Contacts of the helix formed by residues 228 - 248 (chain A) in PDB entry 4A69
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLY 3.4 3.6 + - - +
227A ILE* 1.3 74.3 - - - +
229A ASP* 1.3 64.5 + - - +
230A GLN* 3.3 24.8 + - - +
231A SER* 2.6 29.0 + - - -
232A TYR* 3.1 23.7 + - - +
270A ASN* 3.6 19.1 - - - +
271A LEU* 3.6 5.2 - - - -
348A ASN* 2.7 23.4 + - + +
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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
----------------------------------------------------------
228A ASP* 1.3 75.3 - - - +
230A GLN* 1.3 59.3 + - - +
232A TYR* 3.3 1.7 + - - +
233A LYS* 2.8 37.4 + - - +
270A ASN 4.2 2.1 + - - -
271A LEU* 3.3 12.7 - - - +
272A SER* 2.5 50.3 + - - -
274A ARG* 5.4 0.2 - - - +
275A GLY* 3.4 22.3 + - - -
278A GLU* 5.1 4.7 - - - +
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Residues in contact with GLN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASP* 3.3 11.0 + - - +
229A ASP* 1.3 79.7 - - + +
231A SER* 1.3 61.8 + - - +
233A LYS* 3.6 16.9 + - + +
234A HIS* 3.1 23.6 + - + +
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ILE* 4.1 11.2 - - - -
228A ASP* 2.6 31.6 + - - -
230A GLN* 1.3 74.9 - - - +
232A TYR* 1.3 65.3 + - - +
234A HIS* 3.2 16.7 + - - +
235A LEU* 3.3 17.2 + - - +
348A ASN* 3.9 6.1 + - - -
350A ASN* 5.6 0.4 + - - -
355A LEU* 4.1 25.1 - - - +
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Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 3.4 26.9 + - + +
192A PHE* 3.3 28.7 + + + +
223A LEU* 4.1 17.3 - - + -
227A ILE* 3.8 31.6 - - + +
228A ASP 3.1 18.2 + - - +
229A ASP 3.5 4.0 - - - +
231A SER* 1.3 77.1 - - - +
233A LYS* 1.3 52.5 + - - +
235A LEU* 3.1 6.6 + - - +
236A PHE* 2.7 51.4 + + + +
260A SER* 5.5 0.4 - - - -
269A PHE* 4.2 12.3 - + - -
271A LEU* 3.7 28.3 - - + -
279A CYS* 3.7 31.0 - - - -
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASP* 2.8 24.0 + - - +
230A GLN* 3.7 16.1 - - + +
232A TYR* 1.3 74.2 - - - +
234A HIS* 1.3 60.4 + - - +
236A PHE* 4.4 5.8 - - - -
237A GLN* 3.2 53.0 + - + +
238A PRO* 3.7 0.9 - - - +
278A GLU* 2.8 46.3 + - + +
279A CYS* 6.0 2.7 - - - -
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLN* 3.1 15.5 + - + +
231A SER* 3.3 14.4 - - - +
232A TYR 3.2 0.6 - - - -
233A LYS* 1.3 76.2 - - - +
235A LEU* 1.3 54.7 - - + +
238A PRO* 3.2 14.8 - - + +
355A LEU* 5.8 9.0 - - + -
356A ASP* 5.4 4.6 + - - -
359A ARG* 2.4 64.1 + - + -
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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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192A PHE* 4.7 8.7 - - + -
221A VAL* 4.1 12.6 - - + -
223A LEU* 3.7 30.3 - - + -
227A ILE* 4.5 6.1 - - + -
231A SER 3.3 12.2 + - - +
232A TYR* 3.1 6.6 + - - +
234A HIS* 1.3 80.4 - - + +
236A PHE* 1.3 66.5 + - - +
237A GLN 3.3 0.6 + - - -
238A PRO* 3.4 3.3 - - - +
239A VAL* 3.1 34.6 + - + +
355A LEU* 4.0 22.2 - - + +
358A ILE* 4.3 16.6 - - + -
359A ARG* 3.6 35.7 - - + +
362A ILE* 5.9 0.9 - - + -
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Residues in contact with PHE 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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167A ILE* 4.0 4.5 - - + -
169A ILE* 3.0 34.5 - - + -
192A PHE* 3.4 35.9 - + + -
232A TYR* 2.7 37.5 + + + +
233A LYS* 4.3 3.4 - - - +
235A LEU* 1.3 74.4 - - - +
237A GLN* 1.3 70.2 + - + +
239A VAL* 3.8 0.7 - - - +
240A ILE* 2.9 54.2 + - + +
254A LEU* 5.4 0.2 - - + -
279A CYS* 3.8 37.2 - - + -
282A TYR* 4.3 10.8 - + - -
283A VAL* 4.1 16.4 - - + -
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Residues in contact with GLN 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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233A LYS* 3.2 35.6 + - + +
236A PHE* 1.3 82.6 - - + +
238A PRO* 1.4 66.6 - - + +
241A ASN* 2.9 33.1 + - - +
278A GLU* 4.5 9.9 - - - +
282A TYR* 3.5 56.8 + - + +
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Residues in contact with PRO 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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233A LYS 3.7 2.7 - - - +
234A HIS* 3.2 29.2 - - + +
235A LEU 3.4 4.7 - - - +
237A GLN* 1.4 93.4 - - + +
239A VAL* 1.3 61.7 + - - +
241A ASN* 3.7 5.9 - - + +
242A GLN* 3.1 25.3 + - - +
359A ARG* 4.0 12.6 - - - +
363A PHE* 3.7 22.2 - - + -
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A VAL* 4.5 5.4 - - + -
