Contacts of the helix formed by residues 131 - 141 (chain N) in PDB entry 3O3U
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 131 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126N PRO* 3.5 31.8 - - + +
127N LYS* 3.4 5.1 + - - +
128N THR* 2.7 46.9 + - - +
129N TRP 3.1 0.2 + - - -
130N GLU* 1.3 76.1 - - - +
132N ILE* 1.3 63.9 + - - +
133N PRO* 3.5 0.7 - - - -
134N ALA* 3.4 10.2 + - + +
135N LEU* 3.1 20.9 + - + +
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Residues in contact with ILE 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N LEU* 6.0 0.7 - - + -
126N PRO* 4.1 15.3 - - + -
128N THR 3.8 9.4 - - - +
129N TRP* 3.0 45.0 + - + +
131N GLU* 1.3 76.7 - - - +
133N PRO* 1.3 69.9 - - + +
135N LEU* 3.1 4.7 + - + +
136N ASP* 2.8 23.7 + - + +
146N ALA* 4.2 18.2 - - + -
147N LEU* 4.3 20.6 - - + -
198N LEU* 4.8 11.2 - - + -
203N HIS* 5.8 2.5 - - + -
224N MET* 4.2 16.8 - - + -
248N PRO* 4.2 15.0 - - + -
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Residues in contact with PRO 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N TRP 3.6 7.9 - - - +
130N GLU 3.4 16.8 - - - +
131N GLU 3.7 0.2 - - - -
132N ILE* 1.3 91.0 - - + +
134N ALA* 1.3 60.6 + - - +
136N ASP* 3.3 3.1 + - - +
137N LYS* 3.1 20.1 + - - +
194N PHE* 4.3 9.2 - - + -
198N LEU* 3.8 21.3 - - + -
203N HIS* 3.6 34.6 - - + +
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Residues in contact with ALA 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130N GLU 5.1 0.6 + - - -
131N GLU* 3.4 11.5 + - + +
132N ILE 3.3 0.6 - - - -
133N PRO* 1.3 79.7 - - - +
135N LEU* 1.3 63.8 + - - +
137N LYS* 3.3 19.1 + - - +
138N GLU* 3.1 27.3 + - + +
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Residues in contact with LEU 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122N LEU* 3.5 36.8 - - + -
126N PRO* 4.2 16.2 - - + -
131N GLU* 3.1 14.4 + - + +
132N ILE* 3.1 10.0 + - - +
134N ALA* 1.3 76.9 - - - +
136N ASP* 1.3 63.2 + - - +
138N GLU* 3.1 24.0 + - - +
139N LEU* 2.9 35.1 + - + +
146N ALA* 4.2 2.2 - - + -
224N MET* 3.8 26.7 - - + -
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Residues in contact with ASP 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132N ILE* 2.8 16.9 + - + +
133N PRO 3.6 4.7 - - - +
135N LEU* 1.3 76.5 - - - +
137N LYS* 1.3 57.1 + - - +
139N LEU 3.7 0.4 - - - +
140N LYS* 2.8 63.6 + - - +
145N SER* 3.5 11.6 - - - -
146N ALA* 2.9 37.9 + - + +
203N HIS* 2.8 40.1 + - + +
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Residues in contact with LYS 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133N PRO 3.1 13.5 + - - +
134N ALA* 3.5 19.0 - - - +
135N LEU 3.3 0.2 - - - -
136N ASP* 1.3 76.9 + - - +
138N GLU* 1.3 62.9 + - - +
140N LYS* 3.5 6.5 + - - +
141N ALA* 3.3 21.7 + - - +
203N HIS* 4.9 4.9 - - + -
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Residues in contact with GLU 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134N ALA* 3.1 18.7 + - - +
135N LEU* 3.4 24.1 - - - +
137N LYS* 1.3 75.9 - - + +
139N LEU* 1.3 65.3 + - + +
141N ALA* 3.3 18.9 + - - +
142N LYS* 3.6 26.2 + - - +
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Residues in contact with LEU 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121N LEU* 4.4 26.5 - - + +
122N LEU* 4.1 2.0 - - + -
135N LEU* 2.9 37.0 + - + +
136N ASP 3.2 3.1 + - - +
138N GLU* 1.3 75.0 - - + +
140N LYS* 1.3 59.9 + - - +
142N LYS* 2.9 38.4 + - + +
144N LYS* 2.9 35.4 + - + -
145N SER 3.7 19.3 - - - +
146N ALA* 3.6 27.8 - - - -
223N ALA* 3.8 13.2 - - + -
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Residues in contact with LYS 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N ASP* 2.8 59.5 + - - +
137N LYS* 3.8 7.2 - - - +
139N LEU* 1.3 75.8 - - - +
141N ALA* 1.3 58.7 + - - +
143N GLY* 3.0 17.8 + - - -
144N LYS 3.3 13.2 + - - +
145N SER* 3.8 17.9 - - - -
202N LYS 3.2 22.2 + - - -
203N HIS* 4.3 2.6 + - - +
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Residues in contact with ALA 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137N LYS 3.3 10.6 + - - +
138N GLU* 3.5 12.6 - - - +
139N LEU 3.2 0.8 - - - -
140N LYS* 1.3 76.9 - - - +
142N LYS* 1.3 60.5 + - + +
143N GLY 3.4 1.3 + - - -
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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