Contacts of the helix formed by residues 51 - 62 (chain R) in PDB entry 5GJQ
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 ALA 51 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50R MET* 1.3 79.6 - - - +
52R PRO* 1.4 72.7 - - + +
53R TYR 2.8 1.7 - - - -
54R TYR* 2.3 41.5 + - - +
55R GLU* 3.4 6.1 + - - +
70R LEU* 5.7 2.5 - - + +
73R MET* 5.3 0.7 - - + -
74R LYS* 4.5 19.7 - - + +
77R ASN* 4.1 15.7 - - - +
114R ILE* 5.0 0.6 - - + +
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Residues in contact with PRO 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R MET* 5.4 0.2 - - + -
51R ALA* 1.4 93.9 - - + +
53R TYR* 1.3 64.7 + - + +
55R GLU* 3.5 11.6 - - + +
56R ALA* 2.8 22.1 + - - +
114R ILE* 3.5 31.0 - - + +
115R GLY 4.2 13.5 - - - +
116R ASP* 4.2 22.4 - - + +
151R TYR* 5.2 3.1 - - - +
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Residues in contact with TYR 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R ILE* 2.9 24.0 - - + +
20R ALA* 6.3 0.2 - - - -
23R ARG* 6.1 5.4 - - + -
45R VAL* 4.8 7.0 - - + -
50R MET* 2.5 58.8 - - + +
51R ALA 2.7 6.6 + - - +
52R PRO* 1.3 71.2 - - + +
54R TYR* 1.3 56.6 + - - +
55R GLU 2.4 2.6 + - - -
56R ALA* 2.1 40.4 + - + -
57R LEU* 2.7 43.6 + - + -
114R ILE 5.8 1.1 - - - -
115R GLY* 5.5 10.7 - - - -
150R PHE* 2.6 43.5 - + - -
151R TYR* 6.4 0.4 - + - -
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Residues in contact with TYR 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R VAL* 5.6 13.0 - - + +
50R MET 5.0 3.8 - - - +
51R ALA* 2.3 27.6 + - - +
53R TYR* 1.3 73.6 - - - +
55R GLU* 1.3 58.7 + - + +
57R LEU* 4.3 4.6 - - - +
58R CYS* 2.9 35.0 + - + +
64R GLN* 4.6 14.6 - - + -
65R ILE 2.1 48.1 + - - -
66R ASP* 4.4 2.9 - - + -
67R VAL* 5.6 3.1 - - - -
69R LEU* 6.1 7.0 - - + -
70R LEU* 4.0 39.9 - - + -
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Residues in contact with GLU 55 (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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51R ALA 3.4 2.9 + - - +
52R PRO* 3.5 19.3 - - + +
53R TYR 2.4 7.2 + - - -
54R TYR* 1.3 76.9 - - + +
56R ALA* 1.3 73.4 + - - +
58R CYS* 3.1 11.6 - - - -
59R LYS* 2.9 27.8 + - - +
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Residues in contact with ALA 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R PRO 2.8 22.4 + - - +
53R TYR* 2.1 20.8 + - + +
55R GLU* 1.3 73.2 - - + +
57R LEU* 1.3 60.5 + - + +
59R LYS* 3.4 4.9 + - - +
60R SER* 2.9 29.6 + - - -
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Residues in contact with LEU 57 (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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19R ILE* 6.3 0.2 - - + -
23R ARG* 4.9 25.4 - - + +
26R LEU* 6.5 1.8 - - + -
41R LEU* 4.5 21.5 - - + -
45R VAL* 5.4 6.3 - - + -
53R TYR* 2.7 57.5 + - + +
54R TYR* 4.3 3.8 - - - +
56R ALA* 1.3 74.6 - - + +
58R CYS* 1.3 59.0 + - - +
60R SER* 2.8 8.3 + - - -
61R LEU* 2.7 38.0 + - + +
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Residues in contact with CYS 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 TYR* 2.9 31.0 + - + +
55R GLU* 3.1 22.4 - - - -
57R LEU* 1.3 72.7 - - - +
59R LYS* 1.3 69.8 + - - +
61R LEU* 5.1 1.6 - - - -
62R ASP* 2.6 36.9 + - - +
63R TRP 3.6 5.6 + - - +
64R GLN* 3.5 35.0 - - + +
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Residues in contact with LYS 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 GLU 2.9 19.6 + - - +
56R ALA* 3.6 5.6 - - - +
58R CYS* 1.3 81.2 - - - +
60R SER* 1.3 61.9 + - - +
62R ASP* 4.3 6.5 + - - +
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Residues in contact with SER 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R ARG* 5.8 4.6 + - - -
56R ALA 2.9 14.4 + - - -
57R LEU* 2.8 13.2 + - - -
59R LYS* 1.3 79.3 - - - +
61R LEU* 1.3 66.1 + - - -
62R ASP* 3.5 2.8 + - - +
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Residues in contact with LEU 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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26R LEU* 4.2 25.6 - - + -
57R LEU* 2.7 18.8 + - + +
58R CYS* 5.1 1.6 - - - -
60R SER* 1.3 73.3 + - - +
62R ASP* 1.3 70.0 + - - +
63R TRP* 4.8 8.0 - - + +
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Residues in contact with ASP 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 CYS 2.6 23.3 + - - -
59R LYS 4.6 5.6 - - - +
60R SER 3.3 5.1 - - - +
61R LEU* 1.3 76.7 - - - +
63R TRP* 1.3 64.1 + - - +
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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