Contacts of the helix formed by residues 59 - 70 (chain B) in PDB entry 2ETK
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 TYR 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 2.8 41.8 + - + +
25A VAL* 3.9 7.4 - - + -
29A CYS* 3.7 15.1 + - + +
395A VAL* 3.7 21.6 + - + +
34B LEU* 4.0 23.1 - - + -
38B VAL* 4.9 10.3 - - + +
55B PHE* 3.2 41.9 + + + +
56B LEU* 3.7 3.8 - - - -
58B ARG* 1.3 114.6 + - - +
60B LYS* 1.3 64.0 + - - +
62B THR* 3.9 20.0 - - - -
63B ILE* 3.2 25.9 + - + +
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B VAL* 6.4 0.2 - - - -
47B ARG* 5.5 9.6 - - - +
56B LEU 3.0 17.4 + - - +
57B SER* 3.8 15.7 - - - +
58B ARG 3.1 1.8 - - - -
59B TYR* 1.3 79.7 - - - +
61B ASP* 1.3 73.0 + - - +
62B THR 3.2 0.2 + - - -
63B ILE* 3.4 4.5 + - - +
64B ASN* 2.7 40.1 + - - +
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER 5.3 2.1 - - - +
58B ARG 4.3 6.7 + - - +
59B TYR 3.7 0.2 - - - -
60B LYS* 1.3 89.7 + - - +
62B THR* 1.3 66.0 + - - +
64B ASN* 3.5 10.9 + - - +
65B LYS* 3.4 21.7 + - - +
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Residues in contact with THR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 5.2 5.3 - - + +
24A GLU* 3.2 31.0 + - + +
25A VAL* 3.6 39.7 - - + -
58B ARG 3.9 9.0 + - - -
59B TYR* 3.9 14.4 - - - -
60B LYS 3.2 0.6 - - - -
61B ASP* 1.3 80.0 - - - +
63B ILE* 1.3 56.8 + - - +
64B ASN 3.3 0.2 + - - -
65B LYS* 3.4 4.9 + - - +
66B ILE* 3.0 33.9 + - + +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 5.6 0.4 - - + -
31B LEU* 5.1 2.0 - - + +
34B LEU* 3.9 28.5 - - + +
35B ASP* 3.8 30.1 - - + +
38B VAL* 3.9 30.7 - - + -
59B TYR* 3.2 22.6 + - + +
60B LYS* 3.6 2.7 - - - +
62B THR* 1.3 78.6 - - - +
64B ASN* 1.3 71.5 - - - +
66B ILE* 3.8 14.2 - - + +
67B ARG* 3.1 55.4 + - - +
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Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 2.7 43.0 + - - +
61B ASP* 3.5 12.0 + - - +
62B THR 3.2 0.6 - - - -
63B ILE* 1.3 82.3 - - - +
65B LYS* 1.3 60.4 + - - +
67B ARG* 3.1 15.1 + - - +
68B ASP* 2.9 29.0 + - - +
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.3 30.2 - - - +
17A LEU* 4.8 20.2 - - + -
61B ASP 3.4 14.0 + - - +
62B THR* 3.9 4.7 - - - +
64B ASN* 1.3 77.9 - - - +
66B ILE* 1.3 57.1 + - + +
68B ASP* 3.4 6.7 + - + +
69B LEU* 3.0 51.8 + - + +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MET* 3.7 26.8 - - + +
17A LEU* 3.7 24.7 - - + -
25A VAL* 3.8 24.7 - - + -
31B LEU* 3.9 20.4 - - + +
35B ASP* 6.0 2.0 - - + +
62B THR* 3.0 31.3 + - + +
63B ILE* 3.8 15.5 - - + +
65B LYS* 1.3 75.5 - - - +
67B ARG* 1.3 64.0 + - + +
69B LEU 3.2 0.9 + - - -
70B ARG* 3.0 54.8 + - + +
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Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASP* 2.6 49.5 + - - +
38B VAL* 3.4 26.1 - - - +
39B TYR* 3.4 44.9 + - - -
63B ILE* 3.1 38.4 + - + +
64B ASN* 3.1 12.8 + - - +
66B ILE* 1.3 77.5 - - + +
68B ASP* 1.3 61.2 + - - +
70B ARG* 4.0 12.6 + - - +
72B LYS* 3.8 17.5 - - - +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.4 4.0 + - - -
64B ASN 2.9 14.2 + - - +
65B LYS* 3.8 7.9 - - - +
66B ILE 3.2 0.2 - - - -
67B ARG* 1.3 77.1 - - - +
69B LEU* 1.3 66.5 + - + +
72B LYS* 2.8 46.9 + - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.0 62.7 + - + +
13A LYS* 4.2 35.7 - - + +
14A MET* 3.6 22.2 - - + -
17A LEU* 4.8 6.1 - - + -
65B LYS* 3.0 48.7 + - + +
68B ASP* 1.3 80.0 - - + +
70B ARG* 1.3 65.1 + - - +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.0 11.4 + - - -
14A MET* 3.6 19.7 - - + -
28B ASP* 2.9 33.5 + - - +
31B LEU* 3.5 35.0 + - + +
32B ASP* 3.1 19.8 + - - +
35B ASP* 4.1 15.7 + - - +
66B ILE* 3.0 36.8 + - - +
67B ARG* 4.0 9.4 - - - +
68B ASP 3.6 4.0 - - - +
69B LEU* 1.3 81.1 - - - +
71B MET* 1.3 67.6 + - - +
72B LYS* 3.1 4.9 + - - +
398B THR* 3.4 20.5 - - - +
400B TYR* 3.4 15.1 + - + +
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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