Contacts of the helix formed by residues 241 - 255 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B ARG 5.6 0.7 - - - +
219B TYR* 3.9 27.3 - - - +
235B LYS* 4.9 0.7 + - - -
237B PHE* 3.5 19.7 - - + -
238B SER* 3.0 17.7 + - - +
240B ARG* 1.3 76.5 - - - +
242B GLU* 1.3 63.8 + - - +
243B LYS 3.3 3.1 - - - +
244B SER* 2.7 39.3 + - - -
245B TRP 3.4 7.1 + - - -
373B ASN* 4.5 3.6 - - - +
375B ARG* 3.4 25.5 + - - +
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B SER 3.7 0.8 + - - -
239B SER 3.4 17.5 + - - +
240B ARG 3.5 1.8 - - - -
241B ASP* 1.3 77.4 - - - +
243B LYS* 1.3 60.0 + - + +
245B TRP* 3.2 9.0 + - + +
246B PHE* 3.0 27.0 + - + +
270B MET* 3.7 23.3 - - + +
272B SER* 5.5 0.5 + - - -
277B THR* 4.0 14.3 + - - +
279B LEU* 4.0 23.3 - - + +
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Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ARG 5.4 0.2 + - - -
241B ASP 3.3 1.0 - - - -
242B GLU* 1.3 81.1 - - + +
244B SER* 1.3 58.8 + - - +
246B PHE* 3.9 6.3 - - + +
247B ARG* 3.0 29.5 + - - +
372B ASN* 2.9 41.8 + - + +
373B ASN* 4.0 17.7 + - + -
374B PRO* 4.1 14.8 - - + +
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Residues in contact with SER 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B PHE* 4.0 6.7 - - - -
241B ASP* 2.7 39.9 + - - -
243B LYS* 1.3 74.3 - - - +
245B TRP* 1.3 66.3 + - - +
247B ARG* 3.4 0.3 + - - +
248B GLU* 3.1 27.0 + - - +
356B GLY* 3.8 10.8 - - - -
373B ASN* 3.1 20.1 + - - +
375B ARG* 3.2 25.2 + - - -
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Residues in contact with TRP 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B PHE* 3.6 46.8 - + + -
241B ASP 3.4 2.8 + - - +
242B GLU* 3.2 16.5 + - + +
244B SER* 1.3 78.9 - - - +
246B PHE* 1.3 94.9 + + + +
248B GLU* 3.9 1.6 - - - +
249B THR* 2.9 47.8 + - + -
268B SER* 3.0 28.7 + - - -
269B ASP* 4.1 5.8 - - - -
270B MET* 3.7 34.8 - - + -
279B LEU* 3.6 31.2 - - + -
280B TRP 3.2 18.1 + - - +
281B LEU* 4.5 2.5 - - + -
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLU* 3.0 16.7 + - + +
243B LYS* 3.9 7.2 - - + +
244B SER 3.3 0.2 - - - -
245B TRP* 1.3 102.1 - + + +
247B ARG* 1.3 64.1 + - - +
249B THR* 4.4 6.1 - - + -
250B GLU* 2.9 60.7 + - + +
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B LYS 3.0 19.0 + - - +
244B SER 3.4 0.6 + - - +
246B PHE* 1.3 78.6 - - - +
248B GLU* 1.3 64.4 + - - +
250B GLU* 3.7 22.6 + - - +
251B LEU* 3.1 30.7 + - - +
355B LEU 3.7 9.2 - - - +
356B GLY 3.6 22.4 - - - +
357B LEU 4.9 0.2 - - - -
358B ALA 3.0 32.7 + - - +
360B MET* 3.5 23.0 - - - -
369B ASP* 2.9 48.5 + - - -
370B VAL 3.3 11.9 + - - -
371B GLY* 3.9 12.3 - - - -
373B ASN* 5.4 0.4 - - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LYS* 4.5 0.9 + - - -
