Contacts of the helix formed by residues 117 - 132 (chain A) in PDB entry 5JRE
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLN* 2.6 34.1 + - - +
85A GLU* 3.7 31.2 - - - +
113A PHE 3.4 6.7 - - - +
114A GLY 3.1 9.3 + - - +
115A ILE 3.0 1.2 + - - -
116A GLY* 1.3 80.5 - - - +
118A ILE* 1.3 62.5 + - - +
119A ALA 3.3 3.6 + - - -
120A GLY* 3.6 9.0 + - - -
121A GLU* 4.3 2.4 + - - +
165A LYS* 3.1 20.8 + - - +
168A TYR* 4.3 15.0 + - + -
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Residues in contact with ILE 118 (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 GLU* 3.9 18.2 - - - +
88A ALA* 3.6 26.2 - - + -
89A LEU* 4.9 4.5 - - - +
98A ILE* 3.7 32.5 - - + -
114A GLY 3.8 15.0 - - - +
115A ILE* 3.2 23.3 + - + +
117A ASP* 1.3 76.3 - - - +
119A ALA* 1.3 69.0 + - - +
121A GLU* 3.0 8.4 + - + +
122A ILE* 3.0 37.4 + - + +
148A LEU* 3.8 22.9 - - + -
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Residues in contact with ALA 119 (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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115A ILE 4.8 0.4 + - - -
116A GLY 5.0 0.2 + - - -
117A ASP 3.3 1.0 - - - -
118A ILE* 1.3 81.4 - - - +
120A GLY* 1.3 55.9 + - - +
122A ILE* 3.3 3.3 + - - +
123A LEU 2.9 24.1 + - - -
145A LEU* 3.8 27.3 - - + +
148A LEU* 5.0 1.1 - - + +
168A TYR* 4.5 4.7 - - + -
169A VAL* 4.0 28.0 - - + -
172A ILE* 3.5 30.7 - - + +
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Residues in contact with GLY 120 (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 ASP 3.6 2.7 + - - -
118A ILE 3.2 1.0 - - - -
119A ALA* 1.3 79.3 - - - +
121A GLU* 1.3 62.0 + - - +
123A LEU* 3.5 5.0 + - - +
124A ARG* 3.1 25.5 + - - +
168A TYR* 3.2 29.1 + - - -
172A ILE* 4.2 10.3 - - - -
174F ASN* 5.8 1.9 + - - -
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Residues in contact with GLU 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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37A ILE* 3.2 31.8 - - + +
41A ILE* 4.3 7.8 - - - +
85A GLU* 2.9 37.4 - - + +
89A LEU* 3.9 26.3 - - + +
117A ASP 4.3 2.4 - - - +
118A ILE* 3.0 9.1 + - - +
120A GLY* 1.3 78.0 - - - +
122A ILE* 1.3 59.7 + - - +
124A ARG* 3.3 8.6 + - - +
125A LYS* 3.0 27.9 + - - +
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Residues in contact with ILE 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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89A LEU* 4.2 10.8 - - + -
92A TYR* 4.0 44.9 - - + +
98A ILE* 5.3 0.4 - - + -
118A ILE* 3.0 36.7 + - + +
119A ALA 3.7 7.4 - - - +
121A GLU* 1.3 75.2 - - - +
123A LEU* 1.3 55.8 + - - +
125A LYS* 3.5 5.4 + - - +
126A SER* 2.7 37.0 + - - +
137A TYR* 5.7 0.9 - - + -
141A ALA* 3.9 25.1 - - + -
144A ASP* 5.9 1.3 - - + -
145A LEU* 3.9 32.3 - - + -
176A LEU* 5.6 0.2 - - + -
1B MET* 6.4 0.7 - - - -
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Residues in contact with LEU 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 ALA 2.9 14.8 + - - +
120A GLY* 3.5 9.9 - - - +
122A ILE* 1.3 76.2 - - - +
124A ARG* 1.3 57.1 + - - +
126A SER* 3.2 5.8 + - - -
127A SER* 2.8 36.8 + - - +
145A LEU* 5.5 0.2 - - - -
172A ILE* 3.8 32.3 - - + +
175A LYS* 4.3 20.6 - - + -
176A LEU* 3.9 31.9 - - + +
179A PHE* 3.7 28.3 - - + -
174F ASN* 6.2 4.7 - - + +
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Residues in contact with ARG 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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38A TYR* 4.3 23.6 - - - -
41A ILE* 3.9 33.0 - - + +
120A GLY 3.1 13.0 + - - +
121A GLU* 3.5 15.0 - - - +
123A LEU* 1.3 77.0 - - - +
125A LYS* 1.3 61.9 + - - +
127A SER* 3.3 4.2 + - - -
128A GLU* 3.1 23.3 + - - +
