Contacts of the helix formed by residues 46 - 54 (chain D) in PDB entry 2OVI
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 LYS 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D VAL* 2.7 42.0 - - + +
43D PRO* 3.0 28.3 - - - +
45D ASP* 1.3 94.0 - - + +
47D PHE* 1.3 55.2 + - - +
48D ASP 3.1 3.3 - - - +
49D THR* 2.8 19.7 + - + +
50D VAL* 2.5 40.0 + - + +
107D ILE* 4.3 1.8 - - + -
160D LEU* 3.6 28.8 + - + +
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Residues in contact with PHE 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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44D GLY 3.4 13.5 - - - +
45D ASP* 2.9 6.8 + - - +
46D LYS* 1.3 74.2 - - - +
48D ASP* 1.3 64.3 + - - +
50D VAL* 2.7 11.0 - - - +
51D TRP* 2.6 59.8 + + + +
82D HIS* 4.5 2.9 - + + -
87D PHE* 3.3 50.3 - + + -
99D ILE* 4.4 12.8 - - + -
101D ALA* 4.1 32.5 - - + +
104D CYS* 4.6 10.8 - - + -
107D ILE* 3.6 4.2 - - + +
124D PHE* 3.9 31.2 - + - -
132D MET* 5.5 0.7 - - + -
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Residues in contact with ASP 48 (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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46D LYS* 3.1 1.2 - - - +
47D PHE* 1.3 78.7 - - - +
49D THR* 1.3 68.7 + - - +
51D TRP 2.8 23.1 - - - +
52D ASP* 2.8 27.0 - - - +
82D HIS* 3.5 31.7 + - - -
87D PHE* 3.7 15.6 - - - -
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Residues in contact with THR 49 (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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46D LYS* 2.8 29.2 + - + +
48D ASP* 1.3 77.8 - - - +
50D VAL* 1.3 57.7 + - - +
52D ASP* 4.1 2.1 - - - +
53D THR* 2.5 36.9 + - - +
156D LEU* 4.5 13.7 - - + -
159D SER* 6.0 1.8 - - - +
160D LEU* 4.6 10.8 - - + -
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Residues in contact with VAL 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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46D LYS* 2.5 25.7 + - + +
47D PHE* 2.7 24.2 - - - +
49D THR* 1.3 73.4 - - - +
51D TRP* 1.3 56.1 + - - +
52D ASP 3.1 0.7 + - - -
53D THR* 3.2 5.5 + - - -
54D VAL* 2.9 43.5 + - + +
107D ILE* 3.3 32.1 - - + -
109D LEU* 5.1 3.4 - - + -
122D ILE* 4.0 29.6 - - + -
124D PHE* 4.0 13.5 - - + -
156D LEU* 4.5 14.8 - - + -
160D LEU* 5.7 4.7 - - + +
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Residues in contact with TRP 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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47D PHE* 2.6 44.0 + + + +
48D ASP* 2.8 9.1 - - - +
50D VAL* 1.3 70.8 - - + +
52D ASP* 1.3 73.9 + - - +
54D VAL* 3.6 7.2 - - - -
55D CYS* 3.6 15.1 - - - -
77D LEU* 3.4 36.1 - - + -
78D PRO* 2.9 22.5 + - + -
80D GLY 4.6 1.1 - - - -
87D PHE* 3.6 27.7 - + - -
89D LEU* 3.9 22.9 - - + -
95D MET* 4.9 3.1 - - + -
99D ILE* 3.3 28.5 - - + -
124D PHE* 3.8 21.8 - + - -
133D LEU* 3.6 21.3 - - + -
135D ILE* 4.8 1.6 - - + -
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Residues in contact with ASP 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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48D ASP* 2.8 32.4 - - - +
49D THR* 4.1 2.2 - - - +
50D VAL 3.1 0.8 + - - -
51D TRP* 1.3 86.6 - - - +
53D THR* 1.3 68.0 + - - +
54D VAL* 3.8 3.2 - - - +
55D CYS* 3.6 18.1 + - - +
56D GLU* 3.1 23.0 + - - +
79D SER* 5.7 0.7 - - - -
80D GLY* 4.9 7.3 + - - -
87D PHE* 5.3 0.9 - - - -
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Residues in contact with THR 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 THR* 2.5 25.6 + - - +
50D VAL 3.2 4.6 + - - -
52D ASP* 1.3 79.1 - - - +
54D VAL* 1.3 57.8 + - - +
56D GLU* 2.7 36.3 + - + +
57D TRP* 3.3 31.4 + - + +
152D ALA 5.4 1.3 - - - +
156D LEU* 4.0 25.3 - - + +
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Residues in contact with VAL 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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50D VAL* 2.9 25.4 + - + +
51D TRP* 3.6 11.4 - - + -
53D THR* 1.3 77.5 - - - +
55D CYS* 1.3 56.5 + - - +
56D GLU 2.9 5.5 + - - -
57D TRP* 2.9 46.5 + - + +
58D GLY 4.8 2.4 - - - +
60D VAL* 5.3 4.8 - - + +
77D LEU* 3.0 40.6 + - + +
122D ILE* 3.3 34.3 - - + -
124D PHE* 5.8 1.1 - - + -
135D ILE* 5.4 9.2 - - + -
156D LEU* 4.8 1.1 - - + -
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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