Contacts of the helix formed by residues 22 - 31 (chain B) in PDB entry 2OUX
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 GLN 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B GLU 4.8 0.3 - - - -
17B THR* 2.9 32.0 + - - +
20B ASN* 3.6 37.1 + - + +
21B GLN* 1.3 71.9 - - - +
23B MSE 1.3 65.3 + - - +
24B ASN 3.2 2.2 - - - -
25B GLU* 3.0 44.2 + - + +
26B PHE* 3.0 11.3 + - - +
56B TYR* 5.2 0.2 - - - -
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Residues in contact with MSE 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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21B GLN 3.4 6.0 + - - +
22B GLN* 1.3 71.9 - - - +
24B ASN* 1.3 82.5 + - - +
26B PHE* 3.4 2.1 + - - +
27B ARG* 3.0 48.7 + - - +
55B ASN 4.5 4.9 - - - +
56B TYR* 3.6 53.1 - - + +
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Residues in contact with ASN 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 GLN 3.0 1.2 + - - -
23B MSE 1.3 96.9 - - - +
25B GLU* 1.3 71.0 + - - +
27B ARG* 3.5 9.0 + - - +
28B GLU* 3.2 23.6 + - - +
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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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17B THR* 4.1 17.0 - - + -
22B GLN* 3.0 38.8 + - + +
24B ASN* 1.3 86.7 + - - +
26B PHE* 1.3 62.3 + - - +
28B GLU* 3.3 8.1 + - - +
29B LEU* 3.2 27.7 + - + +
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Residues in contact with PHE 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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14B LEU* 3.5 24.4 - - + +
17B THR* 3.3 29.5 - - - +
18B LEU* 3.5 27.1 - - + -
22B GLN 3.0 10.8 + - - +
23B MSE 3.5 9.4 - - - +
25B GLU* 1.3 77.3 - - - +
27B ARG* 1.3 63.2 + - + +
29B LEU 3.2 1.4 + - - -
30B PHE* 2.8 61.6 + + + +
41B PHE* 3.9 15.3 - + - -
53B LEU* 4.1 20.0 - - + -
56B TYR* 3.9 30.5 - + + -
57B LEU* 4.3 15.5 - - + -
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Residues in contact with ARG 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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23B MSE 3.0 44.2 + - + +
24B ASN* 3.9 9.3 + - - +
25B GLU 3.4 0.2 - - - -
26B PHE* 1.3 86.9 - - + +
28B GLU* 1.3 57.2 + - - +
30B PHE* 4.4 3.6 - - - -
31B LEU* 2.9 50.9 + - + +
56B TYR 2.5 39.6 + - - +
57B LEU* 3.6 6.7 - - + +
58B SER 4.5 0.4 - - - +
61B GLU* 2.9 40.0 + - - -
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Residues in contact with GLU 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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24B ASN 3.2 14.4 + - - +
25B GLU* 3.8 6.9 - - - +
26B PHE 3.3 0.2 - - - -
27B ARG* 1.3 79.6 - - - +
29B LEU* 1.3 63.8 + - + +
31B LEU* 4.5 1.2 - - - +
32B ALA* 3.4 19.8 + - - +
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Residues in contact with LEU 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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10B GLN* 4.1 27.9 - - - +
13B LEU* 4.1 39.9 - - + +
14B LEU* 3.7 18.8 - - + -
17B THR* 4.5 7.2 - - + -
25B GLU* 3.2 13.9 + - + +
26B PHE 3.2 1.8 + - - -
28B GLU* 1.3 80.5 - - + +
30B PHE* 1.3 65.3 + - - +
32B ALA* 3.3 17.6 + - + +
33B LEU* 3.7 12.0 - - - +
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Residues in contact with PHE 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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14B LEU* 3.8 13.6 - - + +
26B PHE* 2.8 40.9 + + + +
27B ARG* 4.1 1.8 - - - +
29B LEU* 1.3 73.1 - - - +
31B LEU* 1.3 73.1 + - + +
32B ALA 3.0 4.7 - - - -
33B LEU* 3.1 24.0 + - + +
38B GLN* 3.3 64.3 + - + +
41B PHE* 4.2 22.2 - + - -
53B LEU* 4.4 9.4 - - + -
57B LEU* 3.5 32.8 - - + -
61B GLU 5.6 2.7 - - - -
62B LEU* 6.4 0.2 - - - -
65B MSE 4.2 13.2 - - + -
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Residues in contact with LEU 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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27B ARG* 2.9 47.3 + - + +
28B GLU* 4.5 1.6 - - - +
30B PHE* 1.3 96.3 - - + +
32B ALA* 1.3 59.0 + - - +
33B LEU 3.2 6.2 + - - +
38B GLN* 4.0 8.8 + - - +
57B LEU* 3.9 12.8 - - + -
61B GLU* 3.7 28.9 - - + +
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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