Contacts of the helix formed by residues 190 - 198 (chain C) in PDB entry 1HJX
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 190 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C LYS* 3.9 18.5 + - + +
148C GLN* 4.7 10.2 + - - +
150C PHE* 5.8 0.4 - - - -
151C THR* 3.5 22.6 + - - +
189C TYR* 1.3 71.8 - - - +
191C ILE* 1.3 61.9 + - - +
192C ALA* 3.7 6.8 + - - +
193C LYS* 3.0 51.8 + - + +
194C ILE* 3.1 25.3 + - - +
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Residues in contact with ILE 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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178C LEU* 3.7 25.4 - - + -
185C ILE* 4.3 5.6 - - + -
189C TYR* 3.3 26.9 + - + +
190C ASP* 1.3 73.4 - - - +
192C ALA* 1.3 61.5 + - - +
194C ILE* 3.7 5.3 - - + +
195C SER* 2.7 31.3 + - - -
201C ILE* 4.9 1.8 - - + -
244C MET* 3.9 25.6 - - + +
247C LEU* 3.9 33.8 - - + +
249C ALA* 3.5 38.8 - - + +
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Residues in contact with ALA 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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190C ASP* 3.4 6.9 + - - +
191C ILE* 1.3 78.2 - - - +
193C LYS* 1.3 67.1 + - + +
195C SER* 3.1 14.9 + - - -
196C GLN* 3.3 16.6 - - - +
247C LEU 3.6 17.4 + - - +
248C GLY* 4.5 9.2 - - - +
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Residues in contact with LYS 193 (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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148C GLN* 5.6 3.4 - - - +
151C THR* 4.0 21.5 - - + -
190C ASP* 3.0 34.9 + - - +
192C ALA* 1.3 77.4 - - + +
194C ILE* 1.3 66.7 + - - +
196C GLN* 3.0 35.0 + - - +
197C HIS* 3.8 12.9 - - + +
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Residues in contact with ILE 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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150C PHE* 4.1 17.9 - - + -
151C THR* 3.9 30.3 - - + +
154C ILE* 3.8 31.6 - - + +
178C LEU* 3.9 26.0 - - + -
189C TYR* 4.1 11.4 - - + -
190C ASP 3.1 21.1 + - - +
191C ILE* 3.7 15.9 - - + +
193C LYS* 1.3 75.1 - - - +
195C SER* 1.3 61.5 + - - +
197C HIS* 3.2 6.7 + - - +
198C LEU* 3.1 37.7 + - + +
201C ILE* 5.0 1.1 - - + -
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Residues in contact with SER 195 (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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191C ILE 2.7 23.5 + - - -
192C ALA 3.1 9.4 + - - -
193C LYS 3.1 0.2 + - - -
194C ILE* 1.3 76.8 - - - +
196C GLN* 1.3 59.8 + - - +
198C LEU* 3.8 5.4 - - - +
201C ILE* 4.0 24.0 - - - -
248C GLY 3.8 3.3 + - - -
249C ALA* 3.8 7.5 - - - -
250C PRO* 3.6 27.5 - - - +
253C LYS* 2.7 33.1 + - - +
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Residues in contact with GLN 196 (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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158C LYS* 5.0 2.4 + - - -
192C ALA 3.3 14.8 + - - +
193C LYS* 3.0 27.3 + - - +
195C SER* 1.3 78.9 - - - +
197C HIS* 1.3 76.8 + - + +
253C LYS* 3.2 13.7 + - - +
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Residues in contact with HIS 197 (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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151C THR* 5.4 3.4 - - + -
154C ILE* 4.0 14.6 - - + +
155C LYS* 3.6 43.6 + - + +
158C LYS* 2.8 51.3 + - + +
174C LEU* 4.5 2.8 - - - +
193C LYS* 3.8 19.2 + - + +
194C ILE* 3.2 7.9 + - - +
196C GLN* 1.3 94.9 + - + +
198C LEU* 1.3 60.6 + - - +
199C ASP 3.9 0.3 + - - -
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Residues in contact with LEU 198 (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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137C LEU* 4.9 0.4 - - + -
154C ILE* 3.8 25.6 - - + -
158C LYS* 4.8 0.8 + - - -
174C LEU* 3.6 25.4 - - + +
175C SER 4.0 11.9 - - - +
176C ALA* 3.8 20.4 - - + -
178C LEU* 5.2 0.2 - - + -
194C ILE* 3.1 34.8 + - + +
195C SER* 4.0 2.4 + - - -
196C GLN 3.6 0.4 - - - -
197C HIS* 1.3 76.5 - - - +
199C ASP* 1.3 60.3 + - - +
200C PHE 3.2 12.3 - - - +
201C ILE* 3.5 31.4 - - + -
253C LYS* 2.7 34.4 + - + +
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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