Contacts of the helix formed by residues 233 - 248 (chain A) in PDB entry 3ADB
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ILE* 5.1 0.9 - - - -
232A VAL* 1.3 77.6 - - - +
234A ALA* 1.3 70.9 + - - +
235A ASP* 3.5 30.5 + - - +
236A ARG* 3.2 32.6 + - - +
237A VAL* 3.1 21.7 + - - +
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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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186A ILE* 4.3 14.0 - - + +
189A LYS* 4.1 33.4 - - + +
190A ILE* 4.1 25.8 - - + -
232A VAL 4.2 1.4 + - - -
233A ASP* 1.3 73.4 + - - +
235A ASP* 1.3 57.7 + - - +
237A VAL* 3.1 1.8 + - - -
238A LEU* 2.6 44.2 + - + +
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Residues in contact with ASP 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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189A LYS* 4.3 16.3 + - - -
233A ASP* 3.3 15.9 + - - +
234A ALA* 1.3 76.1 - - - +
236A ARG* 1.3 63.5 + - + +
238A LEU* 4.0 8.8 - - - +
239A LYS* 3.1 23.4 + - - +
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Residues in contact with ARG 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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233A ASP* 3.2 29.9 + - + +
235A ASP* 1.3 77.1 - - + +
237A VAL* 1.3 63.2 + - + +
239A LYS* 3.2 7.7 + - - +
240A GLU* 2.9 33.7 + - + +
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Residues in contact with VAL 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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190A ILE* 4.0 18.4 - - + -
222A PHE* 3.4 8.4 - - + -
226A ILE* 3.1 31.9 - - + -
229A MSE 3.8 17.9 - - + -
232A VAL* 3.3 32.8 - - + -
233A ASP 3.1 5.8 + - - +
234A ALA 3.1 7.5 + - - +
236A ARG* 1.3 74.9 - - + +
238A LEU* 1.3 67.3 + - - +
240A GLU* 2.9 18.3 + - - +
241A PHE 2.9 19.6 + - - -
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Residues in contact with LEU 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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189A LYS* 5.0 7.0 - - - +
190A ILE* 4.1 12.1 - - + +
193A GLU* 3.4 42.6 - - + +
194A THR* 3.8 25.4 - - + +
197A ILE* 4.2 12.8 - - + +
234A ALA* 2.6 38.6 + - + +
235A ASP* 4.0 8.7 - - - +
237A VAL* 1.3 73.0 - - - +
239A LYS* 1.3 61.6 + - - +
241A PHE* 3.3 4.5 + - - +
242A LYS* 3.0 31.6 + - - +
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Residues in contact with LYS 239 (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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235A ASP 3.1 14.4 + - - +
236A ARG* 3.6 9.6 - - - +
237A VAL 3.1 0.2 - - - -
238A LEU* 1.3 77.1 - - - +
240A GLU* 1.3 64.5 + - + +
242A LYS* 3.2 11.7 + - + +
243A ASP* 2.5 67.9 + - - +
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Residues in contact with GLU 240 (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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222A PHE* 4.4 14.2 - - + -
226A ILE* 5.6 1.2 - - - +
229A MSE 5.3 7.8 - - - +
236A ARG* 2.9 22.2 + - + +
237A VAL* 2.9 22.1 + - - +
239A LYS* 1.3 77.7 - - + +
241A PHE* 1.3 61.3 + - - +
243A ASP* 3.5 8.8 + - - +
244A LEU* 2.9 24.1 + - - +
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Residues in contact with PHE 241 (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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194A THR* 3.5 33.7 - - + -
197A ILE* 3.5 36.3 - - + -
198A VAL* 3.6 21.3 - - + -
215A VAL 5.5 0.2 - - - -
218A LEU* 4.9 0.7 - - + -
219A ARG* 3.6 32.3 - - + -
222A PHE* 3.4 40.1 - + + -
237A VAL 2.9 6.4 + - - +
238A LEU* 3.6 7.6 - - - +
239A LYS 3.2 0.2 - - - -
240A GLU* 1.3 76.5 - - - +
242A LYS* 1.3 63.0 + - - +
244A LEU* 3.0 15.5 + - + +
245A LEU* 2.9 41.8 + - + +
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Residues in contact with LYS 242 (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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197A ILE* 3.6 40.6 - - + -
200A GLU* 5.8 3.4 - - - -
238A LEU* 3.0 16.4 + - - +
239A LYS* 3.5 14.4 - - + +
241A PHE* 1.3 80.0 - - - +
243A ASP* 1.3 64.3 + - - +
245A LEU* 3.3 6.7 + - - +
246A ASN* 2.9 36.1 + - - +
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Residues in contact with ASP 243 (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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239A LYS* 2.5 57.9 + - - +
240A GLU* 3.7 8.0 - - - +
242A LYS* 1.3 75.2 - - - +
244A LEU* 1.3 67.8 + - - +
246A ASN* 2.9 23.7 + - - +
247A SER* 3.1 14.1 + - - -
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Residues in contact with LEU 244 (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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218A LEU* 3.8 37.7 - - + +
222A PHE* 4.4 18.6 - - + -
240A GLU 2.9 14.7 + - - +
241A PHE* 3.2 26.2 - - + +
243A ASP* 1.3 76.7 - - - +
245A LEU* 1.3 61.0 + - - +
247A SER* 3.2 21.1 + - - +
248A TYR* 3.2 9.4 + - - +
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Residues in contact with LEU 245 (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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197A ILE* 3.7 17.3 - - + -
198A VAL* 4.3 6.5 - - + -
201A TYR* 3.3 44.8 + - + -
215A VAL* 3.6 32.1 - - + +
218A LEU* 4.1 18.4 - - + -
241A PHE* 2.9 46.6 + - + +
242A LYS 3.6 7.9 - - - +
244A LEU* 1.3 77.5 - - - +
246A ASN* 1.3 62.5 + - - +
248A TYR* 3.1 21.7 - - + +
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Residues in contact with ASN 246 (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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201A TYR* 4.6 13.1 - - - -
205A LYS* 4.8 10.5 + - - +
242A LYS* 2.9 28.8 + - - +
243A ASP* 2.9 17.8 + - - +
245A LEU* 1.3 79.0 - - - +
247A SER* 1.3 58.4 + - - +
248A TYR* 4.5 2.7 - - - +
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Residues in contact with SER 247 (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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243A ASP 3.1 9.1 + - - -
244A LEU* 3.2 14.8 + - - +
245A LEU 3.2 0.2 - - - -
246A ASN* 1.3 74.8 - - - +
248A TYR* 1.3 71.7 + - - +
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Residues in contact with TYR 248 (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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201A TYR* 3.0 35.6 + + - -
205A LYS* 5.1 3.8 + - - -
207A LEU* 5.5 2.7 - - + -
211A LYS* 3.7 25.1 + - + +
214A GLU* 2.4 49.6 + - + +
215A VAL* 3.8 19.3 - - + -
218A LEU* 4.4 22.2 - - + -
244A LEU 3.2 9.9 + - - +
245A LEU* 3.1 17.3 - - + +
246A ASN 4.5 2.8 - - - +
247A SER* 1.3 88.5 + - - +
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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