Contacts of the helix formed by residues 52 - 62 (chain R) in PDB entry 6QY3
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 52 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50R LEU 4.4 0.2 + - - -
51R THR* 1.3 70.8 - - - +
53R MET* 1.3 60.9 + - - +
55R VAL* 3.2 11.8 + - - +
56R LYS* 2.9 26.2 + - - +
43S LEU* 5.5 6.1 - - - -
45S THR 3.8 21.8 - - - -
46S THR* 3.9 6.9 + - - -
48S ILE* 3.4 23.3 + - - -
67S PHE* 5.7 7.9 - - - +
68S CYS 5.2 5.3 - - - +
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Residues in contact with MET 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R TYR* 4.8 9.1 - - + +
51R THR* 3.2 5.6 - - - -
52R THR* 1.3 77.2 - - - +
54R LEU* 1.3 56.3 + - - +
56R LYS* 3.1 5.7 + - - +
57R ARG* 2.9 27.4 + - - +
46S THR* 3.1 34.2 + - - +
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Residues in contact with LEU 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R LEU* 5.0 6.7 - - + +
16R SER* 4.5 13.7 - - - +
17R TYR* 4.0 24.5 - - + +
50R LEU* 6.0 1.1 - - + -
51R THR* 3.2 20.2 + - - +
53R MET* 1.3 77.8 - - - +
55R VAL* 1.3 58.2 + - - +
57R ARG* 3.8 3.6 - - - +
58R LEU* 2.9 27.7 + - - +
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Residues in contact with VAL 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R THR 3.1 12.9 + - - +
52R THR* 3.3 15.3 - - - +
53R MET 3.1 0.4 - - - -
54R LEU* 1.3 79.2 - - - +
56R LYS* 1.3 56.3 + - - +
58R LEU* 3.3 7.6 + - - +
59R VAL* 2.9 26.0 + - - +
67S PHE* 5.3 12.3 - - + -
76S ALA* 5.8 1.2 - - - +
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Residues in contact with LYS 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52R THR 2.9 12.3 + - - +
53R MET* 3.1 10.3 + - - +
55R VAL* 1.3 75.7 - - - +
57R ARG* 1.3 61.0 + - - +
59R VAL* 3.1 9.6 + - - +
60R ASP* 2.9 26.9 + - - +
46S THR* 5.4 4.3 - - - -
68S CYS 4.6 13.7 - - - +
69S ASP* 4.9 11.0 - - + -
70S ASP 5.7 0.7 - - - +
75S THR* 5.3 7.2 - - - -
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Residues in contact with ARG 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R TYR* 4.8 10.3 - - + -
53R MET 2.9 16.7 + - - +
54R LEU* 3.9 8.5 - - - +
55R VAL 3.4 0.2 - - - -
56R LYS* 1.3 75.4 - - - +
58R LEU* 1.3 57.4 + - - +
60R ASP* 3.4 7.8 + - - +
61R GLU* 2.9 29.0 + - - +
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Residues in contact with LEU 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R LEU 2.9 17.8 + - - +
55R VAL* 3.5 9.2 - - - +
56R LYS 3.2 0.2 - - - -
57R ARG* 1.3 75.2 - - - +
59R VAL* 1.3 58.0 + - - +
61R GLU* 4.2 5.8 - - - +
62R ASN* 2.8 25.6 + - - -
63R ILE* 3.3 27.2 + - + +
65R VAL* 5.8 6.7 - - + -
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Residues in contact with VAL 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55R VAL 2.9 14.2 + - - +
56R LYS* 3.1 13.0 + - - +
58R LEU* 1.3 76.1 - - - +
60R ASP* 1.3 61.4 + - - +
62R ASN* 3.5 10.7 + - - +
80R PRO* 5.1 10.3 - - + -
82R TYR 5.2 5.2 - - - +
83R ALA* 5.2 7.3 - - - +
75S THR* 4.6 17.5 - - - -
76S ALA* 4.8 13.2 - - + -
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Residues in contact with ASP 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R LYS 2.9 12.9 + - - +
57R ARG* 3.8 9.9 - - - +
58R LEU 3.3 0.2 - - - -
59R VAL* 1.3 76.3 - - - +
61R GLU* 1.3 59.5 + - - +
62R ASN* 3.4 1.6 + - - +
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Residues in contact with GLU 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R LEU* 5.2 18.8 - - + +
57R ARG 2.9 16.7 + - - +
58R LEU* 3.2 8.0 + - - +
60R ASP* 1.3 75.4 - - - +
62R ASN* 1.3 63.8 + - - +
63R ILE* 2.9 18.1 + - + +
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Residues in contact with ASN 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58R LEU 2.8 7.9 + - - -
59R VAL* 3.5 8.2 + - - +
60R ASP 3.4 4.5 - - - +
61R GLU* 1.3 76.5 - - - +
63R ILE* 1.3 64.9 + - - +
64R LEU* 3.4 1.6 + - - -
83R ALA* 4.2 21.5 - - + +
84R ARG 5.4 0.4 - - - +
85R HIS* 4.0 23.6 + - - +
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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