Contacts of the helix formed by residues 47 - 57 (chain A) in PDB entry 2D8S
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 ALA 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU 6.0 0.4 - - - +
29A SER* 5.0 12.4 - - - -
45A HIS* 3.0 1.4 - - + +
46A GLN* 1.3 77.2 - - + +
48A CYS* 1.3 70.2 + - - +
49A LEU 3.0 1.3 - - - -
50A GLN* 2.7 43.8 + - - +
51A GLN 3.9 0.7 + - - -
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Residues in contact with CYS 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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18A CYS* 4.0 0.7 - - - -
20A ILE* 4.0 24.3 - - + +
21A CYS* 4.0 12.6 - - - -
45A HIS* 3.1 13.8 + - + +
47A ALA* 1.3 78.6 - - - +
49A LEU* 1.3 66.8 + - - +
50A GLN 2.7 1.9 + - - -
51A GLN* 2.9 21.4 + - - +
52A TRP* 3.2 8.8 + - - +
201A ZN 2.3 37.2 - - - -
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Residues in contact with LEU 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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20A ILE* 4.3 5.8 - - + -
32A ILE* 5.8 4.0 - - + -
34A PRO* 4.3 12.1 - - + -
44A VAL* 3.6 23.9 - - + +
45A HIS 2.8 20.5 + - - +
46A GLN* 3.5 11.7 - - - +
48A CYS* 1.3 71.0 - - - +
50A GLN* 1.3 65.8 + - + +
52A TRP* 3.4 8.8 + - + +
53A ILE* 3.0 32.8 + - + +
68A PHE* 3.6 47.6 - - + -
69A ILE 3.4 28.0 - - - +
70A MET* 5.0 2.9 - - + -
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Residues in contact with GLN 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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46A GLN* 3.9 12.9 + - - +
47A ALA* 2.7 39.8 + - - +
49A LEU* 1.3 68.8 - - + +
51A GLN* 1.3 58.8 + - - +
53A ILE* 2.5 27.2 + - - -
54A LYS* 3.0 30.4 + - - +
70A MET* 3.9 38.0 - - + +
71A GLU* 5.9 2.2 + - - +
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Residues in contact with GLN 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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20A ILE* 4.8 15.0 - - + +
47A ALA 3.9 0.6 + - - +
48A CYS* 2.9 16.9 + - - +
50A GLN* 1.3 75.2 - - - +
52A TRP* 1.3 63.5 + - - +
54A LYS* 3.3 10.9 + - + +
55A SER* 3.1 28.6 + - - -
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Residues in contact with TRP 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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19A ARG* 3.6 28.2 - - - +
20A ILE* 3.9 33.6 - - + +
48A CYS 3.2 1.6 + - - -
49A LEU* 3.4 11.7 - - + +
50A GLN 2.7 4.2 + - - -
51A GLN* 1.3 78.9 - - - +
53A ILE* 1.3 83.3 + - + +
54A LYS 3.2 0.2 + - - -
55A SER* 3.2 3.2 + - - -
56A SER* 2.7 59.6 + - - -
58A THR* 3.1 46.7 - - + -
60A CYS 4.4 0.9 - - - -
61A CYS* 6.0 0.2 - - - -
62A GLU* 6.0 6.1 - - + -
68A PHE* 3.5 27.4 - + - -
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Residues in contact with ILE 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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49A LEU* 3.0 35.2 + - + +
50A GLN* 2.5 17.0 + - - +
52A TRP* 1.3 80.6 - - + +
54A LYS* 1.3 62.9 + - + +
57A ASP* 2.9 27.6 + - - -
58A THR 3.2 28.8 + - - +
59A ARG* 4.2 20.4 - - + +
68A PHE* 4.3 13.5 - - + -
70A MET* 3.1 34.8 - - + -
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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 GLN* 3.0 38.7 + - - +
51A GLN* 3.5 10.8 - - + +
53A ILE* 1.3 80.6 - - + +
55A SER* 1.3 55.6 + - - +
57A ASP* 2.6 30.1 + - - +
70A MET* 4.9 12.4 - - - +
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Residues in contact with SER 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 GLN* 3.1 23.9 + - - -
52A TRP* 3.9 3.8 - - - -
54A LYS* 1.3 74.8 - - - +
56A SER* 1.3 55.1 + - - +
57A ASP* 2.6 34.9 - - - +
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Residues in contact with SER 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 TRP* 2.7 61.6 + - - -
55A SER* 1.3 74.5 + - - +
57A ASP* 1.3 70.8 + - - +
58A THR* 3.2 9.9 + - - -
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Residues in contact with ASP 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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53A ILE* 2.9 16.2 + - - -
54A LYS 2.6 21.6 - - - +
55A SER 2.6 18.8 + - - +
56A SER* 1.3 81.2 - - - +
58A THR* 1.3 59.6 + - - +
59A ARG* 5.6 2.4 - - - +
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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