Contacts of the helix formed by residues 131 - 135 (chain C) in PDB entry 1DXO
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 MET 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A MET* 5.8 1.3 - - - +
160A ILE* 3.6 20.2 - - + -
161A HIS* 4.6 8.1 - - - -
127C THR 3.3 16.2 - - - +
128C TYR* 3.4 24.8 + - + +
129C ALA 3.7 2.0 - - - -
130C ALA* 1.3 77.5 - - - +
132C TYR* 1.3 85.1 + - + +
133C ASP* 3.3 1.7 + - - +
134C LYS* 3.1 15.9 + - - +
178C PHE* 3.5 32.8 - - + -
225C SER* 4.5 6.5 + - - -
230C LEU* 4.6 8.9 - - + +
236C PHE* 3.2 44.0 - - + -
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Residues in contact with TYR 132 (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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106A PHE* 3.7 10.6 - - - -
160A ILE* 3.7 42.8 - - + -
161A HIS* 2.9 31.9 + - - -
131C MET* 1.3 75.9 - - + +
133C ASP* 1.3 62.2 + - - +
134C LYS 2.6 0.9 + - - -
135C GLY 2.6 28.8 + - - -
173C SER* 3.4 32.0 + - - -
174C GLY* 4.8 0.9 - - - -
177C HIS* 3.1 41.5 - + - +
178C PHE* 3.0 44.7 + + - -
180C GLY* 3.1 10.5 - - - -
225C SER* 4.8 5.4 - - - +
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Residues in contact with ASP 133 (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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132C TYR* 1.3 77.9 - - - +
134C LYS* 1.3 71.7 + - - +
135C GLY 3.4 0.9 - - - -
138C ARG* 3.6 21.7 - - - +
177C HIS* 3.8 20.5 + - + +
180C GLY* 4.8 3.4 - - - -
223C ALA 5.0 0.3 - - - +
224C PRO* 3.7 7.7 - - + +
225C SER* 2.6 51.7 + - - -
226C SER 5.3 0.2 - - - -
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Residues in contact with LYS 134 (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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129C ALA 3.6 22.3 + - - -
130C ALA* 3.1 25.8 - - - +
131C MET 3.1 9.0 + - - +
132C TYR 2.6 6.3 + - - -
133C ASP* 1.3 90.7 - - - +
135C GLY* 1.3 63.6 + - - +
138C ARG* 4.1 12.6 + - - +
225C SER* 4.3 3.3 + - - +
230C LEU* 4.0 23.4 - - - +
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Residues in contact with GLY 135 (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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130C ALA* 3.0 12.6 + - - -
131C MET 4.7 0.7 - - - -
132C TYR 2.6 21.0 + - - -
133C ASP 3.4 1.0 - - - -
134C LYS* 1.3 73.3 - - - +
136C PRO* 1.3 70.9 - - - +
137C PHE 3.3 3.4 - - - -
138C ARG* 3.0 31.0 + - - +
179C CYS* 3.4 10.1 - - - -
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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