Contacts of the helix formed by residues 125 - 138 (chain A) in PDB entry 5XVO
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 TYR 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LEU* 3.1 30.9 + - + +
121A ALA 4.0 0.2 + - - -
123A ARG* 3.4 37.9 - - + -
124A ASP* 1.3 79.2 - - - +
126A GLY* 1.3 66.0 + - - +
127A GLN* 2.8 5.8 + - - -
128A LYS* 3.3 16.4 + - + +
129A ALA* 3.2 20.4 + - - +
158A THR* 3.5 33.1 + - - -
159A LEU* 4.6 7.6 + - + -
230A TYR* 4.2 14.2 + - - -
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Residues in contact with GLY 126 (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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121A ALA* 4.8 6.7 + - - +
124A ASP* 3.3 6.5 + - - +
125A TYR* 1.3 75.1 - - - +
127A GLN* 1.3 58.7 + - - +
129A ALA* 3.5 7.2 - - - +
130A ALA* 3.4 21.1 + - - +
69N ARG* 5.0 16.4 - - - +
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Residues in contact with GLN 127 (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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125A TYR 2.8 4.0 + - - -
126A GLY* 1.3 74.9 - - - +
128A LYS* 1.3 68.6 + - + +
129A ALA 3.1 1.8 - - - -
130A ALA* 3.3 8.3 + - - +
131A ALA* 3.2 18.0 + - - +
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Residues in contact with LYS 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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120A LEU* 4.2 14.8 - - + -
125A TYR* 3.3 16.8 + - + +
127A GLN* 1.3 82.5 - - + +
129A ALA* 1.3 65.2 + - - +
131A ALA* 3.2 12.3 - - + +
132A LEU* 3.1 26.2 + - - +
154A SER* 4.2 14.0 + - - +
158A THR* 2.7 40.6 - - + +
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Residues in contact with ALA 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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117A SER* 3.4 31.6 - - - +
120A LEU* 4.1 8.1 - - + +
121A ALA* 3.9 17.0 - - + +
125A TYR 3.2 16.8 + - - +
126A GLY 3.5 7.4 - - - +
127A GLN 3.1 0.2 - - - -
128A LYS* 1.3 79.2 - - - +
130A ALA* 1.3 61.0 + - - +
132A LEU 3.3 7.8 + - - -
133A LEU* 3.2 23.4 + - + +
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Residues in contact with ALA 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 GLY 3.4 9.6 + - - +
127A GLN* 3.3 10.8 + - - +
129A ALA* 1.3 79.3 - - - +
131A ALA* 1.3 61.7 + - - +
133A LEU* 3.2 12.5 + - - +
134A ALA* 3.1 20.8 + - - +
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Residues in contact with ALA 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 3.2 7.1 + - - +
128A LYS* 3.2 21.3 + - + +
129A ALA 3.1 0.2 - - - -
130A ALA* 1.3 79.9 - - - +
132A LEU* 1.3 60.9 + - + +
134A ALA* 3.2 10.3 - - - +
135A MET* 3.1 38.0 + - + +
154A SER* 5.6 1.8 - - - +
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Residues in contact with LEU 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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113A ILE* 3.6 15.4 - - + +
116A GLN* 3.7 31.0 - - + +
117A SER* 3.8 11.7 - - - +
120A LEU* 3.7 25.1 - - + -
128A LYS 3.1 16.4 + - - +
129A ALA 3.6 8.5 - - - +
130A ALA 3.2 0.4 - - - -
131A ALA* 1.3 78.1 - - + +
133A LEU* 1.3 59.3 + - - +
134A ALA 3.1 1.6 - - - -
135A MET* 3.0 16.4 + - + +
136A ARG 2.9 24.8 + - - -
151A ALA* 4.1 22.0 - - + +
154A SER* 4.0 21.5 - - - +
155A TYR* 4.2 9.2 - - + +
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Residues in contact with LEU 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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113A ILE* 5.4 0.7 - - - -
114A THR* 4.7 8.7 - - + -
117A SER* 2.9 31.6 - - - +
129A ALA* 3.2 23.2 + - + +
130A ALA* 3.2 13.9 + - - +
132A LEU* 1.3 77.7 - - - +
134A ALA* 1.3 56.7 + - - +
136A ARG* 3.0 43.2 + - - +
137A ALA* 3.1 26.9 + - - +
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Residues in contact with ALA 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 ALA 3.1 12.1 + - - +
131A ALA* 3.2 13.9 - - - +
132A LEU 3.1 0.4 - - - -
133A LEU* 1.3 74.1 - - - +
135A MET* 1.3 65.5 + - + +
137A ALA* 3.1 16.5 + - - +
138A GLU* 3.3 15.2 + - - +
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Residues in contact with MET 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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113A ILE* 5.2 1.8 - - + -
131A ALA* 3.1 27.6 - - + +
132A LEU* 3.0 13.4 + - + +
134A ALA* 1.3 76.4 - - + +
136A ARG* 1.3 62.3 + - - +
138A GLU* 3.2 27.2 + - - +
139A LEU* 3.5 4.7 + - - +
147A ARG* 3.9 28.8 - - + +
150A HIS* 4.1 11.4 - - + +
151A ALA* 3.6 35.0 - - + -
154A SER* 4.5 20.4 - - - +
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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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110A ALA* 3.6 24.7 + - + +
113A ILE* 4.0 13.4 - - + +
114A THR* 3.2 33.7 - - - +
132A LEU 2.9 11.9 + - - +
133A LEU* 3.0 46.2 + - - +
135A MET* 1.3 77.3 - - - +
137A ALA* 1.3 63.5 + - - +
139A LEU* 3.1 36.8 + - + +
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Residues in contact with ALA 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 LEU 3.1 14.4 + - - +
134A ALA* 3.1 11.4 + - - +
136A ARG* 1.3 80.2 - - - +
138A GLU* 1.3 58.7 + - - +
139A LEU 3.3 4.1 + - - +
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Residues in contact with GLU 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 ALA 3.3 7.6 + - - +
135A MET* 3.2 18.4 + - - +
136A ARG 3.1 0.4 - - - -
137A ALA* 1.3 75.5 - - - +
139A LEU* 1.3 62.5 + - - +
140A ARG* 3.5 10.4 + - - +
145A ALA* 5.7 1.2 - - - +
147A ARG* 3.1 48.3 + - - +
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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