Contacts of the helix formed by residues 164 - 173 (chain I) in PDB entry 2BDI
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 SER 164 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132I ALA* 4.0 21.2 - - - +
163I VAL* 1.3 80.9 - - - +
165I GLU* 1.3 67.8 + - - +
166I GLU* 4.2 1.9 + - - +
167I VAL* 3.4 25.3 + - - +
168I CYS* 3.0 19.8 + - - +
96J ARG* 5.8 3.6 - - - -
97J PRO* 5.9 1.0 - - - +
165O GLU* 3.3 17.6 + - - -
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Residues in contact with GLU 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I VAL 3.6 1.2 + - - -
164I SER* 1.3 72.7 - - - +
166I GLU* 1.3 63.8 + - - +
168I CYS* 3.2 6.5 + - - +
169I SER* 2.8 26.4 + - - -
176I TYR* 3.7 25.6 + - + +
164O SER* 3.5 15.5 - - - -
165O GLU* 3.5 25.3 + - + +
166O GLU* 3.1 38.0 + - + +
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Residues in contact with GLU 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I SER* 4.2 2.5 + - - +
165I GLU* 1.3 79.8 - - - +
167I VAL* 1.3 72.2 + - + +
168I CYS 3.0 0.7 + - - -
169I SER* 3.2 6.3 + - - -
170I LYS* 3.0 50.8 + - + +
174J PRO* 5.5 2.9 - - + +
165O GLU* 2.9 22.9 + - + +
166O GLU* 5.3 1.1 - - - +
169O SER* 3.7 18.2 - - - +
176O TYR* 2.9 38.7 + - - +
178O PRO* 4.8 8.5 - - - +
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Residues in contact with VAL 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I VAL* 4.0 17.5 - - + -
164I SER* 3.2 20.7 + - - +
166I GLU* 1.3 86.9 - - + +
168I CYS* 1.3 57.4 + - - +
170I LYS* 4.0 0.3 - - - +
171I LEU* 2.7 50.8 + - + +
97J PRO* 5.1 12.3 - - + -
98J LEU* 4.7 8.7 - - + +
174J PRO* 4.0 23.3 - - + +
175J LEU* 4.0 21.1 - - + -
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Residues in contact with CYS 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163I VAL* 4.5 1.0 - - - +
164I SER 3.0 13.2 + - - +
165I GLU* 3.3 11.9 - - - +
167I VAL* 1.3 78.5 - - - +
169I SER* 1.3 60.5 - - - +
171I LEU* 3.1 3.9 + - - +
172I TYR* 2.8 37.1 + - - +
176I TYR* 3.8 24.9 - - + -
181I PHE* 4.1 3.4 - - - -
182I CYS* 2.1 64.2 - - + +
227I VAL* 5.6 2.7 - - - -
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Residues in contact with SER 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I GLU 2.8 20.1 + - - -
166I GLU* 3.2 7.8 + - - -
168I CYS* 1.3 75.3 - - - +
170I LYS* 1.3 63.3 + - - +
173I ASP* 2.8 32.9 + - - +
176I TYR* 3.4 38.1 - - - +
166O GLU* 4.0 25.7 - - - +
169O SER* 5.4 0.9 + - - -
170O LYS* 4.3 6.8 + - - -
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Residues in contact with LYS 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166I GLU* 3.0 46.1 + - + +
169I SER* 1.3 78.4 - - - +
171I LEU* 1.3 68.4 + - - +
172I TYR 3.0 1.0 + - - -
173I ASP* 3.4 16.7 + - - +
173J ASP* 4.6 7.1 + - - +
174J PRO* 3.7 33.7 - - + +
169O SER* 4.1 16.3 + - - -
170O LYS* 4.5 21.3 - - - +
173O ASP* 3.2 28.1 + - - +
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Residues in contact with LEU 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167I VAL* 2.7 34.5 + - + +
168I CYS 3.6 3.6 - - - +
170I LYS* 1.3 80.5 - - - +
172I TYR* 1.3 64.2 + - + +
173I ASP 4.8 1.8 - - - +
217I LYS* 3.1 33.6 + - - +
223I GLY 3.4 26.5 - - - +
224I VAL* 5.4 4.9 - - + -
225I PRO* 3.4 24.7 - - + -
173J ASP 5.6 0.4 - - - +
174J PRO* 4.1 20.2 - - + +
175J LEU* 4.6 8.3 - - + -
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Residues in contact with TYR 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I CYS* 2.8 18.1 + - - +
169I SER 3.7 0.9 - - - -
171I LEU* 1.3 88.0 - - + +
173I ASP* 1.3 64.7 - - - +
175I LEU* 2.9 30.3 + - + +
176I TYR* 2.9 20.0 + - + +
180I MET* 6.3 0.4 - - - -
182I CYS* 3.8 19.3 - - - -
215I PHE* 3.8 23.3 - + + -
216I GLY* 3.6 4.0 - - - -
217I LYS* 3.4 46.9 + - + +
224I VAL* 4.2 6.1 - - + +
225I PRO* 2.7 37.1 + - + -
227I VAL* 3.6 21.9 - - + +
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Residues in contact with ASP 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I SER 2.8 18.0 + - - +
170I LYS* 3.4 12.6 + - - +
171I LEU 4.8 1.4 - - - +
172I TYR* 1.3 81.4 - - - +
174I PRO* 1.3 93.1 - - - +
176I TYR* 4.4 2.5 - - - +
170L LYS* 4.4 9.5 + - - +
170O LYS* 3.2 27.4 + - - +
173P ASP* 5.0 6.1 - - - +
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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