Contacts of the helix formed by residues 129 - 137 (chain A) in PDB entry 1YI3
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 LEU 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 GLN 3.9 0.8 + - - -
128A ASP* 1.3 71.2 - - - +
130A PHE* 1.3 55.4 + - - +
132A PHE* 3.8 6.1 - - + -
133A ILE* 2.9 56.1 + - + +
139A LEU* 4.4 4.5 - - + -
147A PHE* 3.9 28.5 - - + -
151A VAL* 5.8 0.4 - - + -
170A ASP* 3.3 18.1 + - + +
173A ILE* 2.7 35.4 + - + +
175A ILE* 4.0 13.8 - - + +
182A LEU* 5.3 2.2 - - + -
231A LEU* 3.8 28.9 - - + -
235A MET* 4.3 15.5 - - + -
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Residues in contact with PHE 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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128A ASP* 3.0 10.5 + - - +
129A LEU* 1.3 80.5 - - - +
131A ASP* 1.3 73.3 + - - +
133A ILE* 3.3 3.2 + - - +
134A THR* 2.8 49.4 + - + -
170A ASP* 3.3 43.6 + - - +
171A GLU* 4.0 26.9 - - + +
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Residues in contact with ASP 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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127A GLN* 3.7 20.8 - - + +
128A ASP* 2.7 36.3 + - - +
130A PHE* 1.3 86.6 - - - +
132A PHE* 1.3 61.3 + - - +
134A THR* 3.6 6.6 - - - -
135A GLU* 2.9 29.6 + - - +
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Residues in contact with PHE 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 GLN* 3.4 28.6 + - - +
128A ASP 3.1 16.6 + - - +
129A LEU* 3.7 8.3 - - + +
131A ASP* 1.3 76.4 - - - +
133A ILE* 1.3 61.6 + - - +
135A GLU* 3.1 7.1 + - + +
136A ARG* 3.1 61.8 + - + +
139A LEU* 3.3 32.3 - - + -
143A LEU* 4.0 10.5 - - + -
147A PHE* 4.1 9.4 - + - -
175A ILE* 3.7 24.0 - - + -
177A LEU* 4.6 7.0 - - + -
304A LEU* 3.6 28.9 - - + -
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Residues in contact with ILE 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 LEU* 2.9 47.0 + - + +
130A PHE* 3.8 3.4 - - - +
132A PHE* 1.3 74.6 - - - +
134A THR* 1.3 60.4 + - - +
137A GLY* 2.6 44.0 + - - +
139A LEU* 4.2 13.9 - - + -
170A ASP* 4.6 1.3 - - + +
234A ASP* 3.4 26.5 - - - +
235A MET* 4.0 23.6 - - + +
238A GLY* 3.9 34.5 - - - +
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Residues in contact with THR 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 PHE* 2.8 44.2 + - + -
131A ASP* 3.6 9.4 - - - -
133A ILE* 1.3 78.1 - - - +
135A GLU* 1.3 61.2 + - - +
137A GLY* 4.4 2.1 + - - -
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Residues in contact with GLU 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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127A GLN* 3.0 27.9 + - - +
131A ASP* 2.9 12.5 + - - +
132A PHE* 3.2 10.8 - - + +
133A ILE 3.0 0.2 - - - -
134A THR* 1.3 82.6 - - - +
136A ARG* 1.3 67.7 + - + +
137A GLY 3.8 0.2 + - - -
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Residues in contact with ARG 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 PHE* 3.1 49.8 + - + +
135A GLU* 1.3 81.1 - - + +
137A GLY* 1.3 66.4 + - - +
138A ALA 3.8 6.6 + - - +
139A LEU* 4.7 7.2 - - + -
143A LEU* 4.4 4.6 - - - +
303A HIS* 2.6 39.8 + - - +
304A LEU* 4.0 11.9 + - - +
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Residues in contact with GLY 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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133A ILE* 2.6 32.8 + - - +
134A THR 4.3 2.1 + - - -
135A GLU 3.5 2.2 - - - -
136A ARG* 1.3 74.7 - - - +
138A ALA* 1.3 66.3 + - - +
139A LEU* 3.2 13.2 + - - +
238A GLY* 4.4 8.3 - - - -
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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