Contacts of the helix formed by residues 128 - 135 (chain C) in PDB entry 3RIE
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 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C GLY 2.9 14.1 + - - -
126C GLY 3.1 0.6 - - - -
127C ASP* 1.4 75.9 + - - +
129C GLY* 1.3 65.9 + - - +
130C ILE 3.2 3.1 - - - -
131C ILE* 3.0 12.9 + - - +
132C ARG 2.8 20.8 + - - -
163C ILE 3.3 13.3 - - - +
164C SER* 4.5 0.9 - - - -
166C GLY 5.5 0.5 + - - -
167C TYR* 3.9 19.1 - - - -
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Residues in contact with GLY 129 (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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103C HIS* 3.7 20.5 - - - +
125C GLY 4.5 0.2 + - - -
127C ASP* 2.8 16.5 + - - -
128C GLY* 1.3 77.8 - - - +
130C ILE* 1.3 62.7 + - - +
132C ARG* 3.2 9.0 + - - +
133C GLU* 3.2 26.3 + - - +
163C ILE* 3.6 17.8 - - - +
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Residues in contact with ILE 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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102C TYR* 4.9 0.2 - - + -
103C HIS* 3.8 19.2 - - + +
106C MET* 3.7 27.8 - - + -
107C THR* 3.5 22.4 - - - +
122C VAL* 3.8 25.1 - - + -
125C GLY* 5.2 2.2 + - - +
127C ASP* 4.7 0.2 + - - -
128C GLY 3.2 0.6 - - - -
129C GLY* 1.3 72.6 - - - +
131C ILE* 1.3 60.7 + - + +
133C GLU* 3.1 3.1 + - - +
134C LEU* 2.7 30.8 + - + +
194C ILE* 3.7 32.3 - - + -
196C ASP* 3.5 33.8 + - + +
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Residues in contact with ILE 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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122C VAL* 4.3 7.9 - - + -
125C GLY 5.3 0.4 + - - +
128C GLY* 3.0 11.8 + - - +
130C ILE* 1.3 79.0 - - - +
132C ARG* 1.3 53.1 + - - +
134C LEU* 3.2 8.7 + - - +
135C CYS* 2.7 35.8 + - - -
143C ILE* 4.2 15.5 - - + -
145C ILE* 3.4 42.6 - - + -
166C GLY* 3.8 32.1 - - - +
167C TYR* 3.7 25.8 - - + +
172C VAL* 3.9 19.3 - - + -
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Residues in contact with ARG 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLU* 2.8 43.2 + - - -
100C PHE* 4.3 9.3 - - - +
103C HIS* 4.1 10.1 - - - +
128C GLY 2.8 15.9 + - - +
129C GLY* 3.4 9.9 - - - +
130C ILE 3.2 0.2 - - - -
131C ILE* 1.3 77.5 - - - +
133C GLU* 1.3 92.7 + - - +
135C CYS* 3.3 14.6 + - - +
136C LYS* 3.6 21.3 - - - +
162C ASN* 3.0 30.1 + - - +
163C ILE* 3.7 15.2 - - - +
165C CYS* 3.8 20.2 - - - -
166C GLY* 4.6 7.0 - - - +
295C ASP* 6.2 0.2 - - - -
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Residues in contact with GLU 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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103C HIS* 3.8 23.1 - - + +
104C GLU* 3.6 17.7 - - - +
107C THR* 3.5 24.7 - - - +
108C HIS* 2.9 34.5 + - - +
129C GLY 3.2 11.2 + - - +
130C ILE 3.1 2.8 + - - +
132C ARG* 1.3 109.4 + - - +
134C LEU* 1.3 65.5 + - - +
136C LYS* 2.9 46.9 + - - +
137C TYR* 3.7 2.6 - - - -
296C LEU* 3.7 0.2 - - - +
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Residues in contact with LEU 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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107C THR* 3.6 19.7 - - + +
111C MET* 3.7 33.2 - - + -
120C VAL* 3.6 30.1 - - + -
122C VAL* 3.6 25.8 - - + -
130C ILE* 2.7 27.8 + - + +
131C ILE* 3.6 4.0 - - - +
133C GLU* 1.3 69.6 - - - +
135C CYS* 1.3 56.1 + - - +
136C LYS 3.0 11.0 + - - -
137C TYR* 3.0 27.7 + - - +
140C VAL* 4.4 5.3 - - + +
143C ILE* 3.8 27.7 - - + +
194C ILE* 4.1 3.4 - - + -
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Residues in contact with CYS 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 ILE* 2.7 39.9 + - - +
132C ARG* 3.6 9.9 - - - +
133C GLU 3.3 1.0 - - - -
134C LEU* 1.3 71.1 - - - +
136C LYS* 1.3 60.5 + - - +
137C TYR 3.3 1.5 + - - +
138C LYS* 4.8 3.3 + - - +
143C ILE* 4.0 11.0 - - - -
166C GLY* 4.0 9.0 - - - -
169C ASP* 3.4 37.1 - - - +
171C ARG* 3.1 22.8 + - - +
172C VAL* 4.2 0.2 - - - -
292C GLU* 5.7 0.5 - - - +
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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