Contacts of the helix formed by residues 142 - 149 (chain D) 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 PRO 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D ILE* 3.6 30.5 - - + -
112D HIS* 3.8 15.2 - - + +
115D VAL* 4.2 13.5 - - + +
131D ASP 4.5 1.3 - - - +
132D LEU* 3.1 47.3 - - + +
134D ARG 3.8 7.9 - - - +
141D THR* 1.3 82.0 - - - +
143D LEU* 1.3 51.3 + - - +
145D LEU* 2.9 5.1 + - + +
146D ALA* 2.7 34.7 + - - +
158D LEU* 3.7 15.9 - - + -
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Residues in contact with LEU 143 (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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132D LEU* 5.0 4.8 + - + +
141D THR* 3.3 8.7 + - - +
142D PRO* 1.3 78.9 - - - +
144D GLU* 1.3 60.7 + - + +
147D LEU* 2.7 52.4 + - + +
155D VAL* 3.6 32.3 - - + +
158D LEU* 3.5 20.2 - - + +
159D GLN* 3.5 23.6 - - - +
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Residues in contact with GLU 144 (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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139D GLY 3.8 11.3 - - - +
140D LEU* 3.8 18.8 - - + +
141D THR* 3.0 47.6 + - - +
143D LEU* 1.3 76.8 - - + +
145D LEU* 1.3 51.3 + - - +
147D LEU* 3.4 13.2 - - + +
148D GLN* 2.7 32.6 + - - +
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Residues in contact with LEU 145 (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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112D HIS* 4.1 27.8 - - + +
115D VAL* 4.0 11.9 - - + -
116D GLN* 3.8 30.1 - - + +
136D ASP* 5.0 2.9 - - - +
138D ARG* 3.8 24.7 - - - +
140D LEU* 4.1 11.8 - - + +
141D THR 2.9 11.5 + - - +
142D PRO* 3.5 7.2 - - + +
144D GLU* 1.3 73.2 - - - +
146D ALA* 1.3 58.9 + - - +
147D LEU 3.0 1.6 - - - -
148D GLN* 3.7 20.0 - - - +
149D ARG* 2.7 52.5 + - + +
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Residues in contact with ALA 146 (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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115D VAL* 3.5 19.7 - - + +
142D PRO 2.7 17.2 + - - +
143D LEU* 3.3 8.3 - - - +
145D LEU* 1.3 70.5 - - - +
147D LEU* 1.3 51.5 + - - +
149D ARG* 3.3 1.6 + - - +
150D GLY 2.7 30.1 + - - -
151D ALA* 3.0 12.1 + - - -
154D LEU* 4.3 3.8 - - + -
155D VAL* 3.9 21.5 - - + +
158D LEU* 3.4 23.3 - - + -
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Residues in contact with LEU 147 (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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143D LEU* 2.7 45.4 + - + +
144D GLU* 3.4 9.4 - - + +
146D ALA* 1.3 73.7 - - - +
148D GLN* 1.3 64.9 + - - +
149D ARG 2.7 5.9 + - - -
150D GLY* 2.9 14.1 + - - +
155D VAL* 4.3 16.8 - - + -
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Residues in contact with GLN 148 (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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138D ARG* 3.3 27.7 + - - +
140D LEU* 3.1 35.1 - - + +
144D GLU 2.7 22.0 + - - +
145D LEU* 2.9 14.6 + - - +
147D LEU* 1.3 71.1 - - - +
149D ARG* 1.3 72.7 + - - +
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Residues in contact with ARG 149 (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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115D VAL* 5.1 8.3 - - + +
116D GLN* 4.0 37.0 + - - +
138D ARG* 5.3 2.4 - - - +
145D LEU* 2.7 31.6 + - + +
146D ALA* 3.5 5.4 - - - +
147D LEU 2.7 1.2 + - - -
148D GLN* 1.3 94.0 + - - +
150D GLY* 1.3 57.8 + - - +
151D ALA* 4.3 8.7 - - + +
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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