Contacts of the helix formed by residues 22 - 33 (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 ALA 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B MET* 4.7 0.7 - - - -
20B GLY 4.3 0.2 + - - -
21B TYR* 1.3 73.7 - - - +
23B PHE* 1.3 66.2 + - - +
24B GLU* 3.3 17.0 - - - +
25B GLU* 3.3 20.6 + - + +
26B VAL* 3.0 24.4 + - - +
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Residues in contact with PHE 23 (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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13B ILE* 3.8 21.5 - - + -
17B MET* 3.7 40.6 - - + +
22B ALA* 1.3 73.4 - - - +
24B GLU* 1.3 64.0 + - + +
26B VAL* 3.3 1.1 + - - +
27B LYS* 2.8 63.6 + - + +
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Residues in contact with GLU 24 (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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22B ALA* 4.2 13.6 - - + +
23B PHE* 1.3 84.4 + - + +
25B GLU* 1.3 72.2 + - + +
27B LYS* 4.1 3.3 - - - +
28B ARG* 3.2 25.2 + - - +
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Residues in contact with GLU 25 (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* 4.4 3.6 - - + -
22B ALA* 3.3 28.2 + - + +
24B GLU* 1.3 80.3 - - + +
26B VAL* 1.3 60.6 + - - +
28B ARG* 3.4 15.7 + - - +
29B ALA* 2.9 29.8 + - - +
44B LEU* 3.8 19.0 - - + +
47B PHE* 4.4 24.5 - - - +
48B SER* 5.5 3.5 - - - -
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Residues in contact with VAL 26 (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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13B ILE* 3.4 42.0 - - + +
16B LEU* 3.6 17.7 - - + -
17B MET* 3.8 24.0 - - + +
21B TYR* 3.7 21.3 - - + -
22B ALA 3.0 17.9 + - - +
23B PHE 3.7 3.1 - - - +
25B GLU* 1.3 72.4 - - - +
27B LYS* 1.3 66.7 + - - +
29B ALA* 3.1 3.1 + - - +
30B LEU* 2.9 32.9 + - + +
44B LEU* 4.4 6.5 - - + -
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Residues in contact with LYS 27 (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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13B ILE* 3.6 31.4 - - + +
23B PHE* 2.8 52.7 + - + +
24B GLU* 4.1 3.6 - - - +
26B VAL* 1.3 73.4 - - - +
28B ARG* 1.3 60.9 + - - +
30B LEU* 3.6 3.0 + - - +
31B GLU* 3.2 56.1 + - - +
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Residues in contact with ARG 28 (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* 2.8 42.9 + - - -
24B GLU 3.2 19.4 + - - +
25B GLU* 3.5 15.5 + - - +
26B VAL 3.1 0.6 - - - -
27B LYS* 1.3 73.3 - - - +
29B ALA* 1.3 65.6 + - - +
31B GLU* 3.1 22.1 + - - +
32B ILE* 3.1 28.2 + - + +
47B PHE* 3.9 24.5 - - + -
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Residues in contact with ALA 29 (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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25B GLU 2.9 17.8 + - - +
26B VAL 3.1 4.2 + - - +
28B ARG* 1.3 76.9 - - - +
30B LEU* 1.3 61.4 + - - +
32B ILE* 3.4 2.1 + - - -
33B ALA* 3.0 23.9 + - - +
40B ALA* 3.9 13.7 - - + +
43B ILE* 3.4 29.4 - - + +
44B LEU* 3.7 26.7 - - + -
47B PHE* 5.8 1.3 - - + -
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Residues in contact with LEU 30 (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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9B VAL* 5.3 4.0 - - + +
12B LYS* 3.6 29.4 - - + +
13B ILE* 4.5 8.7 - - + -
16B LEU* 4.1 11.7 - - + -
26B VAL* 2.9 44.2 + - + +
27B LYS* 4.0 6.3 - - - +
29B ALA* 1.3 75.4 - - - +
31B GLU* 1.3 59.4 + - + +
33B ALA* 3.2 7.7 + - - +
35B ASN* 2.8 40.7 + - + +
36B ASN 3.4 40.8 - - - +
37B VAL* 3.9 1.6 - - - +
40B ALA* 3.7 13.5 - - + -
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Residues in contact with GLU 31 (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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42A SER* 4.7 2.6 + - - -
27B LYS* 3.2 41.1 + - - +
28B ARG* 3.1 16.6 + - - +
30B LEU* 1.3 75.2 - - + +
32B ILE* 1.3 64.8 + - + +
34B GLN* 3.6 9.4 + - - +
35B ASN* 3.8 12.4 - - - +
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Residues in contact with ILE 32 (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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39A VAL* 3.7 9.6 - - - +
42A SER* 3.1 53.3 + - - +
43A ILE* 4.0 12.6 - - + +
46A GLU* 3.6 34.8 - - + +
28B ARG* 3.1 33.3 + - + +
29B ALA 3.7 6.3 - - - +
30B LEU 3.2 0.2 - - - -
31B GLU* 1.3 80.1 - - + +
33B ALA* 1.3 53.9 + - - +
34B GLN 3.2 5.6 + - - -
43B ILE* 3.8 18.6 - - + -
47B PHE* 4.0 15.7 - - + -
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Residues in contact with ALA 33 (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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39A VAL* 3.9 19.0 - - - +
29B ALA 3.0 18.4 + - - +
30B LEU* 3.2 6.0 + - - +
32B ILE* 1.3 71.8 - - - +
34B GLN* 1.3 68.5 + - - +
36B ASN* 3.4 37.4 - - - +
39B VAL* 3.8 4.6 - - + +
40B ALA* 3.6 14.1 - - - +
43B ILE* 3.6 9.6 - - + +
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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