Contacts of the helix formed by residues 146 - 151 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143I LYS 6.0 0.9 - - - +
83O VAL* 5.0 9.0 - - + -
84O GLU* 5.4 6.5 - - + +
141O ILE* 3.8 29.6 + - + +
145O GLY* 1.3 69.9 - - - -
147O GLN* 1.3 60.9 + - + +
149O TYR* 3.1 11.2 + - + +
150O LEU* 2.7 56.8 + - + +
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Residues in contact with GLN 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I GLN 4.7 2.8 + - - -
143I LYS 3.5 15.8 + - - +
144I MET* 3.4 44.0 + - - +
145I GLY* 3.5 7.9 - - - +
148I ASN* 3.6 9.5 + - - +
145O GLY 3.5 0.6 - - - -
146O LEU* 1.3 74.8 - - + +
148O ASN* 1.3 62.3 + - - +
150O LEU* 3.4 2.2 + - - +
151O GLN* 3.0 24.4 + - - +
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Residues in contact with ASN 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I ASN* 2.9 25.7 + - - +
144O MET* 3.3 28.6 + - + +
145O GLY 3.5 1.0 + - - -
146O LEU 3.4 0.4 - - - -
147O GLN* 1.3 73.7 - - - +
149O TYR* 1.3 65.7 + - - +
151O GLN 3.3 1.2 + - - -
152O ALA* 3.1 11.8 + - - +
147W GLN* 3.4 29.0 + - - +
148W ASN* 3.1 26.9 + - - +
151W GLN* 2.9 35.4 + - - +
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Residues in contact with TYR 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O LEU* 3.6 17.4 - - + +
83O VAL* 4.1 14.8 - - + -
87O LEU* 3.8 5.5 - - - +
137O GLU* 2.6 45.4 + - + +
140O LEU* 4.5 11.4 - - + -
141O ILE* 3.7 46.2 - - + -
144O MET* 3.8 16.6 - - + +
145O GLY 2.9 18.8 + - - +
146O LEU* 3.4 14.8 - - + +
148O ASN* 1.3 70.9 - - - +
150O LEU* 1.3 72.8 + - + +
152O ALA* 3.1 7.0 + - + +
153O GLN* 2.9 47.1 + - + -
154W ILE* 6.0 1.8 - - + -
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Residues in contact with LEU 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I LEU* 5.8 0.9 - - + -
143I LYS* 3.7 44.6 - - + +
144I MET* 4.2 12.3 - - + -
37O LEU* 4.1 22.2 - - + +
83O VAL* 4.0 27.8 - - + -
146O LEU* 2.7 44.6 + - + +
147O GLN 3.9 3.4 - - - +
149O TYR* 1.3 77.8 - - + +
151O GLN* 1.3 63.0 + - - +
153O GLN* 3.0 21.0 + - + +
154O ILE* 3.8 9.7 - - - +
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Residues in contact with GLN 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I MET* 3.8 26.1 - - - +
148I ASN* 2.8 40.3 + - - +
151I GLN* 2.9 24.9 + - - +
152I ALA* 3.8 19.1 - - + +
147O GLN 3.0 18.0 + - - +
148O ASN* 3.5 3.6 - - - +
150O LEU* 1.3 75.3 - - - +
152O ALA* 1.3 60.0 + - - +
153O GLN 3.1 1.4 + - - -
154O ILE* 3.5 17.6 - - + +
151W GLN* 2.7 32.0 + - - +
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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