Contacts of the helix formed by residues 189 - 194 (chain C) in PDB entry 3Q3G
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 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C LEU* 3.4 40.6 + - + +
132C THR* 5.8 1.4 - - - +
134C GLY* 2.9 31.5 + - - +
135C GLY 4.5 0.2 - - - +
136C ALA* 4.3 9.2 - - - -
188C THR* 1.3 71.6 - - - +
190C ASP* 1.3 63.6 + - - +
192C TYR* 3.3 3.0 + - - +
193C GLU* 2.9 65.5 + - - +
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Residues in contact with ASP 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C THR* 3.3 5.9 + - - +
189C LYS* 1.3 81.6 - - - +
191C GLU* 1.4 63.9 + - - +
193C GLU* 3.4 18.0 + - - +
194C ARG* 3.3 38.6 + - - +
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Residues in contact with GLU 191 (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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161C ARG* 3.5 26.3 + - - +
187C LEU* 4.0 16.7 - - + -
188C THR* 3.0 49.2 + - - +
190C ASP* 1.4 73.9 - - - +
192C TYR* 1.4 62.3 + - - +
194C ARG* 3.2 37.3 + - - +
195C HIS* 3.1 25.4 + - + -
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Residues in contact with TYR 192 (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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125C PRO* 4.0 3.8 - - - +
126C PRO* 3.4 34.4 - - + +
131C LEU* 4.0 27.4 - - + -
136C ALA* 3.5 13.2 - - + -
138C VAL* 4.3 5.2 - - + -
187C LEU* 4.3 6.2 - - + +
188C THR 3.1 19.6 + - - +
189C LYS 3.4 2.7 - - - +
190C ASP 3.3 0.2 - - - -
191C GLU* 1.4 76.1 - - - +
193C GLU* 1.3 68.3 + - + +
194C ARG 3.3 1.4 + - - -
195C HIS 3.4 4.7 + - - +
198C TYR* 3.0 52.3 + + - -
215C PHE* 3.2 27.6 - + - -
217C ARG* 3.3 38.4 - - + +
224D ARG* 4.7 5.2 + - - -
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Residues in contact with GLU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU* 5.5 4.7 - - + +
189C LYS* 2.9 53.0 + - + +
190C ASP* 3.4 16.7 + - - +
191C GLU 3.4 0.2 - - - -
192C TYR* 1.3 84.0 - - + +
194C ARG* 1.3 58.4 + - - +
195C HIS 3.3 0.9 - - - -
217C ARG* 3.1 43.2 + - - +
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Residues in contact with ARG 194 (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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157C ASP* 4.6 0.7 - - - +
190C ASP* 3.3 17.6 + - - +
191C GLU* 3.2 58.1 + - - +
193C GLU* 1.3 77.3 - - - +
195C HIS* 1.3 80.4 + - + +
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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