Contacts of the helix formed by residues 230 - 238 (chain A) in PDB entry 3IPA
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ALA* 3.6 16.3 - - - +
18A PHE* 3.7 23.3 - - - -
21A GLN* 4.2 5.1 + - - -
203A HIS* 5.0 3.4 - - - -
228A ILE 2.8 6.8 + - - -
229A VAL* 1.3 75.4 - - - +
231A ASN* 1.3 67.6 + - - +
232A GLU* 3.0 22.4 + - - +
233A LEU* 2.9 21.6 + - - +
273A GLU* 3.6 11.5 + - - -
335A TRP* 3.4 10.7 - - - -
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Residues in contact with ASN 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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230A SER* 1.3 73.1 + - - +
232A GLU* 1.3 73.6 + - - +
234A ALA* 3.0 20.9 + - - +
235A SER* 3.2 12.4 + - - -
271A ASN* 5.7 3.4 - - - +
273A GLU* 2.9 22.0 + - - +
335A TRP* 5.0 4.0 - - - -
342A LYS* 4.4 22.9 - - - +
343A PHE 4.4 13.6 + - - -
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Residues in contact with GLU 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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17A ALA* 3.7 19.5 - - + +
203A HIS* 3.7 21.8 - - + -
230A SER* 3.0 16.9 + - - +
231A ASN* 1.3 88.5 - - - +
233A LEU* 1.3 64.7 + - - +
235A SER* 2.6 37.3 + - - +
236A ILE* 3.0 16.8 + - + +
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Residues in contact with LEU 233 (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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203A HIS* 3.5 37.6 + - + +
206A ALA* 3.9 12.1 - - + -
207A GLY* 3.6 18.8 - - - +
210A ILE* 4.5 7.2 - - + -
228A ILE* 3.8 25.4 - - + +
230A SER 2.9 15.3 + - - +
232A GLU* 1.3 78.5 - - - +
234A ALA* 1.3 55.9 + - - +
236A ILE* 3.4 2.5 + - - +
237A ALA* 2.9 28.2 + - - +
241A VAL* 3.7 19.1 - - + -
244A THR* 4.7 0.9 - - + -
335A TRP* 3.4 33.0 - - + +
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Residues in contact with ALA 234 (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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230A SER 4.2 0.4 + - - -
231A ASN* 3.0 15.9 + - - +
233A LEU* 1.3 78.0 - - - +
235A SER* 1.3 58.9 + - - +
238A GLY* 2.8 30.7 + - - +
241A VAL* 4.3 13.9 - - + -
335A TRP* 4.3 6.9 - - + -
343A PHE* 4.0 37.9 - - + +
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Residues in contact with SER 235 (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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211A ARG* 4.8 0.7 + - - -
231A ASN* 3.2 11.7 + - - +
232A GLU* 2.6 47.2 + - - +
234A ALA* 1.3 78.3 - - - +
236A ILE* 1.3 64.4 + - - +
238A GLY 4.2 2.1 + - - -
357A SO4 4.7 7.4 + - - -
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Residues in contact with ILE 236 (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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203A HIS* 4.1 14.8 - - + +
204A THR* 3.9 35.4 - - + +
207A GLY* 3.6 25.1 - - - -
208A LEU* 3.7 19.1 - - + +
211A ARG* 3.2 24.7 + - - -
232A GLU* 3.0 21.8 + - + +
233A LEU* 3.9 2.9 - - - +
235A SER* 1.3 81.1 + - - +
237A ALA* 1.3 63.5 + - - +
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Residues in contact with ALA 237 (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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207A GLY* 3.7 23.1 - - - +
210A ILE* 3.8 23.1 - - + -
211A ARG* 3.4 17.5 + - - +
233A LEU 2.9 16.9 + - - +
236A ILE* 1.3 77.8 - - - +
238A GLY* 1.3 60.9 + - - +
240A ALA* 3.7 15.1 - - - +
241A VAL* 3.9 18.2 - - + -
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Residues in contact with GLY 238 (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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211A ARG* 3.6 0.9 - - - +
234A ALA 2.8 17.7 + - - +
235A SER 4.2 0.9 + - - -
236A ILE 3.4 2.8 + - - -
237A ALA* 1.3 73.1 - - - +
239A ASP* 1.3 64.1 + - - -
240A ALA 3.0 8.2 + - - -
241A VAL* 3.0 23.2 + - - +
343A PHE* 5.3 2.2 - - - -
357A SO4 3.3 24.5 - - - -
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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