Contacts of the helix formed by residues 103 - 114 (chain F) in PDB entry 3WBR
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 103 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102F GLN* 1.3 74.6 - - - +
104F TRP* 1.3 53.2 + - - +
105F THR* 3.7 6.3 + - - -
106F LYS* 3.2 31.6 + - - +
107F SER* 2.7 38.1 + - - -
141F PHE* 3.6 2.7 - - - -
198F CYS 3.7 11.7 - - - -
199F HIS* 3.8 25.8 + - - -
200F VAL 4.2 0.7 - - - -
201F PRO* 4.1 3.0 - - - +
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Residues in contact with TRP 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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103F SER* 1.3 71.4 - - - +
105F THR* 1.3 71.4 + - - +
107F SER* 3.1 3.9 + - - -
108F GLN* 2.8 41.7 + - + +
118F LEU* 3.5 16.8 - - + +
141F PHE* 3.4 36.9 - + + -
142F LEU 2.8 21.6 + - - -
143F GLY* 4.1 16.4 - - - -
144F LEU 3.9 6.5 + - - -
145F SER* 3.9 24.9 - - - -
180F CYS* 3.3 30.7 - - + -
181F ALA 4.8 0.2 - - - -
198F CYS* 3.0 21.8 + - + +
156H VAL* 3.6 27.6 - - + -
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Residues in contact with THR 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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103F SER* 3.7 6.0 + - - -
104F TRP* 1.3 92.1 - - - +
106F LYS* 1.3 69.3 + - + +
108F GLN* 3.2 6.6 + - - +
109F LYS* 2.9 29.1 + - + +
198F CYS* 4.9 2.0 + - - +
199F HIS* 5.8 3.3 + - - -
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Residues in contact with LYS 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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102F GLN* 3.3 33.3 + - + +
103F SER* 3.2 21.1 + - - +
105F THR* 1.3 85.2 - - + +
107F SER* 1.3 57.7 + - - +
109F LYS* 3.3 11.7 + - + +
110F ASN* 2.9 28.9 + - - +
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Residues in contact with SER 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F GLN* 3.4 24.5 + - - +
103F SER 2.7 27.5 + - - -
104F TRP* 3.5 7.0 - - - -
106F LYS* 1.3 72.9 - - - +
108F GLN* 1.3 62.8 + - - +
110F ASN* 3.3 5.0 + - - +
111F CYS* 3.1 26.9 + - - -
118F LEU* 4.1 9.0 - - - -
141F PHE* 4.0 5.1 - - - -
202F GLN 4.2 2.6 + - - -
204F SER* 3.7 31.0 + - - -
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Residues in contact with GLN 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 TRP* 2.8 24.4 + - + +
105F THR* 3.2 8.9 + - - +
107F SER* 1.3 72.9 - - - +
109F LYS* 1.3 60.3 + - - +
111F CYS* 3.4 2.0 + - - +
112F SER* 3.0 36.1 + - - -
116F ALA 4.3 1.2 + - - -
117F ASP* 2.8 28.9 + - - +
118F LEU* 2.9 45.4 + - + +
156H VAL* 3.9 24.3 - - + +
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Residues in contact with LYS 109 (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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105F THR* 2.9 15.5 + - + +
106F LYS* 3.3 17.0 + - + +
108F GLN* 1.3 76.6 - - - +
110F ASN* 1.3 61.6 + - - +
112F SER* 3.3 10.1 + - - -
113F VAL* 3.1 43.6 + - + +
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Residues in contact with ASN 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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96F PHE* 5.5 0.2 - - - -
98F SER* 3.0 29.3 + - - -
102F GLN* 3.6 18.4 + - - +
106F LYS 2.9 13.4 + - - +
107F SER 3.5 9.0 + - - +
108F GLN 3.3 0.2 - - - -
109F LYS* 1.3 74.3 - - - +
111F CYS* 1.3 66.1 + - - +
113F VAL* 3.1 24.2 - - - +
114F MET* 3.8 26.3 + - - +
204F SER* 4.9 2.4 + - - -
206F CYS* 5.1 3.8 - - - -
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Residues in contact with CYS 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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107F SER 3.1 20.2 + - - -
108F GLN 3.7 6.3 - - - +
110F ASN* 1.3 75.4 - - - +
112F SER* 1.3 58.3 + - - +
114F MET* 3.1 16.8 + - - +
116F ALA* 2.9 24.3 + - - +
117F ASP 3.6 27.1 - - - +
118F LEU* 3.8 14.4 - - - -
204F SER* 4.9 1.6 - - - -
206F CYS* 2.0 55.4 - - + -
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Residues in contact with SER 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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108F GLN* 3.0 25.8 + - - -
109F LYS* 3.5 14.1 - - - -
110F ASN 3.2 0.2 - - - -
111F CYS* 1.3 77.3 - - - +
113F VAL* 1.3 58.0 + - - +
115F GLY* 2.9 18.7 + - - -
116F ALA 3.2 14.3 + - - -
117F ASP* 5.2 0.7 + - - -
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Residues in contact with VAL 113 (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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109F LYS* 3.1 32.1 + - + +
110F ASN* 3.1 31.6 - - - +
112F SER* 1.3 76.1 - - - +
114F MET* 1.3 64.1 + - + +
115F GLY 3.1 3.3 + - - -
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Residues in contact with MET 114 (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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87F TRP* 3.7 34.1 - - + -
96F PHE* 4.0 29.8 - - + -
110F ASN* 3.8 30.5 - - - +
111F CYS* 3.1 11.9 + - - +
113F VAL* 1.3 81.3 - - + +
115F GLY* 1.3 61.1 + - - +
116F ALA 3.3 0.2 - - - -
206F CYS* 5.5 1.8 - - - -
208F MET* 3.5 16.3 - - - +
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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