Contacts of the helix formed by residues 185 - 194 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180Q LEU* 2.9 36.7 + - + +
181Q MET 4.2 0.2 + - - -
183Q GLN* 3.2 39.5 + - + +
184Q GLY* 1.3 74.6 - - - +
186Q PHE* 1.3 64.9 - - - +
187Q ASP 3.4 2.5 - - - +
188Q ASP* 3.3 21.2 + - + +
189Q ALA* 3.1 21.0 + - - +
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Residues in contact with PHE 186 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181Q MET* 3.5 49.8 - - + -
184Q GLY* 3.3 24.0 + - - -
185Q LYS* 1.3 72.5 - - - +
187Q ASP* 1.3 61.8 + - - +
189Q ALA* 3.0 6.9 + - + +
190Q TYR* 2.8 28.9 + - - +
195Q MET 4.6 2.0 - - - +
196Q GLY* 5.8 0.2 - - - -
355Q LYS* 4.1 15.5 - - - -
358Q GLU* 5.8 0.2 - - - -
359Q THR* 3.8 16.8 - - + -
382Q PRO 4.0 10.3 - - - +
383Q SER 3.3 25.5 + - - +
384Q ASN* 4.3 13.2 - - - -
385Q PRO* 3.5 25.8 - - + -
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Residues in contact with ASP 187 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Q LYS 3.4 0.6 - - - -
186Q PHE* 1.3 72.8 - - - +
188Q ASP* 1.3 71.5 + - - +
190Q TYR* 3.2 7.5 + - - +
191Q GLN* 2.8 43.5 + - - +
382Q PRO* 4.3 4.7 - - - +
383Q SER* 3.2 42.1 + - - -
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Residues in contact with ASP 188 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180Q LEU* 4.1 19.4 - - + +
185Q LYS* 3.3 31.5 + - + +
186Q PHE 3.2 0.4 - - - -
187Q ASP* 1.3 78.0 - - - +
189Q ALA* 1.3 65.4 + - - +
191Q GLN* 4.2 13.9 + - - +
192Q LEU* 2.8 36.4 + - + +
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Residues in contact with ALA 189 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177Q ALA* 3.9 14.8 - - + +
180Q LEU* 4.0 12.7 - - + +
181Q MET* 3.9 27.1 - - + -
185Q LYS 3.1 10.3 + - - +
186Q PHE* 3.0 9.5 + - + +
188Q ASP* 1.3 79.2 - - - +
190Q TYR* 1.3 57.5 + - - +
193Q HIS* 2.9 33.8 + - - +
194Q GLN 3.6 0.9 + - - -
195Q MET* 3.7 12.3 + - - +
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Residues in contact with TYR 190 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q MET* 2.6 43.2 + - + -
17Q LEU* 3.2 16.1 - - + -
153Q ILE* 3.4 10.9 - - + +
154Q PRO* 3.3 22.0 - - + +
186Q PHE 2.8 15.2 + - - +
187Q ASP* 3.6 11.4 - - - +
189Q ALA* 1.3 74.6 - - - +
191Q GLN* 1.3 69.5 + - + +
194Q GLN* 2.6 50.8 + - + +
195Q MET 3.7 10.5 + - - +
196Q GLY* 3.7 8.5 - - - -
197Q GLY* 3.6 33.7 - - - +
382Q PRO* 6.3 1.1 - - + -
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Residues in contact with GLN 191 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q MET* 4.5 26.3 - - + +
187Q ASP* 2.8 35.2 + - - +
188Q ASP* 3.9 15.6 + - - +
190Q TYR* 1.3 84.9 - - + +
192Q LEU* 1.3 67.9 + - + +
194Q GLN* 3.3 12.8 + - - -
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Residues in contact with LEU 192 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169Q ARG* 5.3 3.8 + - - -
176Q GLU* 4.2 9.4 - - - +
180Q LEU* 4.4 11.4 - - + -
188Q ASP* 2.8 26.8 + - + +
191Q GLN* 1.3 82.4 - - + +
193Q HIS* 1.3 92.0 + - + +
194Q GLN* 3.8 6.2 + - - +
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Residues in contact with HIS 193 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169Q ARG* 4.7 12.5 + - + +
170Q ALA* 6.0 0.2 - - - -
173Q LYS* 3.3 40.0 - - + +
176Q GLU* 3.1 30.7 + - - +
177Q ALA* 4.0 22.9 - - + -
180Q LEU* 4.3 6.2 - - + +
189Q ALA 2.9 13.6 + - - +
192Q LEU* 1.3 105.5 + - + +
194Q GLN* 1.3 81.4 + - - +
195Q MET* 3.0 21.1 + - + +
278Q ALA* 3.2 13.9 - - - +
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Residues in contact with GLN 194 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154Q PRO* 3.6 36.1 - - + +
155Q TYR* 3.5 28.8 + - + +
169Q ARG* 5.8 4.0 - - - +
190Q TYR* 2.6 34.9 + - + +
191Q GLN 3.3 21.0 + - - -
192Q LEU 3.8 3.9 + - - +
193Q HIS* 1.3 82.8 - - - +
195Q MET* 1.3 57.3 + - - +
196Q GLY 3.6 4.2 + - - -
276Q PRO* 4.3 12.5 - - - +
278Q 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