - - + +
71E LEU* 5.2 7.2 - - - -
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Residues in contact with ASP 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 3.3 16.2 - - + +
36E ARG* 5.3 8.9 + - - +
54E ILE* 2.9 30.8 + - - +
55E GLU* 3.6 9.8 - - - +
57E MSE 1.3 76.9 - - - +
59E PHE* 1.3 66.5 + - - +
61E ARG* 3.1 7.8 + - - +
62E GLY 2.9 20.1 + - - -
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Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E LEU* 4.3 23.8 - - + -
30E LEU* 3.7 18.4 - - + +
34E LEU* 4.1 11.2 - - + +
40E PHE* 4.1 22.2 - + + -
41E VAL* 4.5 10.5 - - + -
44E THR* 3.2 40.8 - - + -
45E GLU* 4.2 18.6 - - + -
51E LEU* 4.2 9.2 - - + -
55E GLU 2.7 20.8 + - - +
56E PHE* 3.3 9.6 - - - +
58E ASP* 1.3 72.4 - - - +
60E CYS* 1.3 64.2 + - - +
62E GLY* 3.2 11.4 + - - -
63E ILE* 3.4 33.8 - - + +
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Residues in contact with CYS 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E LEU* 3.8 13.0 - - - -
56E PHE* 2.9 50.2 + - - -
57E MSE 3.6 9.6 - - - +
59E PHE* 1.3 77.4 - - - +
61E ARG* 1.3 57.5 + - - +
63E ILE 3.1 2.6 + - - -
64E GLY 3.0 21.1 + - - -
65E THR* 3.1 37.5 + - - +
67E PRO* 3.8 23.3 - - + -
70E LEU* 4.6 3.1 - - - -
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Residues in contact with ARG 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ARG* 4.9 2.4 + - - -
57E MSE 3.3 27.6 + - - +
58E ASP* 3.1 11.0 + - - +
60E CYS* 1.3 73.5 - - - +
62E GLY* 1.3 59.0 + - - +
63E ILE 2.8 10.5 + - - -
64E GLY* 3.1 14.1 + - - +
65E THR 4.4 3.7 + - - -
66E ASP* 5.2 2.2 + - - +
67E PRO* 3.6 35.3 - - - +
68E TYR* 4.6 9.3 - - - -
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Residues in contact with GLY 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ILE* 3.4 2.3 - - - +
30E LEU* 2.8 35.4 - - - +
33E ARG* 2.9 31.9 + - - -
34E LEU* 3.8 9.4 - - - +
58E ASP 2.9 14.2 + - - -
59E PHE 3.2 2.1 + - - -
61E ARG* 1.3 74.6 - - - +
63E ILE* 1.3 55.6 + - - +
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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