Contacts of the helix formed by residues 146 - 151 (chain Q) 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 Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Q VAL* 5.0 9.6 - - + -
84Q GLU* 5.4 6.5 - - + +
141Q ILE* 3.8 29.8 + - + +
145Q GLY* 1.3 69.5 - - - -
147Q GLN* 1.3 61.5 + - + +
149Q TYR* 3.1 10.8 + - + -
150Q LEU* 2.7 55.2 + - + +
143V LYS 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145Q GLY 3.5 1.0 - - - -
146Q LEU* 1.3 75.9 - - + +
148Q ASN* 1.3 61.3 + - - +
150Q LEU* 3.4 1.3 + - - -
151Q GLN* 3.0 20.4 + - - +
142V GLN 4.6 3.0 + - - -
143V LYS 3.6 15.5 + - - +
144V MET* 3.4 42.8 + - - +
145V GLY* 3.6 9.7 - - - +
148V ASN* 3.5 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 148 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J GLN* 3.6 26.1 + - - +
148J ASN* 3.1 26.3 + - - +
151J GLN* 3.0 35.4 + - - +
144Q MET* 3.3 29.1 + - + +
145Q GLY 3.5 1.2 + - - -
146Q LEU 3.4 0.2 - - - -
147Q GLN* 1.3 73.1 - - - +
149Q TYR* 1.3 66.3 + - - +
151Q GLN* 3.3 1.7 + - - +
152Q ALA* 3.1 11.3 + - - +
148V ASN* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J ILE* 6.1 1.6 - - + -
40Q LEU* 3.6 17.6 - - + +
83Q VAL* 4.1 15.0 - - + -
87Q LEU* 3.8 6.1 - - - +
137Q GLU* 2.6 44.8 + - + +
140Q LEU* 4.5 10.8 - - + -
141Q ILE* 3.7 47.8 - - + -
144Q MET* 3.8 16.2 - - + +
145Q GLY 2.9 18.2 + - - +
146Q LEU* 3.4 14.4 - - + +
148Q ASN* 1.3 71.6 - - - +
150Q LEU* 1.3 72.1 + - + +
152Q ALA* 3.1 7.8 + - + +
153Q GLN* 2.9 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q LEU* 4.1 21.6 - - + +
83Q VAL* 4.0 27.4 - - + -
146Q LEU* 2.7 44.8 + - + +
147Q GLN 3.9 3.1 - - - +
149Q TYR* 1.3 78.4 - - + +
151Q GLN* 1.3 63.7 + - - +
153Q GLN* 3.0 21.3 + - + +
154Q ILE* 3.8 9.0 - - - +
140V LEU* 5.8 0.4 - - + -
143V LYS* 3.7 46.7 - - + +
144V MET* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J GLN* 2.9 22.9 + - - +
147Q GLN 3.0 17.9 + - - +
148Q ASN* 3.3 3.7 + - - +
150Q LEU* 1.3 75.8 - - - +
152Q ALA* 1.3 61.1 + - - +
153Q GLN 3.1 1.4 + - - -
154Q ILE* 3.5 17.3 + - - +
144V MET* 3.7 26.3 - - - +
148V ASN* 2.7 42.6 + - - +
151V GLN* 2.9 30.7 + - - +
152V ALA* 3.8 14.9 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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