Contacts of the helix formed by residues 116 - 125 (chain A) in PDB entry 1JUL
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 GLU 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LYS* 1.3 73.5 - - - +
117A SER* 1.3 62.1 + - - +
119A ILE* 2.9 17.9 + - - +
120A ASP* 3.1 9.4 + - - +
144A SER* 4.3 14.0 + - - +
145A LEU* 3.8 16.2 - - + +
148A TYR* 3.6 52.0 + - + +
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Residues in contact with SER 117 (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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19A ARG 4.6 2.9 + - - -
21A SER* 4.4 17.2 + - - -
115A LYS* 3.3 29.3 + - - +
116A GLU* 1.3 78.4 - - - +
118A GLN* 1.3 59.1 + - - +
119A ILE 3.2 0.2 - - - -
120A ASP* 3.2 18.1 + - - +
121A ASP* 2.8 33.8 + - - +
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Residues in contact with GLN 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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16A SER* 3.7 16.5 + - - +
19A ARG* 5.1 9.5 - - + +
93A TYR* 4.1 12.9 + - - +
109A MET* 3.7 9.1 - - + +
111A ASP* 4.5 10.0 - - - +
112A PHE 3.2 15.4 - - - +
113A ILE* 3.8 19.4 - - + +
114A VAL* 2.8 42.2 - - - +
115A LYS* 3.2 29.8 + - + +
116A GLU 3.0 1.2 + - - -
117A SER* 1.3 78.0 + - - +
119A ILE* 1.3 59.0 + - - +
121A ASP* 3.4 12.3 - - - +
122A ALA* 3.0 25.3 + - - +
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Residues in contact with ILE 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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113A ILE* 3.9 19.1 - - + -
115A LYS 4.5 0.9 - - - +
116A GLU 2.9 9.5 + - - +
118A GLN* 1.3 76.7 - - - +
120A ASP* 1.3 63.9 + - - +
122A ALA* 3.3 6.2 + - - +
123A TYR* 3.0 22.3 + - - +
130A VAL* 4.6 12.3 - - + -
132A LEU* 4.9 1.6 - - + -
145A LEU* 3.6 49.1 - - + +
148A TYR* 3.9 22.7 - - + -
149A ALA* 4.0 18.6 - - + +
152A TYR* 3.9 14.8 - - + -
154A MET* 4.5 9.8 - - - +
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Residues in contact with ASP 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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21A SER* 6.0 1.6 - - - -
116A GLU* 3.1 7.1 + - - +
117A SER* 3.3 23.5 + - - +
119A ILE* 1.3 76.8 - - - +
121A ASP* 1.3 58.0 + - - +
123A TYR* 3.3 1.6 + - - +
124A ASN* 2.8 44.1 + - - +
148A TYR* 2.6 30.9 + - - -
152A TYR* 2.8 27.2 + - - +
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Residues in contact with ASP 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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19A ARG* 5.3 1.0 - - - +
20A PRO 4.1 1.6 - - - +
21A SER* 3.1 19.9 - - - -
22A PHE 3.0 24.8 + - - +
93A TYR* 2.6 45.8 + - + +
117A SER* 2.8 18.9 + - - +
118A GLN* 3.4 13.6 - - - +
120A ASP* 1.3 78.2 - - - +
122A ALA* 1.3 56.5 + - - +
124A ASN* 3.3 6.4 + - - +
125A LEU* 2.9 41.5 + - + +
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Residues in contact with ALA 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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109A MET* 3.6 25.1 - - - -
118A GLN 3.0 10.1 + - - +
119A ILE 3.3 6.7 + - - +
121A ASP* 1.3 75.4 - - - +
123A TYR* 1.3 62.1 + - - +
125A LEU* 3.5 2.8 + - - +
126A GLY 3.3 4.0 + - - -
127A ALA* 2.9 37.2 + - + +
130A VAL* 3.5 32.5 - - + -
154A MET* 4.2 3.1 - - + -
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Residues in contact with TYR 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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26A ARG* 2.9 64.6 + - + +
30A ILE* 4.0 20.4 - - + +
119A ILE 3.0 17.0 + - - +
120A ASP 3.6 3.1 - - - +
122A ALA* 1.3 76.3 - - - +
124A ASN* 1.3 77.2 + - - +
126A GLY 3.3 2.4 + - - -
152A TYR* 3.5 57.2 - + + -
154A MET* 3.7 12.0 - - + +
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Residues in contact with ASN 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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22A PHE 4.5 9.5 - - - +
24A ALA* 3.3 34.8 + - + +
25A SER* 3.4 24.0 - - - +
26A ARG* 3.5 8.8 + - - +
27A GLN* 4.1 0.5 - - - +
97A ARG* 5.8 0.2 - - - +
120A ASP* 2.8 32.8 + - - +
121A ASP* 3.9 5.2 + - - +
123A TYR* 1.3 90.7 - - - +
125A LEU* 1.3 62.3 + - + +
126A GLY 3.5 0.3 + - - -
152A TYR* 5.4 2.2 + - - -
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Residues in contact with LEU 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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22A PHE* 3.3 36.8 - - + -
24A ALA* 3.8 11.2 - - + -
27A GLN* 3.8 6.2 - - - +
93A TYR* 3.6 51.4 - - + +
96A LEU* 3.7 21.8 - - + +
97A ARG* 3.8 25.2 - - + +
100A ALA* 3.5 16.3 - - - +
121A ASP* 2.9 31.4 + - + +
122A ALA 4.0 0.9 - - - +
124A ASN* 1.3 77.5 - - + +
126A GLY* 1.3 58.0 + - - +
127A ALA 3.7 0.2 - - - -
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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