Contacts of the strand formed by residues 230 - 237 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226C SER* 3.4 4.4 - - - -
227C TRP* 2.8 36.5 + - + +
228C GLN* 3.9 10.9 - - + +
229C GLY* 1.3 85.6 - - - +
231C ASN* 1.3 69.2 + - - +
232C VAL* 4.2 4.1 - - + +
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Residues in contact with ASN 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C LEU* 4.5 3.6 - - - +
224C ARG* 3.3 36.5 + - + +
225C GLY 3.3 10.3 - - - +
226C SER* 5.0 1.7 + - - -
229C GLY 4.4 0.2 + - - -
230C GLU* 1.3 79.3 + - - +
232C VAL* 1.3 63.9 + - - +
284C HIS* 5.3 3.1 - - - -
285C TYR* 4.0 31.3 + - + +
287C GLU* 4.9 8.9 + - - -
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 4.6 5.6 - - + -
224C ARG* 3.7 3.5 - - - -
225C GLY 2.8 46.4 + - - +
226C SER 4.4 0.4 - - - +
227C TRP* 4.1 36.6 - - + -
230C GLU* 3.5 4.2 + - + +
231C ASN* 1.3 79.6 - - - +
233C ALA* 1.3 59.6 + - - +
234C VAL* 4.2 12.6 - - + -
266C ILE* 3.8 23.6 - - + -
282C ILE* 4.0 17.3 - - + -
283C THR 3.6 8.5 - - - +
285C TYR* 3.7 10.8 - - - +
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C VAL* 4.7 1.8 - - + -
223C TRP 3.4 6.7 - - - +
232C VAL* 1.3 73.6 - - - +
234C VAL* 1.3 60.2 - - - +
282C ILE* 3.3 5.7 - - - +
283C THR* 2.9 50.5 + - - +
284C HIS 3.7 3.6 - - - +
285C TYR* 3.9 9.8 - - + +
1000C 844 3.5 36.7 - - + +
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Residues in contact with VAL 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ILE* 4.1 26.0 - - + -
210C LEU* 4.1 15.7 - - + -
221C GLU 3.7 0.7 - - - +
222C VAL* 3.3 3.3 - - - -
223C TRP* 2.8 44.0 + - + +
225C GLY* 4.9 2.0 - - - -
232C VAL* 4.2 11.2 - - + +
233C ALA* 1.3 77.0 - - - +
235C LYS* 1.3 62.5 + - - +
236C ILE* 3.9 9.8 + - + -
280C TRP* 3.6 38.1 - - + -
281C LEU 3.5 2.5 - - - +
282C ILE* 3.8 15.9 - - + -
1000C 844 4.0 2.0 - - - -
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Residues in contact with LYS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C TYR* 4.0 36.4 - - - +
221C GLU 3.4 9.6 - - - +
222C VAL* 4.1 9.2 - - + -
234C VAL* 1.3 73.6 - - - +
236C ILE* 1.3 65.5 + - - +
237C PHE* 3.6 47.3 - - + -
244C SER* 6.0 0.4 - - - -
248C GLU* 4.7 1.4 + - - -
279C LEU 3.6 1.2 - - - +
280C TRP* 3.2 5.4 - - - -
281C LEU* 2.7 40.1 + - + +
354C ASP* 4.0 23.4 + - - -
1000C 844 3.5 41.4 + - - +
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C LEU* 4.4 13.9 - - + -
220C GLY* 3.3 4.0 - - - -
221C GLU* 2.8 45.8 + - + +
223C TRP* 3.7 30.3 - - + +
234C VAL* 4.1 7.9 - - + -
235C LYS* 1.3 76.7 - - - +
237C PHE* 1.3 67.1 + - - +
273C ARG* 5.9 1.6 - - - +
278C GLN* 3.6 35.4 - - + +
279C LEU 3.4 3.8 - - - +
280C TRP* 3.6 30.3 - - + +
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Residues in contact with PHE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C TYR 3.9 4.5 - - - -
220C GLY* 4.6 0.2 - - - -
235C LYS* 3.6 47.6 - - + -
236C ILE* 1.3 80.9 - - - +
238C SER* 1.3 71.0 + - - +
239C SER 3.7 1.0 + - - -
241C ASP* 3.7 24.2 - - + +
244C SER* 4.0 10.3 - - - -
245C TRP* 3.6 43.1 - + + -
248C GLU* 3.7 18.2 - - + -
277C THR 5.6 0.9 - - - +
278C GLN* 5.4 3.5 - - - +
279C LEU* 3.0 42.6 + - + +
281C LEU* 3.8 16.6 - - + -
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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