Contacts of the helix formed by residues 182 - 190 (chain D) in PDB entry 1H5R
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 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D ASP* 3.1 15.3 + - - +
181D ASN* 1.3 78.9 - - - +
183D VAL* 1.3 62.8 + - - +
184D VAL 3.2 1.0 + - - -
185D GLN* 3.4 9.4 + - - +
186D MET* 3.3 25.3 + - + +
207D TYR* 3.8 4.5 - - - +
212D ARG* 2.9 36.6 + - - +
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Residues in contact with VAL 183 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D PHE* 3.6 45.8 - - + -
100D ILE* 5.1 3.4 - - + -
105D CYS* 5.4 3.6 - - + -
179D TYR* 3.8 17.9 - - + -
180D ASP 3.6 12.1 - - - +
181D ASN* 3.0 2.9 + - - +
182D ASP* 1.3 78.7 - - - +
184D VAL* 1.3 75.0 + - + +
186D MET* 3.3 5.5 + - + +
187D ALA* 2.9 22.3 + - - +
203D ILE* 3.7 28.9 - - + -
207D TYR* 3.3 14.7 + - - +
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Residues in contact with VAL 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D PHE* 4.1 17.3 - - + +
94D ILE* 5.2 0.2 - - - +
97D GLU* 3.9 26.2 - - + +
100D ILE* 3.7 43.3 - - + -
101D GLY 5.4 1.3 - - - +
181D ASN* 3.5 12.8 + - - +
182D ASP 3.2 1.2 - - - -
183D VAL* 1.3 81.7 - - + +
185D GLN* 1.3 66.2 + - - +
187D ALA* 3.2 2.4 + - - +
188D LYS* 2.9 41.3 + - + +
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Residues in contact with GLN 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D ASN 4.7 0.8 + - - +
182D ASP* 3.4 9.9 + - - +
183D VAL 3.2 0.6 - - - -
184D VAL* 1.3 81.7 - - - +
186D MET* 1.3 62.6 + - + +
188D LYS* 3.2 26.2 + - - +
189D ASN* 3.0 58.8 + - - +
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Residues in contact with MET 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D ASP* 3.3 16.1 + - + +
183D VAL* 3.6 7.2 - - - +
184D VAL 3.3 0.4 - - - -
185D GLN* 1.3 75.5 - - + +
187D ALA* 1.3 66.2 + - - +
189D ASN* 3.1 15.1 + - - +
190D LEU* 3.1 19.0 + - - +
203D ILE* 4.2 13.9 - - + -
206D ILE* 3.8 45.4 - - + +
207D TYR* 3.4 52.9 - - + +
210D GLN* 4.0 7.0 - - - +
212D ARG* 3.7 15.3 - - - +
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Residues in contact with ALA 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ALA* 3.6 27.5 - - + +
93D PHE* 3.8 15.9 - - + -
94D ILE* 3.7 19.2 - - + +
183D VAL 2.9 17.7 + - - +
184D VAL 3.6 3.6 - - - +
186D MET* 1.3 77.7 - - - +
188D LYS* 1.3 63.4 - - - +
190D LEU* 3.2 30.7 + - - +
198D LEU* 5.4 1.2 - - - +
203D ILE* 4.8 2.4 - - + +
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Residues in contact with LYS 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 4.1 28.4 - - + +
97D GLU* 2.7 40.0 + - + +
184D VAL* 2.9 31.7 + - + +
185D GLN* 3.2 27.6 + - - +
187D ALA* 1.3 77.5 - - - +
189D ASN* 1.3 62.8 + - - +
190D LEU 4.6 2.5 - - - +
191D LYS* 5.5 3.8 + - - -
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Residues in contact with ASN 189 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D GLN* 3.0 46.9 + - - +
186D MET* 3.1 6.1 + - - +
187D ALA 3.0 0.6 - - - -
188D LYS* 1.3 80.7 - - - +
190D LEU* 1.3 62.5 + - - +
191D LYS* 3.8 11.1 + - - +
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ALA* 3.6 31.2 - - + -
186D MET 3.1 16.0 + - - +
187D ALA* 3.2 14.7 + - - +
188D LYS 4.6 2.8 - - - +
189D ASN* 1.3 80.1 - - - +
191D LYS* 1.3 72.0 + - - +
192D PRO* 4.5 0.2 - - - +
198D LEU* 3.7 18.3 - - + +
199D GLU 3.7 20.6 - - - +
202D ASP* 3.6 27.6 - - + +
203D ILE* 3.9 10.5 - - + +
206D ILE* 4.5 16.2 - - + -
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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