146F GLU* 4.3 15.8 + - - +
149F TYR* 6.0 2.6 - - - -
170F SER* 4.6 11.9 + - - -
173F ILE* 4.1 22.7 - - - +
174F ASN* 3.3 31.6 + - - +
177F ILE* 4.0 18.4 - - - +
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Residues in contact with LYS 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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40A MET 4.6 2.4 + - - -
41A ILE* 3.9 28.3 + - + +
43A GLU* 3.5 27.9 + - - +
45A TYR* 4.8 3.6 + - - -
89A LEU* 4.9 1.6 - - + -
92A TYR* 5.9 0.4 - - + -
93A ILE* 4.0 32.5 - - + -
121A GLU 3.0 16.3 + - - +
122A ILE* 3.7 7.2 - - - +
124A ARG* 1.3 75.3 - - - +
126A SER* 1.3 62.8 + - - +
128A GLU* 3.2 10.3 + - + +
129A GLU* 3.0 48.7 + - - +
137A TYR* 3.3 37.0 - - + +
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Residues in contact with SER 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 ILE 2.7 22.2 + - - -
123A LEU* 3.5 6.5 - - - -
125A LYS* 1.3 76.2 - - - +
127A SER* 1.3 58.1 + - - +
129A GLU* 3.2 3.3 + - - +
130A LEU* 2.8 33.8 + - - +
137A TYR* 4.0 14.2 - - - -
138A ALA* 4.4 9.2 - - - +
141A ALA* 3.2 25.6 - - - +
176A LEU* 3.9 24.4 - - - +
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 2.8 22.2 + - - +
124A ARG* 3.6 8.1 - - - -
126A SER* 1.3 75.1 - - - +
128A GLU* 1.3 64.6 + - - +
130A LEU* 3.2 12.2 + - - +
131A ILE* 3.0 29.7 + - - +
179A PHE* 3.5 24.9 - - - -
177F ILE* 3.7 28.4 - - - +
181F ILE* 4.2 3.8 - - - +
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Residues in contact with GLU 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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41A ILE* 3.6 36.8 - - + +
42A ARG* 5.6 3.6 - - + -
124A ARG* 3.1 12.1 + - - +
125A LYS* 3.2 13.4 + - + +
127A SER* 1.3 79.5 - - - +
129A GLU* 1.3 62.2 + - + +
131A ILE* 3.6 19.7 + - + +
132A LYS* 3.6 20.9 + - - +
142F LYS* 5.6 6.7 - - - +
177F ILE* 6.1 1.9 - - + +
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Residues in contact with GLU 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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43A GLU* 3.7 1.6 - - - +
125A LYS* 3.0 44.2 + - - +
126A SER 3.2 7.4 + - - +
128A GLU* 1.3 75.6 - - - +
130A LEU* 1.3 64.6 + - - +
132A LYS* 3.2 37.3 + - - +
134A ASN* 2.9 55.0 + - - +
137A TYR* 3.6 38.9 - - + -
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Residues in contact with LEU 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 SER 2.8 24.7 + - - +
127A SER* 3.2 7.6 + - - +
129A GLU* 1.3 75.9 - - - +
131A ILE* 1.3 54.6 + - - +
133A GLY* 2.8 24.7 + - - +
134A ASN 4.4 2.7 - - - +
135A ILE* 4.1 30.1 - - + -
138A ALA* 3.9 27.6 - - + -
176A LEU* 4.7 3.1 - - + -
179A PHE* 3.6 42.4 - - + +
180A ILE* 5.3 0.9 - - - -
183A LYS* 3.9 37.6 - - + +
181F ILE* 4.6 9.6 - - + -
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Residues in contact with ILE 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 SER 3.0 22.7 + - - +
128A GLU* 3.7 13.2 - - + +
129A GLU 3.3 0.2 - - - -
130A LEU* 1.3 76.9 - - - +
132A LYS* 1.3 64.3 + - + +
133A GLY 3.1 1.4 + - - -
183A LYS* 4.8 9.8 + - - +
139F LYS* 6.4 2.5 - - - -
142F LYS* 4.2 28.5 - - + +
177F ILE* 4.5 12.6 - - + -
180F ILE* 5.2 14.8 - - + -
181F ILE* 4.8 12.1 - - + -
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Residues in contact with LYS 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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43A GLU* 2.7 31.3 + - - -
128A GLU* 3.6 15.0 - - - +
129A GLU* 3.2 34.0 + - - +
130A LEU 3.2 0.8 - - - -
131A ILE* 1.3 82.3 - - + +
133A GLY* 1.3 58.9 + - - +
134A ASN* 3.4 3.6 + - + +
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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