Contacts of the strand formed by residues 230 - 235 (chain C) in PDB entry 6BW4
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 VAL 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C TYR 5.2 2.6 + - - -
196C ALA* 3.5 30.7 - - + +
197C SER 3.1 22.3 + - - +
198C ASP* 4.8 1.0 - - - +
200C HIS 3.5 32.1 - - - +
201C THR 3.9 8.1 - - - +
202C ILE* 3.9 14.6 - - + -
226C HIS* 3.8 23.8 - - + -
228C ALA 3.7 6.3 - - - +
229C VAL* 1.3 72.9 - - - +
231C GLU* 1.3 61.4 + - - +
232C ASP 3.9 7.9 - - - +
245C SER* 4.2 1.1 - - - -
246C VAL 3.5 15.3 - - - +
247C ALA* 3.9 1.1 - - - -
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Residues in contact with GLU 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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1B MET* 2.9 27.0 + - - -
2B ARG* 3.0 41.8 + - - -
129C ARG* 4.8 0.9 + - - -
181C TYR* 4.0 7.0 - - - +
182C GLY* 3.5 16.4 + - - -
196C ALA* 4.5 0.2 - - - -
198C ASP* 5.2 0.2 - - - +
229C VAL* 3.8 12.8 - - - +
230C VAL* 1.3 74.8 - - - +
232C ASP* 1.3 62.3 + - - +
246C VAL 2.9 5.4 + - - +
248C ASP* 2.6 32.4 - - - +
276C VAL 3.3 25.8 - - - +
277C ASN* 3.5 24.0 - - - +
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Residues in contact with ASP 232 (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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129C ARG* 3.4 25.1 + - - -
182C GLY* 3.6 9.1 - - - -
183C LEU 4.4 1.6 + - - +
196C ALA* 4.2 2.4 - - - +
230C VAL* 3.6 3.0 - - - +
231C GLU* 1.3 80.2 - - - +
233C VAL* 1.3 79.7 + - - +
234C SER* 5.7 0.2 - - - -
245C SER* 3.3 5.5 - - - -
246C VAL* 3.1 38.0 + - + +
277C ASN 3.6 13.2 - - - +
278C CYS* 3.4 9.0 - - - +
279C LEU* 3.2 33.5 + - + +
322C GLN* 4.7 3.8 - - - +
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Residues in contact with VAL 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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182C GLY* 3.9 12.8 - - - -
183C LEU* 4.0 6.2 - - - +
184C SER* 3.6 9.4 - - - +
194C LEU* 3.9 29.4 - - + +
195C SER 4.0 2.2 - - - +
196C ALA* 3.9 27.8 - - + +
202C ILE* 4.0 12.1 - - + -
232C ASP* 1.3 87.4 + - - +
234C SER* 1.3 66.5 + - - +
243C PHE* 3.7 22.2 - - + -
244C GLY 3.3 14.4 - - - +
245C SER* 4.5 3.8 - - - -
279C LEU* 4.0 2.5 - - - -
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Residues in contact with SER 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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184C SER* 3.6 10.8 + - - -
194C LEU* 4.7 1.1 - - - -
233C VAL* 1.3 77.3 - - - +
235C TRP* 1.3 72.7 + - - +
237C LEU* 5.8 1.7 - - - +
243C PHE* 3.2 4.7 - - - +
244C GLY 2.8 33.5 + - - -
279C LEU* 4.0 26.2 + - - -
280C SER* 5.3 1.1 - - - -
281C PHE* 3.4 15.9 + - - +
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Residues in contact with TRP 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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184C SER* 3.0 47.9 + - - +
185C TRP 3.2 3.4 - - - -
186C ASN* 3.2 53.7 - - + +
187C PRO* 4.0 11.4 - - + -
189C LEU* 5.8 0.9 - - + -
192C HIS* 3.5 11.6 + - + -
194C LEU* 3.2 28.8 - - + +
204C LEU* 3.5 25.1 - - + -
234C SER* 1.3 84.0 + - - +
236C HIS* 1.3 70.7 + - - +
237C LEU* 3.6 8.7 + - - +
239C HIS 5.2 0.4 - - - -
240C GLU 3.4 13.0 - - - -
241C SER 4.4 0.9 - - - -
242C LEU 3.6 20.0 - - - -
243C PHE* 3.8 11.0 - + + -
257C THR* 3.9 24.9 - - + -
281C PHE* 3.4 6.8 - - - -
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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