Contacts of the helix formed by residues 50 - 61 (chain B) in PDB entry 1O6V
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 ASP 50 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE 3.2 1.6 - - - +
49B THR* 1.3 78.4 + - - +
51B THR* 1.3 61.4 + - - +
52B ALA* 3.1 16.7 + - - +
53B LEU* 3.0 28.1 + - + +
54B ALA* 2.8 30.7 + - - +
87B GLY 4.5 1.3 - - - +
88B ILE* 3.7 6.2 - - - +
89B LYS* 2.8 42.8 + - - +
90B SER* 3.2 32.8 + - - +
92B ASP 5.2 0.6 + - - -
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Residues in contact with THR 51 (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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45B ASN* 6.5 0.2 - - - -
49B THR 3.4 5.7 + - - -
50B ASP* 1.3 73.5 + - - +
52B ALA* 1.3 62.4 + - - +
54B ALA* 3.4 6.2 + - - +
55B GLU* 3.1 22.4 + - + +
66B VAL* 5.2 1.4 - - - +
89B LYS* 6.2 2.0 - - - -
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Residues in contact with ALA 52 (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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50B ASP* 3.1 10.3 + - - +
51B THR* 1.3 77.9 - - - +
53B LEU* 1.3 66.2 + - - +
55B GLU* 3.3 8.2 + - - +
56B LYS* 3.1 21.5 + - - +
86B LEU* 3.2 32.0 - - + +
87B GLY 4.2 7.0 - - - +
88B ILE* 3.9 8.5 - - + -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.8 28.5 - - + -
50B ASP* 3.0 22.8 + - + +
52B ALA* 1.3 76.6 - - - +
54B ALA* 1.3 58.3 + - - +
56B LYS* 3.2 11.7 + - + -
57B MET* 2.9 44.0 + - + +
81B LEU* 4.7 2.2 - - + -
83B ALA* 4.6 1.8 - - + -
88B ILE* 3.9 25.5 - - + +
90B SER 3.9 16.2 - - - +
91B ILE* 3.9 12.1 - - + -
92B ASP 4.2 3.1 - - - +
94B VAL* 3.9 17.3 - - + -
105B PHE* 4.4 11.7 - - + -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.6 15.6 - - + +
45B ASN* 4.0 23.8 - - + -
48B PHE* 3.4 24.4 - - - +
50B ASP 2.8 12.2 + - - +
51B THR* 3.8 7.4 - - - +
53B LEU* 1.3 76.4 - - - +
55B GLU* 1.3 58.6 + - - +
57B MET 3.3 0.3 + - - -
58B LYS* 2.9 29.5 + - - +
66B VAL* 3.7 9.6 - - + +
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Residues in contact with GLU 55 (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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51B THR* 3.1 14.1 + - + +
52B ALA* 3.6 11.7 - - - +
53B LEU 3.2 0.2 - - - -
54B ALA* 1.3 77.4 - - - +
56B LYS* 1.3 63.1 + - - +
58B LYS* 2.4 49.0 + - - +
59B THR* 3.5 10.1 + - - +
66B VAL* 3.5 18.9 - - + +
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Residues in contact with LYS 56 (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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52B ALA 3.1 12.5 + - - +
53B LEU* 3.2 14.3 + - + +
55B GLU* 1.3 76.8 - - - +
57B MET* 1.3 57.6 - - - +
59B THR* 3.2 9.8 + - - +
60B VAL* 3.0 44.3 + - + +
81B LEU* 3.8 20.4 - - + -
82B GLN* 2.8 33.5 + - - +
83B ALA* 4.4 4.5 - - + -
86B LEU* 3.9 27.3 - - + +
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Residues in contact with MET 57 (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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44B ILE* 4.0 4.3 - - + -
48B PHE* 3.7 43.3 - - + -
53B LEU* 2.9 27.1 + - + +
54B ALA 3.8 3.6 - - - +
56B LYS* 1.3 72.5 - - - +
58B LYS* 1.3 66.8 + - - +
60B VAL* 4.1 18.8 - - + -
61B LEU* 2.8 46.2 + - + +
78B VAL* 4.5 3.1 - - + -
81B LEU* 3.7 35.2 - - - -
97B LEU* 3.8 30.3 - - + -
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Residues in contact with LYS 58 (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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44B ILE* 3.8 16.3 - - + +
54B ALA 2.9 17.4 + - - +
55B GLU* 2.4 35.6 + - - +
57B MET* 1.3 78.1 - - - +
59B THR* 1.4 74.4 + - - +
62B GLY 3.2 2.1 + - - -
63B LYS* 2.9 53.2 + - + +
64B THR* 3.6 10.1 + - - +
65B ASN* 3.5 33.7 - - - +
66B VAL* 3.9 10.5 - - + +
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Residues in contact with THR 59 (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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55B GLU* 3.5 10.0 + - - -
56B LYS* 3.2 13.2 + - - +
58B LYS* 1.4 87.4 + - - +
60B VAL* 1.3 66.0 + - + +
62B GLY* 3.2 13.2 + - - -
63B LYS 4.8 3.6 - - - -
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LYS* 3.0 44.4 + - - +
57B MET* 3.3 16.1 + - + +
59B THR* 1.3 78.3 - - - +
61B LEU* 1.3 60.6 + - - +
62B GLY 3.3 0.9 + - - -
78B VAL* 3.8 38.8 - - + +
80B THR 5.2 1.6 - - - +
81B LEU* 4.0 12.1 - - + -
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Residues in contact with LEU 61 (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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44B ILE* 4.2 10.8 - - + -
48B PHE* 4.5 1.6 - - + -
57B MET* 2.8 38.8 + - + +
58B LYS 4.2 1.6 - - - +
59B THR 3.2 0.2 - - - -
60B VAL* 1.3 75.5 - - - +
62B GLY* 1.3 61.6 + - - +
63B LYS* 3.3 14.1 + - + +
70B VAL* 4.0 24.9 - - + -
74B ASP* 3.7 31.2 - - + +
75B LEU* 3.8 24.5 - - + -
78B VAL* 3.7 28.3 - - + -
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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