Contacts of the helix formed by residues 36 - 48 (chain B) in PDB entry 2DO6
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 ASN 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLN* 4.4 7.1 - - - +
39A VAL* 6.2 0.8 - - - +
4B GLY* 5.2 14.0 + - - +
12B LYS* 4.1 3.1 - - - +
30B LEU* 3.4 5.5 - - - +
33B ALA* 3.4 20.2 + - - +
34B GLN 3.5 2.7 - - - +
35B ASN* 1.3 76.0 - - - +
37B VAL* 1.3 62.8 + - - +
38B GLU* 3.1 25.6 + - - +
39B VAL* 3.4 20.4 + - + +
40B ALA* 3.0 28.4 + - - +
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Residues in contact with VAL 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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11B ALA 5.0 0.4 - - - +
12B LYS* 3.6 43.9 - - + +
15B LYS* 4.1 31.0 - - + +
16B LEU* 3.7 27.7 - - + +
30B LEU* 3.9 1.0 - - - +
36B ASN* 1.3 73.8 + - - +
38B GLU* 1.3 68.6 + - + +
40B ALA* 3.2 2.3 + - - +
41B ARG* 3.2 23.8 + - - +
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Residues in contact with GLU 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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34A GLN* 3.4 37.8 + - - +
1B GLY* 2.7 35.5 + - - -
36B ASN* 3.1 14.7 + - - +
37B VAL* 1.3 83.1 - - + +
39B VAL* 1.3 59.2 + - - +
41B ARG* 4.0 10.1 - - - +
42B SER* 3.9 9.0 + - - -
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Residues in contact with VAL 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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32A ILE 3.6 17.5 - - - +
33A ALA* 3.7 21.8 - - - +
34A GLN* 3.6 27.1 - - + +
36A ASN* 6.0 0.4 - - + -
39A VAL* 3.7 20.9 - - + -
43A ILE* 5.3 0.7 - - + -
33B ALA* 3.8 15.7 - - + +
36B ASN* 3.4 18.2 + - + +
37B VAL 3.2 0.4 - - - -
38B GLU* 1.3 72.2 - - - +
40B ALA* 1.3 68.2 + - - +
41B ARG 3.1 2.2 - - - -
42B SER* 2.9 18.7 + - - -
43B ILE* 3.3 16.6 + - + +
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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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16B LEU* 4.2 6.7 - - + -
29B ALA* 4.1 12.8 - - + +
30B LEU* 3.7 30.7 - - + -
33B ALA* 3.6 6.6 - - - +
36B ASN 3.0 18.3 + - - +
37B VAL* 3.2 6.5 + - - +
39B VAL* 1.3 75.1 - - - +
41B ARG* 1.3 62.3 + - - +
43B ILE* 3.2 9.6 + - - +
44B LEU* 2.9 28.1 + - - +
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Residues in contact with ARG 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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15B LYS* 6.3 1.0 - - - +
16B LEU* 4.2 13.5 - - + +
19B GLU* 2.8 42.0 + - - +
21B TYR* 5.4 0.8 + - + -
37B VAL* 3.2 14.8 + - + +
38B GLU* 4.0 8.7 - - - +
39B VAL 3.0 0.8 + - - -
40B ALA* 1.3 75.9 - - - +
42B SER* 1.3 58.5 + - - +
44B LEU* 3.2 6.1 + - - +
45B ARG* 2.9 48.5 + - + +
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Residues in contact with SER 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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31A GLU 5.2 0.3 + - - -
32A ILE* 3.3 40.9 + - - +
34A GLN* 4.9 4.0 - - - +
38B GLU 3.9 9.5 + - - -
39B VAL 2.9 7.5 + - - -
41B ARG* 1.3 78.6 - - - +
43B ILE* 1.3 60.8 + - - +
45B ARG* 3.5 12.0 - - - +
46B GLU* 3.4 24.4 + - - +
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Residues in contact with ILE 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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32A ILE* 3.8 19.3 - - + -
43A ILE* 4.8 5.8 - - + -
29B ALA* 3.4 37.9 - - + +
32B ILE* 3.8 18.8 - - + -
33B ALA* 3.6 28.3 - - + +
39B VAL* 3.6 13.7 - - + +
40B ALA* 3.2 6.9 + - - +
41B ARG 3.2 0.6 - - - -
42B SER* 1.3 74.8 - - - +
44B LEU* 1.3 60.4 + - - +
46B GLU* 2.9 21.2 + - + +
47B PHE* 3.0 39.8 + - + -
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Residues in contact with LEU 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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16B LEU* 3.5 41.5 - - + -
21B TYR* 3.7 46.4 - - + -
25B GLU* 3.8 37.7 - - + +
26B VAL* 4.5 2.9 - - + -
29B ALA* 3.7 11.7 - - + -
40B ALA 2.9 17.4 + - - +
41B ARG* 3.2 4.2 + - - +
43B ILE* 1.3 74.6 - - - +
45B ARG* 1.3 56.6 + - - +
47B PHE* 4.5 8.3 - - + +
48B SER* 2.9 32.4 + - - -
49B GLY 3.2 4.7 + - - -
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Residues in contact with ARG 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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21B TYR* 4.9 11.1 + - - +
41B ARG* 2.9 34.0 + - + +
42B SER* 3.5 15.3 - - - +
43B ILE 3.1 0.2 - - - -
44B LEU* 1.3 77.5 - - - +
46B GLU* 1.3 59.4 + - + +
49B GLY* 3.1 31.4 + - - +
50B PRO* 4.4 18.4 + - - -
52B SER* 5.8 1.8 + - - -
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Residues in contact with GLU 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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28A ARG* 2.7 45.9 + - - -
32A ILE* 3.8 27.3 - - + +
47A PHE* 4.5 14.8 - - + -
42B SER 3.4 12.8 + - - +
43B ILE* 2.9 10.3 + - - +
45B ARG* 1.3 81.6 - - + +
47B PHE* 1.3 65.8 + - + +
48B SER* 3.4 1.8 - - - -
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Residues in contact with PHE 47 (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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46A GLU* 4.0 28.9 - - + -
47A PHE* 6.1 9.6 - + - -
25B GLU* 4.4 18.6 - - - +
28B ARG* 3.9 28.0 - - + -
29B ALA* 5.8 1.3 - - + -
32B ILE* 4.0 11.9 - - + -
43B ILE* 3.0 46.2 + - + +
44B LEU* 4.5 8.3 - - + +
46B GLU* 1.3 78.4 - - + +
48B SER* 1.3 57.2 + - - +
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 3.7 28.7 - - - -
25B GLU* 5.5 4.3 - - - -
44B LEU* 2.9 15.0 + - - -
45B ARG 4.1 0.7 - - - -
46B GLU 4.7 1.3 - - - -
47B PHE* 1.3 79.5 - - - +
49B GLY* 1.3 67.4 + - - +
50B PRO* 3.6 8.0 - - - +
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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