Contacts of the helix formed by residues 104 - 115 (chain E) in PDB entry 5DO9
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 GLU 104 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E TYR* 5.2 0.8 + - - -
102E LYS 4.0 1.8 + - - -
103E TYR* 1.3 70.6 - - - +
105E HIS* 1.3 66.0 + - + +
106E ASN 3.0 1.3 + - - -
107E LYS* 3.1 36.1 + - - +
108E ALA 4.3 0.5 + - - -
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Residues in contact with HIS 105 (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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103E TYR* 3.4 32.7 - + + +
104E GLU* 1.3 82.4 - - + +
106E ASN* 1.3 66.1 + - - +
107E LYS 3.3 0.9 + - - -
108E ALA* 3.4 16.9 + - - +
109E HIS* 3.5 37.9 + + + -
134E SER* 3.4 16.8 + - - -
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Residues in contact with ASN 106 (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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101E TYR* 3.9 13.7 - - + -
103E TYR* 2.9 29.3 + - - +
105E HIS* 1.3 83.0 + - - +
107E LYS* 1.3 56.2 + - - +
108E ALA 3.5 0.2 - - - -
109E HIS* 3.3 13.6 + - - +
110E ALA* 2.9 23.6 + - - +
134E SER* 2.5 42.1 + - - -
135E LEU* 3.5 14.5 + - + +
138E ASP* 2.9 34.8 + - - +
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Residues in contact with LYS 107 (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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101E TYR* 4.0 33.0 - - + +
104E GLU* 3.1 31.1 + - - +
106E ASN* 1.3 74.3 - - - +
108E ALA* 1.3 66.6 + - - +
110E ALA* 3.1 7.7 + - - +
111E GLN* 3.0 23.6 + - - +
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Residues in contact with ALA 108 (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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104E GLU 4.3 0.6 + - - -
105E HIS* 3.4 12.4 + - - +
107E LYS* 1.3 77.5 - - - +
109E HIS* 1.3 61.4 + - + +
111E GLN* 3.4 7.3 + - - +
112E LEU* 2.9 30.0 + - - +
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Residues in contact with HIS 109 (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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105E HIS* 3.5 31.6 + + + -
106E ASN* 3.3 25.1 + - - +
107E LYS 3.2 0.6 - - - -
108E ALA* 1.3 81.1 - - + +
110E ALA* 1.3 56.8 + - - +
112E LEU* 3.3 10.1 + - + +
113E VAL* 3.0 33.1 + - - +
127E PRO* 5.6 1.1 - - + -
130E ASP* 4.9 3.0 - - + +
131E ALA* 3.7 29.7 + - + -
134E SER* 3.7 15.2 + - - -
135E LEU* 4.0 13.0 - - + -
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Residues in contact with ALA 110 (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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91E ILE* 3.7 26.8 - - + +
101E TYR* 3.3 29.4 - - + +
106E ASN 2.9 16.3 + - - +
107E LYS* 3.1 8.3 + - - +
109E HIS* 1.3 70.1 - - - +
111E GLN* 1.3 58.4 + - - +
113E VAL 3.3 0.2 + - - -
114E ARG* 2.8 40.5 + - - +
135E LEU* 4.1 4.5 - - + +
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Residues in contact with GLN 111 (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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107E LYS 3.0 12.4 + - - +
108E ALA* 3.6 12.6 - - - +
110E ALA* 1.3 78.2 - - - +
112E LEU* 1.3 65.2 + - - +
114E ARG* 3.3 29.1 + - - +
115E GLU* 2.6 60.4 + - - +
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Residues in contact with LEU 112 (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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108E ALA 2.9 14.8 + - - +
109E HIS* 3.5 11.7 - - + +
111E GLN* 1.3 76.7 - - - +
113E VAL* 1.3 60.9 + - - +
115E GLU* 3.4 23.6 + - - +
116E VAL* 4.0 8.3 - - - +
127E PRO* 4.1 26.2 - - + +
128E TYR* 3.6 40.6 + - + +
131E ALA* 4.1 22.0 - - + -
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Residues in contact with VAL 113 (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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84E PHE* 4.4 9.0 - - + +
87E MET* 4.1 16.2 - - + -
88E GLN* 3.0 30.2 + - + -
91E ILE* 3.8 21.5 - - + -
109E HIS 3.0 20.3 + - - +
112E LEU* 1.3 76.6 - - + +
114E ARG* 1.3 59.9 + - - +
116E VAL* 3.2 15.0 + - - +
128E TYR* 4.7 8.7 - - + -
131E ALA* 4.1 12.1 - - + -
132E ILE* 3.9 29.6 - - + -
135E LEU* 3.9 8.5 - - + -
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Residues in contact with ARG 114 (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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88E GLN* 3.5 20.2 + - + +
91E ILE* 3.5 27.4 - - + +
92E ARG* 4.0 26.5 - - - +
95E ASP* 3.4 27.0 + - - -
110E ALA* 2.8 19.2 + - - +
111E GLN* 3.3 49.7 + - - +
113E VAL* 1.3 73.8 - - - +
115E GLU* 1.3 61.4 + - + +
116E VAL 3.3 2.6 + - - +
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Residues in contact with GLU 115 (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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111E GLN* 2.6 46.0 + - - +
112E LEU* 3.6 18.5 - - - +
113E VAL 3.2 1.2 - - - -
114E ARG* 1.3 77.8 - - + +
116E VAL* 1.3 60.8 + - - +
117E ASP 3.6 1.6 + - - -
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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