Contacts of the helix formed by residues 128 - 139 (chain D) in PDB entry 1IO4
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 ASP 128 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D SER 4.9 2.2 - - - +
84D GLU* 5.1 1.4 - - - +
107D CYS 3.5 9.2 + - - +
108D VAL* 3.7 7.8 - - - +
109D ILE* 2.8 42.1 - - + +
126D GLU 2.8 7.7 + - - -
127D PHE* 1.3 69.6 - - - +
129D GLU* 1.3 63.0 + - - +
130D GLU* 3.1 10.9 + - - +
131D ARG* 2.5 54.3 + - + +
132D ALA* 3.1 26.3 + - - +
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Residues in contact with GLU 129 (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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9D ARG* 4.4 21.5 - - - +
82D SER 5.7 2.9 + - - -
127D PHE* 3.6 19.1 - - + +
128D ASP* 1.3 78.2 - - - +
130D GLU* 1.3 61.8 + - - +
132D ALA* 3.6 5.8 - - - +
133D GLN* 2.9 32.2 + - - +
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Residues in contact with GLU 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 6.7 + - - +
129D GLU* 1.3 81.9 + - - +
131D ARG* 1.3 80.4 + - - +
133D GLN* 3.4 8.4 + - - +
134D GLN* 2.9 34.6 + - + +
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Residues in contact with ARG 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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156C PRO* 4.2 26.7 - - - +
70D PRO* 5.4 10.9 - - - +
84D GLU* 6.0 1.3 - - - +
100D PRO* 5.4 5.9 - - - +
107D CYS* 3.2 28.6 - - + -
109D ILE* 5.7 0.7 - - + -
128D ASP* 2.5 38.2 + - + +
130D GLU* 1.3 86.9 - - - +
132D ALA* 1.3 53.8 + - - +
134D GLN* 2.7 33.5 + - - +
135D GLU* 2.7 66.5 + - - +
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Residues in contact with ALA 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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8D GLN* 3.7 33.7 + - + +
107D CYS* 3.9 10.3 - - + +
127D PHE* 6.5 1.6 - - + -
128D ASP 3.1 20.4 + - - +
129D GLU* 3.6 7.9 - - - +
131D ARG* 1.3 78.9 - - - +
133D GLN* 1.3 56.1 + - - +
135D GLU* 4.7 0.4 - - - -
136D ASP* 3.1 34.1 + - - +
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Residues in contact with GLN 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 GLU 2.9 17.3 + - - +
130D GLU* 3.8 7.5 - - - +
132D ALA* 1.3 73.6 - - - +
134D GLN* 1.3 66.2 + - - +
136D ASP* 3.4 6.8 + - - +
137D ALA* 3.1 24.7 + - + +
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Residues in contact with GLN 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 GLU* 2.9 24.1 + - + +
131D ARG* 2.7 47.5 + - - +
133D GLN* 1.3 74.0 - - - +
135D GLU* 1.3 67.6 + - - +
137D ALA* 3.2 6.5 + - - +
138D LEU* 2.9 36.1 + - + +
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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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3D ARG* 3.4 41.1 + - + +
4D VAL* 3.9 30.7 - - + -
102D ILE* 4.9 4.3 - - - +
107D CYS* 3.5 18.2 - - + -
131D ARG* 2.7 45.9 + - - +
132D ALA* 4.1 3.1 - - - +
134D GLN* 1.3 73.8 - - - +
136D ASP* 1.3 53.9 + - - +
138D LEU* 3.2 13.0 + - + +
139D ALA* 2.8 40.5 + - + +
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Residues in contact with ASP 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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4D VAL* 3.6 8.2 - - - +
5D VAL 3.6 1.9 - - - +
6D PRO 3.3 25.7 - - - +
7D ASP* 4.7 2.6 - - - +
8D GLN* 3.3 21.5 + - - +
132D ALA 3.1 21.4 + - - +
133D GLN* 3.6 7.9 - - - +
135D GLU* 1.3 76.2 - - - +
137D ALA* 1.3 57.5 + - - +
139D ALA* 3.1 24.9 - - - +
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Residues in contact with ALA 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 GLN* 3.1 17.3 + - + +
134D GLN* 3.7 5.4 - - - +
136D ASP* 1.3 74.7 - - - +
138D LEU* 1.3 63.4 + - - +
139D ALA 3.1 9.5 + - - +
140D GLN* 4.8 5.4 + - - -
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Residues in contact with LEU 138 (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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134D GLN* 2.9 28.5 + - + +
135D GLU* 3.9 11.7 - - + +
137D ALA* 1.3 75.6 - - - +
139D ALA* 1.3 59.4 + - - +
140D GLN* 4.0 14.5 + - - +
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Residues in contact with ALA 139 (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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2D PRO* 5.2 13.7 - - + -
3D ARG* 5.4 5.4 - - + +
4D VAL* 5.0 10.1 - - + +
135D GLU* 2.8 20.9 + - + +
136D ASP* 3.1 20.5 - - - +
137D ALA 3.1 6.4 - - - +
138D LEU* 1.3 78.0 - - - +
140D GLN* 1.3 65.7 + - - +
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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