Contacts of the helix formed by residues 34 - 43 (chain A) 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 HIS 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ALA 3.9 1.4 + - - -
33A LEU* 1.3 72.5 - - - +
35A ILE* 1.3 82.2 + - + +
36A TYR* 2.9 39.3 - - + +
37A GLU* 2.8 27.1 + - + +
38A GLN 3.0 9.2 + - - -
68A VAL* 6.0 0.4 - - - +
207B ASN* 6.4 0.2 - - - +
209B ARG* 6.1 0.8 - - - +
211B ILE* 5.0 7.9 - - + +
228B ASP 4.7 0.6 + - - -
229B TYR* 3.1 56.0 + + + -
230B ASP* 5.5 1.0 + - - +
231B PHE* 3.8 18.5 - + - -
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Residues in contact with ILE 35 (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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33A LEU 3.7 1.2 + - - -
34A HIS* 1.3 87.0 - - + +
36A TYR* 1.3 58.8 + - - +
38A GLN* 3.4 25.2 - - - +
39A GLY* 3.0 21.3 + - - -
64A ASP* 3.4 41.5 - - + +
65A MSE 4.0 3.3 - - - +
67A ASP* 5.3 1.6 - - + -
68A VAL* 3.4 39.8 - - + +
230B ASP* 5.3 1.8 - - + +
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Residues in contact with TYR 36 (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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7A MSE 5.9 2.5 - - + -
34A HIS* 2.9 20.5 - - + +
35A ILE* 1.3 75.3 - - + +
37A GLU* 1.3 68.8 + - + +
39A GLY* 3.2 2.6 + - - +
40A GLN* 3.2 58.0 + - + +
68A VAL* 4.1 17.0 - - + -
228B ASP* 3.4 60.6 + - + +
229B TYR* 3.9 30.7 - + + -
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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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7A MSE 3.0 38.3 - - + +
11A PHE* 3.4 9.1 - - - -
33A LEU* 3.5 27.2 - - + +
34A HIS* 2.8 25.4 + - + +
36A TYR* 1.3 77.9 - - + +
38A GLN* 1.3 66.1 + - - +
40A GLN* 3.2 6.4 + - - +
41A PHE* 2.9 21.3 + - - +
209B ARG* 5.0 10.8 - - - +
211B ILE* 4.8 7.3 - - - +
229B TYR* 3.1 34.2 + - + +
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Residues in contact with GLN 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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30A PHE* 3.3 59.8 + - + +
31A LEU* 4.2 13.0 + - - +
33A LEU* 2.7 29.9 + - + +
34A HIS 3.0 9.4 + - - +
35A ILE* 3.4 29.4 - - - +
37A GLU* 1.3 77.7 - - - +
39A GLY* 1.3 57.2 + - - +
41A PHE* 3.5 2.5 + - - +
42A TYR* 3.0 30.7 + - - +
61A GLU 4.6 5.0 - - - +
64A ASP* 5.3 0.9 - - - +
65A MSE 3.4 18.9 - - + +
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Residues in contact with GLY 39 (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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35A ILE 3.0 12.3 + - - -
36A TYR* 3.2 5.3 + - - -
37A GLU 3.1 0.4 - - - -
38A GLN* 1.3 78.3 - - - +
40A GLN* 1.3 57.1 + - - +
42A TYR* 3.4 1.2 + - - +
43A GLN* 2.9 41.3 + - - +
65A MSE 3.7 8.5 - - - +
69A ILE* 3.2 26.2 - - - -
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Residues in contact with GLN 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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7A MSE 5.9 1.1 - - + -
11A PHE* 4.0 15.2 - - + -
36A TYR* 3.2 55.5 + - + +
37A GLU* 3.2 7.4 + - - +
39A GLY* 1.3 71.5 - - - +
41A PHE* 1.3 69.9 + - - +
43A GLN* 3.2 30.8 + - - +
44A SER* 3.3 13.2 + - - -
69A ILE* 5.5 0.4 - - - +
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Residues in contact with PHE 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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11A PHE* 3.5 45.4 - + + -
14A LEU* 3.5 50.7 - - + -
15A LEU* 3.9 15.9 - - + -
18A LEU* 4.3 5.6 - - + -
26A PHE* 4.0 16.8 - + - -
30A PHE* 4.1 13.9 - + - -
33A LEU* 4.7 0.4 - - + -
37A GLU 2.9 15.7 + - - +
38A GLN* 3.7 5.8 - - - +
40A GLN* 1.3 76.0 - - - +
42A TYR* 1.3 66.4 + - - +
44A SER* 2.5 27.7 + - - -
45A LEU* 3.4 39.1 - - + +
53A LEU* 4.6 0.9 - - + -
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Residues in contact with TYR 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 GLN 3.0 18.6 + - - +
39A GLY 3.7 2.5 - - - +
41A PHE* 1.3 79.2 - - + +
43A GLN* 1.3 69.7 + - + +
44A SER 3.2 3.8 + - - -
45A LEU* 3.3 26.3 + - + +
50A ARG* 4.2 17.3 + - + +
53A LEU* 3.7 22.4 - - + -
54A TYR* 2.6 42.4 + + - -
65A MSE 3.5 28.9 - - + -
66A PHE* 3.6 22.4 - + - -
69A ILE* 5.3 4.3 - - + -
79A TYR* 3.2 46.3 - + - +
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Residues in contact with GLN 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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39A GLY 2.9 19.9 + - - +
40A GLN* 3.2 22.1 + - - +
42A TYR* 1.3 82.9 - - + +
44A SER* 1.3 57.6 + - - +
45A LEU 4.7 2.5 - - - +
50A ARG* 6.1 0.4 - - - +
69A ILE* 2.8 41.3 - - + +
70A GLU 5.2 0.8 - - - +
73A ASN* 3.2 23.2 - - - +
79A TYR* 3.7 25.0 + - + +
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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