Contacts of the helix formed by residues 129 - 137 (chain A) in PDB entry 2ERR
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 ARG 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ARG 4.2 7.1 + - - +
128A PHE* 1.3 79.5 - - - +
130A ASP* 1.3 65.7 + - - +
131A PRO* 3.6 16.6 - - + -
132A ASP* 3.3 22.3 + - - +
133A LEU* 3.1 25.3 + - - +
148A ILE* 3.7 13.0 - - - +
150A PHE* 4.4 22.3 - - + -
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Residues in contact with ASP 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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129A ARG* 1.3 72.5 - - - +
131A PRO* 1.4 69.4 - - + +
133A LEU* 3.2 5.2 + - - +
134A ARG 3.0 18.9 + - - -
146A VAL* 3.5 36.9 - - + +
147A GLU* 3.2 8.3 + - - -
148A ILE* 2.8 39.8 + - - +
150A PHE* 4.9 7.0 - - + -
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Residues in contact with PRO 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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129A ARG* 3.7 16.2 - - + -
130A ASP* 1.4 92.2 - - + +
132A ASP* 1.3 61.9 + - - +
134A ARG* 3.4 32.1 + - + +
135A GLN* 3.0 28.2 + - - +
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Residues in contact with ASP 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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127A ARG 4.8 2.4 - - - +
128A PHE* 4.6 22.5 - - + -
129A ARG* 3.3 39.3 + - - +
130A ASP 3.3 0.6 - - - -
131A PRO* 1.3 78.6 - - - +
133A LEU* 1.3 61.8 + - - +
135A GLN* 3.5 10.8 + - - +
136A MET* 3.0 26.7 + - - +
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Residues in contact with LEU 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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121A VAL* 3.7 33.4 - - + -
124A ILE* 4.6 2.9 - - + -
128A PHE* 3.6 24.2 - - + -
129A ARG 3.1 10.3 + - - +
130A ASP* 3.8 6.1 - - - +
132A ASP* 1.3 74.5 - - - +
134A ARG* 1.3 57.7 + - - +
136A MET* 3.2 28.4 + - + -
137A PHE* 2.8 41.7 + - + +
146A VAL* 4.3 11.4 - - + -
148A ILE* 3.7 30.1 - - + +
159A GLY* 4.4 9.2 - - - -
160A PHE 5.0 7.0 - - - +
161A VAL* 5.4 0.9 - - + -
186A ILE* 4.3 0.2 - - + -
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Residues in contact with ARG 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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130A ASP 3.0 9.1 + - - +
131A PRO* 3.4 33.2 + - + +
133A LEU* 1.3 74.0 - - - +
135A GLN* 1.3 57.0 + - + +
138A GLY* 2.8 28.1 + - - -
143A ILE* 3.3 22.4 - - + +
146A VAL* 3.8 29.3 - - + +
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Residues in contact with GLN 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 PRO 3.0 17.8 + - - +
132A ASP* 3.9 10.0 + - - +
134A ARG* 1.3 75.0 - - + +
136A MET* 1.3 55.9 + - - +
138A GLY* 3.0 20.0 + - - +
139A GLN* 3.0 13.2 + - - +
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Residues in contact with MET 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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128A PHE* 3.9 17.9 - - + -
132A ASP 3.0 18.4 + - - +
133A LEU* 3.3 26.2 - - + -
135A GLN* 1.3 74.2 - - - +
137A PHE* 1.3 90.1 + - + +
138A GLY 3.1 0.4 - - - -
139A GLN* 2.8 40.5 + - - +
176A LEU* 4.2 10.6 - - + +
179A THR* 5.2 10.5 - - + -
181A VAL* 5.0 9.0 - - + -
186A ILE* 3.4 28.3 - - + -
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Residues in contact with PHE 137 (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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119A LEU* 3.5 21.5 - - + -
121A VAL* 3.6 32.1 - - + -
133A LEU* 2.8 24.8 + - + +
136A MET* 1.3 99.0 - - + +
138A GLY* 1.3 51.5 + - - +
139A GLN* 5.0 0.2 - - - -
140A PHE* 2.8 30.3 + - - +
141A GLY 3.0 7.3 + - - -
143A ILE* 3.5 20.4 - - + +
161A VAL* 3.6 22.4 - - + -
163A PHE* 3.6 28.5 - + + -
173A ARG* 5.3 2.0 - - - -
176A LEU* 3.5 22.2 - - + -
188A VAL* 3.8 20.6 - - + -
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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