Contacts of the helix formed by residues 241 - 255 (chain D) in PDB entry 4BGG
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 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D ARG 5.6 0.7 - - - +
219D TYR* 3.9 35.5 - - - +
235D LYS* 5.4 1.4 + - - -
237D PHE* 3.7 12.4 - - + -
238D SER* 3.1 14.6 + - - +
240D ARG* 1.3 79.9 - - - +
242D GLU* 1.3 64.8 + - - +
243D LYS 3.3 3.4 - - - +
244D SER* 2.8 40.9 + - - -
245D TRP 3.4 8.1 + - - -
373D ASN* 4.8 1.7 - - - +
375D ARG* 4.7 10.4 - - - +
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Residues in contact with GLU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ASN 5.6 1.1 - - - +
254C THR* 4.4 17.0 - - - -
238D SER 3.7 2.2 + - - -
239D SER* 3.8 12.4 + - - +
240D ARG 3.9 0.2 - - - -
241D ASP* 1.3 76.6 - - - +
243D LYS* 1.3 57.7 + - - +
245D TRP* 3.2 5.2 + - - +
246D PHE* 2.6 49.0 + - + -
279D LEU* 4.1 24.2 - - + -
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Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C GLU* 3.2 28.7 - - + +
254C THR* 5.0 14.1 - - - -
255C VAL* 5.5 8.0 - - - +
330C PRO* 5.9 3.0 - - - +
360C MET* 4.7 16.2 - - - +
241D ASP 3.3 0.8 - - - -
242D GLU* 1.3 76.0 - - - +
244D SER* 1.3 60.6 + - - +
246D PHE* 3.7 6.0 - - + +
247D ARG* 3.0 29.8 + - - +
372D ASN* 2.9 38.4 + - + +
373D ASN* 4.0 18.7 + - + +
374D PRO* 4.1 14.4 - - + +
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Residues in contact with SER 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D PHE* 4.1 10.1 - - - -
241D ASP* 2.8 34.9 + - - -
243D LYS* 1.3 73.6 - - - +
245D TRP* 1.3 66.4 + - - +
247D ARG 3.5 0.2 + - - -
248D GLU* 3.0 27.2 + - - +
354D ASP* 5.7 0.7 - - - -
356D GLY* 3.8 21.4 + - - -
357D LEU* 5.4 0.9 - - - +
373D ASN* 3.1 21.1 + - - +
375D ARG* 4.7 4.0 - - - +
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Residues in contact with TRP 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C TRP* 6.3 3.6 - + - -
246C PHE* 5.1 3.8 - + - -
249C THR* 6.4 0.2 - - + -
237D PHE* 3.6 47.7 - + + -
241D ASP 3.4 3.0 + - - +
242D GLU* 3.2 9.9 + - - +
244D SER* 1.3 78.5 - - - +
246D PHE* 1.3 113.2 + + - +
248D GLU* 3.9 2.1 - - - +
249D THR* 2.9 48.0 + - + -
268D SER* 3.0 29.5 + - - -
269D ASP 4.0 17.0 - - - -
270D MET* 5.2 5.4 - - + -
279D LEU* 3.6 31.9 - - + -
280D TRP 3.1 18.4 + - - +
281D LEU* 4.4 2.5 - - + -
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Residues in contact with PHE 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C PHE* 3.6 24.3 - + + -
249C THR* 4.3 12.3 - - + -
250C GLU* 3.2 61.7 - - + +
253C ASN* 4.2 17.7 - - + -
254C THR* 4.3 4.9 - - - -
242D GLU* 2.6 48.4 + - + -
243D LYS* 3.7 9.0 - - + +
244D SER 3.3 0.2 - - - -
245D TRP* 1.3 106.4 - + - +
247D ARG* 1.3 65.2 + - - +
249D THR* 3.4 0.4 + - - -
250D GLU* 3.0 26.7 + - - +
279D LEU* 4.7 6.7 - - + -
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Residues in contact with ARG 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D LYS 3.0 17.5 + - - +
244D SER 3.9 0.4 - - - +
246D PHE* 1.3 76.7 - - - +
248D GLU* 1.3 63.9 + - - +
250D GLU* 3.4 17.6 + - - +
251D LEU* 3.1 24.8 + - + +
355D LEU 3.8 10.8 - - - +
356D GLY 3.6 23.8 - - - +
357D LEU 5.0 0.4 - - - -
358D ALA 2.9 24.8 + - - +
360D MET* 3.6 21.5 - - - +
369D ASP* 2.9 50.7 + - - -
