Contacts of the helix formed by residues 146 - 151 (chain W) in PDB entry 1BFR
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 146 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143O LYS 6.0 0.9 - - - +
83W VAL* 5.0 9.9 - - + -
84W GLU* 5.4 6.1 - - + +
141W ILE* 3.8 29.1 + - + +
145W GLY* 1.3 70.5 - - - -
147W GLN* 1.3 59.6 + - + +
149W TYR* 3.1 11.8 + - + +
150W LEU* 2.7 55.8 + - + +
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Residues in contact with GLN 147 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142O GLN 4.9 1.8 + - - -
143O LYS 3.8 14.2 + - - +
144O MET* 3.5 39.1 + - - +
145O GLY* 3.8 8.5 - - - +
148O ASN* 3.4 14.0 + - - +
145W GLY 3.5 0.6 - - - -
146W LEU* 1.3 76.1 - - + +
148W ASN* 1.3 62.0 + - - +
150W LEU* 3.4 2.9 + - - +
151W GLN* 3.0 19.8 + - - +
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Residues in contact with ASN 148 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G GLN* 3.5 26.7 + - - +
148G ASN* 2.9 29.2 + - - +
151G GLN* 2.7 38.1 + - - +
148O ASN* 3.1 22.9 + - - +
144W MET* 3.3 27.8 + - + +
145W GLY 3.5 1.4 + - - -
146W LEU 3.4 0.2 - - - -
147W GLN* 1.3 74.6 - - - +
149W TYR* 1.3 64.6 + - - +
151W GLN* 3.3 1.7 + - - +
152W ALA* 3.1 11.1 + - - +
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Residues in contact with TYR 149 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ILE* 5.9 2.2 - - + -
39W ARG* 5.1 0.2 - - - -
40W LEU* 3.6 17.2 - - + +
83W VAL* 4.1 15.0 - - + -
87W LEU* 3.8 5.7 - - - +
137W GLU* 2.6 45.3 + - + +
140W LEU* 4.5 11.2 - - + -
141W ILE* 3.7 44.9 - - + -
144W MET* 3.8 16.2 - - + +
145W GLY 2.9 18.4 + - - +
146W LEU* 3.4 13.5 - - + +
148W ASN* 1.3 70.9 - - - +
150W LEU* 1.3 72.3 + - + +
152W ALA* 3.1 6.6 + - + -
153W GLN* 2.9 46.9 + - + +
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Residues in contact with LEU 150 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140O LEU* 6.1 0.9 - - + -
143O LYS* 3.8 44.0 - - + +
144O MET* 4.3 12.8 - - + -
37W LEU* 4.1 21.6 - - + +
83W VAL* 4.0 28.3 - - + -
146W LEU* 2.7 46.6 + - + +
147W GLN 3.9 3.1 - - - +
149W TYR* 1.3 76.9 - - + +
151W GLN* 1.3 63.8 + - - +
153W GLN* 3.0 21.8 + - + +
154W ILE* 3.8 9.4 - - - +
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Residues in contact with GLN 151 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G GLN* 2.9 24.1 + - - +
144O MET* 4.0 24.0 - - - +
148O ASN* 2.9 41.7 + - - +
151O GLN* 2.7 32.6 + - - +
152O ALA* 4.0 13.2 - - + +
147W GLN 3.0 17.0 + - - +
148W ASN* 3.3 3.7 + - - +
150W LEU* 1.3 76.1 - - - +
152W ALA* 1.3 60.6 + - - +
153W GLN 3.1 1.2 + - - -
154W ILE* 3.5 17.9 - - + +
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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