Contacts of the helix formed by residues 228 - 232 (chain A) in PDB entry 2IHB
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 SER 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ASP* 4.0 8.1 + - - -
227A LEU* 1.3 75.5 - - - +
229A ASP* 1.3 63.1 + - - +
230A TYR* 3.2 7.8 + - - -
232A LEU* 4.1 1.6 - - - +
270A LYS* 3.4 26.3 - - - +
273A LEU* 3.8 25.5 - - - +
274A PHE* 4.1 12.8 - - - -
277A LYS* 2.7 47.6 + - - -
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Residues in contact with ASP 229 (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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42A GLY 4.7 6.9 - - - +
43A GLU 5.1 0.9 - - - +
150A ASP* 5.2 0.7 - - - +
226A ALA* 2.9 36.7 + - - +
228A SER* 1.3 81.4 + - - +
230A TYR* 1.3 63.2 + - - +
231A ASP 3.1 2.9 - - - -
232A LEU* 3.0 33.8 + - - +
242A ARG* 3.2 50.9 + - + +
243A MET* 4.1 9.4 + - + +
270A LYS* 4.8 4.9 + - - -
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Residues in contact with TYR 230 (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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227A LEU 3.4 19.1 + - - -
228A SER 3.2 4.0 - - - -
229A ASP* 1.3 77.2 - - - +
231A ASP* 1.3 66.1 + - + +
241A ASN* 2.8 26.2 + - - -
243A MET* 3.6 29.3 - - + +
274A PHE* 3.6 26.2 - + - -
277A LYS* 3.4 35.6 + - + +
278A ILE* 3.5 11.0 - - + -
281A SER* 2.4 39.0 + - - -
282A PRO 3.5 15.9 - - - -
283A LEU* 3.9 22.7 - - + -
285A ILE* 4.1 0.8 - - + +
286A CYS* 3.2 22.2 - - + +
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Residues in contact with ASP 231 (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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144A ARG* 3.2 39.1 + - - +
230A TYR* 1.3 83.8 - - + +
232A LEU* 1.3 68.4 + - - +
233A VAL* 5.1 3.1 - - - +
241A ASN* 4.4 1.3 - - - +
277A LYS* 3.1 38.5 + - - -
281A SER* 2.8 23.0 + - - +
285A ILE* 3.7 35.4 - - + +
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Residues in contact with LEU 232 (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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143A SER* 5.1 4.3 - - - +
144A ARG* 3.8 32.8 - - + +
146A TYR 5.3 3.6 - - - +
147A GLN* 5.8 1.3 - - - +
148A LEU 6.0 1.6 - - - +
150A ASP* 5.4 6.5 - - - +
228A SER* 4.1 4.7 - - - +
229A ASP* 3.0 28.7 + - - +
231A ASP* 1.3 99.6 + - - +
233A VAL* 1.3 65.5 + - - +
241A ASN* 3.6 9.4 + - - -
242A ARG* 3.2 42.4 + - - +
277A LYS* 3.8 17.9 - - - +
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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