Contacts of the strand formed by residues 263 - 268 (chain C) in PDB entry 3BRW
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 263 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191C ASN 2.9 7.2 + - - +
192C ASN* 3.7 20.5 + - - +
193C PHE* 3.1 26.9 + - - +
238C GLY* 4.0 4.5 - - - -
239C PHE* 3.3 33.1 + - + +
256C TYR* 2.9 26.4 + - - +
258C ASN* 4.1 13.0 - - - +
261C ASN 3.7 6.0 + - - +
262C LYS* 1.3 74.4 - - - +
264C ILE* 1.3 60.6 + - - +
265C MET 4.2 0.4 + - - -
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Residues in contact with ILE 264 (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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193C PHE* 3.7 11.9 - - + +
195C PHE* 3.6 35.7 - - + -
255C VAL 4.5 0.2 - - - +
256C TYR* 3.2 9.0 - - - -
257C CYS* 3.2 45.5 + - - +
259C PHE* 3.8 28.0 - - + -
262C LYS* 4.4 9.0 - - + +
263C GLU* 1.3 75.9 - - - +
265C MET* 1.3 62.6 + - - +
266C PHE* 4.1 19.1 + - + -
366C LEU* 3.8 22.7 - - + -
370C ILE* 4.6 11.4 - - + -
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Residues in contact with MET 265 (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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193C PHE 3.4 7.1 + - - -
194C LYS* 3.5 26.3 - - + +
195C PHE 3.7 1.0 + - - -
231C VAL* 4.6 4.9 - - + -
233C LEU* 4.8 6.3 - - + -
236C PHE* 3.6 26.5 - - + -
239C PHE* 3.3 42.0 - - + +
240C ARG* 3.4 18.2 - - - +
243C LEU* 3.8 20.2 - - + -
254C SER* 3.8 14.1 - - - -
255C VAL 3.9 7.4 - - - +
256C TYR* 3.7 17.5 - - + -
264C ILE* 1.3 73.2 - - - +
266C PHE* 1.3 74.6 + - - +
267C HIS* 4.9 2.8 + - - +
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Residues in contact with PHE 266 (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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195C PHE* 3.4 42.6 - + + -
197C VAL* 3.8 21.1 - - + -
227C LEU* 3.8 34.1 - - + -
243C LEU* 4.5 0.7 - - - +
254C SER* 3.0 20.1 + - - -
255C VAL* 3.1 38.3 + - + +
256C TYR 4.9 0.4 - - - -
257C CYS* 4.4 17.7 - - - -
264C ILE* 4.3 7.4 - - + -
265C MET* 1.3 80.1 - - - +
267C HIS* 1.3 66.5 + - - +
268C VAL* 3.9 7.9 - - + -
295C VAL* 4.5 8.7 - - + -
365C LEU* 5.9 0.2 - - + -
366C LEU* 3.9 22.0 - - + -
369C LEU* 4.4 7.9 - - + -
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Residues in contact with HIS 267 (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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194C LYS* 4.0 12.5 - - + +
195C PHE 2.8 9.2 + - - +
196C GLY* 3.4 0.9 - - - -
197C VAL* 2.5 34.6 + - - +
240C ARG 4.4 1.8 + - - -
241C GLY* 3.2 28.2 + - - -
242C GLY 3.7 12.7 + - - -
243C LEU* 3.9 28.9 - - + +
254C SER* 5.0 0.2 - - - -
265C MET* 5.0 1.9 + - + -
266C PHE* 1.3 76.2 - - - +
268C VAL* 1.3 56.7 + - - +
272C LEU* 4.8 6.1 - - + -
287C HIS* 3.7 19.0 + - + -
288C ILE* 3.8 18.3 - - + +
291C ASP* 2.7 37.4 + - - +
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Residues in contact with VAL 268 (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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197C VAL* 3.6 33.7 - - + +
220C PHE* 5.2 3.6 - - + -
224C LEU* 4.6 10.8 - - + -
254C SER* 4.3 12.9 + - - +
255C VAL* 4.6 14.4 - - + +
266C PHE* 3.9 12.1 + - + -
267C HIS* 1.3 75.9 - - - +
269C SER* 1.3 67.4 + - - +
270C THR* 3.8 21.1 - - - +
271C LYS* 3.4 29.2 + - + +
272C LEU* 3.3 22.1 + - - +
288C ILE* 4.3 0.4 - - - -
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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