Contacts of the helix formed by residues 46 - 57 (chain D) in PDB entry 3OX4
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 GLY 46 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ASN 3.4 9.3 + - - -
44D LYS 3.0 6.3 - - - -
45D SER* 1.3 80.3 + - - +
47D VAL* 1.3 63.4 + - - +
48D VAL 3.4 2.2 - - - -
49D LYS* 3.6 11.3 + - - +
50D GLN* 3.1 24.3 + - - +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 5.9 0.4 - - + -
42D MET* 3.0 40.0 + - + +
45D SER* 3.3 21.5 - - - +
46D GLY* 1.3 76.1 - - - +
48D VAL* 1.3 66.0 + - - +
50D GLN* 3.3 16.7 + - - +
51D VAL* 3.0 26.0 + - + +
95D LEU* 3.9 15.7 - - + -
179D LEU* 4.4 20.0 - - + +
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ILE* 4.3 8.3 - - + +
38D SER* 3.8 25.1 - - - +
42D MET 3.0 8.9 + - - +
43D ASN* 3.4 45.3 - - + +
46D GLY 3.4 0.2 - - - -
47D VAL* 1.3 76.0 - - - +
49D LYS* 1.3 59.3 + - - +
51D VAL* 3.4 2.8 + - - +
52D ALA* 2.9 27.8 + - + +
64D VAL* 3.6 38.8 - - + -
95D LEU* 3.8 11.2 - - + -
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ASN* 5.0 5.1 + - - +
46D GLY* 3.6 15.1 + - - +
47D VAL 3.3 0.2 - - - -
48D VAL* 1.3 76.4 - - - +
50D GLN* 1.3 60.8 + - - +
52D ALA* 3.1 8.3 + - + +
53D ASP* 2.8 71.7 + - - +
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Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.5 24.7 - - + +
20D GLU* 5.3 0.7 - - - +
46D GLY 3.1 10.3 + - - +
47D VAL* 3.3 26.8 + - - +
49D LYS* 1.3 80.4 - - - +
51D VAL* 1.3 63.2 + - + +
53D ASP* 3.3 8.8 + - - +
54D LEU* 3.1 33.5 + - + +
179D LEU* 4.8 6.6 - - - +
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.6 16.2 - - + -
23D ILE* 5.0 1.8 - - + -
36D ILE* 4.3 16.8 - - + -
47D VAL* 3.0 24.8 + - + +
48D VAL 3.7 3.8 - - - +
50D GLN* 1.3 77.1 - - + +
52D ALA* 1.3 62.2 + - - +
54D LEU* 3.2 8.3 + - - +
55D LEU* 3.0 45.0 + - + +
93D ILE* 4.9 4.7 - - + -
95D LEU* 3.7 25.1 - - + -
136D ILE* 4.2 27.1 - - + -
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ILE* 4.1 8.7 - - + -
48D VAL* 2.9 21.1 + - + +
49D LYS* 3.6 9.4 - - + +
51D VAL* 1.3 78.6 - - - +
53D ASP* 1.3 61.3 + - - +
55D LEU* 3.4 5.2 + - - +
56D LYS* 2.9 33.1 + - + +
60D ILE 4.6 0.5 - - - +
62D SER* 3.8 21.7 + - - +
64D VAL* 5.5 2.9 - - + -
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Residues in contact with ASP 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LYS* 2.8 58.1 + - - +
50D GLN* 3.7 7.7 + - - +
52D ALA* 1.3 77.3 - - - +
54D LEU* 1.3 64.5 + - + +
56D LYS* 3.2 18.3 + - - +
57D ALA* 3.0 21.5 + - - +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.9 33.7 - - + -
20D GLU* 4.3 22.9 - - + +
23D ILE* 3.4 32.8 - - + +
24D LYS* 6.4 1.3 - - + -
50D GLN* 3.1 25.5 + - + +
51D VAL* 3.2 8.3 + - - +
53D ASP* 1.3 76.3 - - + +
55D LEU* 1.3 64.2 + - - +
57D ALA* 3.1 22.6 + - + +
58D GLN* 3.5 3.8 + - - +
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ILE* 3.3 35.9 - - + -
26D LEU* 5.0 1.3 - - + -
34D ALA* 3.9 17.0 - - + -
36D ILE* 4.3 9.6 - - + -
51D VAL* 3.0 32.2 + - + +
52D ALA* 3.5 7.4 - - - +
53D ASP 3.2 0.2 - - - -
54D LEU* 1.3 76.8 - - - +
56D LYS* 1.3 58.1 + - - +
58D GLN* 2.8 20.5 + - - -
60D ILE* 3.0 42.1 + - + +
62D SER* 4.0 18.2 - - - +
93D ILE* 3.6 24.9 - - + -
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Residues in contact with LYS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ALA* 2.9 18.7 + - - +
53D ASP* 3.4 20.9 + - - +
55D LEU* 1.3 76.6 - - - +
57D ALA* 1.3 62.1 + - - +
58D GLN 2.9 1.8 + - - -
59D GLY* 3.0 12.8 + - - -
60D ILE 3.7 14.1 - - - +
61D ASN* 4.6 17.3 - - - -
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASN* 5.6 0.3 + - - -
53D ASP 3.0 13.0 + - - +
54D LEU* 3.1 19.9 + - + +
56D LYS* 1.3 75.9 - - - +
58D GLN* 1.3 72.8 + - - +
59D GLY 3.5 0.4 - - - -
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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