Contacts of the helix formed by residues 127 - 138 (chain A) in PDB entry 3PAR
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 ASN 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 1.3 79.6 - - - +
128A PHE* 1.3 70.5 + - - +
129A ASP* 3.3 10.4 + - - +
130A THR* 2.9 29.8 + - - -
131A ILE* 3.0 17.2 + - - +
166A TYR* 4.0 1.1 - - - -
218A CYS 3.3 12.4 - - - +
219A LEU* 3.8 19.6 + - - +
220A GLN 2.9 19.4 + - - +
221A TYR* 3.7 14.0 + - + -
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Residues in contact with PHE 128 (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 ASN* 1.3 73.2 - - - +
129A ASP* 1.3 79.2 + - - +
131A ILE* 2.6 31.2 + - - +
132A LYS* 3.0 44.2 + - + -
142A ILE* 3.9 15.3 - - + -
166A TYR* 3.5 22.8 - - + -
167A LEU 3.7 21.3 - - - -
169A MET 4.5 0.9 - - - -
170A ILE* 4.0 22.9 - - + -
181A LEU* 4.4 11.9 - - + -
204A CYS* 3.4 23.1 - - + -
218A CYS* 3.1 26.7 + - + +
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Residues in contact with ASP 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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127A ASN* 3.3 7.8 + - - +
128A PHE* 1.3 96.4 - - - +
130A THR* 1.3 63.9 + - - +
132A LYS* 3.1 16.8 + - - +
133A GLU* 3.0 23.9 + - - +
218A CYS* 5.9 1.9 - - - +
219A LEU* 5.7 5.2 - - - +
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Residues in contact with THR 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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126A VAL* 3.5 29.7 - - + +
127A ASN* 2.9 32.1 + - - -
128A PHE 2.9 1.8 + - - -
129A ASP* 1.3 76.2 - - - +
131A ILE* 1.3 64.5 + - - +
133A GLU* 3.2 13.1 + - - +
134A MET* 3.0 31.6 + - + +
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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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126A VAL* 3.3 32.3 - - + +
127A ASN 3.0 14.9 + - - +
128A PHE 2.6 13.4 + - - +
130A THR* 1.3 71.2 - - - +
132A LYS* 1.3 64.9 + - - +
134A MET* 3.2 7.8 + - - +
135A CYS* 3.1 29.6 + - - -
142A ILE* 3.7 27.1 - - + -
166A TYR* 3.9 25.8 - - + +
222A ARG 3.5 13.0 - - - +
223A LEU 3.8 5.6 - - - +
224A ALA* 3.7 27.8 - - + -
225A VAL 4.5 1.3 - - - +
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Residues in contact with LYS 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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128A PHE* 3.0 39.2 + - + +
129A ASP* 3.4 19.1 - - - +
131A ILE* 1.3 77.1 - - - +
133A GLU* 1.3 60.4 + - - +
135A CYS* 3.5 2.0 + - - +
136A THR* 2.9 38.7 + - + +
142A ILE* 4.2 14.8 + - + +
181A LEU* 3.4 33.2 - - + +
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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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129A ASP 3.0 11.8 + - - +
130A THR* 3.2 19.4 - - - +
132A LYS* 1.3 76.7 - - - +
134A MET* 1.3 65.2 + - - +
136A THR* 2.7 22.4 + - - -
137A ARG* 2.4 63.2 + - - +
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Residues in contact with MET 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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122A ASN* 2.7 46.0 - - - +
124A GLN* 3.4 22.7 - - + +
126A VAL* 4.1 22.4 - - - -
130A THR* 3.0 20.9 + - + +
131A ILE 3.2 5.6 + - - +
133A GLU* 1.3 89.0 + - - +
135A CYS* 1.3 66.2 + - - +
137A ARG* 3.1 27.4 + - - +
138A ALA* 3.0 23.4 + - - +
224A ALA* 4.3 13.5 - - + -
226A CYS* 4.8 3.1 - - - -
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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* 3.1 22.0 + - - +
132A LYS 3.8 2.2 - - - +
134A MET* 1.3 80.4 - - - +
136A THR* 1.3 55.7 + - - +
138A ALA* 3.1 10.9 + - - +
140A GLY* 2.7 30.8 + - - -
141A ASN 3.5 20.0 - - - -
142A ILE* 3.6 16.8 - - - +
224A ALA* 5.5 0.7 - - - -
225A VAL 3.7 4.5 - - - -
226A CYS* 2.0 56.8 - - + -
228A PHE* 4.6 0.2 - - - -
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Residues in contact with THR 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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132A LYS* 2.9 19.8 + - + +
133A GLU* 2.7 23.4 + - - -
135A CYS* 1.3 76.0 - - - +
137A ARG* 1.3 56.6 + - - +
139A GLY* 2.9 18.8 + - - -
140A GLY 3.2 16.6 - - - +
141A ASN* 4.4 14.4 - - - +
142A ILE 5.8 0.2 - - - +
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Residues in contact with ARG 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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124A GLN* 5.9 0.8 + - - -
133A GLU* 2.4 67.5 + - - +
134A MET* 3.1 27.1 + - - +
136A THR* 1.3 77.2 + - - +
138A ALA* 1.3 58.7 + - - +
139A GLY 3.2 1.1 + - - -
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Residues in contact with ALA 138 (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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134A MET 3.0 11.4 + - - +
135A CYS* 3.1 10.5 + - - +
137A ARG* 1.3 76.8 - - - +
139A GLY* 1.3 59.9 + - - +
140A GLY 3.4 0.4 - - - -
226A CYS* 5.6 1.6 - - - -
228A PHE* 3.6 25.4 - - + -
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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