Contacts of the helix formed by residues 108 - 120 (chain C) in PDB entry 3ITX
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 ASP 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C ALA* 1.3 72.6 - - - +
109C PRO* 1.3 69.1 - - - +
110C LYS* 3.1 36.1 + - - +
111C GLU* 2.8 60.0 + - + +
112C LEU* 3.0 10.8 + - - +
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Residues in contact with PRO 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ALA 3.0 11.2 - - - +
108C ASP* 1.3 89.0 - - - +
110C LYS* 1.3 64.5 + - + +
112C LEU* 3.3 5.4 + - + +
113C LYS* 3.0 25.5 + - - +
167C ILE* 4.7 19.5 - - + -
170C ALA* 3.6 33.6 - - + +
171C ILE* 3.7 16.5 - - + +
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Residues in contact with LYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASP* 3.0 23.9 + - - +
109C PRO* 1.3 77.9 - - + +
111C GLU* 1.3 56.6 + - + +
113C LYS* 3.8 5.5 - - - +
114C ALA* 3.1 28.1 + - - +
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Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C PHE* 3.9 28.0 - - + -
108C ASP* 2.8 40.2 + - + +
110C LYS* 1.3 71.5 - - + +
112C LEU* 1.3 59.4 + - - +
114C ALA* 3.7 6.0 - - - +
115C ARG* 2.9 31.0 + - - +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ILE* 3.7 41.7 - - + -
79C PHE* 4.0 11.4 - - + -
82C LEU* 4.3 5.9 - - + +
100C LEU* 3.9 24.5 - - + -
105C ASP 4.2 8.5 - - - +
107C ALA* 4.0 24.7 - - + +
108C ASP 3.0 11.7 + - - +
109C PRO* 3.7 13.5 - - + +
111C GLU* 1.3 74.7 - - - +
113C LYS* 1.3 58.8 + - - +
115C ARG* 3.2 2.9 + - - +
116C GLY 2.8 25.5 + - - -
123C PHE* 3.4 20.5 - - + -
167C ILE* 5.1 6.5 - - + -
171C ILE* 4.3 8.3 - - + -
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Residues in contact with LYS 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C PRO 3.0 17.3 + - - +
110C LYS* 3.8 6.1 - - - +
112C LEU* 1.3 77.5 - - - +
114C ALA* 1.3 57.4 + - - +
116C GLY* 3.2 1.2 + - - -
117C ASP* 2.9 71.1 + - - +
123C PHE* 4.1 11.6 - - + -
170C ALA 5.0 4.9 - - - +
171C ILE* 3.7 32.3 - - - +
172C GLY* 5.6 1.6 - - - -
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS 3.1 18.6 + - - +
111C GLU* 3.7 7.2 - - - +
113C LYS* 1.3 78.4 - - - +
115C ARG* 1.3 60.9 + - - +
117C ASP* 3.6 7.9 + - - +
118C ALA* 3.2 23.4 + - - +
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Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C PHE* 3.4 58.2 + - + +
82C LEU* 4.1 9.9 - - + -
83C ASP* 3.6 15.9 + - - -
111C GLU 2.9 17.9 + - - +
112C LEU 3.7 3.6 - - - +
114C ALA* 1.3 73.9 - - - +
116C GLY* 1.3 66.7 + - - +
118C ALA* 3.3 7.5 + - - +
119C LEU* 3.0 47.3 + - + +
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Residues in contact with GLY 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 5.0 3.3 - - - +
112C LEU 2.8 16.0 + - - -
113C LYS 3.7 1.8 - - - -
115C ARG* 1.3 78.1 - - - +
117C ASP* 1.3 57.2 + - - +
119C LEU* 3.1 5.1 + - - -
120C GLY 2.8 10.0 + - - -
121C LEU* 2.8 48.1 + - - -
123C PHE* 4.5 10.8 - - - -
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Residues in contact with ASP 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LYS* 2.9 61.8 + - - +
114C ALA* 3.9 6.9 - - - +
116C GLY* 1.3 74.6 - - - +
118C ALA* 1.3 62.3 + - - +
120C GLY* 3.3 12.0 + - - +
121C LEU 4.5 5.2 - - - +
123C PHE* 6.1 0.2 - - - -
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Residues in contact with ALA 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ALA 3.2 17.5 + - - +
115C ARG* 3.6 11.4 - - - +
116C GLY 3.2 0.2 - - - -
117C ASP* 1.3 80.0 - - - +
119C LEU* 1.3 62.8 + - + +
120C GLY 3.5 0.5 + - - -
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ARG* 4.2 14.1 - - + +
82C LEU* 3.5 37.0 - - + +
83C ASP* 3.8 15.5 - - - +
86C ALA* 3.9 26.9 - - + +
89C GLN* 5.5 2.1 - - - +
115C ARG* 3.0 43.3 + - + +
116C GLY* 3.8 3.4 - - - +
118C ALA* 1.3 78.1 - - + +
120C GLY* 1.3 62.0 + - - +
121C LEU* 4.1 14.2 - - + +
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Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C GLN* 4.2 11.6 + - - +
96C PRO* 4.0 6.8 - - - +
116C GLY 2.8 4.1 + - - -
117C ASP* 3.3 9.0 + - - -
118C ALA 3.3 4.0 + - - -
119C LEU* 1.3 80.2 - - - +
121C LEU* 1.3 66.9 + - - +
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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