Contacts of the helix formed by residues 105 - 119 (chain E) in PDB entry 5UQ9
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 105 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77E ALA* 5.5 0.2 - - - +
104E SER* 1.3 74.1 - - - +
106E TYR* 1.3 69.0 + - + +
107E ARG* 4.4 10.9 - - + +
108E ASP* 3.0 33.7 + - - +
109E THR* 3.2 10.9 + - - -
266E TRP* 3.5 53.7 + - + -
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Residues in contact with TYR 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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104E SER 3.6 2.0 + - - -
105E GLU* 1.3 75.1 - - + +
107E ARG* 1.3 99.1 + - + +
109E THR* 3.9 2.7 - - - -
110E THR* 2.9 36.1 + - - -
177E GLU 4.5 0.3 - - - +
178E GLY 3.7 18.3 - - - +
181E HIS* 4.3 9.5 - - - +
182E PHE* 3.4 46.9 - + + +
185E MET* 4.2 19.7 - - + -
266E TRP* 6.3 0.2 - - + -
270E SER* 3.6 18.7 + - - -
274E TYR* 3.7 8.3 - - - -
349E PHE* 3.5 25.4 - + - -
351E TRP* 4.3 11.7 - + + -
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Residues in contact with ARG 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E GLU* 3.1 10.2 - - + +
106E TYR* 1.3 113.8 + - + +
108E ASP* 1.3 61.8 + - - +
110E THR* 3.5 5.8 + - - +
111E ARG* 3.0 27.7 + - - +
273E GLU* 3.0 41.1 + - - -
274E TYR* 3.1 24.0 + - - -
349E PHE* 4.3 5.8 - - + -
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Residues in contact with ASP 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E GLY* 5.3 6.2 + - - -
104E SER* 5.1 0.6 + - - +
105E GLU* 3.0 29.7 + - - +
107E ARG* 1.3 79.8 - - - +
109E THR* 1.3 58.3 + - - +
111E ARG* 3.1 23.3 + - - +
112E ARG* 2.8 64.3 + - - +
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Residues in contact with THR 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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100E ASP* 4.6 1.2 + - - -
104E SER* 3.8 6.1 - - - -
105E GLU 3.2 10.5 + - - -
106E TYR* 3.4 8.0 + - - -
108E ASP* 1.3 76.0 - - - +
110E THR* 1.3 59.3 + - - +
112E ARG* 3.4 2.7 + - - +
113E CYS* 2.8 29.0 + - + +
123E PHE* 3.5 27.1 - - + -
125E GLY* 3.6 11.9 - - - +
178E GLY* 3.6 23.1 - - - +
181E HIS* 2.4 37.3 + - - +
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Residues in contact with THR 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E TYR* 2.9 22.8 + - - -
107E ARG* 3.7 6.5 - - - +
109E THR* 1.3 76.8 - - - +
111E ARG* 1.3 61.6 + - - +
113E CYS* 3.2 2.8 + - - +
114E ARG* 3.0 59.2 + - - +
177E GLU* 2.4 43.9 + - + +
349E PHE* 6.4 1.8 - - + -
351E TRP* 4.2 7.8 - - + -
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Residues in contact with ARG 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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82E ASP* 3.0 39.2 + - - -
107E ARG 3.0 16.7 + - - +
108E ASP* 3.5 23.7 + - - +
110E THR* 1.3 77.1 - - - +
112E ARG* 1.3 76.0 + - - +
114E ARG* 3.5 5.1 + - - +
115E ASP* 3.1 54.6 + - - +
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Residues in contact with ARG 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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78E GLY 3.3 16.6 + - - +
81E VAL* 3.1 24.4 - - - +
82E ASP* 2.8 42.3 + - - +
85E ILE* 3.8 22.7 - - + -
100E ASP* 3.3 6.9 + - - -
104E SER* 3.0 27.3 + - - -
108E ASP* 2.8 47.2 + - - +
109E THR* 4.4 2.8 + - - +
111E ARG* 1.3 83.7 - - - +
113E CYS* 1.3 61.7 + - - +
115E ASP* 4.8 3.1 - - - -
116E LEU* 3.1 33.8 + - + +
123E PHE* 3.7 24.7 - - + -
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Residues in contact with CYS 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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109E THR 2.8 19.0 + - - +
110E THR* 3.2 7.2 + - - +
112E ARG* 1.3 77.5 - - - +
114E ARG* 1.3 57.6 + - - +
116E LEU* 4.0 0.5 - - - +
117E LYS* 3.0 36.2 + - - +
123E PHE* 3.7 21.4 + - + +
145E GLY* 3.6 36.8 - - - -
146E ASN* 4.1 11.4 + - - -
176E ASP* 5.2 0.7 - - - -
177E GLU* 4.1 17.3 - - + -
178E GLY 4.9 0.2 - - - +
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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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110E THR* 3.0 32.3 + - - +
111E ARG* 4.1 3.1 - - - +
113E CYS* 1.3 77.9 - - - +
115E ASP* 1.3 70.5 + - - +
117E LYS* 3.4 5.9 + - - +
118E ALA* 3.1 24.3 + - - +
177E GLU* 2.7 44.5 + - + +
349E PHE* 5.9 4.8 - - - -
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Residues in contact with ASP 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 ARG* 3.1 39.7 + - - +
112E ARG* 4.4 3.4 - - - +
114E ARG* 1.3 82.5 - - - +
116E LEU* 1.3 63.7 + - + +
118E ALA* 3.7 5.5 + - - +
119E LYS* 3.3 30.9 + - - +
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Residues in contact with LEU 116 (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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85E ILE* 3.8 27.6 - - + -
89E VAL* 3.6 29.6 - - + -
98E ILE* 4.6 4.9 - - + -
112E ARG* 3.1 20.4 + - - +
115E ASP* 1.3 77.3 - - + +
117E LYS* 1.3 62.9 + - - +
118E ALA 3.2 0.2 - - - -
119E LYS* 3.0 24.1 + - - +
120E GLY 3.0 0.2 + - - -
121E ILE* 2.8 50.6 + - + +
123E PHE* 3.6 36.8 - - + -
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Residues in contact with LYS 117 (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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113E CYS* 3.0 25.3 + - - +
114E ARG* 3.8 6.3 - - - +
116E LEU* 1.3 76.3 - - - +
118E ALA* 1.3 61.3 + - - +
120E GLY* 3.4 10.8 + - - +
121E ILE 3.4 9.7 + - - +
122E LEU* 5.5 2.9 - - + -
146E ASN* 3.7 28.9 + - - +
148E GLU* 5.9 2.0 - - - -
176E ASP* 5.5 5.1 + - - -
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Residues in contact with ALA 118 (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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114E ARG 3.1 16.1 + - - +
115E ASP* 3.9 7.6 - - - +
116E LEU 3.2 0.2 - - - -
117E LYS* 1.3 76.9 - - - +
119E LYS* 1.3 60.8 + - + +
120E GLY 3.3 1.2 + - - -
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Residues in contact with LYS 119 (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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85E ILE* 6.2 0.2 - - - +
86E GLU* 6.0 4.4 - - - +
89E VAL* 4.0 26.4 - - + +
94E THR* 5.0 2.6 + - - -
115E ASP* 3.3 20.4 + - - +
116E LEU* 3.0 24.5 + - - +
118E ALA* 1.3 77.7 - - + +
120E GLY* 1.3 60.7 + - - +
121E ILE* 3.4 11.2 + - + +
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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