Contacts of the helix formed by residues 105 - 117 (chain B) in PDB entry 3ADB
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 SER 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B ALA* 1.3 76.1 - - - +
106B LEU* 1.3 64.5 + - - +
107B ASP* 3.3 11.9 + - - +
108B VAL* 2.9 38.1 + - - +
109B LEU* 2.9 10.7 + - - +
129B TYR* 5.0 4.3 - - - -
151B THR* 4.6 3.9 - - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA 3.6 1.8 + - - -
105B SER* 1.3 72.9 - - - +
107B ASP* 1.3 56.9 + - - +
109B LEU* 4.2 5.8 - - + -
110B ILE* 2.8 60.1 + - + +
125B ILE* 4.1 12.6 - - + -
126B LYS* 4.2 25.8 - - + +
129B TYR* 4.0 52.8 + - + -
130B GLU* 6.1 0.4 - - + +
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B SER* 3.0 11.4 + - - +
106B LEU* 1.3 78.8 - - - +
108B VAL* 1.3 58.3 + - + +
110B ILE* 3.8 6.4 - - - +
111B ARG* 3.0 28.3 + - - +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA* 4.4 6.7 - - + -
105B SER* 2.9 27.7 + - - +
107B ASP* 1.3 73.3 - - + +
109B LEU* 1.3 62.1 + - - +
111B ARG* 3.3 10.5 + - + +
112B ARG* 2.8 67.8 + - + +
151B THR* 4.1 18.4 - - + -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.5 36.6 - - + +
9B PRO 3.4 23.3 - - - +
10B GLY* 3.9 3.0 - - - +
11B VAL* 3.5 29.4 - - + +
104B ALA* 3.9 25.6 - - + +
105B SER 2.9 13.8 + - - +
106B LEU* 3.6 9.9 - - + +
108B VAL* 1.3 78.3 - - - +
110B ILE* 1.3 58.3 + - - +
112B ARG* 3.3 4.6 + - - +
113B ASN* 2.8 30.4 + - - +
125B ILE* 4.2 16.9 - - + +
129B TYR* 4.1 9.4 - - + -
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 2.8 47.7 + - + +
107B ASP* 3.8 6.7 - - - +
109B LEU* 1.3 71.0 - - - +
111B ARG* 1.3 66.3 + - - +
113B ASN* 3.1 14.2 + - - +
114B ILE* 3.1 29.5 + - + +
122B ASN* 3.9 27.4 - - + +
125B ILE* 3.9 13.5 - - + -
126B LYS* 3.7 31.0 - - + -
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Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASP 3.0 17.8 + - - +
108B VAL* 3.6 11.2 - - - +
110B ILE* 1.3 76.9 - - - +
112B ARG* 1.3 66.4 + - + +
114B ILE* 3.2 13.5 + - - +
115B GLU* 3.1 41.9 + - + +
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLY* 2.8 34.2 + - - +
11B VAL* 2.9 24.4 + - - +
104B ALA* 4.6 1.6 - - - +
108B VAL* 2.8 43.5 + - + +
109B LEU* 3.7 5.1 - - - +
111B ARG* 1.3 78.9 - - + +
113B ASN* 1.3 66.8 + - - +
114B ILE 3.0 0.9 + - - -
115B GLU* 3.1 20.9 + - + +
116B ARG* 3.2 18.9 + - - +
150B THR* 3.1 24.4 + - - -
151B THR* 4.6 3.6 - - - +
2002B ANP 3.0 60.7 + - - +
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Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO 6.1 0.4 - - - +
10B GLY* 5.7 2.4 - - - -
109B LEU 2.8 21.1 + - - +
110B ILE* 3.1 6.9 + - - +
112B ARG* 1.3 73.8 - - - +
114B ILE* 1.3 59.4 + - - +
116B ARG* 3.5 18.7 + - - +
117B GLY 3.5 0.3 + - - -
118B GLU* 3.0 34.5 + - - +
119B LYS 4.5 0.7 + - - -
120B ILE* 2.8 42.1 + - - +
122B ASN* 2.9 29.9 + - - +
125B ILE* 3.9 21.7 - - + +
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE* 3.1 29.6 + - + +
111B ARG* 3.4 10.3 - - - +
112B ARG 3.0 0.4 - - - -
113B ASN* 1.3 72.7 - - - +
115B GLU* 1.3 59.1 + - - +
116B ARG 2.6 5.1 + - - -
117B GLY* 2.6 28.9 + - - -
118B GLU* 4.3 17.5 - - + +
122B ASN* 3.9 16.6 - - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG* 3.2 30.3 - - + +
112B ARG* 3.1 15.2 + - + +
114B ILE* 1.3 78.4 - - - +
116B ARG* 1.3 61.3 + - + +
2002B ANP 5.3 6.1 - - - +
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 4.0 3.4 - - - +
10B GLY* 3.1 17.8 - - - +
112B ARG 3.2 15.2 + - - +
113B ASN* 3.7 16.8 + - - +
114B ILE 2.6 6.1 + - - -
115B GLU* 1.3 78.0 - - + +
117B GLY* 1.3 55.0 + - - +
118B GLU 4.8 0.2 - - - +
119B LYS* 4.8 14.9 - - + +
120B ILE* 5.5 3.4 - - - +
2002B ANP 2.8 94.9 + - - +
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ILE 2.6 18.1 + - - -
115B GLU 3.5 0.2 - - - -
116B ARG* 1.3 73.7 - - - +
118B GLU* 1.3 71.9 + - - +
119B LYS* 3.2 10.2 + - - +
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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