Contacts of the helix formed by residues 230 - 243 (chain A) in PDB entry 3O71
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 HIS 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ARG* 3.5 16.0 - - - +
229A LYS* 1.3 86.0 - - + +
231A TYR* 1.3 66.7 + + + +
232A LEU* 3.6 13.6 + - + +
233A ASP* 3.2 42.5 + - + +
234A GLN* 2.8 28.8 + - - +
359A SCN 5.0 0.7 - - - -
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Residues in contact with TYR 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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183A THR* 5.5 4.5 - - + -
197A MET* 3.4 46.9 - - + +
230A HIS* 1.3 80.6 - - + +
232A LEU* 1.3 104.6 + - + +
234A GLN* 3.5 0.4 + - - -
235A LEU* 3.1 20.7 + - + +
359A SCN 3.8 27.1 + - - +
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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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230A HIS* 3.4 12.0 + - + +
231A TYR* 1.3 123.5 - - + +
233A ASP* 1.3 60.3 + - - +
235A LEU* 3.5 11.0 + - + +
236A ASN* 2.9 40.3 + - - +
261A TYR* 3.8 35.9 - - + +
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Residues in contact with ASP 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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227A PRO 4.2 0.2 - - - +
228A GLY* 3.3 4.9 - - - -
229A LYS* 2.8 35.3 + - - +
230A HIS* 3.2 32.4 + - + +
232A LEU* 1.3 72.9 - - - +
234A GLN* 1.3 60.8 + - - +
236A ASN* 3.2 9.8 + - - +
237A HIS* 2.8 52.8 + - - -
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Residues in contact with GLN 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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189A ARG* 3.2 36.7 + - + +
190A TRP* 3.2 17.1 + - - -
192A ARG 4.6 1.8 + - - +
197A MET* 3.6 25.1 - - + -
226A PHE* 2.9 34.0 + - - +
228A GLY* 2.9 29.6 + - - -
230A HIS 2.8 16.8 + - - +
231A TYR* 3.6 6.5 - - - +
233A ASP* 1.3 77.0 - - - +
235A LEU* 1.3 62.0 + - - +
237A HIS* 3.3 3.9 + - - +
238A ILE* 3.2 31.5 + - - +
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Residues in contact with LEU 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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194A PRO* 4.3 23.8 - - + +
197A MET* 4.0 17.6 - - + +
198A LEU* 3.8 37.5 - - + -
231A TYR 3.1 13.5 + - - +
232A LEU* 3.6 14.4 - - + +
234A GLN* 1.3 79.0 - - - +
236A ASN* 1.3 59.8 + - - +
238A ILE* 3.2 8.0 + - + +
239A LEU* 3.0 42.0 + - + +
261A TYR* 3.9 25.8 - - + -
262A LEU* 4.2 7.9 - - + -
294A PHE* 4.8 5.2 - - + -
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Residues in contact with ASN 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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230A HIS* 6.2 0.2 - - - -
232A LEU* 2.9 29.7 + - - +
233A ASP* 3.2 10.8 + - - +
235A LEU* 1.3 74.3 - - - +
237A HIS* 1.3 60.3 + - - +
239A LEU* 3.4 16.9 + - - +
240A GLY* 2.8 26.5 + - - -
261A TYR* 3.9 18.1 + - - -
265A LEU* 4.5 4.5 - - - +
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Residues in contact with HIS 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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225A ILE 4.5 2.4 + - - -
226A PHE* 3.5 26.4 - - + -
227A PRO* 3.5 39.7 + - + +
228A GLY* 3.8 10.1 - - - -
233A ASP* 2.8 50.2 + - - -
234A GLN* 3.5 8.7 - - - +
235A LEU 3.3 0.2 - - - -
236A ASN* 1.3 71.6 - - - +
238A ILE* 1.3 62.2 + - - +
240A GLY* 3.4 9.5 + - - -
241A ILE* 3.5 11.8 + - - +
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Residues in contact with ILE 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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192A ARG 3.9 9.0 - - - +
194A PRO* 4.2 16.2 - - + -
197A MET* 3.6 31.0 - - + -
210A TRP* 3.6 36.3 - - + +
226A PHE* 3.7 27.1 - - + -
234A GLN* 3.2 14.1 + - - +
235A LEU* 3.2 9.7 + - + +
237A HIS* 1.3 73.4 - - - +
239A LEU* 1.3 62.4 + - + +
241A ILE* 3.2 2.4 + - - +
242A LEU* 2.9 41.7 + - + +
294A PHE* 4.7 6.7 - - + -
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Residues in contact with LEU 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 LEU* 3.0 26.6 + - + +
236A ASN* 3.8 14.6 - - - +
238A ILE* 1.3 73.7 - - + +
240A GLY* 1.3 59.8 + - - +
242A LEU* 5.1 0.9 - - + -
243A GLY* 2.9 41.2 + - - +
244A SER* 4.7 2.2 - - - +
245A PRO* 3.9 28.0 - - + -
262A LEU* 3.8 19.5 - - + -
265A LEU* 3.5 32.1 - - + -
268A LYS* 3.6 9.0 - - + +
294A PHE* 4.4 16.4 - - + -
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Residues in contact with GLY 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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236A ASN 2.8 17.2 + - - -
237A HIS* 3.4 4.2 + - - -
238A ILE 3.2 0.4 - - - -
239A LEU* 1.3 75.9 - - - +
241A ILE* 1.3 63.2 + - - +
268A LYS* 2.7 38.9 + - - -
271A VAL* 3.6 5.0 - - - +
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Residues in contact with ILE 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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225A ILE* 4.6 10.1 - - + +
226A PHE* 3.8 26.5 - - + -
237A HIS 3.5 5.1 + - - +
238A ILE 3.2 1.8 + - - -
239A LEU 3.2 0.4 - - - -
240A GLY* 1.3 81.9 - - - +
242A LEU* 1.3 64.6 + - + +
243A GLY 3.2 2.0 - - - -
270A LYS* 3.6 0.9 + - - +
271A VAL* 2.8 41.2 + - + +
273A TRP* 3.8 28.3 - - + -
276A LEU* 3.6 44.4 - - + -
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Residues in contact with LEU 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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210A TRP* 3.9 15.9 - - + -
226A PHE* 4.1 17.0 - - + -
238A ILE* 2.9 26.9 + - + +
239A LEU* 5.1 0.4 - - + -
241A ILE* 1.3 73.8 - - + +
243A GLY* 1.3 66.1 + - - +
244A SER 4.7 2.1 - - - +
270A LYS* 3.5 34.3 + - - +
273A TRP* 3.9 28.5 - - + -
292A LEU 3.5 21.5 - - - +
294A PHE* 3.8 32.5 - - + +
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Residues in contact with GLY 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 LEU* 2.9 31.7 + - - +
241A ILE 3.2 3.6 + - - -
242A LEU* 1.3 87.2 - - - +
244A SER* 1.3 65.9 + - - -
245A PRO* 3.5 2.6 - - - +
268A LYS* 3.1 16.8 - - - -
269A ASN 3.9 12.8 - - - -
270A LYS* 3.9 0.6 - - - +
294A PHE* 5.9 0.9 - - - -
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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