Contacts of the helix formed by residues 166 - 174 (chain A) in PDB entry 6DC0
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 ASP 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ASP* 5.4 0.4 - - - +
165A GLY* 1.3 75.8 - - - -
167A MET* 1.3 63.2 + - - +
168A HIS* 2.9 32.6 + - - +
169A SER* 3.0 29.6 + - - -
170A TYR* 3.2 21.2 + - - +
209A ARG* 3.7 30.6 - - - +
211A PHE 3.2 11.7 - - - +
212A VAL* 3.9 8.1 - - + -
213A PHE* 4.6 3.3 - - - -
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Residues in contact with MET 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASP* 1.3 73.2 - - - +
168A HIS* 1.3 60.0 + - - +
170A TYR* 3.6 17.5 - - + +
171A VAL* 3.2 28.1 + - + +
177A LEU* 4.1 0.7 - - + -
185A LEU* 3.7 26.5 - - + -
189A ILE* 4.5 2.7 - - + -
208A LEU* 3.5 26.5 + - + +
211A PHE* 2.8 16.2 + - + +
213A PHE* 3.7 27.8 - - - -
221A LEU* 3.4 33.9 - - + -
277A LEU* 3.4 32.8 - - + -
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Residues in contact with HIS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASP* 2.9 11.4 + - - +
167A MET* 1.3 75.4 - - - +
169A SER* 1.3 72.8 + - - +
170A TYR 3.1 1.1 - - - -
171A VAL* 3.3 4.5 + - - +
172A ARG* 3.2 35.0 + - - +
208A LEU* 3.7 10.6 + - + +
209A ARG* 3.7 15.7 - - + +
282A TYR* 4.0 2.9 - - - -
497B ILE* 3.9 12.4 - - + +
498B CYS 3.3 23.6 - - - -
499B GLU 3.5 24.0 + - - -
500B HIS 4.1 0.2 + - - -
501B GLU* 3.2 52.3 + - + +
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Residues in contact with SER 169 (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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166A ASP* 3.0 28.9 + - - -
168A HIS* 1.3 81.8 - - - +
170A TYR* 1.3 56.3 + - - +
172A ARG* 3.2 14.1 + - - +
173A SER* 2.8 37.1 + - - -
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Residues in contact with TYR 170 (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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166A ASP 3.2 15.2 + - - +
167A MET* 3.6 29.8 - - + +
169A SER* 1.3 77.0 - - - +
171A VAL* 1.3 57.4 + - - +
173A SER* 3.4 10.0 + - - -
174A ARG* 2.8 54.3 + - - +
177A LEU* 3.9 19.3 - - + -
181A GLU* 2.6 31.6 + - - -
185A LEU* 4.0 4.9 - - + -
213A PHE* 3.7 37.2 - + + -
218A ARG* 4.7 12.3 + - + +
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A MET* 3.2 21.3 + - + +
168A HIS 3.9 4.0 - - - +
169A SER 3.3 0.4 - - - -
170A TYR* 1.3 75.6 - - - +
172A ARG* 1.3 62.1 + - - +
174A ARG* 2.4 27.7 - - - +
175A LYS* 3.6 16.7 - - - +
176A ARG* 5.1 0.7 - - - -
177A LEU* 4.8 7.6 - - + -
208A LEU* 4.0 7.9 - - + -
276A THR* 3.7 21.8 - - + +
277A LEU* 3.5 34.5 - - + +
280A GLY* 4.4 4.0 - - - +
497B ILE* 4.0 19.1 - - + -
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Residues in contact with ARG 172 (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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168A HIS* 3.2 23.8 + - - +
169A SER* 3.2 16.2 + - - +
171A VAL* 1.3 78.2 - - - +
173A SER* 1.3 63.6 - - - +
175A LYS* 3.8 22.7 + - - +
497B ILE* 3.6 28.5 - - + +
498B CYS 3.2 23.1 + - - -
499B GLU* 3.3 35.8 + - - +
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Residues in contact with SER 173 (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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169A SER 2.8 21.6 + - - -
170A TYR* 3.4 11.9 - - - -
172A ARG* 1.3 73.8 - - - +
174A ARG* 1.3 60.8 + - - +
175A LYS* 3.7 9.0 + - - +
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Residues in contact with ARG 174 (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* 2.8 46.5 + - - +
171A VAL* 2.4 26.6 - - - +
173A SER* 1.3 74.3 - - - +
175A LYS* 1.3 59.9 + - - +
176A ARG* 3.0 12.4 + - - +
177A LEU* 3.7 17.4 - - + +
178A ARG* 3.5 38.0 - - - +
181A GLU* 3.4 18.4 + - - -
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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