Contacts of the helix formed by residues 63 - 73 (chain C) in PDB entry 3BSU
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 THR 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C PHE* 3.2 12.3 - - - +
61C PHE* 3.7 5.9 - - - +
62C ALA* 1.3 86.5 - - + +
64C GLU* 1.3 63.9 + - - +
65C ASP* 3.6 10.8 + - - +
66C GLU* 3.0 39.3 + - - +
67C ALA 3.3 13.9 + - - -
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 3.2 42.3 - - + -
39C VAL* 4.8 4.8 - - + +
41C LEU* 5.8 0.8 - - - +
63C THR* 1.3 72.9 - - - +
65C ASP* 1.3 68.0 + - - +
67C ALA* 3.1 3.9 + - - +
68C TRP* 2.7 58.2 + - + +
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Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C THR* 3.8 9.2 - - - +
64C GLU* 1.3 81.0 - - - +
66C GLU* 1.3 57.5 + - + +
68C TRP* 3.6 7.3 + - - +
69C ALA* 3.0 26.5 + - - +
72C ARG* 4.8 2.3 + - - -
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C PHE* 3.3 34.2 - - + -
62C ALA* 4.2 7.4 + - - +
63C THR* 3.0 41.1 + - - +
65C ASP* 1.3 75.0 - - + +
67C ALA* 1.3 67.0 + - - +
69C ALA* 3.3 7.8 + - - +
70C PHE* 3.1 22.3 + - - +
73C LYS* 5.4 0.3 + - - -
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 3.7 21.1 - - + +
30C ALA* 3.3 9.9 - - + +
39C VAL* 3.4 32.3 - - + -
61C PHE* 3.7 14.0 - - + -
63C THR 3.3 2.0 + - - -
64C GLU 3.1 8.5 + - - +
66C GLU* 1.3 78.5 - - - +
68C TRP* 1.3 63.5 + - - +
70C PHE* 3.2 6.8 - - - +
71C VAL* 3.0 23.7 + - - +
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Residues in contact with TRP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLY* 3.8 17.5 - - - -
39C VAL* 3.3 39.4 - - + +
64C GLU* 2.7 58.7 + - + +
65C ASP* 3.9 6.5 - - - +
67C ALA* 1.3 74.2 - - - +
69C ALA* 1.3 65.9 + - - +
71C VAL* 3.1 20.3 + - + +
72C ARG* 3.0 48.2 + - + +
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ASP 3.0 16.1 + - - +
66C GLU* 3.3 12.1 + - - +
68C TRP* 1.3 76.2 - - - +
70C PHE* 1.3 62.9 + - - +
72C ARG* 3.2 20.0 + - - +
73C LYS* 3.1 36.3 + - + +
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Residues in contact with PHE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ALA* 3.7 16.4 - - + -
32C ARG* 3.0 64.4 + - + -
57C ARG* 3.9 25.1 - - - -
58C PHE* 3.9 26.5 - - - -
59C LYS* 3.8 24.5 - - + -
61C PHE* 3.6 24.7 - + + -
66C GLU 3.1 11.5 + - - +
67C ALA 3.2 10.3 - - - +
69C ALA* 1.3 74.6 - - - +
71C VAL* 1.3 65.0 + - - +
73C LYS* 3.0 21.9 + - - +
10E G 6.5 0.2 - - - -
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ALA* 4.1 6.5 - - + -
31C VAL 4.3 12.6 - - - +
32C ARG* 3.8 16.4 - - - +
37C THR* 4.8 6.1 - - - +
38C GLY* 3.9 18.8 - - - +
39C VAL* 3.8 10.1 - - + -
67C ALA 3.0 16.8 - - - +
68C TRP* 3.1 36.5 + - + +
70C PHE* 1.3 77.8 - - - +
72C ARG* 1.3 64.1 + - + +
73C LYS 3.1 3.3 + - - -
74C SER 3.5 18.9 + - - +
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Residues in contact with ARG 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ASP 4.8 2.2 + - - -
68C TRP* 3.0 37.7 + - + +
69C ALA* 3.2 19.3 + - - +
71C VAL* 1.3 80.9 - - + +
73C LYS* 1.3 55.0 + - - +
74C SER* 2.8 15.3 + - - -
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Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ARG* 3.0 25.3 + - - +
61C PHE* 5.7 1.8 - - - -
66C GLU 5.4 0.4 + - - -
69C ALA* 3.1 17.4 + - - +
70C PHE* 3.0 47.2 + - - +
72C ARG* 1.3 74.2 - - - +
74C SER* 1.3 64.3 + - - +
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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