Contacts of the helix formed by residues 146 - 151 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143R LYS 6.0 1.3 - - - +
83T VAL* 5.0 9.0 - - + -
84T GLU* 5.5 6.5 - - + +
141T ILE* 3.8 29.4 + - + +
145T GLY* 1.3 70.1 - - - -
147T GLN* 1.3 59.5 + - + +
149T TYR* 3.1 11.0 + - + +
150T LEU* 2.8 56.1 + - + +
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Residues in contact with GLN 147 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142R GLN 4.8 2.4 + - - -
143R LYS 3.7 16.3 + - - +
144R MET* 3.4 42.6 + - - +
145R GLY* 3.7 9.3 - - - +
148R ASN* 3.4 13.0 + - - +
145T GLY 3.5 0.8 - - - -
146T LEU* 1.3 75.5 - - + +
148T ASN* 1.3 61.9 + - - +
150T LEU* 3.5 1.9 + - - -
151T GLN* 3.0 19.4 + - - +
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Residues in contact with ASN 148 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147N GLN* 3.4 27.7 + - - +
148N ASN* 2.9 30.5 + - - +
151N GLN* 2.7 37.0 + - - +
148R ASN* 2.9 23.9 + - - +
144T MET* 3.3 27.4 + - + +
145T GLY 3.5 1.2 + - - -
146T LEU 3.4 0.2 - - - -
147T GLN* 1.3 73.8 - - - +
149T TYR* 1.3 65.1 + - - +
151T GLN 3.3 0.9 + - - -
152T ALA* 3.1 10.6 + - - +
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Residues in contact with TYR 149 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N ILE* 5.9 2.2 - - + -
40T LEU* 3.6 17.7 - - + +
83T VAL* 4.1 15.3 - - + -
87T LEU* 3.8 5.5 - - - +
137T GLU* 2.6 44.1 + - - +
140T LEU* 4.5 11.0 - - + -
141T ILE* 3.7 46.2 - - + -
144T MET* 3.9 15.6 - - + +
145T GLY 2.9 18.0 + - - +
146T LEU* 3.5 14.6 - - + +
148T ASN* 1.3 71.3 - - - +
150T LEU* 1.3 72.4 + - + +
152T ALA* 3.2 6.9 + - - +
153T GLN* 2.9 46.6 + - + +
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Residues in contact with LEU 150 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140R LEU* 5.9 0.7 - - + -
143R LYS* 3.7 44.6 - - + +
144R MET* 4.1 12.8 - - + -
37T LEU* 4.1 21.6 - - + +
83T VAL* 3.9 27.4 - - + -
146T LEU* 2.8 44.6 + - + +
147T GLN 4.0 3.6 - - - +
149T TYR* 1.3 77.2 - - + +
151T GLN* 1.3 63.4 + - - +
153T GLN* 3.0 19.9 + - + +
154T ILE* 3.8 9.7 - - - +
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Residues in contact with GLN 151 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N GLN* 2.8 26.0 + - - +
144R MET* 3.8 27.2 - - - +
148R ASN* 2.8 40.1 + - - +
151R GLN* 2.8 30.6 + - - +
152R ALA* 3.8 14.3 - - + +
147T GLN 3.0 17.2 + - - +
148T ASN* 3.6 3.3 - - - +
150T LEU* 1.3 74.8 - - - +
152T ALA* 1.3 60.1 + - - +
153T GLN 3.2 1.0 + - - -
154T ILE* 3.5 18.3 - - + +
155T ARG 5.1 0.2 + - - -
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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