Contacts of the helix formed by residues 105 - 109 (chain A) in PDB entry 1BI8
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 LEU 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ASP* 1.3 71.9 - - - +
106A THR* 1.3 56.7 + - - +
108A TYR* 3.6 3.8 - - + +
109A LEU* 2.8 61.7 + - + +
125A MET* 4.3 11.9 - - + -
129A LEU* 5.1 1.6 - - + -
148A PRO* 3.5 26.7 + - + +
151A ILE* 2.6 32.3 + - + +
153A VAL* 3.7 16.3 - - + +
159A ILE* 5.4 1.3 - - + -
208A ILE* 3.8 28.5 - - + -
211A GLU* 6.3 1.3 - - + -
212A MET* 4.2 18.2 - - + -
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Residues in contact with THR 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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104A ASP* 2.9 11.3 + - - -
105A LEU* 1.3 74.6 - - - +
107A THR* 1.3 56.4 + - + +
108A TYR 3.0 1.6 - - - -
109A LEU* 3.0 8.8 + - + +
110A ASP* 2.6 45.3 + - + +
148A PRO* 3.6 30.8 + - + +
149A GLN* 3.9 16.6 + - - +
211A GLU* 5.7 3.8 - - - +
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Residues in contact with THR 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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103A GLN* 3.6 5.7 - - - +
104A ASP* 3.0 31.7 + - - +
106A THR* 1.3 78.5 - - + +
108A TYR* 1.3 60.2 + - - +
110A ASP* 3.4 15.1 - - - +
111A LYS* 2.9 27.3 + - - +
18B ARG 5.6 0.2 - - - +
19B GLY 4.0 14.6 - - - +
21B VAL* 5.5 3.1 - - + -
50B MET* 3.6 26.1 - - + -
52B GLY 4.7 3.4 - - - -
53B SER* 3.9 26.0 - - - +
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Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLN* 3.4 30.9 + - - +
104A ASP 3.2 10.2 + - - +
105A LEU* 3.6 11.7 - - + +
107A THR* 1.3 80.0 + - - +
109A LEU* 1.3 72.2 + - + +
111A LYS* 2.9 22.3 + - - +
112A VAL* 2.9 32.8 + - + +
117A VAL* 3.5 31.9 - - + +
118A PRO* 4.4 3.3 - - - +
121A THR* 3.3 25.2 - - + +
125A MET* 3.4 29.8 - - + -
153A VAL* 4.7 4.7 - - + -
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Residues in contact with LEU 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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105A LEU* 2.8 49.8 - - + +
106A THR* 3.0 6.4 + - + +
108A TYR* 1.3 86.5 - - + +
110A ASP* 1.3 59.9 + - - +
111A LYS 2.8 10.8 + - - -
112A VAL* 3.4 13.2 + - - +
117A VAL* 3.6 21.3 - - + -
148A PRO* 5.6 0.9 - - + -
211A GLU* 3.9 33.0 - - + +
212A MET* 4.4 16.8 - - + +
215A ARG* 3.5 35.6 + - + +
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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