Contacts of the helix formed by residues 47 - 55 (chain A) in PDB entry 2QNU
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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44A LEU* 3.1 20.7 + - + +
46A ALA* 1.3 79.1 - - - +
48A TRP* 1.3 63.1 + - - +
49A LEU 3.5 0.7 - - - -
50A ASP* 3.8 8.7 + - - +
51A ALA* 3.3 19.6 + - - +
190A ARG* 5.1 1.2 + - - -
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Residues in contact with TRP 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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37A MSE 3.7 19.7 - - + -
40A SER* 2.9 29.2 + - - -
41A GLN* 3.4 58.3 - - + +
44A LEU* 3.7 16.7 + - + -
45A GLY 3.0 20.5 + - - +
46A ALA 3.2 0.6 - - - -
47A ALA* 1.3 76.8 - - - +
49A LEU* 1.3 101.8 + - + +
51A ALA* 3.0 5.4 + - - +
52A TYR* 2.8 65.8 + + + +
86A TYR* 3.9 15.0 - + + -
211A LEU* 3.6 12.4 - - + +
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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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45A GLY 4.7 0.4 + - - -
46A ALA 4.4 5.6 + - - +
47A ALA 3.5 0.2 - - - -
48A TRP* 1.3 99.1 - - + +
50A ASP* 1.3 59.6 + - - +
52A TYR* 3.3 1.4 + - + +
53A LEU* 2.9 57.2 + - + +
86A TYR* 3.6 43.7 - - + +
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Residues in contact with ASP 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 ALA 5.3 1.5 + - - +
47A ALA* 3.8 10.9 + - - +
48A TRP 3.2 0.6 - - - -
49A LEU* 1.3 81.2 - - - +
51A ALA* 1.3 54.3 + - - +
53A LEU* 4.2 8.5 - - - +
54A THR* 2.5 37.4 + - - +
190A ARG* 4.1 10.2 + - - +
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Residues in contact with ALA 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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44A LEU* 4.3 7.9 - - + -
47A ALA 3.3 11.4 + - - +
48A TRP 3.0 9.7 + - - +
50A ASP* 1.3 80.3 - - - +
52A TYR* 1.3 61.7 + - - +
54A THR* 3.4 2.1 + - - -
55A SER* 3.1 23.7 + - - -
190A ARG* 3.3 24.2 - - - +
211A LEU* 3.7 10.0 - - + +
212A THR* 3.6 24.9 - - + -
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Residues in contact with TYR 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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37A MSE 3.7 27.6 - - + -
48A TRP* 2.8 50.6 + + + +
49A LEU 3.7 2.7 - - - +
51A ALA* 1.3 73.7 - - - +
53A LEU* 1.3 69.9 + - + +
55A SER* 2.8 22.4 + - - -
78A PRO* 3.4 32.7 - - + +
79A SER 2.8 43.7 + - - -
86A TYR* 3.6 18.8 - + + -
87A PHE 3.2 17.0 + - - -
88A PRO* 3.4 5.4 - - + -
207A PHE* 5.7 0.7 - + - -
211A LEU* 4.2 22.3 - - + +
228A ACT 4.5 2.7 - - + -
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Residues in contact with LEU 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* 2.9 44.7 + - + +
50A ASP* 3.6 9.2 + - - +
52A TYR* 1.3 82.1 - - + +
54A THR* 1.3 62.8 + - + +
55A SER 5.0 0.9 - - - +
78A PRO* 5.1 2.9 - - - +
86A TYR* 3.8 22.7 - - + +
228A ACT 3.5 44.7 - - + +
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Residues in contact with THR 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 ASP 2.5 23.8 + - - +
51A ALA 3.5 4.4 + - - -
53A LEU* 1.3 80.8 - - + +
55A SER* 1.3 63.9 + - - +
188A SER* 3.6 19.8 + - - -
190A ARG* 3.5 23.1 + - - +
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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 ALA 3.1 15.3 + - - -
52A TYR 2.8 19.7 + - - +
53A LEU 3.6 1.1 - - - +
54A THR* 1.3 81.9 - - - +
56A PRO* 1.4 76.1 + - - +
57A LEU* 4.0 3.3 + - - +
78A PRO* 3.0 26.5 - - - +
188A SER* 4.6 1.8 - - - -
210A PHE 3.7 12.6 - - - -
211A LEU* 3.5 24.0 - - - +
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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