Contacts of the helix formed by residues 46 - 55 (chain A) in PDB entry 2DK6
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 SER 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A TRP 5.4 2.6 - - - +
21A GLY* 5.2 3.1 - - - -
22A TRP* 4.1 20.3 - - - -
33A MET* 3.9 21.5 - - - +
34A PHE* 3.3 35.3 + - - -
36A PRO* 5.4 0.4 - - - +
45A SER* 1.3 71.4 - - - +
47A GLU* 1.3 61.9 + - - +
49A ILE* 4.4 2.4 - - - +
50A GLU* 3.3 24.4 + - - +
95A PHE* 4.7 7.0 - - - -
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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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45A SER* 2.6 14.3 + - - -
46A SER* 1.3 76.3 + - - +
48A ASP* 1.3 55.7 + - - +
50A GLU* 3.4 4.0 + - - +
51A LYS* 2.8 47.7 + - + +
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Residues in contact with ASP 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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44A VAL* 3.5 32.5 - - + +
45A SER* 2.8 20.3 + - - +
47A GLU* 1.3 77.5 - - - +
49A ILE* 1.3 82.3 + - - +
51A LYS* 3.1 27.6 + - - +
52A SER* 3.2 10.7 + - - -
61A ILE* 3.2 25.9 - - - +
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Residues in contact with ILE 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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22A TRP* 4.2 18.6 - - + -
34A PHE* 2.9 57.9 - - + -
44A VAL* 3.6 26.9 - - + -
45A SER 3.4 6.3 + - - +
46A SER* 4.5 2.9 - - - +
48A ASP* 1.3 83.3 + - - +
50A GLU* 1.3 66.6 + - - +
52A SER* 3.0 19.9 + - - -
53A PHE 3.2 4.2 + - - -
61A ILE* 4.6 5.4 - - + -
72A ILE* 4.0 13.9 - - + -
74A PHE* 3.3 36.1 - - + -
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Residues in contact with GLU 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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20A TRP* 3.7 31.0 - - - +
22A TRP* 2.8 37.1 + - + +
46A SER 3.3 19.5 + - - +
47A GLU* 3.4 4.4 + - - +
48A ASP 3.3 0.6 - - - -
49A ILE* 1.3 78.2 - - - +
51A LYS* 1.3 68.1 + - - +
52A SER 2.7 2.1 + - - -
53A PHE* 2.9 30.2 + - - -
54A LYS* 3.0 35.7 + - - +
92A ARG* 3.8 10.2 + - - -
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Residues in contact with LYS 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* 2.8 27.8 + - + +
48A ASP* 3.1 26.9 + - - +
50A GLU* 1.3 73.4 - - - +
52A SER* 1.3 63.4 + - - +
54A LYS* 3.3 29.8 - - + +
55A THR* 3.8 7.1 + - - +
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Residues in contact with SER 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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48A ASP 3.2 3.3 + - - -
49A ILE 3.0 8.9 + - - -
50A GLU 2.7 4.8 + - - -
51A LYS* 1.3 72.4 + - - +
53A PHE* 1.3 54.3 + - - -
54A LYS 2.6 17.2 + - - -
55A THR* 2.8 20.4 + - - +
56A ASN* 2.4 26.9 + - - +
61A ILE* 2.9 35.5 - - - +
74A PHE* 3.7 9.2 - - - -
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Residues in contact with PHE 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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22A TRP* 3.6 31.0 - + + -
49A ILE 3.2 0.8 + - - +
50A GLU* 2.9 22.0 + - - +
52A SER* 1.3 75.1 - - - +
54A LYS* 1.3 64.4 + - + +
56A ASN 3.4 1.6 - - - -
57A PRO* 2.8 57.4 - - + +
74A PHE* 3.1 44.7 - + + -
77A MET* 5.1 8.5 - - + -
92A ARG* 3.8 32.3 - - + -
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Residues in contact with LYS 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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50A GLU* 3.0 38.2 + - - +
51A LYS* 3.3 27.5 - - + +
52A SER 2.6 4.6 + - - -
53A PHE* 1.3 82.3 - - + +
55A THR* 1.3 63.2 + - - +
57A PRO* 3.5 8.5 - - - +
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Residues in contact with THR 55 (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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51A LYS 4.0 6.7 - - - +
52A SER* 2.8 20.3 + - - +
54A LYS* 1.3 78.4 - - - +
56A ASN* 1.3 70.8 + - + +
57A PRO* 3.3 7.4 - - - +
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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