Contacts of the helix formed by residues 46 - 56 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.8 27.6 - - + -
43A PRO* 3.0 17.5 + - + +
44A GLY 3.0 1.8 - - - -
45A ASP* 1.3 95.4 + - + +
47A PHE* 1.3 64.2 + - - +
48A ASP 3.3 2.7 - - - -
49A THR* 3.2 21.9 + - - +
50A VAL* 2.8 26.4 + - + +
107A ILE* 3.7 3.4 - - + -
159A SER 6.0 0.7 - - - -
160A LEU* 4.1 31.4 + - + +
4B VAL* 5.0 6.9 - - - +
5B SER* 4.2 24.4 - - - +
6B LEU 5.3 0.6 - - - +
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Residues in contact with PHE 47 (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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44A GLY 3.1 16.3 + - - +
45A ASP 3.3 1.4 - - - +
46A LYS* 1.3 76.7 - - - +
48A ASP* 1.3 67.4 + - - +
50A VAL* 3.2 1.6 + - - +
51A TRP* 2.7 63.0 + + + +
82A HIS* 4.1 2.7 - - - +
87A PHE* 3.5 44.6 - + + -
99A ILE* 4.5 12.8 - - + -
101A ALA* 3.8 28.3 - - + +
104A CYS* 4.4 12.6 - - + -
107A ILE* 3.4 12.5 - - + +
124A PHE* 3.7 35.4 - + - -
132A MET* 5.9 0.2 - - + -
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Residues in contact with ASP 48 (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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45A ASP 4.6 4.1 + - - +
46A LYS 3.3 0.8 - - - -
47A PHE* 1.3 82.6 - - - +
49A THR* 1.3 62.2 + - - +
51A TRP* 4.6 2.5 - - - -
52A ASP* 2.8 48.7 + - - +
82A HIS* 2.7 36.2 + - - -
87A PHE* 4.3 4.9 - - - -
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Residues in contact with THR 49 (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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45A ASP 5.5 0.5 + - - -
46A LYS* 3.2 27.9 + - + +
48A ASP* 1.3 76.4 - - - +
50A VAL* 1.3 62.8 + - - +
52A ASP* 4.3 2.6 - - - +
53A THR* 2.7 39.8 + - - +
156A LEU* 4.3 14.6 - - + -
159A SER* 6.1 0.4 - - - +
160A LEU* 4.6 9.4 - - + -
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Residues in contact with VAL 50 (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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46A LYS* 2.8 25.2 + - + +
47A PHE 3.7 3.1 - - - +
49A THR* 1.3 81.1 - - - +
51A TRP* 1.3 63.0 + - - +
53A THR* 3.6 1.2 - - - -
54A VAL* 3.0 32.1 + - + +
107A ILE* 4.0 22.9 - - + -
109A LEU* 4.9 1.3 - - + -
122A ILE* 3.9 27.8 - - + -
124A PHE* 3.9 13.5 - - + -
156A LEU* 4.4 14.5 - - + +
160A LEU* 4.0 27.4 - - + -
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Residues in contact with TRP 51 (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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47A PHE* 2.7 48.9 + + + +
48A ASP* 4.0 2.7 - - - +
50A VAL* 1.3 75.3 - - - +
52A ASP* 1.3 64.6 + - - +
54A VAL* 3.1 9.7 - - - +
55A CYS* 3.0 41.6 + - - -
62A THR* 5.5 0.9 - - + -
77A LEU* 3.3 37.2 - - + -
78A PRO 2.8 21.7 + - - -
80A GLY 4.2 2.6 - - - +
87A PHE* 3.5 30.7 - + + -
89A LEU* 3.7 28.9 - - + -
99A ILE* 4.4 6.7 - - + -
124A PHE* 3.8 23.6 - + - -
133A LEU* 3.8 29.6 - - + -
135A ILE* 5.1 0.4 - - + -
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Residues in contact with ASP 52 (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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48A ASP* 2.8 34.5 + - - +
49A THR* 4.4 2.4 - - - +
51A TRP* 1.3 83.1 - - - +
53A THR* 1.3 63.8 + - - +
55A CYS* 3.4 15.1 + - - +
56A GLU* 3.5 16.5 - - - +
79A SER* 6.1 0.2 - - - -
80A GLY 5.2 4.2 + - - +
87A PHE* 4.9 6.2 - - - -
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Residues in contact with THR 53 (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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49A THR* 2.7 28.8 + - - +
50A VAL 3.6 2.9 - - - -
52A ASP* 1.3 78.1 - - - +
54A VAL* 1.3 62.6 + - - +
56A GLU* 3.0 19.5 + - - +
57A TRP* 3.4 36.3 - - + +
152A ALA* 5.5 2.0 - - + +
156A LEU* 4.1 23.8 - - + +
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Residues in contact with VAL 54 (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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50A VAL* 3.0 23.0 + - + +
51A TRP* 3.1 13.7 - - + +
53A THR* 1.3 74.7 - - - +
55A CYS* 1.3 60.8 + - - +
57A TRP* 3.0 55.8 + - + +
58A GLY 4.5 4.2 + - - +
60A VAL* 5.1 4.0 - - + +
77A LEU* 2.9 39.6 - - + +
122A ILE* 4.2 14.8 - - + -
124A PHE* 5.9 1.3 - - + -
135A ILE* 5.6 9.6 - - + -
156A LEU* 4.6 2.7 - - + -
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Residues in contact with CYS 55 (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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51A TRP* 3.0 34.8 + - - +
52A ASP* 3.5 14.8 - - - +
53A THR 3.2 0.4 - - - -
54A VAL* 1.3 77.0 - - - +
56A GLU* 1.3 66.2 + - - +
57A TRP 3.4 0.6 + - - -
58A GLY 4.6 3.6 + - - -
76A GLU* 5.2 5.9 - - - +
77A LEU* 3.5 25.3 + - - +
78A PRO 3.4 26.5 - - - -
79A SER* 3.8 15.0 - - - -
92A LYS* 6.1 0.5 - - - -
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Residues in contact with GLU 56 (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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52A ASP 3.5 16.8 - - - +
53A THR* 3.0 9.2 + - - +
54A VAL 3.0 1.4 - - - -
55A CYS* 1.3 84.5 - - - +
57A TRP* 1.3 63.9 + - + +
58A GLY 3.5 2.8 + - - -
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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