Contacts of the helix formed by residues 128 - 136 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A GLY 2.8 15.1 + - - -
126A GLY 3.1 1.2 - - - -
127A ASP* 1.3 76.0 + - - +
129A GLY* 1.3 57.0 + - - +
130A ILE 3.4 2.7 - - - -
131A ILE* 3.2 13.0 + - - +
132A ARG* 2.7 26.3 + - - +
163A ILE 3.2 13.4 - - - +
164A SER* 4.7 0.9 - - - -
166A GLY 5.4 0.9 + - - -
167A TYR* 3.8 19.5 - - - -
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A HIS* 3.8 21.8 - - - +
125A GLY 4.5 0.4 + - - -
127A ASP* 2.8 24.0 + - - -
128A GLY* 1.3 70.3 - - - +
130A ILE* 1.3 62.2 + - - +
132A ARG* 3.2 17.0 + - - +
133A GLU* 3.2 17.2 + - - +
163A ILE* 3.7 17.1 - - - +
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Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR* 4.9 0.4 - - + -
103A HIS* 3.7 19.8 - - + +
106A MET* 3.7 27.6 - - + -
107A THR* 3.4 23.3 - - - +
122A VAL* 3.7 26.7 - - + -
125A GLY* 5.4 2.4 + - - +
128A GLY 3.4 0.4 - - - -
129A GLY* 1.3 74.6 - - - +
131A ILE* 1.3 60.3 + - - +
133A GLU* 2.9 5.2 + - - +
134A LEU* 2.7 29.6 + - + +
194A ILE* 3.6 29.4 - - + -
196A ASP* 3.5 32.5 - - + +
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Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A VAL* 4.3 10.1 - - + -
128A GLY* 3.2 11.9 + - - +
130A ILE* 1.3 76.7 - - - +
132A ARG* 1.3 63.7 + - - +
134A LEU* 3.6 9.2 - - - +
135A CYS* 3.0 24.8 + - - -
143A ILE* 4.1 17.9 - - + -
145A ILE* 3.7 44.6 - - + -
166A GLY* 3.8 22.2 - - - -
167A TYR* 3.8 21.8 - - + +
172A VAL* 3.8 28.0 - - + -
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLU* 2.8 43.5 + - - -
100A PHE* 4.3 9.1 - - - +
103A HIS* 4.2 10.3 - - - +
128A GLY 2.7 16.0 + - - +
129A GLY* 3.4 9.6 - - - +
130A ILE 3.1 0.2 - - - -
131A ILE* 1.3 77.4 - - - +
133A GLU* 1.3 90.5 + - - +
135A CYS* 3.5 11.4 + - - +
136A LYS* 3.7 20.0 - - - +
162A ASN 3.2 28.5 + - - -
163A ILE* 3.8 18.0 - - - +
165A CYS* 3.7 19.5 - - - -
166A GLY* 4.6 8.7 - - - +
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A HIS* 3.9 22.7 - - + +
104A GLU* 3.9 13.9 - - - +
107A THR* 3.6 15.5 - - + +
108A HIS* 2.9 33.1 + - - +
129A GLY 3.2 11.0 + - - +
130A ILE 2.9 7.2 + - - +
132A ARG* 1.3 106.4 + - - +
134A LEU* 1.3 63.7 + - - +
136A LYS* 2.7 51.3 + - - +
137A TYR* 3.7 1.6 - - - -
296A LEU* 3.7 3.8 - - - +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A THR* 3.4 20.6 - - + -
111A MET* 3.7 28.7 - - + -
120A VAL* 3.7 31.4 - - + -
122A VAL* 3.7 25.8 - - + -
130A ILE* 2.7 21.6 + - + +
131A ILE* 3.3 5.4 + - - +
133A GLU* 1.3 72.6 - - - +
135A CYS* 1.3 61.7 + - - +
136A LYS 2.9 6.7 + - - -
137A TYR* 3.1 25.4 + - - +
140A VAL* 4.3 5.6 - - + +
143A ILE* 3.8 27.5 - - + +
194A ILE* 4.3 3.8 - - + -
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Residues in contact with CYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ILE* 3.0 30.6 + - - +
132A ARG* 3.8 7.6 - - - +
133A GLU 3.4 0.6 - - - -
134A LEU* 1.3 71.8 - - - +
136A LYS* 1.3 62.0 + - + +
137A TYR 3.2 2.6 + - - +
138A LYS* 4.6 1.0 + - - +
143A ILE* 4.0 10.8 - - - -
166A GLY* 4.0 15.5 - - - -
169A ASP* 3.5 34.5 - - - +
171A ARG* 2.8 29.6 + - - +
172A VAL* 4.2 0.7 - - - -
292A GLU* 5.7 0.5 - - - +
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Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLU* 5.2 1.6 + - - -
132A ARG* 3.7 19.6 - - - +
133A GLU* 2.7 53.0 + - - +
134A LEU 2.9 0.4 + - - -
135A CYS* 1.3 78.4 - - + +
137A TYR* 1.3 58.0 + - - +
138A LYS* 3.4 4.9 + - - +
292A GLU* 3.6 47.8 - - + +
293A PHE* 3.6 34.0 - - + -
295A ASP* 3.2 31.8 + - - -
296A LEU* 3.8 6.9 - - - +
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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