Contacts of the strand formed by residues 263 - 268 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ASN 2.9 10.2 + - - +
192A ASN* 3.1 12.7 - - + +
193A PHE 2.8 25.6 + - - +
238A GLY* 3.8 5.5 - - - -
239A PHE* 3.1 43.1 + - + +
256A TYR* 2.5 30.4 + - + +
257A CYS 4.0 3.1 - - - -
258A ASN* 4.1 12.1 - - - +
261A ASN 5.5 2.2 - - - +
262A LYS* 1.3 74.9 - - - +
264A ILE* 1.3 60.7 + - - +
265A MET 4.1 0.4 + - - -
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Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A PHE* 3.4 20.2 - - + +
195A PHE* 3.5 31.0 - - + -
256A TYR* 3.3 9.6 - - - -
257A CYS* 2.9 40.8 + - - +
259A PHE* 3.8 25.8 - - + -
262A LYS 4.9 1.3 - - - +
263A GLU* 1.3 76.1 - - - +
265A MET* 1.3 61.3 + - - +
266A PHE* 3.6 22.4 - - + -
366A LEU* 3.6 25.8 - - + -
370A ILE* 3.9 17.7 - - + -
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Residues in contact with MET 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A PHE 2.8 9.2 + - - +
194A LYS* 3.2 7.4 - - - +
195A PHE 3.0 22.2 + - - +
231A VAL* 5.5 1.1 - - + -
233A LEU* 4.7 8.3 - - + -
236A PHE* 3.9 23.6 - - + -
239A PHE* 3.2 43.5 - - + +
240A ARG* 3.1 28.9 - - - +
241A GLY* 4.7 0.4 - - - -
243A LEU* 3.7 14.1 - - + -
254A SER* 3.6 25.1 - - - -
255A VAL 3.8 9.4 - - - +
256A TYR* 4.1 7.6 - - + -
263A GLU 4.1 0.8 + - - -
264A ILE* 1.3 73.0 - - - +
266A PHE* 1.3 66.8 + - - +
267A HIS* 4.5 5.8 + - - +
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Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PHE* 3.4 27.6 - - + -
196A GLY 4.7 0.2 - - - -
197A VAL* 3.5 27.1 - - + -
227A LEU* 3.4 35.0 - - + -
243A LEU* 4.3 0.5 - - - +
254A SER* 3.1 23.2 + - - -
255A VAL* 3.0 26.8 + - + +
256A TYR 4.7 0.4 - - - -
257A CYS* 4.3 8.7 - - - -
264A ILE* 3.6 21.1 - - + -
265A MET* 1.3 79.1 - - - +
267A HIS* 1.3 66.8 + - - +
268A VAL* 3.7 7.7 + - + -
295A VAL* 4.2 9.9 - - + -
366A LEU* 3.8 25.1 - - + -
369A LEU* 4.0 15.5 - - + -
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Residues in contact with HIS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LYS* 3.7 23.5 - - + +
195A PHE 2.8 12.8 + - - +
197A VAL 3.0 20.8 + - - -
241A GLY 3.0 27.3 + - - -
243A LEU* 3.9 25.0 - - + +
265A MET* 4.5 4.1 - - + +
266A PHE* 1.3 78.5 - - - +
268A VAL* 1.3 63.8 + - - +
272A LEU* 4.1 7.6 - - + -
287A HIS* 3.6 27.6 - - + +
288A ILE* 3.5 24.3 - - + +
291A ASP* 3.1 31.9 + - - -
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A VAL* 3.8 24.9 - - + +
220A PHE* 4.1 15.9 - - + -
224A LEU* 3.9 21.1 - - + -
254A SER* 5.2 1.4 + - - +
255A VAL* 4.4 29.2 - - + +
266A PHE* 3.7 8.4 + - + -
267A HIS* 1.3 70.7 - - - +
269A SER* 1.3 68.7 + - - +
270A THR* 3.7 21.8 - - - +
271A LYS* 3.9 15.2 - - + +
272A LEU* 3.1 26.2 + - - +
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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