Contacts of the helix formed by residues 129 - 137 (chain D) in PDB entry 1YXU
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D GLN 3.9 0.4 + - - -
128D ASP* 1.3 69.1 - - - +
130D PHE* 1.3 66.1 + - - +
132D PHE* 3.7 13.5 - - + -
133D ILE* 3.0 45.5 + - + +
139D LEU* 4.3 4.0 - - + -
147D PHE* 3.9 31.4 - - + -
170D ASP* 3.5 14.5 + - + +
173D ILE* 3.0 32.1 + - + +
175D ILE* 4.2 5.3 - - + +
182D LEU* 5.1 0.9 - - + -
231D LEU* 4.2 15.3 - - + -
235D MET* 3.8 32.3 - - + -
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Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ASP* 3.1 8.9 + - - +
129D LEU* 1.3 79.3 - - - +
131D ASP* 1.3 70.7 + - - +
134D THR* 2.9 44.3 + - + -
170D ASP* 3.4 38.0 + - - -
171D GLU* 3.5 39.3 - - + +
800D IMD 3.2 24.8 - + - -
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Residues in contact with ASP 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLN* 3.9 19.9 + - + +
128D ASP* 2.9 32.5 + - - +
130D PHE* 1.3 86.2 - - - +
132D PHE* 1.3 62.3 + - - +
133D ILE 3.1 1.8 - - - -
134D THR* 3.6 7.4 + - - -
135D GLU* 3.0 34.7 + - + +
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Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLN* 3.3 26.4 - - - +
128D ASP 3.1 14.2 + - - +
129D LEU* 3.4 15.9 + - + +
131D ASP* 1.3 76.9 - - - +
133D ILE* 1.3 57.4 + - - +
135D GLU* 5.0 1.3 - - - -
136D ARG* 3.2 68.0 + - - +
139D LEU* 3.6 28.9 - - + -
143D LEU* 3.9 15.5 - - + -
147D PHE* 4.1 6.5 - + - -
175D ILE* 3.7 20.2 - - + -
177D LEU* 4.7 6.3 - - + -
304D LEU* 3.7 30.5 - - + -
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LEU* 3.0 48.9 + - + +
132D PHE* 1.3 74.9 - - - +
134D THR* 1.3 63.0 + - - +
135D GLU 3.3 0.2 - - - -
137D GLY* 2.8 33.8 + - - +
139D LEU* 4.1 17.0 - - + -
170D ASP* 4.3 2.5 - - - +
234D ASP* 3.7 28.0 - - - +
235D MET* 4.4 9.2 - - + +
238D GLY* 3.6 32.3 - - - +
800D IMD 3.5 20.4 + - + +
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Residues in contact with THR 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PHE* 2.9 36.9 + - + -
131D ASP* 3.2 10.0 + - - -
133D ILE* 1.3 80.1 - - - +
135D GLU* 1.3 66.0 + - + +
137D GLY* 4.0 2.9 + - - -
800D IMD 3.2 17.3 - - - +
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Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLN* 3.0 28.2 + - - +
131D ASP* 3.0 11.6 + - + +
132D PHE* 4.4 0.9 - - - +
134D THR* 1.3 85.6 - - + +
136D ARG* 1.3 69.4 + - + +
137D GLY 3.6 0.4 + - - -
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Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLN* 5.5 0.9 - - - -
132D PHE* 3.2 57.9 + - + +
135D GLU* 1.3 87.1 - - + +
137D GLY* 1.3 66.8 + - - +
138D ALA 4.0 5.7 - - - +
139D LEU* 5.2 2.4 - - + +
140D GLN* 6.1 1.4 - - - +
143D LEU* 4.7 4.8 - - - +
303D HIS* 3.0 36.8 + - - +
304D LEU* 4.7 7.5 + - - +
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Residues in contact with GLY 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 2.8 29.3 + - - +
134D THR 4.0 2.5 + - - -
135D GLU 3.6 2.2 - - - -
136D ARG* 1.3 77.8 - - - +
138D ALA* 1.3 64.8 + - - -
139D LEU* 3.3 13.9 + - - +
238D GLY* 4.4 6.3 - - - -
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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