Contacts of the helix formed by residues 185 - 194 (chain R) in PDB entry 1HI0
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 185 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180R LEU* 2.9 37.6 + - + +
181R MET 4.2 0.2 + - - -
183R GLN* 3.2 38.3 + - + +
184R GLY* 1.3 75.4 - - - +
186R PHE* 1.3 63.5 + - - +
187R ASP 3.4 2.7 - - - -
188R ASP* 3.3 21.6 + - + +
189R ALA* 3.1 20.4 + - - +
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Residues in contact with PHE 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181R MET* 3.5 51.1 - - + -
184R GLY* 3.3 24.0 + - - -
185R LYS* 1.3 73.1 - - - +
187R ASP* 1.3 61.4 + - - +
189R ALA* 3.0 7.1 + - - +
190R TYR* 2.8 29.6 + - - +
195R MET 4.6 2.2 - - - +
355R LYS* 4.1 15.9 - - - -
358R GLU* 5.8 0.2 - - - -
359R THR* 3.8 17.3 - - + -
382R PRO 4.0 10.5 - - - +
383R SER 3.3 26.4 + - - +
384R ASN* 4.3 13.9 - - - -
385R PRO* 3.5 25.1 - - + -
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Residues in contact with ASP 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185R LYS 3.4 0.4 - - - -
186R PHE* 1.3 75.0 - - - +
188R ASP* 1.3 71.2 + - - +
190R TYR* 3.2 8.2 + - - +
191R GLN* 2.8 44.1 + - - +
382R PRO* 4.3 4.5 - - - +
383R SER* 3.2 40.3 + - - -
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Residues in contact with ASP 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463P ARG* 3.9 20.7 + - - -
180R LEU* 4.1 18.7 - - + +
185R LYS* 3.3 31.6 + - + +
186R PHE 3.2 0.2 - - - -
187R ASP* 1.3 80.4 - - - +
189R ALA* 1.3 64.8 + - - +
191R GLN* 4.2 8.4 + - - +
192R LEU* 2.8 36.4 + - + +
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Residues in contact with ALA 189 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177R ALA* 4.0 14.6 - - + +
180R LEU* 4.0 13.4 - - + +
181R MET* 3.9 27.1 - - + -
185R LYS 3.1 10.2 + - - +
186R PHE* 3.0 9.1 + - + +
188R ASP* 1.3 78.5 - - - +
190R TYR* 1.3 57.6 + - - +
193R HIS* 2.9 34.7 + - - +
194R GLN 3.6 0.7 + - - -
195R MET* 3.7 12.7 + - - +
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Residues in contact with TYR 190 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R MET* 2.6 42.6 + - + -
17R LEU* 3.2 15.7 - - + -
153R ILE* 3.4 10.4 - - + +
154R PRO* 3.3 22.1 - - + +
186R PHE 2.8 15.2 + - - +
187R ASP* 3.6 11.4 - - - +
189R ALA* 1.3 74.0 - - - +
191R GLN* 1.3 71.4 + - + +
194R GLN* 2.6 50.4 + - + +
195R MET 3.7 10.7 + - - +
196R GLY* 3.7 8.7 - - - -
197R GLY* 3.6 34.8 - - - +
276R PRO* 5.7 0.2 - - + -
382R PRO* 6.3 1.3 - - + -
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Residues in contact with GLN 191 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420P PRO* 4.1 29.2 - - + +
421P HIS* 3.7 32.4 - - + +
424P SER* 5.8 2.9 - - - -
463P ARG* 4.2 4.8 - - - +
16R MET* 4.5 24.9 - - + +
187R ASP* 2.8 34.3 + - - +
188R ASP* 3.9 15.6 + - - +
190R TYR* 1.3 85.2 - - + +
192R LEU* 1.3 66.8 + - + +
194R GLN* 3.3 12.5 + - - -
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Residues in contact with LEU 192 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420P PRO* 6.1 2.7 - - + -
421P HIS* 6.0 4.7 - - + +
463P ARG* 5.4 16.8 - - + +
470P ARG* 5.9 0.7 + - - -
169R ARG* 5.3 3.8 + - - -
176R GLU* 4.2 8.5 - - - +
180R LEU* 4.4 11.9 - - + -
188R ASP* 2.8 26.8 + - + +
191R GLN* 1.3 81.2 - - + +
193R HIS* 1.3 94.3 + - + +
194R GLN* 3.8 5.8 + - - +
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Residues in contact with HIS 193 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169R ARG* 4.7 10.6 + - + +
173R LYS* 3.3 41.4 - - + +
176R GLU* 3.1 30.9 + - - +
177R ALA* 4.0 22.7 - - + -
180R LEU* 4.3 5.1 - - + +
189R ALA 2.9 13.2 + - - +
192R LEU* 1.3 106.2 + - + +
194R GLN* 1.3 81.7 + - - +
195R MET* 3.0 20.7 + - + +
278R ALA* 3.2 14.6 - - - +
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Residues in contact with GLN 194 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154R PRO* 3.6 35.9 - - + +
155R TYR* 3.5 31.0 + - + +
169R ARG* 5.8 4.0 - - - +
190R TYR* 2.6 34.6 + - + +
191R GLN 3.3 20.6 + - - -
192R LEU 3.8 4.1 + - - +
193R HIS* 1.3 82.7 - - - +
195R MET* 1.3 57.3 + - - +
196R GLY 3.6 4.5 + - - -
276R PRO* 4.3 12.5 - - - +
278R ALA* 3.2 19.1 - - + +
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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