Contacts of the helix formed by residues 103 - 113 (chain D) in PDB entry 1B06
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 GLY 103 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D GLY* 1.3 74.5 - - - +
104D ALA* 1.3 64.0 + - - -
106D ALA* 3.7 2.0 - - - +
107D ASP* 3.3 18.1 + - - +
201D GLU* 3.9 9.6 - - - -
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLY* 1.3 71.3 - - - -
105D LEU* 1.3 62.7 + - - +
107D ASP* 3.2 9.1 + - - +
108D LEU* 2.9 28.4 + - + +
201D GLU* 3.1 7.5 + - - +
204D LEU* 3.9 4.5 - - + -
205D GLN* 3.7 13.9 - - - +
208D LEU* 3.5 31.9 - - + -
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PRO* 4.1 5.4 - - + -
102D GLY 3.7 4.0 - - - +
103D GLY 3.2 0.2 - - - -
104D ALA* 1.3 77.6 - - - +
106D ALA* 1.3 62.7 + - - +
108D LEU* 3.2 2.4 + - - +
109D ILE* 3.0 49.1 + - + +
138D LEU* 4.9 3.8 - - + -
147D LEU* 4.2 15.7 - - + -
166D ILE* 4.4 17.3 - - + -
197D TRP* 3.7 35.0 - - + +
200D ALA* 3.8 21.1 - - + -
201D GLU* 2.9 27.8 + - + +
204D LEU* 3.6 14.5 - - + +
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Residues in contact with ALA 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LYS* 3.9 13.5 + - - +
101D PRO* 3.4 36.1 - - - +
102D GLY* 3.2 18.7 + - - +
103D GLY 3.3 2.4 + - - +
105D LEU* 1.3 78.2 - - - +
107D ASP* 1.3 61.2 + - - +
109D ILE* 3.6 3.8 + - - +
110D ASP* 3.2 30.2 + - - +
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLY 3.3 10.1 + - - +
104D ALA* 3.4 12.8 - - - +
105D LEU 3.1 0.4 - - - -
106D ALA* 1.3 78.6 - - - +
108D LEU* 1.3 66.4 + - - +
110D ASP* 3.4 7.7 + - - +
111D LYS* 2.7 67.1 + - - +
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ALA* 2.9 16.7 + - + +
105D LEU 3.8 2.0 - - - +
107D ASP* 1.3 81.2 - - - +
109D ILE* 1.3 61.9 + - - +
111D LYS* 3.3 15.1 + - + +
112D GLN* 3.0 49.2 + - - +
140D TYR* 4.2 23.6 - - + -
145D GLY 4.6 4.3 - - - +
147D LEU* 3.5 26.7 - - + -
204D LEU* 4.2 22.2 - - + -
208D LEU* 4.8 8.7 - - + -
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LYS* 6.2 0.7 - - - -
101D PRO* 4.0 19.5 - - + -
105D LEU* 3.0 39.8 + - + +
106D ALA* 3.9 5.4 - - - +
107D ASP 3.3 0.2 - - - -
108D LEU* 1.3 75.4 - - - +
110D ASP* 1.3 58.4 + - - +
113D TYR* 2.8 35.0 + - + +
114D GLY 3.6 0.7 + - - -
115D SER 3.9 10.0 + - - +
116D PHE* 4.1 12.3 - - + +
119D PHE* 3.6 53.4 - - + -
138D LEU* 5.4 1.1 - - + -
147D LEU* 3.9 15.5 - - + -
197D TRP* 4.9 3.1 - - + -
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LYS* 4.3 13.8 + - - -
106D ALA 3.2 22.2 + - - +
107D ASP* 3.6 8.7 - - - +
109D ILE* 1.3 78.6 - - - +
111D LYS* 1.3 60.0 + - + +
114D GLY* 2.8 38.2 + - - +
115D SER* 3.4 19.8 - - - -
116D PHE 3.9 5.5 + - - -
4F ILE 4.8 1.7 + - - -
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Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP* 2.7 48.4 + - - +
108D LEU* 3.3 16.8 + - + +
110D ASP* 1.3 79.1 - - + +
112D GLN* 1.3 61.3 + - + +
3F VAL* 5.1 1.5 + - - +
4F ILE* 3.4 11.4 + - - +
5F GLN* 3.2 22.5 + - - +
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Residues in contact with GLN 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D LEU* 3.0 36.1 + - - +
111D LYS* 1.3 83.1 - - + +
113D TYR* 1.3 72.2 + - + +
114D GLY 3.7 0.4 - - - -
145D GLY 3.0 26.7 + - - -
146D ASN* 3.6 10.5 + - - +
147D LEU* 2.9 36.2 + - - +
4F ILE* 3.7 12.8 - - - +
5F GLN 3.8 19.9 + - - +
6F LEU* 3.9 22.9 - - + +
56F ILE* 3.9 6.2 - - - +
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ILE* 2.8 23.8 + - - +
112D GLN* 1.3 92.5 - - + +
114D GLY* 1.3 58.6 + - - +
115D SER 3.1 10.0 + - - +
118D ARG* 3.2 21.5 - - - +
119D PHE* 3.9 53.6 - + + +
122D VAL* 4.4 7.9 - - + -
138D LEU* 4.3 0.7 - - - +
147D LEU* 2.9 34.6 + - + -
149D ILE* 3.6 28.2 + - + +
4F ILE* 4.0 9.5 - - - +
6F LEU* 5.2 3.7 - - + +
52F LEU* 6.0 1.2 - - - +
56F ILE* 3.6 41.6 - - + +
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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