192A PHE* 4.1 22.9 - - + -
219A LEU* 4.0 28.3 - - + -
221A VAL* 4.9 3.8 - - + -
235A LEU* 3.1 29.1 + - + +
236A PHE 3.8 2.7 - - - +
238A PRO* 1.3 78.5 - - - +
240A ILE* 1.3 59.5 + - - +
242A GLN* 3.3 3.8 + - - +
243A VAL* 2.9 36.7 + - + +
362A ILE* 3.9 22.2 - - + -
363A PHE* 4.4 17.0 - - + -
366A LEU* 4.3 1.7 - - + +
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Residues in contact with ILE 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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165A LEU* 5.2 0.9 - - + -
167A ILE* 3.8 43.7 - - + -
190A VAL* 4.2 14.8 - - + -
192A PHE* 4.2 13.2 - - + -
236A PHE* 2.9 42.3 + - + +
237A GLN 4.1 1.8 - - - +
239A VAL* 1.3 72.6 - - + +
241A ASN* 1.3 67.6 + - - +
243A VAL* 3.2 5.7 + - + +
244A VAL* 2.9 29.6 + - + +
282A TYR* 4.3 7.4 - - + -
283A VAL* 4.9 4.5 - - + -
286A PHE* 3.8 25.6 - - + -
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Residues in contact with ASN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLN 2.9 20.3 + - - +
238A PRO* 3.7 6.4 - - + +
240A ILE* 1.3 76.0 - - - +
242A GLN* 1.3 58.3 + - - +
244A VAL* 3.4 1.6 + - - +
245A ASP* 3.1 42.7 + - - +
282A TYR* 3.3 15.9 + - - +
286A PHE* 3.9 19.9 - - - -
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Residues in contact with GLN 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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238A PRO 3.1 17.8 + - - +
239A VAL 3.9 2.7 - - - +
241A ASN* 1.3 73.7 - - - +
243A VAL* 1.3 60.9 + - - +
245A ASP* 3.8 6.9 - - + +
246A PHE* 2.9 75.4 + - + +
363A PHE* 3.1 34.9 - - + +
366A LEU* 3.7 15.8 - - + +
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Residues in contact with VAL 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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165A LEU* 3.7 36.1 - - + -
188A MET* 4.1 16.8 - - + -
190A VAL* 4.3 8.5 - - + -
219A LEU* 4.1 15.0 - - + -
239A VAL* 2.9 31.9 + - + +
240A ILE* 3.5 9.6 - - + +
242A GLN* 1.3 76.1 - - - +
244A VAL* 1.3 57.5 + - - +
246A PHE* 5.0 0.7 - - - -
247A TYR* 2.9 39.1 + - + +
366A LEU* 3.8 23.8 - - + -
369A LEU* 6.0 0.7 - - - -
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Residues in contact with VAL 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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165A LEU* 4.1 20.0 - - + -
240A ILE* 2.9 21.6 + - + +
241A ASN 3.8 3.6 - - - +
243A VAL* 1.3 74.5 - - - +
245A ASP* 1.3 61.5 + - - +
248A GLN* 2.9 37.6 + - - +
249A PRO* 4.0 11.4 - - + -
252A ILE* 4.9 5.2 - - + -
286A PHE* 3.8 43.5 - - + -
288A ILE* 4.0 19.1 - - + -
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Residues in contact with ASP 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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241A ASN* 3.1 35.7 + - - +
242A GLN* 3.8 8.2 - - - +
244A VAL* 1.3 82.5 - - - +
246A PHE* 1.3 73.0 + - + +
248A GLN* 3.4 22.5 - - - +
286A PHE* 5.3 1.2 - - - -
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Residues in contact with PHE 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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242A GLN* 2.9 57.1 + - + +
243A VAL* 4.3 1.1 - - - +
245A ASP* 1.3 87.3 - - + +
247A TYR* 1.3 61.5 + - - +
248A GLN* 3.8 3.3 + - - +
366A LEU* 3.3 35.2 - - + -
367A LYS* 4.5 4.5 - - + -
369A LEU* 3.8 30.2 - - + +
370A ASN* 3.3 32.1 - - - -
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Residues in contact with TYR 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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163A ARG* 3.1 50.5 + - + +
164A VAL 3.6 16.8 - - - -
165A LEU* 4.1 6.1 - - + -
185A ASP 2.9 28.2 + - - -
186A ARG 3.1 22.2 + - - -
187A VAL 3.5 1.7 + - - -
188A MET* 3.5 36.7 + - + -
217A TYR* 3.6 30.5 - + - -
243A VAL* 2.9 22.4 + - + +
246A PHE* 1.3 72.9 - - - +
248A GLN* 1.3 66.6 + - - +
249A PRO* 3.9 16.2 - - + -
369A LEU* 4.7 5.2 - - + -
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Residues in contact with GLN 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG* 2.9 32.9 + - - +
244A VAL* 2.9 32.1 + - - +
245A ASP* 3.4 21.8 - - - +
246A PHE 4.5 2.7 - - - +
247A TYR* 1.3 77.5 - - - +
249A PRO* 1.4 69.9 - - - +
250A THR* 4.2 0.5 - - - +
288A ILE* 6.2 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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