Contacts of the helix formed by residues 146 - 151 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143N LYS 6.0 1.3 - - - +
83P VAL* 5.0 8.7 - - + -
84P GLU* 5.5 6.7 - - + +
141P ILE* 3.8 30.2 + - + +
145P GLY* 1.3 70.5 - - - -
147P GLN* 1.3 60.0 + - + +
149P TYR* 3.1 11.3 + - + +
150P LEU* 2.8 55.6 + - + +
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Residues in contact with GLN 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142N GLN 4.7 2.6 + - - -
143N LYS 3.6 16.3 + - - +
144N MET* 3.5 41.4 + - - +
145N GLY* 3.6 8.1 - - - +
148N ASN* 3.5 13.6 + - - +
145P GLY 3.4 1.0 + - - -
146P LEU* 1.3 76.3 - - + +
148P ASN* 1.3 62.1 + - - +
150P LEU* 3.5 2.0 + - - -
151P GLN* 3.0 19.4 + - - +
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Residues in contact with ASN 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N ASN* 2.9 23.5 + - - +
144P MET* 3.3 27.4 + - + +
145P GLY 3.5 1.0 + - - -
146P LEU 3.4 0.2 - - - -
147P GLN* 1.3 75.9 - - - +
149P TYR* 1.3 65.6 + - - +
151P GLN 3.3 0.9 + - - -
152P ALA* 3.1 11.3 + - - +
147R GLN* 3.4 27.7 + - - +
148R ASN* 3.0 29.4 + - - +
151R GLN* 2.8 37.5 + - - +
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Residues in contact with TYR 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P LEU* 3.6 17.5 - - + +
83P VAL* 4.2 14.6 - - + -
87P LEU* 3.8 5.5 - - - +
137P GLU* 2.6 44.9 + - + +
140P LEU* 4.5 10.3 - - + -
141P ILE* 3.7 45.3 - - + -
144P MET* 3.9 16.8 - - + +
145P GLY 2.9 18.2 + - - +
146P LEU* 3.5 14.4 - - + +
148P ASN* 1.3 70.4 - - - +
150P LEU* 1.3 72.5 + - + +
152P ALA* 3.2 6.9 + - + +
153P GLN* 2.9 47.7 + - + +
154R ILE* 5.9 2.2 - - + -
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Residues in contact with LEU 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140N LEU* 5.8 1.1 - - + -
143N LYS* 3.7 45.1 - - + +
144N MET* 4.1 12.3 - - + -
37P LEU* 4.1 22.2 - - + +
83P VAL* 3.9 27.8 - - + -
146P LEU* 2.8 45.1 + - + +
147P GLN 4.0 3.1 - - - +
149P TYR* 1.3 77.8 - - + +
151P GLN* 1.3 63.8 + - - +
153P GLN* 3.0 20.3 + - + +
154P ILE* 3.8 9.4 - - - +
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Residues in contact with GLN 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144N MET* 3.8 26.9 - - - +
148N ASN* 2.8 40.8 + - - +
151N GLN* 2.9 28.1 + - - +
152N ALA* 3.9 14.9 - - + +
147P GLN 3.0 17.4 + - - +
148P ASN 3.3 3.6 + - - +
150P LEU* 1.3 75.6 - - - +
152P ALA* 1.3 60.7 + - - +
153P GLN 3.2 1.4 + - - -
154P ILE* 3.5 16.9 - - + +
151R GLN* 2.7 31.5 + - - +
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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