370D VAL 3.2 12.9 + - - -
371D GLY* 3.9 11.8 - - - -
373D ASN* 5.3 1.1 - - + +
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D LYS* 4.8 0.7 + - - -
237D PHE* 3.8 19.5 - - + -
244D SER* 3.0 15.7 + - - +
245D TRP* 3.9 3.6 - - - +
247D ARG* 1.3 75.7 - - - +
249D THR* 1.3 64.8 + - - +
251D LEU* 3.4 4.4 + - - +
252D TYR* 3.1 50.6 + - + -
281D LEU* 3.7 19.7 - - + +
354D ASP* 3.3 16.3 + - - +
355D LEU* 3.1 37.4 + - + +
356D GLY* 3.8 12.1 + - - +
1000D 844 3.5 13.9 - - - +
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Residues in contact with THR 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C PHE* 4.2 17.0 - - + -
245D TRP* 2.9 39.5 + - + -
246D PHE* 3.7 4.9 - - - -
248D GLU* 1.3 76.2 - - - +
250D GLU* 1.3 58.0 + - - +
252D TYR* 3.1 6.0 + - - +
253D ASN* 2.8 48.3 + - + +
265D PHE* 5.3 0.2 - - - -
268D SER* 2.8 31.1 + - - +
281D LEU* 4.7 5.7 - - - +
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Residues in contact with GLU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C LYS* 5.1 8.7 - - - +
246C PHE* 3.9 41.1 - - + +
246D PHE 3.0 17.4 + - - +
247D ARG* 3.9 20.9 + - - +
249D THR* 1.3 75.3 - - - +
251D LEU* 1.3 59.9 + - - +
253D ASN* 4.8 2.0 - - - -
254D THR* 2.7 50.0 + - - +
255D VAL* 3.6 0.7 + - - +
360D MET* 5.2 10.4 - - + +
369D ASP* 5.0 4.9 - - - +
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D ARG* 3.1 18.3 + - - +
248D GLU 3.7 6.5 - - - +
250D GLU* 1.3 76.3 - - - +
252D TYR* 1.3 64.8 + - - +
255D VAL* 3.1 39.7 + - + +
256D MET 3.4 2.6 + - - -
257D LEU* 4.0 11.6 + - + +
332D ILE* 4.0 21.3 - - + -
355D LEU* 4.0 26.2 - - + +
358D ALA* 3.6 31.6 - - + -
360D MET* 3.7 40.8 - - + -
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Residues in contact with TYR 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D GLU* 3.1 46.6 + - + +
249D THR 3.7 2.7 - - - +
251D LEU* 1.3 81.7 - - + +
253D ASN* 1.3 58.6 + - - +
256D MET* 3.5 27.2 + - - +
257D LEU* 3.9 27.2 + - + +
262D ILE* 4.1 7.6 - - + +
263D LEU* 2.8 40.6 + - - +
264D GLY 5.2 0.2 - - - -
265D PHE* 3.4 57.7 - + + -
281D LEU* 4.4 9.4 - - + -
283D THR* 5.4 2.2 - - + -
352D ILE 5.1 0.7 + - - -
353D ALA* 5.4 0.3 - - - -
354D ASP 5.4 2.3 + - - -
355D LEU* 4.0 24.4 - - + +
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Residues in contact with ASN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C PHE* 6.2 1.6 - - + -
249D THR* 2.8 40.3 + - + +
250D GLU* 4.6 2.2 - - - +
252D TYR* 1.3 78.6 - - - +
254D THR* 1.3 57.8 + - - +
255D VAL 3.6 0.4 - - - -
256D MET* 3.2 19.7 - - - +
265D PHE* 3.3 34.3 - - - -
268D SER* 4.5 2.6 - - - +
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Residues in contact with THR 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D GLU* 2.7 37.3 + - - -
253D ASN* 1.3 73.7 - - - +
255D VAL* 1.3 65.0 + - - +
256D MET* 3.8 3.5 - - - +
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D GLU 4.8 0.7 - - - +
251D LEU* 3.1 31.5 + - + +
254D THR* 1.3 85.6 - - - +
256D MET* 1.3 71.6 + - - +
257D LEU* 4.2 22.0 - - + +
328D GLY 3.6 19.2 - - - +
329D LYS* 4.6 4.5 - - + -
330D PRO* 3.9 36.3 - - + -
332D ILE* 4.7 7.6 - - + -
360D MET* 5.1 5.6 - - + -
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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