Contacts of the helix formed by residues 146 - 151 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C LYS 6.1 0.9 - - - +
83K VAL* 5.0 9.6 - - + -
84K GLU* 5.4 7.0 - - + +
141K ILE* 3.8 29.4 + - + +
145K GLY* 1.3 70.8 - - - -
147K GLN* 1.3 60.6 + - + +
149K TYR* 3.1 10.5 + - + +
150K LEU* 2.7 55.7 + - + +
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Residues in contact with GLN 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C GLN 4.9 2.2 + - - -
143C LYS 3.8 15.0 + - - +
144C MET* 3.6 38.7 + - - +
145C GLY* 3.8 8.3 - - - +
148C ASN* 3.4 13.5 + - - +
145K GLY 3.5 0.8 - - - -
146K LEU* 1.3 75.9 - - + +
148K ASN* 1.3 62.8 + - - +
150K LEU* 3.4 3.8 + - - +
151K GLN* 3.0 19.4 + - - +
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Residues in contact with ASN 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ASN* 3.1 22.4 + - - +
144K MET* 3.3 26.9 + - + +
145K GLY 3.5 1.4 + - - -
146K LEU 3.4 0.4 - - - -
147K GLN* 1.3 74.2 - - - +
149K TYR* 1.3 65.7 + - - +
151K GLN* 3.3 2.1 + - - +
152K ALA* 3.1 11.4 + - - +
147S GLN* 3.5 25.1 + - - +
148S ASN* 3.0 28.3 + - - +
151S GLN* 2.8 39.7 + - - +
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Residues in contact with TYR 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K LEU* 3.6 16.9 - - + +
83K VAL* 4.1 15.3 - - + -
87K LEU* 3.8 5.7 - - - +
137K GLU* 2.6 45.7 + - + +
140K LEU* 4.5 10.5 - - + -
141K ILE* 3.7 46.0 - - + -
144K MET* 3.8 16.9 - - + +
145K GLY 2.9 18.2 + - - +
146K LEU* 3.1 13.9 + - + +
148K ASN* 1.3 70.5 - - - +
150K LEU* 1.3 73.0 + - + +
152K ALA* 3.1 6.6 + - + +
153K GLN* 2.9 47.0 + - + +
154S ILE* 5.9 2.0 - - + -
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Residues in contact with LEU 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C LEU* 6.1 0.4 - - + -
143C LYS* 3.8 44.2 - - + +
144C MET* 4.3 13.0 - - + -
37K LEU* 4.1 21.8 - - + +
83K VAL* 4.0 28.0 - - + -
146K LEU* 2.7 45.0 + - + +
147K GLN 3.9 3.4 - - - +
149K TYR* 1.3 78.2 - - + +
151K GLN* 1.3 63.8 + - - +
153K GLN* 3.0 20.9 + - + +
154K ILE* 3.8 9.0 - - - +
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Residues in contact with GLN 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C MET* 4.0 24.7 - - - +
148C ASN* 2.9 42.7 + - - +
151C GLN* 2.7 31.9 + - - +
152C ALA* 4.0 13.0 - - + +
147K GLN 3.0 17.6 + - - +
148K ASN* 3.3 3.7 + - - +
150K LEU* 1.3 75.8 - - - +
152K ALA* 1.3 60.8 + - - +
153K GLN 3.1 1.6 + - - -
154K ILE* 3.5 17.0 - - - +
155K ARG 5.1 0.2 + - - -
151S GLN* 2.9 23.4 + - - +
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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