Contacts of the helix formed by residues 136 - 142 (chain B) in PDB entry 3UXO
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 GLN 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 4.6 12.1 - - + +
104B THR 3.4 9.3 - - - +
105B GLY* 3.4 7.7 - - - -
106B ILE* 3.2 49.0 + - - +
110B ALA 5.1 1.6 + - - -
114B LEU* 5.6 5.9 - - - +
132B LEU* 3.2 42.5 + - - +
133B ASN 4.0 0.2 - - - -
134B HIS 3.1 0.2 - - - -
135B HIS* 1.3 101.0 + - + +
137B ARG* 1.3 61.6 + - - +
138B ILE 3.2 1.8 - - - -
139B GLY* 3.0 3.8 + - - -
140B LEU* 2.8 27.6 + - - +
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 4.0 47.3 + - + +
130B ASP* 5.0 1.8 - - - +
132B LEU 4.8 1.3 + - - +
133B ASN* 2.7 49.8 + - - +
134B HIS* 3.1 27.7 + - - +
136B GLN* 1.3 79.8 - - - +
138B ILE* 1.3 58.7 + - + +
140B LEU* 3.2 9.8 + - + +
141B LYS* 2.9 26.0 + - - +
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B HIS* 2.6 45.8 + - + +
137B ARG* 1.3 69.4 - - + +
139B GLY* 1.3 63.0 + - - +
140B LEU 3.0 1.8 - - - -
141B LYS* 3.2 10.5 + - - +
142B TYR* 3.0 36.8 + - + +
146B PHE* 5.1 0.4 - - + -
226B ASP* 4.1 16.4 - - + +
227B THR 3.2 28.7 - - - +
228B LEU* 3.5 18.4 - - + -
238B VAL* 3.7 24.0 - - + -
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 4.5 6.5 - - - +
104B THR* 3.5 33.9 + - - +
135B HIS 4.0 4.0 + - - -
136B GLN 3.0 10.8 + - - -
138B ILE* 1.3 79.1 - - - +
140B LEU* 1.3 57.1 + - - +
142B TYR 3.4 1.2 - - - +
143B PHE* 3.0 32.1 + - - +
146B PHE* 4.0 5.4 - - - -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 4.8 10.8 - - + -
122B LEU* 3.8 30.3 - - + -
125B LEU* 4.4 30.5 - - + +
126B ARG* 3.8 45.2 + - + +
129B GLU* 4.9 7.0 - - + +
136B GLN 2.8 11.3 + - - +
137B ARG* 3.4 15.3 - - + +
138B ILE 3.0 0.2 - - - -
139B GLY* 1.3 76.8 - - - +
141B LYS* 1.3 66.1 + - - +
142B TYR 3.3 0.2 - - - -
143B PHE* 3.8 9.9 + - + +
144B GLU* 4.8 0.5 - - - +
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ARG* 5.5 1.3 + - - +
137B ARG 2.9 13.2 + - - +
138B ILE* 3.6 15.7 - - - +
140B LEU* 1.3 81.2 - - - +
142B TYR* 1.3 103.5 + - + +
143B PHE 3.7 1.7 + - - -
144B GLU* 4.5 5.5 - - - +
226B ASP* 3.6 12.8 + - - -
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Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ILE* 3.0 29.3 + - + +
139B GLY 3.4 4.3 - - - -
141B LYS* 1.3 118.0 + - + +
143B PHE* 1.3 60.4 + - - +
144B GLU* 3.4 2.7 - - - +
145B ASP* 4.0 13.7 - - + +
146B PHE* 3.0 46.1 + + + -
225B THR* 5.0 0.2 - - - -
226B ASP* 2.9 36.5 + - - -
238B VAL* 3.9 12.8 - - + -
252B HIS* 3.4 46.1 - + + -
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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