Contacts of the helix formed by residues 120 - 134 (chain A) in PDB entry 5XJY
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 THR 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LYS 5.5 1.3 - - - -
119A ASP* 1.3 80.5 + - - +
121A SER* 1.3 64.2 + - - +
122A MET* 3.6 1.6 - - - -
123A LYS* 3.5 20.9 - - + +
124A ASP* 2.9 41.7 + - - +
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Residues in contact with SER 121 (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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119A ASP* 3.1 26.9 + - - -
120A THR* 1.3 75.9 - - - +
122A MET* 1.3 71.8 + - - +
124A ASP* 3.1 7.7 + - - +
125A MET* 2.9 31.3 + - - +
261A LEU* 6.1 0.5 - - - -
264A SER* 3.7 29.2 - - - -
265A LEU* 5.5 5.2 - - - -
268A LEU* 3.5 17.4 - - - +
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Residues in contact with MET 122 (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 THR 5.6 0.2 - - - -
121A SER* 1.3 85.5 + - - +
123A LYS* 1.3 63.4 + - + +
125A MET* 3.3 13.0 - - - +
126A ARG* 2.9 23.0 + - - +
426A PHE* 4.9 23.6 - - + -
432A GLU* 5.6 3.5 - - + +
1562A LEU* 3.8 37.0 - - + -
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Residues in contact with LYS 123 (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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119A ASP 5.5 1.3 - - - +
120A THR* 3.5 28.9 - - + +
122A MET* 1.3 81.2 - - + +
124A ASP* 1.3 68.8 + - - +
125A MET 3.2 0.2 - - - -
126A ARG* 3.1 34.0 + - + +
127A LYS* 3.0 25.6 + - - +
1561A HIS* 5.3 16.1 + - + -
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Residues in contact with ASP 124 (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 THR* 2.9 38.2 + - - +
121A SER* 3.1 6.9 + - - +
123A LYS* 1.3 79.5 - - - +
125A MET* 1.3 60.7 + - - +
127A LYS* 3.3 25.6 + - + +
128A VAL* 2.9 32.2 + - - +
257A ALA* 5.3 2.6 - - + +
260A THR* 5.0 21.2 - - - +
261A LEU* 5.9 1.6 - - - +
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Residues in contact with MET 125 (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 SER* 2.9 20.2 + - - +
122A MET* 3.3 15.3 - - - +
124A ASP* 1.3 75.6 - - - +
126A ARG* 1.3 59.6 + - - +
128A VAL* 3.3 15.4 + - + +
129A LEU* 2.9 27.0 + - - +
261A LEU* 3.6 33.7 - - + -
264A SER* 6.5 0.4 - - - -
265A LEU* 4.8 14.8 - - + -
432A GLU* 4.3 22.2 - - + +
435A LEU* 3.8 35.9 - - + +
436A VAL* 4.5 5.2 - - + +
439A LEU* 6.1 2.7 - - + -
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Residues in contact with ARG 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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122A MET 2.9 13.1 + - - +
123A LYS* 3.1 38.7 + - - +
125A MET* 1.3 76.8 - - - +
127A LYS* 1.3 60.1 + - - +
129A LEU* 3.0 12.9 + - + +
130A ARG* 2.9 64.3 + - + +
432A GLU* 5.8 2.7 - - - +
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Residues in contact with LYS 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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123A LYS 3.0 9.4 + - - +
124A ASP* 3.3 38.3 + - + +
126A ARG* 1.3 77.8 - - - +
128A VAL* 1.3 54.9 + - + +
130A ARG* 3.7 9.4 - - + +
131A THR* 2.7 46.4 + - + +
257A ALA* 5.3 10.7 - - + +
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Residues in contact with VAL 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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124A ASP 2.9 20.3 + - - +
125A MET* 3.4 27.4 - - + +
126A ARG 3.3 0.2 - - - -
127A LYS* 1.3 77.6 - - - +
129A LEU* 1.3 58.9 + - - +
131A THR* 2.9 10.4 + - - +
132A LEU* 2.9 35.0 + - + +
254A LEU* 5.7 7.1 - - + +
257A ALA* 3.7 39.7 - - + +
258A THR* 4.2 9.9 - - - +
261A LEU* 5.0 0.4 - - + -
435A LEU* 5.9 4.0 - - + -
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Residues in contact with LEU 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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125A MET 2.9 14.1 + - - +
126A ARG* 3.0 14.6 + - + +
128A VAL* 1.3 78.6 - - - +
130A ARG* 1.3 58.8 + - + +
132A LEU* 3.0 26.6 + - + +
133A GLN* 2.4 47.9 + - + +
431A GLN* 4.5 34.8 - - + +
432A GLU* 4.7 15.3 - - + +
435A LEU* 6.3 2.5 - - + -
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Residues in contact with ARG 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 ARG* 2.9 47.2 + - - +
127A LYS* 4.1 7.6 - - + +
128A VAL 3.3 0.2 - - - -
129A LEU* 1.3 81.3 - - - +
131A THR* 1.3 59.2 + - + +
132A LEU 3.1 4.3 - - - -
133A GLN* 3.8 19.1 - - - +
134A GLN* 3.0 39.2 + - + +
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Residues in contact with THR 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 LYS* 2.7 32.8 + - + +
128A VAL* 2.9 16.4 + - - +
130A ARG* 1.3 75.1 - - + +
132A LEU* 1.3 55.5 + - - +
134A GLN* 4.5 1.8 - - - -
135A ILE* 4.1 23.9 - - + +
136A LYS* 3.8 15.8 + - - +
253A GLU* 5.5 15.0 - - + +
254A LEU* 4.9 18.3 - - - +
257A ALA* 5.1 4.0 - - + +
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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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128A VAL* 2.9 23.5 + - + +
129A LEU* 3.0 25.1 + - + +
131A THR* 1.3 76.4 - - - +
133A GLN* 1.3 57.6 + - - +
134A GLN 3.4 1.6 - - - -
136A LYS* 3.5 12.2 - - + -
137A LYS* 2.7 30.8 + - - -
138A SER* 5.2 0.2 - - - -
139A SER* 3.6 46.4 - - - +
140A SER* 4.7 0.9 - - - +
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Residues in contact with GLN 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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129A LEU* 2.4 39.1 + - + +
130A ARG* 3.3 24.0 + - - +
132A LEU* 1.3 73.9 - - - +
134A GLN* 1.3 72.8 + - - +
137A LYS* 3.3 22.9 + - - +
431A GLN* 5.3 3.6 - - - +
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Residues in contact with GLN 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 ARG* 3.0 23.7 + - + +
133A GLN* 1.3 97.2 + - + +
135A ILE* 1.3 72.8 + - + +
137A LYS* 3.5 11.7 - - - +
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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