Contacts of the helix formed by residues 102 - 115 (chain A) in PDB entry 2JNU
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 PHE 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A PHE* 5.0 4.5 - + - -
47A CYS* 3.6 23.3 - - + -
50A PHE* 3.7 49.7 - + + -
65A ALA* 4.6 13.5 - - - -
68A ILE* 4.2 15.9 - - + -
73A LEU* 3.5 29.8 - - + -
88A TRP* 3.6 19.5 - + - -
89A LEU* 6.0 1.3 - - + -
93A VAL* 3.4 33.7 - - + -
100A ASP 3.7 0.4 - - - -
101A MET* 1.3 75.8 - - - +
103A ARG* 1.3 52.2 + - - +
104A ALA 3.4 2.0 - - - -
105A GLN* 3.3 13.2 + - + +
106A GLN* 2.7 37.7 + - - +
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Residues in contact with ARG 103 (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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100A ASP* 2.7 61.5 + - - +
101A MET 2.9 9.0 + - - +
102A PHE* 1.3 75.6 - - - +
104A ALA* 1.3 75.3 + - + +
106A GLN* 3.1 12.0 + - - +
107A LEU* 3.0 35.2 + - + +
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Residues in contact with ALA 104 (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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101A MET 4.5 0.6 + - - -
102A PHE 3.4 0.4 - - - -
103A ARG* 1.3 87.0 - - + +
105A GLN* 1.3 73.3 + - - +
107A LEU* 3.2 7.0 + - - +
108A GLN* 2.8 27.6 + - - +
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Residues in contact with GLN 105 (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 PHE* 3.6 12.5 - - + -
83A ILE* 3.5 37.5 - - + -
84A ASP* 4.6 10.7 - - - +
88A TRP* 3.5 23.4 - - + +
89A LEU* 4.1 13.3 - - - +
101A MET 3.9 19.6 + - - -
102A PHE* 3.3 13.0 + - + +
104A ALA* 1.3 91.5 - - - +
106A GLN* 1.3 61.8 + - - +
108A GLN* 3.2 10.1 + - - +
109A ILE* 3.1 28.2 + - - +
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Residues in contact with GLN 106 (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 PHE* 4.2 10.1 - - - -
44A TRP* 3.4 55.9 + - + +
47A CYS* 3.2 30.7 - - + +
48A GLU* 4.2 4.9 - - - +
51A GLN* 3.2 28.8 + - - +
102A PHE 2.7 19.9 + - - +
103A ARG* 3.2 13.6 - - - +
105A GLN* 1.3 73.6 - - - +
107A LEU* 1.3 66.5 + - + +
109A ILE* 3.3 4.0 + - - +
110A PHE 2.9 21.3 + - - -
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Residues in contact with LEU 107 (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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44A TRP* 5.3 2.0 - - - +
103A ARG* 3.0 31.4 + - + +
104A ALA* 3.2 8.9 + - - +
106A GLN* 1.3 88.3 - - + +
108A GLN* 1.3 59.8 + - - +
110A PHE* 3.6 28.7 - - + -
111A ASN* 2.8 45.5 + - - +
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Residues in contact with GLN 108 (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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82A ASN 4.1 11.3 + - - +
83A ILE* 3.9 22.2 - - + +
84A ASP* 5.6 1.8 - - - +
104A ALA 2.8 13.8 + - - +
105A GLN* 3.3 17.0 - - - +
106A GLN 3.2 0.2 - - - -
107A LEU* 1.3 78.6 - - - +
109A ILE* 1.3 57.2 + - - +
111A ASN* 3.6 3.3 + - - +
112A LEU* 3.0 34.7 + - + +
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Residues in contact with ILE 109 (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 ASN* 3.1 47.3 - - + +
43A PHE* 3.6 22.7 - - + -
44A TRP* 3.9 15.9 - - + +
81A VAL* 4.2 12.6 - - + -
82A ASN 4.3 6.7 - - - +
83A ILE* 3.4 31.9 - - + -
105A GLN 3.1 9.6 + - - +
106A GLN 3.6 5.6 - - - +
108A GLN* 1.3 77.8 - - - +
110A PHE* 1.3 66.7 + - - +
112A LEU* 2.9 21.4 + - + +
113A MET* 3.0 19.3 + - + +
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Residues in contact with PHE 110 (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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15A PHE* 3.5 21.7 - + + -
16A GLU* 4.3 24.9 - - + -
19A LEU* 3.3 35.7 - - + -
44A TRP* 3.4 19.7 - + + +
106A GLN 2.9 14.7 + - - +
107A LEU* 3.5 26.0 - - + +
109A ILE* 1.3 76.9 - - - +
111A ASN* 1.3 71.0 + - - +
113A MET* 3.4 14.0 - - - +
114A LYS* 2.9 43.5 + - + +
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Residues in contact with ASN 111 (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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107A LEU* 2.8 40.4 + - - +
108A GLN* 4.2 3.8 - - - +
110A PHE* 1.3 84.7 - - - +
112A LEU* 1.3 66.2 + - - +
114A LYS* 3.5 33.8 + - + +
115A PHE* 4.0 6.4 + - - +
116A ASP* 5.0 0.2 - - - +
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Residues in contact with LEU 112 (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 ASN* 5.3 12.1 - - + +
82A ASN* 4.3 29.8 - - + +
108A GLN* 3.0 23.4 + - - +
109A ILE* 2.9 21.0 + - + +
111A ASN* 1.3 79.1 - - - +
113A MET* 1.3 63.4 + - + +
115A PHE 4.1 0.2 + - - -
116A ASP* 2.8 34.0 - - + +
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Residues in contact with MET 113 (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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15A PHE* 3.5 25.6 - - + -
19A LEU* 3.7 21.3 - - + -
28A PHE* 4.4 0.7 - - - -
40A ASN* 3.1 29.2 - - - +
41A VAL* 3.3 19.5 - - + -
44A TRP* 4.0 13.0 - - + -
109A ILE* 3.0 22.6 + - + +
110A PHE* 3.4 22.0 - - - +
112A LEU* 1.3 76.1 - - + +
114A LYS* 1.3 64.0 + - - +
115A PHE 3.2 4.3 + - - -
116A ASP* 3.2 3.3 + - - -
117A SER* 3.0 23.3 + - - +
118A TYR* 3.0 27.0 + - - +
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Residues in contact with LYS 114 (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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15A PHE* 3.8 27.8 - - + -
110A PHE* 2.9 33.3 + - + +
111A ASN* 3.5 30.3 - - + +
112A LEU 3.3 0.6 - - - -
113A MET* 1.3 76.7 - - - +
115A PHE* 1.3 64.7 + - + +
118A TYR* 3.0 29.6 - - + -
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Residues in contact with PHE 115 (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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111A ASN 4.0 6.7 + - - +
112A LEU 4.1 0.6 + - - -
113A MET 3.2 0.2 - - - -
114A LYS* 1.3 87.0 - - + +
116A ASP* 1.3 69.9 + - - +
118A TYR* 5.2 0.2 - - - -
119A ALA* 3.7 19.9 - - + +
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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