Contacts of the helix formed by residues 130 - 142 (chain A) in PDB entry 1XTQ
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 SER 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A TYR* 4.8 0.3 + - - -
127A ARG* 4.0 8.1 - - - +
128A VAL 4.2 0.4 - - - -
129A ILE* 1.3 78.9 - - - +
131A TYR* 1.3 65.1 + - - +
132A GLU* 3.4 16.5 + - - +
133A GLU* 3.0 40.8 + - - +
134A GLY* 3.2 17.2 + - - -
147A GLU* 4.3 1.6 - - - +
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Residues in contact with TYR 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 ARG* 3.8 6.5 - - - +
130A SER* 1.3 73.4 - - - +
132A GLU* 1.3 79.5 + - + +
134A GLY* 3.3 2.4 + - - -
135A LYS* 2.9 52.0 + - + +
145A PHE* 3.5 29.8 + + - -
146A LEU* 5.7 1.0 - - - +
147A GLU* 3.5 42.4 - - + +
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Residues in contact with GLU 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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130A SER* 3.1 19.1 + - - +
131A TYR* 1.3 95.5 + - + +
133A GLU* 1.3 61.2 + - + +
135A LYS* 3.3 6.0 + - + +
136A ALA* 2.8 31.8 + - - +
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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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93A PHE* 3.7 19.8 - - + -
128A VAL 3.9 5.0 - - - +
129A ILE* 3.6 21.4 - - + +
130A SER* 3.0 43.5 + - - +
132A GLU* 1.3 75.7 - - + +
134A GLY* 1.3 63.2 + - - +
136A ALA* 3.3 7.2 + - - +
137A LEU* 3.1 22.2 + - - +
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Residues in contact with GLY 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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85A TYR* 3.3 25.8 - - - -
93A PHE* 4.2 9.8 - - - -
116A LEU* 3.4 10.3 - - - +
129A ILE* 4.5 0.6 - - - +
130A SER 3.2 8.3 + - - -
131A TYR 3.7 2.9 - - - -
133A GLU* 1.3 80.0 - - - +
135A LYS* 1.3 61.1 + - - +
137A LEU* 3.2 2.4 + - - +
138A ALA 3.1 17.3 + - - -
145A PHE* 3.6 11.1 - - - -
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Residues in contact with LYS 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 TYR* 2.9 41.9 + - + +
132A GLU* 3.7 6.7 - - - +
134A GLY* 1.3 76.0 - - - +
136A ALA* 1.3 56.1 + - - +
138A ALA* 3.4 2.5 + - + +
139A GLU* 3.0 61.4 + - + +
145A PHE* 3.6 24.6 - - + +
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Residues in contact with ALA 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 GLU 2.8 20.8 + - - +
133A GLU* 3.6 8.1 - - - +
134A GLY 3.3 0.2 - - - -
135A LYS* 1.3 72.6 - - - +
137A LEU* 1.3 59.0 + - - +
139A GLU* 3.3 13.8 + - - +
140A SER* 2.9 30.7 + - - -
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Residues in contact with LEU 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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93A PHE* 3.5 31.4 - - + -
96A ILE* 4.0 9.2 - - + -
97A LYS* 4.0 30.1 - - + -
116A LEU* 3.9 11.9 - - + -
133A GLU 3.1 12.3 + - - +
134A GLY 3.5 8.7 - - - +
136A ALA* 1.3 74.2 - - - +
138A ALA* 1.3 66.9 + - - +
140A SER* 2.9 22.5 + - - +
141A TRP* 3.1 51.4 + - + +
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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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116A LEU* 3.8 11.5 - - + +
134A GLY 3.1 6.8 + - - +
135A LYS* 3.7 6.3 - - + +
137A LEU* 1.3 78.5 - - - +
139A GLU* 1.3 53.5 + - + +
141A TRP* 3.1 4.5 + - - -
142A ASN 2.7 30.0 + - - -
143A ALA* 2.8 28.6 + - - +
144A ALA 4.0 5.6 - - - +
145A PHE* 3.5 32.5 - - + -
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Residues in contact with GLU 139 (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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135A LYS* 3.0 52.6 + - + +
136A ALA* 3.6 13.4 - - - +
138A ALA* 1.3 75.1 - - + +
140A SER* 1.3 67.1 + - - +
142A ASN* 3.1 14.6 + - - +
143A ALA 5.3 0.4 - - - -
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Residues in contact with SER 140 (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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136A ALA 2.9 16.0 + - - -
137A LEU* 2.9 20.3 + - - +
139A GLU* 1.3 76.5 - - - +
141A TRP* 1.3 66.5 + - - +
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Residues in contact with TRP 141 (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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83A LEU* 3.9 11.9 - - + -
96A ILE* 3.8 13.9 - - + -
97A LYS* 4.1 7.7 + - + +
100A HIS* 3.3 69.2 + + + +
114A ILE* 4.3 3.6 - - + -
116A LEU* 3.9 30.1 - - + -
137A LEU* 3.1 47.9 + - + +
138A ALA* 3.1 7.2 + - - +
140A SER* 1.3 87.7 - - - +
142A ASN* 1.3 69.0 + - - +
143A ALA* 4.0 20.2 - - + +
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Residues in contact with ASN 142 (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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138A ALA 2.7 11.5 + - - -
139A GLU* 3.1 14.1 + - - +
140A SER 5.4 0.2 - - - +
141A TRP* 1.3 78.4 - - - +
143A ALA* 1.3 57.3 + - - +
166A GLU* 4.0 9.7 - - - +
169A LYS* 5.5 6.4 + - - +
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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