Contacts of the helix formed by residues 176 - 186 (chain C) in PDB entry 3BRW
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 LYS 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TYR* 3.7 33.4 - - + +
125B GLU* 4.8 5.4 - - - +
150B PHE* 3.8 19.3 - - + -
174C TYR* 2.9 34.6 + - + +
175C PRO* 1.3 77.8 - - - +
177C ALA* 1.3 62.5 + - - +
178C SER* 3.6 1.3 - - - -
179C ARG* 3.6 30.1 - - - +
180C LEU* 3.5 34.3 + - + +
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Residues in contact with ALA 177 (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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100B PHE* 6.0 1.3 - - + -
101C ASN* 5.0 4.7 - - - +
172C VAL* 3.6 26.5 - - + -
174C TYR* 2.7 20.4 + - + +
175C PRO 3.2 1.6 - - - -
176C LYS* 1.3 73.5 - - - +
178C SER* 1.3 67.8 + - - +
179C ARG 3.1 1.8 - - - -
180C LEU* 2.9 6.8 + - - +
181C ILE* 2.9 32.1 + - + +
401C LEU* 3.7 16.2 - - + -
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Residues in contact with SER 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 2.7 42.4 + - - -
90C TYR* 3.3 26.6 - - - -
95C LEU* 3.7 10.8 - - - +
99C HIS* 4.2 4.0 - - - -
101C ASN* 4.9 2.4 - - - +
175C PRO 4.8 4.6 + - - -
177C ALA* 1.3 79.0 - - - +
179C ARG* 1.3 61.7 + - - +
181C ILE* 3.8 2.9 - - - +
182C VAL* 3.0 33.2 + - - +
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Residues in contact with ARG 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR* 3.1 44.0 + - - -
120B VAL* 4.6 14.6 - - - +
95C LEU* 5.3 4.9 - - + +
175C PRO 4.6 4.9 + - - -
176C LYS* 3.6 31.4 + - - +
177C ALA 3.1 0.4 - - - -
178C SER* 1.3 85.5 + - - +
180C LEU* 1.3 58.1 + - + +
182C VAL* 3.3 16.1 - - + +
183C THR* 2.7 27.7 + - - -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C TYR* 4.3 18.2 - - + -
176C LYS* 3.5 28.0 + - - +
177C ALA* 2.9 7.9 + - - +
179C ARG* 1.3 79.1 - - + +
181C ILE* 1.3 64.9 + - - +
183C THR* 3.5 7.5 + - - -
184C PHE* 3.2 17.2 + - - +
397C LEU* 3.7 22.6 - - + +
400C GLU* 4.1 35.7 - - + +
401C LEU* 4.5 11.0 - - + -
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Residues in contact with ILE 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 3.6 18.2 - - + +
101C ASN* 3.6 40.2 - - + +
113C VAL* 4.5 15.0 - - + -
132C ARG* 3.6 34.8 - - - +
177C ALA* 2.9 25.2 + - + +
178C SER 3.9 4.3 - - - +
180C LEU* 1.3 74.5 - - - +
182C VAL* 1.3 66.7 + - - +
184C PHE* 3.2 6.4 + - + +
185C ASP* 3.0 21.4 + - - +
397C LEU* 4.4 10.8 - - + -
401C LEU* 4.6 16.2 - - + -
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 3.7 19.9 - - + -
91C ARG* 3.9 31.0 - - + +
95C LEU* 4.0 16.2 - - + -
178C SER 3.0 17.6 + - - +
179C ARG* 3.3 20.2 - - + +
181C ILE* 1.3 76.1 - - - +
183C THR* 1.3 67.6 + - - +
185C ASP* 3.3 3.4 + - - +
186C GLU* 3.1 55.4 + - + +
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Residues in contact with THR 183 (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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179C ARG 2.7 18.7 + - - -
180C LEU* 3.5 11.8 - - - -
181C ILE 3.2 0.2 - - - -
182C VAL* 1.3 81.2 - - - +
184C PHE* 1.3 62.5 + - - +
186C GLU* 3.4 5.3 + - - +
187C HIS* 3.3 21.2 + - + +
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Residues in contact with PHE 184 (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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132C ARG* 3.4 31.0 - - + -
180C LEU 3.2 9.6 + - - +
181C ILE* 3.2 9.2 + - + +
183C THR* 1.3 78.5 - - - +
185C ASP* 1.3 73.4 + - - +
186C GLU 3.2 0.5 + - - -
187C HIS* 2.5 39.6 + + - -
390C ARG* 4.0 38.4 - - + -
393C LEU* 3.9 28.3 - - + -
394C LEU* 3.8 39.3 - - + -
397C LEU* 4.2 19.5 - - + -
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Residues in contact with ASP 185 (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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86C THR 4.4 9.0 - - - +
87C ALA* 3.1 33.7 - - - +
90C TYR* 3.2 20.4 - - + +
130C LEU* 4.2 4.0 - - - +
132C ARG* 2.9 48.8 + - - -
137C THR* 5.5 3.3 + - - -
181C ILE 3.0 11.6 + - - +
182C VAL* 3.3 10.7 + - - +
184C PHE* 1.3 83.3 - - - +
186C GLU* 1.3 58.9 + - + +
187C HIS* 4.8 0.3 + - - -
188C VAL* 3.5 11.4 - - - +
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Residues in contact with GLU 186 (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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87C ALA* 3.3 27.4 - - + +
88C ARG* 5.0 5.7 - - - -
91C ARG* 2.5 58.4 + - - +
182C VAL* 3.1 23.0 + - + +
183C THR* 3.4 6.4 + - - +
184C PHE 3.2 0.4 - - - -
185C ASP* 1.3 75.3 - - + +
187C HIS* 1.3 62.6 + - - +
188C VAL 3.2 2.2 - - - -
189C ILE* 3.3 31.9 + - + +
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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