Contacts of the helix formed by residues 173 - 181 (chain A) in PDB entry 4BR6
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 ARG 173 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLN 3.6 18.4 + - - -
170A TYR* 3.0 34.6 + - - +
171A GLU* 2.7 31.5 + - - +
172A ASN* 1.3 89.9 + - - +
174A LYS* 1.3 64.5 + - - +
175A ALA* 3.2 3.6 - - - -
176A GLU* 2.8 57.2 + - + +
177A TYR 3.6 2.4 + - - -
21B ARG* 4.8 3.2 - - - +
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU 5.1 1.5 + - - +
119A THR* 3.3 36.3 + - + +
121A ILE 4.5 8.9 + - - -
166A TYR* 3.6 38.6 - - + +
172A ASN 2.8 15.4 + - - +
173A ARG* 1.3 71.2 - - - +
175A ALA* 1.3 67.2 + - + +
177A TYR* 3.0 6.3 + - - +
178A PHE* 3.0 49.2 + - + -
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR* 4.9 8.3 - - + +
173A ARG* 3.2 0.9 - - - -
174A LYS* 1.3 84.3 - - + +
176A GLU* 1.3 63.7 + - + +
178A PHE* 3.7 11.5 - - - +
179A GLU* 3.0 42.6 + - - +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A TYR* 3.5 21.6 - - + -
173A ARG* 2.8 55.5 + - + +
175A ALA* 1.3 79.2 - - + +
177A TYR* 1.3 57.7 + - - +
179A GLU* 3.5 9.9 + - - +
180A ALA* 3.0 29.8 + - - +
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR 5.0 4.3 - - - -
18A ILE* 4.6 10.9 - - + +
77A PHE* 3.8 9.0 - - - -
159A ILE* 3.9 3.5 - - + +
160A ASP 2.9 28.7 + - - -
165A ALA* 3.8 22.0 - - + +
166A TYR* 3.4 38.6 - + + -
170A TYR* 3.6 35.1 - + + -
173A ARG 3.6 1.4 + - - -
174A LYS 3.0 8.3 + - - +
176A GLU* 1.3 79.8 - - - +
178A PHE* 1.3 90.1 + + - +
180A ALA* 3.1 0.9 + - - +
181A ILE* 3.0 58.2 + - + +
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASN* 3.3 19.0 - - + +
118A LEU* 3.6 59.2 - - + +
119A THR* 3.7 18.4 - - - -
159A ILE* 4.6 2.0 - - + -
160A ASP 4.6 0.2 - - - -
161A ALA* 4.1 16.4 - - + -
166A TYR* 5.0 2.9 - + - -
174A LYS* 3.0 46.6 + - + -
175A ALA* 3.3 7.8 + - - +
177A TYR* 1.3 102.7 - + - +
179A GLU* 1.3 59.4 + - + +
181A ILE* 3.4 9.8 - - - +
182A TRP* 2.9 28.8 + - - -
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 3.8 28.2 + - - +
115A ASN* 4.3 11.2 - - + +
175A ALA* 3.0 32.0 + - - +
176A GLU* 3.9 9.9 - - - +
178A PHE* 1.3 77.0 - - + +
180A ALA* 1.3 64.8 + - - +
182A TRP* 3.3 17.8 + - - +
183A ASN* 4.1 4.9 + - - -
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 3.6 23.7 - - + +
170A TYR* 3.3 25.1 - - + +
176A GLU 3.0 19.0 + - - +
177A TYR 3.1 4.0 + - - +
179A GLU* 1.3 74.8 - - - +
181A ILE* 1.3 60.4 + - - +
182A TRP 3.1 4.7 - - - -
183A ASN* 2.9 27.7 + - - +
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 5.1 2.9 - - - -
18A ILE* 4.2 11.9 - - + -
77A PHE* 3.8 26.2 - - + -
81A LEU* 4.1 15.5 - - + -
159A ILE* 3.8 34.5 - - + -
177A TYR* 3.0 47.8 + - + +
178A PHE* 3.4 17.9 - - - +
180A ALA* 1.3 76.3 - - - +
182A TRP* 1.3 64.4 + - + +
183A ASN 3.1 0.2 - - - -
184A VAL* 3.1 24.3 + - + +
185A ILE* 3.4 10.2 - - + +
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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