Contacts of the strand formed by residues 230 - 237 (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 GLU 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B SER* 3.4 4.8 - - - -
227B TRP* 2.8 41.8 + - + +
228B GLN 3.3 2.9 - - - +
229B GLY* 1.3 73.0 - - - +
231B ASN* 1.3 68.2 + - - +
232B VAL* 3.5 4.6 + - + +
472C LYS* 6.3 0.7 - - - -
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Residues in contact with ASN 231 (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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211B LEU* 4.5 2.9 - - - +
224B ARG* 3.3 36.0 + - + +
225B GLY 3.3 11.5 - - - +
226B SER* 5.1 1.4 - - - -
229B GLY 4.4 0.2 + - - -
230B GLU* 1.3 78.1 - - - +
232B VAL* 1.3 65.1 + - - +
266B ILE* 5.6 0.2 - - - +
284B HIS* 5.4 3.1 - - - -
285B TYR* 4.0 31.2 + - + +
287B GLU* 5.1 7.3 + - - -
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.6 5.2 - - + -
224B ARG* 3.7 4.0 - - - +
225B GLY 2.8 45.6 + - - +
226B SER 4.4 0.4 - - - +
227B TRP* 4.1 35.9 - - + -
230B GLU* 4.2 3.4 - - + +
231B ASN* 1.3 81.0 - - - +
233B ALA* 1.3 59.0 + - - +
234B VAL* 4.2 12.8 - - + -
266B ILE* 3.8 23.6 - - + -
282B ILE* 4.0 17.3 - - + -
283B THR 3.6 8.7 - - - +
284B HIS* 5.2 0.2 - - - +
285B TYR* 3.7 11.1 - - - +
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Residues in contact with ALA 233 (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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222B VAL* 4.7 1.6 - - + -
223B TRP 3.4 6.7 - - - +
232B VAL* 1.3 73.0 - - - +
234B VAL* 1.3 62.1 + - - +
281B LEU 3.7 0.9 - - - +
282B ILE* 3.4 5.5 - - - +
283B THR* 2.9 50.4 + - - +
284B HIS 3.7 3.4 - - - +
285B TYR* 3.9 9.8 - - + +
1000B 844 3.6 35.9 - - + +
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Residues in contact with VAL 234 (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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208B ILE* 4.1 26.0 - - + -
210B LEU* 4.1 16.6 - - + -
221B GLU 3.7 0.9 - - - +
222B VAL* 3.2 4.0 - - - +
223B TRP* 2.8 42.8 + - - +
225B GLY* 5.0 2.0 - - - -
232B VAL* 4.2 12.1 - - + +
233B ALA* 1.3 76.4 - - - +
235B LYS* 1.3 62.0 + - - +
236B ILE* 4.0 10.0 + - + -
280B TRP* 3.6 39.3 - - + -
281B LEU 3.5 5.8 - - - +
282B ILE* 4.4 10.1 - - + -
1000B 844 4.1 1.8 - - - -
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Residues in contact with LYS 235 (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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219B TYR* 4.0 35.5 - - - +
221B GLU 3.4 9.4 - - - +
222B VAL* 4.1 8.1 - - + -
234B VAL* 1.3 73.2 - - - +
236B ILE* 1.3 64.7 + - - +
237B PHE* 3.6 46.2 - - + -
241B ASP* 4.9 2.2 + - - -
248B GLU* 4.5 1.6 + - - -
279B LEU 3.6 1.0 - - - +
280B TRP* 3.3 5.5 - - - -
281B LEU* 2.7 37.9 + - + +
354B ASP* 4.1 23.8 + - - -
375B ARG* 5.1 3.4 - - - +
1000B 844 3.5 43.1 + - + +
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Residues in contact with ILE 236 (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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210B LEU* 4.4 14.4 - - + -
220B GLY* 3.3 2.9 - - - -
221B GLU* 2.8 44.6 + - + +
223B TRP* 3.7 30.3 - - + +
234B VAL* 4.1 8.5 - - + -
235B LYS* 1.3 74.9 - - - +
237B PHE* 1.3 70.6 + - - +
278B GLN* 6.1 2.0 - - + -
279B LEU 3.5 6.7 - - - +
280B TRP* 3.5 37.5 - - + +
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Residues in contact with PHE 237 (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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219B TYR 3.9 4.5 - - - -
235B LYS* 3.6 43.7 - - + -
236B ILE* 1.3 82.6 - - - +
238B SER* 1.3 71.6 + - - +
239B SER 3.6 1.4 + - - -
241B ASP* 3.5 31.0 - - - +
244B SER* 4.0 5.6 - - - -
245B TRP* 3.6 43.5 - + + -
248B GLU* 3.6 21.8 - - + -
277B THR 5.5 1.7 - - - +
278B GLN* 5.7 0.3 - - - -
279B LEU* 3.0 40.0 + - + +
281B LEU* 3.8 14.8 - - + -
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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