Contacts of the helix formed by residues 125 - 138 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120J LEU* 3.1 24.8 + - + +
121J ALA 4.1 0.4 + - - -
123J ARG* 3.4 38.6 - - + -
124J ASP* 1.3 79.1 - - - +
126J GLY* 1.3 65.5 + - - +
127J GLN* 2.8 5.3 + - - -
128J LYS* 3.3 11.0 + - + -
129J ALA* 3.2 20.0 + - - +
158J THR* 3.5 48.7 + - + -
159J LEU* 4.6 7.6 + - + -
230J TYR* 4.3 14.2 + - - -
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Residues in contact with GLY 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F GLN* 6.5 0.7 - - - -
69F ARG* 6.1 5.4 - - - -
121J ALA* 4.8 6.7 - - - +
124J ASP* 3.4 6.3 + - - +
125J TYR* 1.3 75.6 - - - +
127J GLN* 1.3 60.3 + - - +
129J ALA* 3.5 7.7 - - - +
130J ALA* 3.4 20.8 + - - +
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Residues in contact with GLN 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F SER* 6.3 1.0 - - - -
125J TYR 2.8 3.6 + - - -
126J GLY* 1.3 73.4 - - - +
128J LYS* 1.3 67.4 + - + +
129J ALA 3.2 1.1 - - - -
130J ALA* 3.3 9.0 + - + +
131J ALA* 3.2 18.4 + - - +
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Residues in contact with LYS 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J LEU* 4.2 11.9 - - + -
125J TYR* 3.3 11.0 + - + +
127J GLN* 1.3 78.1 - - + +
129J ALA* 1.3 64.4 + - - +
131J ALA* 3.2 12.0 - - + +
132J LEU* 3.1 27.0 + - - +
154J SER* 4.6 11.6 + - - +
158J THR* 3.3 40.7 + - + +
162J ASN* 5.5 6.7 + - - +
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Residues in contact with ALA 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J SER* 2.7 47.3 + - - +
120J LEU* 4.1 6.4 - - + +
121J ALA* 3.8 16.6 - - + +
125J TYR 3.2 12.5 + - - +
126J GLY 3.5 11.7 - - - +
127J GLN 3.2 0.2 - - - -
128J LYS* 1.3 78.6 - - - +
130J ALA* 1.3 61.2 + - - +
132J LEU* 3.3 8.2 + - - -
133J LEU* 3.2 9.2 + - - +
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Residues in contact with ALA 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J GLY 3.4 9.4 + - - +
127J GLN* 3.3 11.7 + - + +
129J ALA* 1.3 79.0 - - - +
131J ALA* 1.3 63.2 + - - +
133J LEU* 3.3 12.7 + - - +
134J ALA* 3.1 21.0 + - - +
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Residues in contact with ALA 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J GLN 3.2 8.5 + - - +
128J LYS* 3.2 19.5 - - + +
130J ALA* 1.3 78.7 - - - +
132J LEU* 1.3 63.1 + - + +
134J ALA* 3.2 10.3 + - - +
135J MET* 3.0 29.5 + - + +
154J SER* 5.6 2.7 - - - +
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Residues in contact with LEU 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J ILE* 3.6 14.3 - - + +
116J GLN* 3.7 30.3 - - + +
117J SER* 3.7 12.3 - - - +
120J LEU* 3.7 24.7 - - + -
128J LYS 3.1 16.6 + - - +
129J ALA 3.7 8.1 - - - +
130J ALA 3.2 0.2 - - - -
131J ALA* 1.3 78.4 - - + +
133J LEU* 1.3 59.0 + - - +
134J ALA 3.0 1.6 - - - -
135J MET* 3.0 12.0 + - - +
136J ARG 2.9 25.5 + - - -
151J ALA* 4.1 24.0 - - + +
154J SER* 4.0 22.7 - - - +
155J TYR* 4.2 9.2 - - + +
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Residues in contact with LEU 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J ILE* 5.3 0.7 - - - -
114J THR* 5.1 14.1 - - + +
117J SER* 2.7 39.3 - - - +
118J LEU* 6.5 0.4 - - + -
129J ALA 3.2 7.6 - - - +
130J ALA* 3.3 13.6 + - - +
132J LEU* 1.3 78.4 - - - +
134J ALA* 1.3 56.4 + - - +
136J ARG* 3.2 46.7 + - - +
137J ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J ALA 3.1 12.5 + - - +
131J ALA* 3.2 14.1 - - - +
132J LEU 3.0 0.4 - - - -
133J LEU* 1.3 74.4 - - - +
135J MET* 1.3 64.7 + - + +
137J ALA* 3.2 17.0 + - - +
138J GLU* 3.2 19.1 + - - +
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Residues in contact with MET 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J ILE* 5.2 1.8 - - + -
131J ALA* 3.0 19.5 - - - +
132J LEU* 3.0 16.5 + - - +
134J ALA* 1.3 75.5 - - - +
136J ARG* 1.3 64.1 + - - +
138J GLU* 3.2 27.7 + - - +
139J LEU* 3.5 5.9 + - - -
147J ARG* 3.0 55.2 - - + +
150J HIS* 3.4 27.1 - - + +
151J ALA* 3.6 28.9 - - + +
154J SER* 5.2 4.7 - - - -
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Residues in contact with ARG 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J ALA* 3.6 33.6 - - + +
113J ILE* 4.0 18.9 - - + +
114J THR* 3.3 29.4 + - - +
132J LEU 2.9 12.5 + - - +
133J LEU* 3.2 43.1 + - - +
134J ALA 3.2 0.2 - - - -
135J MET* 1.3 77.7 - - - +
137J ALA* 1.3 68.7 + - - +
139J LEU* 3.1 22.6 + - + +
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Residues in contact with ALA 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J LEU 3.0 14.0 + - - +
134J ALA* 3.2 11.4 + - - +
136J ARG* 1.3 84.5 - - - +
138J GLU* 1.3 57.3 + - - +
139J LEU 3.3 5.8 + - - +
140J ARG* 5.2 3.5 + - - -
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Residues in contact with GLU 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J ALA* 3.2 17.8 + - - +
135J MET* 3.2 20.9 + - - +
136J ARG 3.1 0.2 - - - -
137J ALA* 1.3 74.8 - - - +
139J LEU* 1.3 64.7 + - - +
140J ARG* 3.5 20.7 + - - +
145J ALA* 5.6 2.6 - - - +
147J ARG* 3.3 45.2 + - + +
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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