Contacts of the helix formed by residues 102 - 112 (chain F) in PDB entry 1JB0
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 102 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84F TYR* 3.0 17.0 + - + +
97F LYS* 3.6 31.9 + - + +
100F ILE 3.6 1.8 + - - +
101F ILE* 1.3 69.0 - - - +
103F VAL* 1.3 66.2 + - - +
104F PRO* 3.5 16.4 - - - +
105F LEU* 2.8 33.6 + - + +
106F ALA* 2.9 20.6 + - - +
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Residues in contact with VAL 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139A CLA 6.5 1.8 - - + -
101F ILE* 3.1 6.2 + - - +
102F ASP* 1.3 71.9 - - - +
104F PRO* 1.4 67.7 - - + +
106F ALA* 3.0 9.1 + - + +
107F ILE* 2.8 55.9 + - + +
110F MET* 6.3 0.4 - - + -
8J LEU 5.9 0.2 - - - -
9J SER* 3.8 25.1 - - - +
14J LEU* 4.4 23.1 - - + -
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Residues in contact with PRO 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ASP* 3.5 13.7 - - - +
103F VAL* 1.4 95.8 - - + +
105F LEU* 1.3 64.1 + - - +
107F ILE* 3.3 9.9 + - + +
108F LYS* 3.1 21.8 + - - +
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Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F TYR* 4.1 6.1 - - + -
87F ALA* 4.1 19.7 - - + -
88F VAL* 3.8 29.8 - - + +
97F LYS* 4.9 5.6 - - - +
102F ASP* 2.8 31.2 + - + +
104F PRO* 1.3 78.5 - - - +
106F ALA* 1.3 62.4 + - - +
108F LYS* 3.2 18.8 + - + +
109F CYS* 3.1 36.5 + - - -
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Residues in contact with ALA 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138A CLA 4.0 12.5 - - + +
1139A CLA 5.2 1.6 - - + -
84F TYR* 3.8 11.6 - - + -
101F ILE* 4.0 19.3 - - + -
102F ASP 2.9 13.2 + - - +
103F VAL* 3.0 12.1 + - + +
105F LEU* 1.3 76.7 - - - +
107F ILE* 1.3 63.2 + - + +
109F CYS* 3.1 5.8 + - - +
110F MET* 3.0 42.3 + - + +
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Residues in contact with ILE 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F VAL* 2.8 46.2 + - + +
104F PRO* 3.8 8.1 - - + +
106F ALA* 1.3 71.2 - - - +
108F LYS* 1.3 63.0 + - - +
110F MET* 3.2 19.1 + - + +
111F LEU* 3.1 46.2 + - + +
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Residues in contact with LYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F PRO 3.1 12.4 + - - +
105F LEU* 3.3 22.7 - - + +
106F ALA 3.2 0.2 - - - -
107F ILE* 1.3 78.3 - - - +
109F CYS* 1.3 62.4 + - - +
111F LEU* 3.6 16.1 + - - +
112F THR* 3.4 13.5 + - - +
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Residues in contact with CYS 109 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80F VAL* 3.0 29.0 - - + +
83F ALA* 4.2 13.4 - - + +
84F TYR* 3.8 28.0 - - + -
87F ALA* 5.0 1.8 - - - -
105F LEU* 3.1 36.9 + - - -
106F ALA 3.1 7.2 + - - +
108F LYS* 1.3 75.7 - - - +
110F MET* 1.3 62.2 + - - +
112F THR* 2.9 32.9 + - - -
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Residues in contact with MET 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138A CLA 4.2 4.9 - - + -
1139A CLA 3.4 30.3 - - + -
76F TRP* 3.2 18.4 + - - -
80F VAL* 3.5 19.5 - - + -
103F VAL* 6.3 0.2 - - + -
106F ALA* 3.0 34.2 + - + +
107F ILE* 3.2 23.3 + - + +
109F CYS* 1.3 76.7 - - - +
111F LEU* 1.3 58.3 + - + +
113F GLY* 2.8 17.7 + - - -
1301F CLA 3.0 47.6 - - + +
18J TRP* 4.8 10.5 - - + -
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Residues in contact with LEU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F TRP* 5.0 1.3 - - - -
107F ILE* 3.1 33.8 + - + +
108F LYS* 3.8 10.1 - - - +
109F CYS 3.2 0.2 - - - -
110F MET* 1.3 76.1 - - + +
112F THR* 1.3 59.0 + - - +
113F GLY 3.0 0.4 - - - -
114F PHE* 3.0 34.7 + - + -
1301F CLA 4.3 17.9 - - - -
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Residues in contact with THR 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F TRP* 4.6 21.3 - - + +
80F VAL* 4.5 1.1 - - - -
108F LYS* 3.4 11.3 + - - +
109F CYS* 2.9 18.3 + - - -
111F LEU* 1.3 78.4 - - - +
113F GLY* 1.3 65.8 + - - +
114F PHE* 3.5 3.4 - - - -
115F ALA* 3.2 18.1 + - + +
116F TRP* 3.8 2.3 + - - -
119F ALA* 5.2 7.6 - - + -
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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