Contacts of the helix formed by residues 51 - 63 (chain E) in PDB entry 5AKF
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 HIS 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E TYR* 2.7 40.3 + + - -
17E LEU* 5.3 0.4 - - + -
47E LEU* 2.8 37.0 + - + +
50E GLN* 1.3 77.1 - - + +
52E ILE* 1.3 77.5 + - + +
54E PRO* 3.4 6.3 - - - +
55E LEU* 3.4 28.8 + - + +
115E VAL* 6.0 2.9 - - + -
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Residues in contact with ILE 52 (chain E).
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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14E LEU* 4.3 4.7 - - + -
17E LEU* 4.3 18.2 - - + -
40E ILE* 3.7 47.8 - - + -
42E ALA* 4.8 3.6 - - + -
47E LEU* 3.1 25.2 + - + +
48E ILE* 3.9 27.6 - - + +
51E HIS* 1.3 88.2 - - + +
53E ALA* 1.3 67.8 + - - +
55E LEU* 2.9 20.4 + - - +
56E MET* 3.0 11.5 + - + +
80E LEU* 3.9 12.8 - - + -
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Residues in contact with ALA 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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48E ILE* 2.8 25.6 + - + +
49E LYS* 4.1 8.5 - - - +
52E ILE* 1.3 72.9 - - - +
54E PRO* 1.3 62.0 - - + +
56E MET* 3.1 2.4 + - - -
57E GLN* 2.7 31.3 + - - +
69E ILE* 3.4 16.0 - - + +
71E ILE* 4.8 4.9 - - + -
80E LEU* 3.6 20.8 - - + +
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Residues in contact with PRO 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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49E LYS 3.5 19.5 - - - +
50E GLN* 3.6 14.6 - - - +
51E HIS 3.4 12.3 - - - +
52E ILE 3.3 5.2 - - - -
53E ALA* 1.3 94.3 - - + +
55E LEU* 1.3 61.7 + - + +
57E GLN* 3.7 7.0 - - + +
58E PHE* 3.1 23.7 + - - +
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Residues in contact with LEU 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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10E ILE* 3.9 33.4 - - + +
13E TYR* 3.5 37.0 - - + -
14E LEU* 4.2 13.7 - - + -
51E HIS* 3.4 29.8 - - + +
52E ILE* 2.9 8.5 + - - +
54E PRO* 1.3 77.5 - - + +
56E MET* 1.3 65.2 + - - +
57E GLN 3.4 0.2 + - - -
58E PHE* 3.4 6.7 + - + +
59E LEU* 3.1 21.8 + - - +
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Residues in contact with MET 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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14E LEU* 4.0 23.1 - - + +
18E ILE* 4.6 1.1 - - + -
38E VAL* 4.2 20.4 - - + -
40E ILE* 4.0 27.6 - - + -
52E ILE* 3.0 11.2 + - + +
53E ALA* 3.6 9.6 - - - +
55E LEU* 1.3 78.0 - - - +
57E GLN* 1.3 51.1 + - - +
59E LEU* 3.2 5.9 + - - +
60E ILE* 2.7 35.7 + - + +
69E ILE* 3.9 10.5 - - + -
80E LEU* 4.3 15.3 - - + -
82E VAL* 3.9 19.3 - - + -
87E LEU* 3.9 22.2 - - - -
91E PHE* 4.3 9.9 - - + -
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Residues in contact with GLN 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 ALA 2.7 19.9 + - - +
54E PRO* 3.7 8.7 - - + +
55E LEU 3.2 0.4 - - - -
56E MET* 1.3 69.1 - - - +
58E PHE* 1.3 68.0 + - - +
60E ILE* 3.2 15.0 + - - +
61E ASP* 2.9 59.5 + - - +
67E SER 5.5 1.2 + - - -
68E LYS* 5.7 0.9 - - - +
69E ILE* 3.1 27.9 + - + +
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Residues in contact with PHE 58 (chain E).
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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6E ASN* 4.1 16.6 - - + -
7E VAL* 4.7 15.3 - - + -
10E ILE* 3.5 34.3 - - + -
54E PRO 3.1 11.7 + - - +
55E LEU* 3.6 9.6 - - + +
57E GLN* 1.3 79.1 - - - +
59E LEU* 1.3 60.4 + - - +
61E ASP* 3.2 8.7 + - + +
62E GLU* 3.0 67.7 + - + +
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Residues in contact with LEU 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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7E VAL* 4.0 17.0 - - + +
10E ILE* 4.7 5.4 - - + -
11E SER* 3.9 24.7 - - - +
14E LEU* 3.7 14.8 - - + -
55E LEU 3.1 13.6 + - - +
56E MET* 3.5 9.9 - - - +
58E PHE* 1.3 77.8 - - - +
60E ILE* 1.3 65.5 + - - +
62E GLU* 3.2 4.0 + - + -
63E LEU* 3.1 47.1 + - + +
87E LEU* 4.3 5.2 - - + -
90E TYR* 4.0 4.9 - - + -
91E PHE* 3.3 37.5 - - + -
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Residues in contact with ILE 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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56E MET* 2.7 23.0 + - + +
57E GLN* 3.2 18.1 + - - +
59E LEU* 1.3 72.9 - - - +
61E ASP* 1.3 62.7 + - - +
63E LEU* 3.5 0.7 + - - -
64E ASN 3.3 2.3 + - - -
65E VAL* 2.9 61.7 + - + +
67E SER 3.9 20.0 - - - +
69E ILE* 3.4 35.7 - - + +
82E VAL* 3.9 20.6 - - + -
87E LEU* 4.5 14.1 - - + -
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Residues in contact with ASP 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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57E GLN* 2.9 46.9 + - - +
58E PHE* 3.6 7.8 - - + +
59E LEU 3.2 0.2 - - - -
60E ILE* 1.3 80.5 - - - +
62E GLU* 1.3 69.7 + - - +
64E ASN* 3.2 13.8 + - - +
65E VAL 5.4 0.7 - - - +
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Residues in contact with GLU 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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7E VAL* 4.8 18.4 - - + -
58E PHE* 3.0 57.4 + - + +
59E LEU* 3.2 5.8 + - - +
61E ASP* 1.3 82.9 - - - +
63E LEU* 1.3 64.4 + - + +
64E ASN* 3.2 2.1 + - - +
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Residues in contact with LEU 63 (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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7E VAL* 4.9 7.9 - - + -
59E LEU* 3.1 36.9 + - + +
60E ILE 3.5 0.2 + - - -
62E GLU* 1.3 79.2 - - - +
64E ASN* 1.3 68.6 + - - +
65E VAL* 3.1 14.8 + - + -
86E LYS* 2.8 31.6 + - + -
87E LEU* 3.7 24.7 - - + -
90E TYR* 3.8 37.7 - - + +
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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