Contacts of the helix formed by residues 156 - 160 (chain C) in PDB entry 1BRR
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 PHE 156 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C LEU 5.0 0.4 - - - -
97C LEU* 3.9 13.2 - - + -
98C ALA* 3.8 24.2 - - + -
101C VAL* 3.5 17.3 - - + +
103C ALA* 3.6 23.8 - - + -
107C THR* 3.9 18.2 - - + -
111C LEU* 3.5 31.2 - - + -
151C VAL* 2.9 25.5 + - + -
152C LEU* 3.3 23.2 + - + +
155C GLY* 1.3 72.9 - - - +
157C THR* 1.3 63.8 + - - +
158C SER 3.5 0.2 - - - -
159C LYS* 3.9 4.9 - - + -
160C ALA* 3.1 23.7 + - - +
171C PHE* 3.2 25.0 - + + -
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Residues in contact with THR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C PHE* 2.7 23.7 + - - -
154C PHE* 5.4 0.7 - - - -
155C GLY 3.2 0.6 - - - -
156C PHE* 1.3 77.7 - - - +
158C SER* 1.3 51.1 + - - +
160C ALA* 2.7 24.9 + - - +
161C GLU* 2.7 42.4 + - + +
171C PHE* 3.5 7.9 - - - -
172C LYS* 4.2 5.8 - - + -
175C ARG* 2.9 39.8 + - - +
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Residues in contact with SER 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C PHE 4.9 3.3 + - - -
155C GLY* 3.1 17.6 + - - -
157C THR* 1.3 78.3 - - - +
159C LYS* 1.3 62.7 + - - +
161C GLU* 3.7 18.3 + - - +
162C SER* 3.3 18.0 + - - -
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 3.1 36.4 + - + +
102C ASP* 3.1 26.8 + - - +
103C ALA* 4.6 9.6 - - + +
104C ASP* 4.7 13.7 - - - +
155C GLY 3.7 10.2 + - - +
156C PHE* 3.6 3.9 + - + -
157C THR 3.1 0.6 - - - -
158C SER* 1.3 80.4 + - - +
160C ALA* 1.3 63.9 + - - +
162C SER* 3.8 10.7 - - - -
163C MET* 3.2 25.5 - - - +
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Residues in contact with ALA 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 4.1 6.3 - - + -
156C PHE 3.1 15.5 + - - +
157C THR* 2.7 12.8 + - - +
159C LYS* 1.3 75.1 - - - +
161C GLU* 1.3 51.2 + - + +
162C SER 2.6 17.4 + - - -
163C MET* 2.9 23.0 + - - +
167C VAL* 5.1 1.1 - - + -
168C ALA* 3.4 27.6 - - - +
171C PHE* 3.6 27.1 - - + -
172C LYS* 6.0 0.7 - - + -
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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