Contacts of the helix formed by residues 36 - 47 (chain A) in PDB entry 1QXJ
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 ASP 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE* 3.4 3.6 - - - +
35A VAL* 1.3 77.4 - - + +
37A GLU* 1.3 60.8 + - - +
38A ARG* 3.2 12.1 + - - +
39A ALA* 3.0 32.5 + - + +
40A TRP* 3.1 19.6 + - - +
78A VAL* 3.7 17.4 + - - +
79A GLY* 4.0 9.4 - - - -
80A LYS 5.4 1.3 - - - +
81A GLU* 4.5 1.6 + - - -
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Residues in contact with GLU 37 (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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31A GLU* 6.4 2.2 - - + -
32A GLY* 6.2 3.1 - - - +
34A PHE 4.6 6.5 - - - +
35A VAL 3.1 10.9 + - - +
36A ASP* 1.3 69.4 - - - +
38A ARG* 1.3 61.0 + - - +
40A TRP* 3.5 16.3 - - + +
41A LYS* 2.5 77.9 + - - +
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Residues in contact with ARG 38 (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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36A ASP* 3.2 9.1 + - - +
37A GLU* 1.3 81.2 + - - +
39A ALA* 1.3 63.4 + - - +
41A LYS* 3.9 4.9 - - - +
42A GLU* 3.0 26.0 + - - +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP* 3.0 30.2 + - - +
38A ARG* 1.3 77.7 - - - +
40A TRP* 1.3 56.1 + - - +
42A GLU* 3.8 7.5 - - - +
43A LEU* 2.8 32.8 + - + +
78A VAL* 4.1 3.1 - - + -
79A GLY* 3.6 25.8 - - - +
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Residues in contact with TRP 40 (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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27A LEU* 3.1 49.7 + - + +
28A SER* 4.1 9.6 - - - -
30A MET 3.3 12.7 + - - -
31A GLU* 3.5 44.9 - - + -
32A GLY 5.5 2.2 - - - -
34A PHE* 3.9 20.0 - + + +
36A ASP 3.1 13.8 + - - +
37A GLU* 3.5 21.3 - - + +
39A ALA* 1.3 75.9 - - - +
41A LYS* 1.3 98.9 + - + +
43A LEU* 3.2 5.0 + - - +
44A VAL* 2.8 52.4 + - + +
78A VAL* 3.6 11.6 - - + +
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Residues in contact with LYS 41 (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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31A GLU* 5.7 3.0 + - - -
37A GLU* 2.5 50.7 + - - +
38A ARG* 3.9 4.9 - - - +
40A TRP* 1.3 95.2 - - + +
42A GLU* 1.3 64.2 + - - +
44A VAL* 3.3 3.8 + - + +
45A GLU* 3.0 44.4 + - + +
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Residues in contact with GLU 42 (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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38A ARG 3.0 19.8 + - - +
39A ALA* 3.8 7.4 - - - +
41A LYS* 1.3 77.6 - - - +
43A LEU* 1.3 61.8 + - + +
45A GLU* 3.3 9.6 + - - +
46A LYS* 2.9 40.6 + - + +
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Residues in contact with LEU 43 (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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27A LEU* 3.6 28.0 - - + -
39A ALA* 2.8 22.1 + - + +
40A TRP 3.8 0.4 - - - +
42A GLU* 1.3 75.5 - - + +
44A VAL* 1.3 57.0 + - - +
46A LYS* 4.6 13.9 - - + +
47A GLU* 3.0 52.2 + - + +
48A ASP 3.0 6.6 + - - -
49A PRO* 4.0 10.1 - - + -
77A LYS 3.6 24.0 - - - +
78A VAL* 4.8 4.3 - - + -
83A PHE* 4.5 7.0 - - + -
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Residues in contact with VAL 44 (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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27A LEU* 3.9 9.9 - - + -
28A SER* 3.8 33.7 - - - +
40A TRP* 2.8 56.2 + - + +
41A LYS* 3.7 7.6 - - + +
43A LEU* 1.3 75.6 - - - +
45A GLU* 1.3 63.3 + - + +
47A GLU 4.2 0.3 - - - -
48A ASP* 3.3 27.1 + - - +
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Residues in contact with GLU 45 (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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41A LYS* 3.0 36.5 + - + +
42A GLU* 3.7 6.6 - - - +
44A VAL* 1.3 78.8 - - + +
46A LYS* 1.3 67.6 + - - +
47A GLU* 4.7 0.2 - - - -
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Residues in contact with LYS 46 (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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42A GLU* 2.9 29.0 + - + +
43A LEU* 4.1 12.0 - - + +
45A GLU* 1.3 78.0 - - - +
47A GLU* 1.3 92.7 + - + +
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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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26A ARG* 4.6 3.3 + - - -
43A LEU* 3.0 21.1 + - + +
44A VAL 4.2 0.9 - - - -
45A GLU 3.6 0.6 - - - -
46A LYS* 1.3 106.9 + - - +
48A ASP* 1.3 75.1 + - - +
49A PRO* 3.3 26.9 - - + +
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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