Contacts of the helix formed by residues 176 - 184 (chain A) in PDB entry 1D2H
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 ASN 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A HIS 3.5 1.8 + - - -
175A LYS* 1.3 67.2 - - - +
177A TYR* 1.3 56.5 + - - +
178A ASP* 3.1 11.9 - - - +
179A TYR* 2.7 39.1 - - + +
180A ILE* 3.0 25.0 + - + +
280A VAL* 4.3 1.2 - - - +
281A PRO* 2.7 43.5 - - - +
282A CYS* 3.0 16.6 + - - +
284A PHE* 3.5 26.1 - - + -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASN* 3.4 20.8 + - - -
141A ALA* 4.2 2.4 - - + +
174A HIS* 5.0 1.8 - - + -
175A LYS* 2.6 52.0 + - + +
176A ASN* 1.3 71.4 - - - +
178A ASP* 1.3 60.4 + - - +
180A ILE* 3.5 28.7 - - + -
181A LEU* 2.7 38.3 + - + +
216A VAL* 4.6 19.0 - - + +
218A LEU* 5.6 2.3 - - + +
242A TYR* 3.5 27.0 - - + +
243A TYR 4.1 8.7 - - - -
244A PRO* 3.5 33.4 - - + +
245A HIS* 3.5 30.4 + - + +
246A CYS* 4.5 1.3 - - - +
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASN* 3.5 7.5 + - - +
177A TYR* 1.3 80.2 + - - +
179A TYR* 1.3 61.9 + - - +
181A LEU* 3.6 8.3 + - - +
182A SER* 3.7 10.6 + - - -
246A CYS* 3.1 27.8 - - - +
247A LEU* 2.7 39.5 + - - +
248A ALA* 4.9 4.0 + - - +
284A PHE* 4.8 3.5 - - + -
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Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASN* 2.7 32.0 - - + +
178A ASP* 1.3 72.0 - - - +
180A ILE* 1.3 71.8 + - + +
182A SER* 3.1 24.9 + - - -
183A THR* 3.2 29.9 + - + -
187A PRO* 5.0 13.0 - - + -
280A VAL* 3.8 30.5 - - + -
281A PRO 5.5 1.3 - - - -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LYS* 3.8 33.9 - - + -
176A ASN* 3.0 24.6 + - + +
177A TYR* 3.3 27.8 + - + -
179A TYR* 1.3 83.7 - - + +
181A LEU* 1.3 59.8 + - + +
182A SER 3.1 0.2 - - - -
183A THR* 3.2 2.1 + - - +
184A GLY* 2.8 33.1 + - - -
185A CYS 3.7 18.6 + - - +
186A ALA* 4.3 20.6 - - + +
187A PRO* 4.3 9.6 - - + -
204A THR* 5.4 5.2 - - + -
216A VAL* 5.5 4.0 - - + -
218A LEU* 6.2 0.4 - - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A TYR* 2.7 27.9 + - + +
178A ASP* 4.0 5.2 - - - +
179A TYR 3.2 0.2 - - - -
180A ILE* 1.3 82.9 - - + +
182A SER* 1.3 57.9 + - - +
184A GLY* 4.0 6.3 + - - +
206A VAL* 4.3 26.5 - - + -
213A ALA* 3.8 17.3 - - + -
216A VAL* 4.4 4.9 - - + -
244A PRO* 3.5 33.2 - - + +
246A CYS* 4.5 15.0 - - - -
211B ASN* 5.5 1.0 + - - -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP 3.7 8.8 + - - -
179A TYR* 3.1 20.0 + - - -
180A ILE 3.1 0.4 - - - -
181A LEU* 1.3 76.6 - - - +
183A THR* 1.3 63.0 + - - +
184A GLY 3.3 4.3 - - - -
211B ASN* 4.8 7.4 + - - +
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TYR* 3.2 32.5 + - + +
180A ILE* 3.9 4.3 - - - +
182A SER* 1.3 79.2 + - - +
184A GLY* 1.3 54.2 + - - +
185A CYS* 2.7 53.4 + - + +
187A PRO* 5.2 4.3 - - + -
211B ASN* 3.9 12.8 + - - +
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Residues in contact with GLY 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ILE* 2.8 13.7 + - - -
181A LEU* 4.0 5.4 - - - -
182A SER 3.3 4.4 - - - +
183A THR* 1.3 76.5 - - - +
185A CYS* 1.3 61.8 + - - +
204A THR* 3.9 16.1 - - - +
206A VAL* 4.4 16.1 - - - +
208B THR* 5.5 0.9 - - - -
211B ASN* 3.2 32.5 + - - +
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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