Contacts of the helix formed by residues 56 - 66 (chain J) in PDB entry 5AYZ
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 GLY 56 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55J ALA* 1.3 74.0 - - - +
57J GLN* 1.3 66.1 + - - +
58J PRO* 3.3 3.4 - - - -
59J PHE* 3.1 25.3 + - - +
60J PHE* 3.1 13.5 + - - +
77J GLU* 2.9 11.0 + - - -
107J THR* 5.3 1.3 - - - +
108J LEU* 3.8 10.0 - - - +
111J CYS* 3.6 19.0 - - - -
150J TYR* 3.8 1.8 - - - -
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Residues in contact with GLN 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J LEU* 3.3 23.9 - - + +
55J ALA 3.7 0.6 - - - -
56J GLY* 1.3 75.0 - - - +
58J PRO* 1.3 63.9 - - + +
60J PHE* 3.1 2.7 + - - +
61J ASP* 2.9 36.0 + - - +
73J TRP* 3.5 53.0 - - + +
75J LEU 2.8 27.7 + - - +
76J PRO* 4.8 0.7 - - - +
77J GLU* 3.1 37.9 + - + +
108J LEU* 4.1 0.6 - - - +
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Residues in contact with PRO 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ALA* 3.6 24.7 - - + +
10J LEU* 3.6 23.8 - - + -
15J LEU* 3.9 11.5 - - + +
56J GLY* 3.4 4.5 - - - -
57J GLN* 1.3 93.7 - - + +
59J PHE* 1.3 60.2 + - - +
61J ASP* 4.0 7.9 - - + +
62J ALA* 3.1 23.9 + - - +
77J GLU* 3.5 13.5 - - + +
150J TYR* 3.5 16.6 - - + +
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Residues in contact with PHE 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J LEU* 3.9 26.5 - - + -
15J LEU* 4.1 26.5 - - + -
18J LEU* 4.7 4.3 - - + -
19J VAL* 4.3 3.0 - - + +
22J TRP* 4.2 13.9 - + + -
56J GLY* 3.1 20.3 + - - +
58J PRO* 1.3 73.8 - - + +
60J PHE* 1.3 59.9 + - - +
62J ALA* 3.3 5.3 + - - +
63J ILE* 3.0 36.3 + - - +
107J THR* 3.6 21.8 - - + -
146J LEU* 4.1 14.4 - - + -
147J VAL* 3.8 42.8 - - + -
150J TYR* 3.6 26.5 - + - -
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Residues in contact with PHE 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J LEU* 4.0 31.6 - - + -
56J GLY 3.1 12.0 + - - +
57J GLN 3.5 7.6 - - - +
59J PHE* 1.3 76.0 - - - +
61J ASP* 1.3 65.0 + - - +
63J ILE* 3.4 7.8 + - - +
64J PHE* 3.3 46.8 + + - -
71J VAL* 3.8 22.0 - - + -
73J TRP* 3.4 23.6 - + + -
88J ALA* 5.4 0.2 - - + -
90J VAL* 3.9 12.8 - - + -
104J ALA* 3.6 35.2 - - + +
105J LEU* 4.7 4.9 - - + -
107J THR* 5.3 1.2 - - - +
108J LEU* 4.0 19.1 - - + -
283J LEU* 4.7 3.8 - - + -
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Residues in contact with ASP 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J GLN* 2.9 24.4 + - - +
58J PRO* 4.0 7.1 - - + +
60J PHE* 1.3 70.8 - - - +
62J ALA* 1.3 53.7 + - - +
64J PHE* 3.3 1.9 + - - +
65J THR* 2.7 43.1 + - - +
71J VAL* 3.4 23.2 - - - +
73J TRP* 2.7 33.3 + - - -
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Residues in contact with ALA 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 4.3 22.0 - - + +
16J ALA* 5.9 0.7 - - - -
19J VAL* 3.8 19.3 - - + +
58J PRO 3.1 18.0 + - - +
59J PHE* 3.6 5.2 - - - +
60J PHE 3.2 0.4 - - - -
61J ASP* 1.3 76.4 - - - +
63J ILE* 1.3 66.6 + - - +
65J THR* 3.7 6.1 - - - +
66J GLN* 3.1 27.9 + - - +
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Residues in contact with ILE 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J VAL* 3.6 24.9 - - + -
22J TRP* 4.2 5.6 - - + -
23J LEU* 4.2 19.5 - - + +
59J PHE 3.0 25.6 + - - +
60J PHE 3.7 4.0 - - - +
61J ASP 3.3 0.2 - - - -
62J ALA* 1.3 78.6 - - - +
64J PHE* 1.3 66.0 + - + +
66J GLN* 3.2 14.4 + - - +
67J LEU* 3.5 9.2 + - - +
100J GLY* 4.1 15.9 - - - +
103J VAL* 3.6 22.2 - - + +
104J ALA* 3.5 38.6 - - + +
107J THR* 3.9 11.4 - - - +
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Residues in contact with PHE 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J PHE* 3.3 44.7 + + - +
61J ASP 3.3 4.0 + - - +
63J ILE* 1.3 79.3 - - + +
65J THR* 1.3 55.8 + - - +
67J LEU* 2.7 26.1 + - + +
69J CYS* 3.0 48.4 + - + +
71J VAL* 4.1 8.5 - - + -
90J VAL* 3.9 15.3 - - + -
96J CYS 4.5 2.5 - - - -
97J LEU* 3.6 28.0 - - + -
100J GLY* 3.9 24.7 - - - -
101J GLU* 4.0 7.0 - - - -
104J ALA* 3.4 23.3 - - + -
283J LEU* 4.2 12.3 - - + -
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Residues in contact with THR 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J ASP* 2.7 28.8 + - - +
62J ALA* 3.7 7.9 - - - +
63J ILE 3.3 0.2 - - - -
64J PHE* 1.3 71.7 - - - +
66J GLN* 1.3 64.7 + - - +
67J LEU 3.2 0.7 + - - -
68J ASN* 3.2 17.1 + - - +
69J CYS 3.6 12.5 + - - -
70J GLN* 5.2 4.5 + - - -
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Residues in contact with GLN 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H PRO* 4.5 8.7 - - - +
13H VAL* 3.6 14.9 - - + +
16J ALA* 3.8 27.5 - - - +
19J VAL* 3.9 11.9 - - + +
20J ASP* 3.1 33.3 + - - +
23J LEU* 4.3 4.9 - - + -
62J ALA* 3.1 14.0 + - - +
63J ILE 3.4 11.7 - - - +
64J PHE 3.2 0.4 - - - -
65J THR* 1.3 78.5 - - - +
67J LEU* 1.3 64.3 + - - +
68J ASN* 3.5 5.3 + - - +
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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