Contacts of the helix formed by residues 146 - 151 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83M VAL* 5.0 9.4 - - + -
84M GLU* 5.4 6.5 - - + +
141M ILE* 3.8 29.4 + - + +
145M GLY* 1.3 70.2 - - - -
147M GLN* 1.3 60.8 + - + +
149M TYR* 3.1 10.9 + - + +
150M LEU* 2.7 55.7 + - + +
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Residues in contact with GLN 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145M GLY 3.5 0.8 + - - -
146M LEU* 1.3 75.2 - - + +
148M ASN* 1.3 62.7 + - - +
150M LEU* 3.4 2.8 + - - +
151M GLN* 3.0 23.7 + - - +
142X GLN 4.7 2.8 + - - -
143X LYS 3.5 21.9 + - - +
144X MET* 3.6 36.6 + - - +
145X GLY* 3.8 7.3 - - - +
148X ASN* 3.7 8.6 + - - +
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Residues in contact with ASN 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L GLN* 3.3 29.3 + - - +
148L ASN* 3.1 28.1 + - - +
151L GLN* 2.9 37.6 + - - +
144M MET* 3.3 27.6 + - + +
145M GLY 3.5 1.2 + - - -
146M LEU 3.4 0.4 - - - -
147M GLN* 1.3 74.0 - - - +
149M TYR* 1.3 65.6 + - - +
151M GLN* 3.3 1.6 + - - +
152M ALA* 3.1 10.7 + - - +
148X ASN* 3.0 23.0 + - - +
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Residues in contact with TYR 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L ILE* 6.0 2.0 - - + -
40M LEU* 3.6 17.0 - - + +
83M VAL* 4.1 15.0 - - + -
87M LEU* 3.8 5.7 - - - +
137M GLU* 2.6 45.9 + - + +
140M LEU* 4.5 11.2 - - + -
141M ILE* 3.7 46.2 - - + -
144M MET* 3.8 16.6 - - + +
145M GLY 2.9 18.4 + - - +
146M LEU* 3.4 13.5 - - + +
148M ASN* 1.3 70.5 - - - +
150M LEU* 1.3 73.6 + - + +
152M ALA* 3.1 6.1 + - - +
153M GLN* 2.9 46.7 + - + +
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Residues in contact with LEU 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M LEU* 4.1 21.1 - - + +
83M VAL* 4.0 28.0 - - + -
146M LEU* 2.7 47.0 + - + +
147M GLN* 3.9 3.8 - - - +
149M TYR* 1.3 77.4 - - + +
151M GLN* 1.3 64.1 + - - +
153M GLN* 3.0 21.3 + - + +
154M ILE* 3.8 9.4 - - - +
140X LEU* 5.9 0.9 - - + -
143X LYS* 3.8 43.3 - - + +
144X MET* 4.3 11.9 - - + -
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Residues in contact with GLN 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L GLN* 2.7 31.5 + - - +
147M GLN 3.0 17.8 + - - +
148M ASN 3.5 3.1 - - - +
150M LEU* 1.3 75.6 - - - +
152M ALA* 1.3 60.1 + - - +
153M GLN 3.1 1.6 + - - -
154M ILE* 3.5 18.0 - - + +
155M ARG 5.1 0.2 + - - -
144X MET* 3.8 27.6 - - - +
148X ASN* 2.9 42.4 + - - +
151X GLN* 3.0 26.6 + - - +
152X ALA* 4.0 12.7 - - + +
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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