237B PHE* 3.6 24.2 - - + -
244B SER 3.1 14.2 + - - +
245B TRP* 3.9 3.1 - - - +
247B ARG* 1.3 77.8 - - - +
249B THR* 1.3 65.3 + - - +
251B LEU* 3.4 3.6 + - - +
252B TYR* 3.1 46.6 + - + -
281B LEU* 3.7 21.3 - - + +
354B ASP* 3.2 18.7 + - - +
355B LEU* 2.7 46.4 + - + +
356B GLY* 4.1 2.4 + - - -
1000B 844 3.7 10.4 - - - +
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Residues in contact with THR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B TRP* 2.9 40.0 + - + -
246B PHE* 3.8 10.8 - - + -
248B GLU* 1.3 77.6 - - - +
250B GLU* 1.3 54.9 + - - +
252B TYR* 3.1 7.4 + - - +
253B ASN* 2.8 43.8 + - + +
265B PHE* 5.4 0.9 - - + -
268B SER* 2.8 37.2 + - - +
281B LEU* 4.6 6.2 - - - +
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B PHE* 2.9 50.8 + - + +
247B ARG* 3.7 35.7 + - - +
249B THR* 1.3 78.8 - - - +
251B LEU* 1.3 64.4 + - + +
253B ASN* 4.8 2.0 - - - -
254B THR* 2.9 42.8 + - - +
255B VAL* 3.6 1.6 + - - +
360B MET* 4.7 12.1 - - + +
369B ASP* 4.9 2.6 - - - +
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ARG* 3.1 27.0 + - - +
248B GLU* 3.6 4.5 - - - +
250B GLU* 1.3 78.0 - - - +
252B TYR* 1.3 60.7 + - - +
255B VAL* 3.1 40.4 + - + +
256B MET 3.4 2.6 + - - -
257B LEU* 3.9 12.7 - - + +
332B ILE* 4.0 21.8 - - + -
355B LEU* 4.1 21.1 - - + +
358B ALA* 3.7 30.3 - - + -
360B MET* 3.8 38.1 - - + -
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Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B GLU* 3.1 43.5 + - + -
249B THR 3.1 6.9 + - - +
251B LEU* 1.3 77.3 - - - +
253B ASN* 1.3 59.1 + - - +
256B MET* 3.5 25.3 + - - +
257B LEU* 3.8 28.2 + - + +
262B ILE* 4.1 8.0 - - + +
263B LEU* 2.8 41.8 + - + +
265B PHE* 3.4 58.5 - + + -
281B LEU* 4.3 10.5 - - + -
283B THR* 5.3 2.0 - - + -
352B ILE 5.0 0.9 + - - -
353B ALA* 5.5 1.9 - - - -
354B ASP 5.5 0.3 + - - -
355B LEU* 4.0 23.1 - - + +
1000B 844 6.2 0.2 - - - -
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Residues in contact with ASN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B THR* 2.8 31.1 + - + +
250B GLU* 4.7 2.2 - - - +
252B TYR* 1.3 73.0 - - - +
254B THR* 1.3 57.9 + - - +
256B MET* 3.2 17.6 - - - +
265B PHE* 4.9 13.7 - - + -
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLU* 2.9 25.1 + - - -
253B ASN* 1.3 76.2 - - - +
255B VAL* 1.3 65.4 + - - +
256B MET* 3.4 7.4 - - - +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLU 4.7 1.1 - - - +
251B LEU* 3.1 32.0 + - + +
254B THR* 1.3 81.5 - - - +
256B MET* 1.3 71.3 + - - +
257B LEU* 4.2 14.4 - - + -
328B GLY 3.7 14.9 - - - +
329B LYS* 4.2 16.8 - - + +
330B PRO* 3.8 35.9 - - + -
332B ILE* 4.7 6.5 - - + -
360B MET* 5.3 4.0 - - + -
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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