Contacts of the helix formed by residues 182 - 190 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180C ASP* 3.0 16.9 + - - +
181C ASN* 1.3 82.2 - - - +
183C VAL* 1.3 61.8 + - - +
184C VAL 3.1 1.0 + - - -
185C GLN* 3.4 9.1 + - - +
186C MET* 3.2 28.1 + - + +
207C TYR* 3.8 4.7 - - - +
212C ARG* 2.9 33.9 + - - +
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Residues in contact with VAL 183 (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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93C PHE* 3.6 44.2 - - + -
100C ILE* 5.4 2.7 - - + -
105C CYS* 5.5 3.6 - - + -
179C TYR* 3.8 19.1 - - + -
180C ASP 3.6 13.2 - - - +
181C ASN* 4.6 1.1 - - - +
182C ASP* 1.3 78.8 - - - +
184C VAL* 1.3 66.7 + - + +
186C MET* 3.3 6.5 + - - +
187C ALA* 2.9 28.1 + - - +
203C ILE* 3.7 28.9 - - + -
207C TYR* 3.3 16.1 + - - +
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Residues in contact with VAL 184 (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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93C PHE* 4.0 18.8 - - + +
97C GLU* 3.8 37.9 - - + +
100C ILE* 3.9 39.9 - - + -
101C GLY 5.2 2.5 - - - +
181C ASN* 4.0 13.9 - - - +
182C ASP 3.1 0.4 - - - -
183C VAL* 1.3 83.0 - - + +
185C GLN* 1.3 64.2 + - - +
187C ALA* 3.2 5.7 + - - +
188C LYS* 3.2 29.1 + - + +
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Residues in contact with GLN 185 (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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181C ASN 4.7 0.6 + - - +
182C ASP* 3.4 10.1 + - - +
184C VAL* 1.3 77.6 - - - +
186C MET* 1.3 64.3 + - - +
188C LYS* 3.4 30.3 + - - +
189C ASN* 2.7 55.4 + - - +
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Residues in contact with MET 186 (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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182C ASP* 3.2 19.6 + - + +
183C VAL* 3.6 6.1 - - - +
185C GLN* 1.3 75.6 - - + +
187C ALA* 1.3 66.1 + - - +
189C ASN* 3.1 15.1 + - - +
190C LEU* 3.4 15.6 + - - +
203C ILE* 4.0 14.6 - - + +
206C ILE* 3.7 49.1 - - + +
207C TYR* 3.4 53.6 - - + +
210C GLN* 4.1 5.4 - - - +
212C ARG* 4.1 12.1 - - - +
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Residues in contact with ALA 187 (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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90C ALA 3.7 23.8 - - - +
93C PHE* 3.7 14.1 - - + -
94C ILE* 3.5 18.6 - - + +
183C VAL 2.9 18.0 + - - +
184C VAL 3.2 5.6 + - - +
186C MET* 1.3 79.1 - - - +
188C LYS* 1.3 62.0 + - - +
189C ASN 3.3 0.5 + - - -
190C LEU* 3.4 20.4 + - - +
198C LEU* 4.5 3.3 - - - +
203C ILE* 3.7 15.0 - - + +
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Residues in contact with LYS 188 (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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94C ILE* 4.1 28.9 - - + -
97C GLU* 3.1 39.2 + - - -
184C VAL* 3.2 26.1 + - + +
185C GLN* 3.9 27.0 + - - +
186C MET 3.2 0.8 - - - -
187C ALA* 1.3 76.9 - - - +
189C ASN* 1.3 64.8 + - - +
190C LEU 3.4 2.6 - - - +
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Residues in contact with ASN 189 (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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185C GLN* 2.7 49.5 + - - +
186C MET* 3.1 9.7 + - - +
187C ALA 3.1 0.6 - - - -
188C LYS* 1.3 81.7 - - - +
190C LEU* 1.3 63.9 + - - +
191C LYS* 3.8 3.5 + - - +
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Residues in contact with LEU 190 (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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90C ALA* 3.3 33.4 - - + -
186C MET 3.4 12.3 + - - +
187C ALA* 3.4 16.3 + - - +
188C LYS 4.7 2.8 - - - +
189C ASN* 1.3 81.0 - - - +
191C LYS* 1.3 63.1 + - - +
198C LEU* 3.7 19.4 - - + +
199C GLU 3.7 16.6 - - - +
202C ASP* 3.8 27.6 - - + +
203C ILE* 3.7 16.8 - - + +
206C ILE* 4.2 19.3 - - + -
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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