Contacts of the helix formed by residues 72 - 83 (chain E) in PDB entry 4GTU
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 SER 72 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E LEU* 4.0 38.0 - - - +
16E ILE* 4.5 8.2 - - - +
58E ASN* 5.0 1.7 + - - +
60E PRO* 5.0 4.3 + - - +
71E GLN* 1.3 86.7 + - - +
73E ASN* 1.4 69.9 + - - +
75E ILE* 3.2 14.5 + - - +
76E LEU* 3.2 21.5 + - - +
104E MET* 4.5 17.3 - - - +
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Residues in contact with ASN 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E SER* 1.4 79.4 - - - +
74E ALA* 1.3 50.8 + - - +
76E LEU* 3.2 16.8 + - - +
77E CYS* 2.8 41.1 + - - -
100E GLU* 3.0 54.7 + - - +
101E ASN* 5.1 5.5 + - - +
104E MET* 4.1 25.2 - - - +
158E LEU* 4.5 4.0 - - - +
73F ASN* 5.8 0.8 - - - +
97F ASP* 5.2 0.4 - - - -
100F GLU* 5.1 0.6 + - - -
101F ASN* 3.0 28.8 + - - +
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Residues in contact with ALA 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E ILE* 3.3 24.4 - - + +
71E GLN* 3.4 24.9 - - + +
72E SER 3.2 0.4 - - - -
73E ASN* 1.3 77.9 - - - +
75E ILE* 1.3 60.0 + - - +
78E TYR* 3.3 17.2 + - - +
81E ARG* 4.2 0.2 + - - -
97F ASP* 3.5 35.3 - - + +
98F ILE* 3.8 12.3 - - + +
101F ASN* 3.5 4.0 + - - -
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Residues in contact with ILE 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LEU* 5.4 0.9 - - + -
16E ILE* 3.7 42.4 - - + -
60E PRO* 3.8 12.1 - - + +
61E TYR* 3.7 22.2 - - - +
62E LEU* 3.6 26.5 - - + -
69E ILE* 3.3 32.5 - - - +
71E GLN 3.0 21.4 + - - +
72E SER 3.6 3.4 - - - +
74E ALA* 1.3 76.1 - - - +
76E LEU* 1.3 63.8 + - - +
78E TYR* 3.2 16.5 + - - +
79E ILE* 3.3 12.6 + - + +
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Residues in contact with LEU 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LEU 6.0 1.1 - - - +
15E ALA* 3.8 27.1 - - + +
16E ILE* 3.8 22.9 - - + -
19E LEU* 3.7 23.5 - - + +
72E SER* 3.5 18.4 - - - +
73E ASN* 3.2 15.7 + - - +
75E ILE* 1.3 73.7 - - - +
77E CYS* 1.3 61.0 + - - +
78E TYR 3.0 1.3 + - - -
79E ILE* 3.3 2.3 + - - -
80E ALA* 3.0 27.9 + - - +
154E PHE* 3.9 18.6 - - + +
157E PHE* 5.8 0.7 - - + -
158E LEU* 3.5 41.3 - - + -
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Residues in contact with CYS 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ASN 2.8 21.7 + - - +
76E LEU* 1.3 72.4 - - - +
78E TYR* 1.3 55.7 + - - +
80E ALA* 3.3 10.3 - - - +
81E ARG* 3.0 36.0 + - - +
86E CYS* 4.6 2.3 - - - -
100E GLU* 3.8 20.4 - - - -
154E PHE* 3.7 24.9 - - + -
97F ASP* 3.2 28.9 - - - +
100F GLU* 6.1 0.7 - - - -
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Residues in contact with TYR 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E MET* 5.0 2.2 - - + -
62E LEU* 3.9 16.2 - - + -
64E ASP* 2.7 46.5 + - + -
67E HIS* 3.0 14.2 + - - -
69E ILE* 3.6 18.8 - - + -
74E ALA 3.3 14.0 + - - +
75E ILE* 3.2 13.2 + - - +
76E LEU 3.0 0.2 - - - -
77E CYS* 1.3 76.8 - - - +
79E ILE* 1.3 72.6 + - + +
81E ARG* 3.0 34.9 + - - +
82E LYS* 3.0 45.4 + - + +
90F GLU* 3.2 18.3 + - + -
94F ILE* 3.4 21.8 - - + -
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Residues in contact with ILE 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E MET* 5.1 6.7 - - + -
16E ILE* 5.1 6.5 - - + +
19E LEU* 3.9 26.9 - - + -
20E LEU* 3.3 45.1 - - + +
23E THR* 3.8 10.5 - - - +
25E SER* 4.1 6.1 - - - +
62E LEU* 4.4 14.6 - - + -
75E ILE 3.3 12.6 + - - +
76E LEU* 4.0 0.4 - - - +
78E TYR* 1.3 79.0 - - + +
80E ALA* 1.3 52.7 + - - +
82E LYS* 3.1 7.9 + - - -
83E HIS* 2.8 57.2 + - + +
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Residues in contact with ALA 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 4.5 2.2 - - - +
76E LEU 3.0 15.5 + - - +
77E CYS* 3.3 14.6 - - - +
79E ILE* 1.3 75.8 - - - +
81E ARG* 1.3 51.1 + - - +
83E HIS 3.0 2.3 + - - -
84E ASN 2.6 31.5 + - - -
85E LEU* 2.6 26.9 + - - +
86E CYS* 2.9 27.4 - - - -
154E PHE* 3.6 10.5 - - + -
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Residues in contact with ARG 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ALA 4.2 1.0 + - - -
77E CYS* 3.0 11.6 + - - +
78E TYR* 3.0 41.0 + - - +
80E ALA* 1.3 77.6 - - - +
82E LYS* 1.3 61.0 + - - +
83E HIS 3.0 1.5 + - - -
84E ASN* 3.3 12.3 + - - +
86E CYS* 3.6 9.8 - - - -
90F GLU* 2.9 43.6 + - - +
93F LYS* 3.8 31.1 - - - +
94F ILE* 3.8 15.5 - - - +
97F ASP* 3.0 28.3 + - - -
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Residues in contact with LYS 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E MET* 5.3 7.1 - - + +
64E ASP* 3.0 33.7 + - - +
67E HIS* 4.9 2.6 - - - -
78E TYR* 3.0 43.9 + - + +
79E ILE* 3.1 9.8 + - - +
81E ARG* 1.3 76.1 - - - +
83E HIS* 1.3 71.5 + - + +
84E ASN 3.7 0.2 - - - -
90F GLU* 4.3 11.4 + - - +
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Residues in contact with HIS 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E MET* 6.1 0.2 - - - +
23E THR* 3.2 42.6 + - + -
25E SER* 2.7 20.9 + - - -
79E ILE* 2.8 42.0 + - + +
80E ALA 3.9 1.1 - - - +
82E LYS* 1.3 86.1 + - + +
84E ASN* 1.3 65.1 + - - +
85E LEU* 2.9 20.5 + - + +
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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