Contacts of the helix formed by residues 129 - 136 (chain C) in PDB entry 2RHB
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 GLY 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C VAL 3.0 2.8 + - - -
128C GLU* 1.3 74.3 - - - +
130C GLN* 1.3 62.0 + - - +
131C VAL* 3.2 5.4 - - - -
132C ASP* 3.4 20.0 + - - +
133C LEU* 3.4 16.1 + - - +
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Residues in contact with GLN 130 (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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81C ALA* 3.4 29.7 + - - +
82C ASN* 4.2 9.9 - - - +
122C LEU 4.4 0.2 + - - -
123C PHE* 3.5 24.0 - - + +
124C ASP* 3.0 43.0 - - - +
127C VAL* 3.0 38.8 + - + +
128C GLU 3.2 4.1 + - - +
129C GLY* 1.3 74.0 - - - +
131C VAL* 1.3 64.4 + - - +
132C ASP 3.2 0.4 - - - -
133C LEU* 3.2 21.6 + - + +
134C PHE* 3.0 21.8 + - - +
142C LEU* 5.0 0.7 - - - -
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Residues in contact with VAL 131 (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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125C GLY* 3.6 31.2 - - - +
127C VAL 5.8 0.2 - - - +
129C GLY* 3.2 2.4 - - - -
130C GLN* 1.3 78.8 - - - +
132C ASP* 1.3 60.7 + - - +
134C PHE* 3.3 5.7 + - - +
135C ARG* 3.2 33.0 + - + +
142C LEU* 4.1 15.5 - - + -
144C THR* 4.2 11.4 - - + -
148C VAL* 3.8 30.3 - - + -
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Residues in contact with ASP 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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129C GLY* 3.4 15.4 + - - +
130C GLN 3.2 0.6 - - - -
131C VAL* 1.3 79.0 - - - +
133C LEU* 1.3 63.7 + - - +
135C ARG* 3.4 28.9 + - - +
136C ASN* 3.3 32.8 + - - +
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Residues in contact with LEU 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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82C ASN* 5.9 1.1 - - - +
110C LYS* 5.8 7.2 - - + -
111C PRO* 4.3 24.9 - - + -
112C THR* 3.5 31.3 - - + +
123C PHE* 3.8 16.3 - - + -
128C GLU 5.6 0.9 - - - +
129C GLY 3.4 9.8 + - - +
130C GLN* 3.2 31.2 + - + +
132C ASP* 1.3 77.4 - - + +
134C PHE* 1.3 60.3 + - - +
136C ASN* 3.4 14.8 + - - +
137C ALA* 3.5 16.3 + - - +
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Residues in contact with PHE 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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123C PHE* 3.6 31.3 - + + -
130C GLN 3.0 12.3 + - - +
131C VAL 3.4 9.9 - - - +
132C ASP 3.2 0.2 - - - -
133C LEU* 1.3 72.9 - - - +
135C ARG* 1.3 67.9 + - + +
136C ASN 3.1 2.6 + - - -
137C ALA* 3.3 11.3 + - + +
140C GLY* 3.3 28.0 - - - -
142C LEU* 3.6 33.9 - - + -
151C LEU* 4.2 12.6 - - + -
179C PHE* 4.0 21.8 - - + -
180C LYS 3.9 21.3 - - - -
181C LYS* 3.3 23.8 + - + +
186C ILE* 3.8 20.6 - - + -
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Residues in contact with ARG 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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131C VAL* 3.2 18.0 + - + +
132C ASP* 3.4 29.6 + - - +
134C PHE* 1.3 83.4 - - + +
136C ASN* 1.3 64.8 + - - +
148C VAL* 3.4 22.3 - - - +
149C LYS* 2.8 44.6 + - - +
150C GLY 5.0 1.2 + - - -
151C LEU* 4.0 16.2 - - + +
181C LYS* 2.6 22.8 + - - +
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Residues in contact with ASN 136 (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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112C THR* 5.0 16.6 - - + +
132C ASP* 3.3 22.4 + - - +
133C LEU* 3.4 9.0 + - - +
134C PHE 3.1 0.8 - - - -
135C ARG* 1.3 87.7 - - - +
137C ALA* 1.3 57.9 + - - +
138C ARG 4.4 0.2 + - - -
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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