Contacts of the helix formed by residues 36 - 46 (chain B) in PDB entry 1ADO
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 THR 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B SER* 1.3 73.0 - - - +
37B GLY* 1.3 57.5 + - - +
39B ILE* 3.2 9.8 - - - +
40B ALA* 3.0 30.7 + - - +
50B ASN* 3.3 23.0 + - - +
55B ARG* 3.6 26.2 + - - +
79B PHE* 4.2 18.3 - - - -
81B GLU* 5.1 2.6 + - - -
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Residues in contact with GLY 37 (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 SER* 3.2 5.6 + - - -
36B THR* 1.3 80.5 - - - +
38B SER* 1.3 61.0 + - - +
40B ALA* 3.5 15.3 - - - +
41B LYS* 3.6 6.8 + - - +
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Residues in contact with SER 38 (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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34B GLU* 3.8 20.0 - - - -
35B SER* 3.1 21.6 + - - -
37B GLY* 1.3 71.3 - - - +
39B ILE* 1.3 68.2 + - - +
40B ALA 3.1 1.6 - - - -
41B LYS* 3.1 21.5 + - - +
42B ARG* 3.5 23.9 + - - +
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Residues in contact with ILE 39 (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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34B GLU* 3.9 19.5 - - + +
35B SER 2.9 15.3 + - - +
36B THR* 3.2 15.3 - - - +
38B SER* 1.3 77.2 - - - +
40B ALA* 1.3 66.2 + - - +
42B ARG* 3.2 15.6 + - + +
43B LEU* 3.1 36.0 + - + +
50B ASN* 4.0 2.7 - - - +
55B ARG* 3.5 33.7 - - + -
58B TYR* 3.9 33.4 - - + -
59B ARG* 3.9 24.9 - - - +
306B GLN* 5.3 0.2 - - - +
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Residues in contact with ALA 40 (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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36B THR 3.0 20.7 + - - +
37B GLY* 3.5 10.3 - - - +
38B SER 3.1 0.2 - - - -
39B ILE* 1.3 77.7 - - - +
41B LYS* 1.3 60.7 + - - +
43B LEU* 3.4 2.7 + - - +
44B GLN* 3.0 34.5 + - - +
50B ASN* 3.4 31.6 - - + +
363B TYR* 6.0 0.7 - - - -
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Residues in contact with LYS 41 (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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37B GLY 3.6 6.0 + - - +
38B SER* 3.1 13.1 + - - +
40B ALA* 1.3 78.4 - - - +
42B ARG* 1.3 85.5 + - - +
44B GLN* 3.2 8.0 + - - +
45B SER* 3.0 23.7 + - - +
303B ARG* 5.5 7.0 - - - +
363B TYR* 3.1 47.3 + - + +
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Residues in contact with ARG 42 (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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34B GLU* 4.7 21.1 + - - +
38B SER* 3.5 29.4 + - - +
39B ILE* 3.2 18.9 + - + +
41B LYS* 1.3 101.6 - - - +
43B LEU* 1.3 62.8 - - + +
45B SER* 2.6 22.4 + - - -
46B ILE* 3.4 11.5 - - - +
58B TYR* 6.1 1.1 - - + +
303B ARG* 3.1 51.5 - - - +
310B LEU* 3.6 31.4 - - + +
354B GLU* 5.9 1.8 - - - +
1053B 13P 4.5 10.3 - - - -
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Residues in contact with LEU 43 (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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39B ILE* 3.1 24.1 + - + +
40B ALA* 3.7 6.3 - - - +
42B ARG* 1.3 76.5 - - - +
44B GLN* 1.3 61.6 + - - +
46B ILE* 3.0 15.9 - - + +
48B THR* 2.8 41.6 + - + +
49B GLU 4.0 5.8 - - - +
50B ASN* 3.5 38.6 - - + +
51B THR 4.5 0.2 - - - +
54B ASN* 4.9 8.5 - - + +
55B ARG* 4.2 15.3 - - + -
58B TYR* 5.1 7.0 - - + -
310B LEU* 5.1 2.2 - - + -
313B TRP* 3.9 32.1 - - + -
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Residues in contact with GLN 44 (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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40B ALA* 3.0 25.2 + - - +
41B LYS 3.2 8.7 + - - +
43B LEU* 1.3 76.9 - - - +
45B SER* 1.3 57.4 + - - +
47B GLY* 2.8 21.1 + - - +
48B THR 2.7 31.9 + - - +
49B GLU* 4.0 7.9 - - - +
50B ASN* 4.3 13.5 + - - +
363B TYR* 3.2 39.5 + - + +
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Residues in contact with SER 45 (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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41B LYS* 3.0 12.4 + - - +
42B ARG* 2.6 30.5 + - - +
44B GLN* 1.3 73.7 - - - +
46B ILE* 1.3 60.3 + - - +
47B GLY 3.5 0.4 - - - -
310B LEU* 4.5 5.9 - - - +
354B GLU* 5.7 1.5 + - - -
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Residues in contact with ILE 46 (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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42B ARG 3.4 8.1 - - - +
43B LEU* 3.0 18.4 - - - +
45B SER* 1.3 82.1 - - - +
47B GLY* 1.3 61.0 + - - +
48B THR* 3.6 12.6 + - - +
310B LEU* 3.7 40.6 - - + +
311B LYS* 4.0 17.3 - - + +
313B TRP* 3.6 37.9 - - + -
314B GLY* 4.0 18.2 - - - +
315B GLY 4.3 4.5 - - - +
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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