Contacts of the strand formed by residues 263 - 268 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B ASN 3.0 7.1 + - - +
192B ASN* 3.5 19.4 + - - +
193B PHE* 3.1 24.9 + - - +
238B GLY* 4.2 5.7 - - - -
239B PHE* 3.4 32.5 + - + +
256B TYR* 3.0 27.2 + - + +
257B CYS 3.7 3.8 - - - -
258B ASN* 3.8 11.1 - - - +
261B ASN 5.8 0.2 - - - +
262B LYS* 1.3 77.6 - - - +
264B ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 264 (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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193B PHE* 3.7 9.6 - - + +
195B PHE* 3.5 34.8 - - + -
256B TYR* 3.1 11.0 - - - -
257B CYS* 2.9 40.4 + - - +
259B PHE* 3.9 29.2 - - + +
262B LYS* 4.8 3.4 - - + -
263B GLU* 1.3 79.1 - - - +
265B MET* 1.3 64.1 + - - +
266B PHE* 3.7 19.5 - - + -
366B LEU* 3.9 19.3 - - + -
370B ILE* 4.2 24.7 - - + -
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Residues in contact with MET 265 (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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193B PHE 3.1 7.2 + - - +
194B LYS* 3.2 24.9 - - - +
195B PHE 3.2 3.8 + - - -
231B VAL* 5.3 2.2 - - + -
233B LEU* 4.8 9.0 - - + -
236B PHE* 3.7 27.6 - - + -
239B PHE* 3.6 38.4 - - + +
240B ARG* 4.2 6.1 - - - +
241B GLY* 3.9 13.7 - - - -
243B LEU* 3.7 32.5 - - + -
254B SER* 4.0 7.0 - - - -
255B VAL 3.9 10.1 - - - +
256B TYR* 4.0 9.4 - - + -
263B GLU 4.2 0.2 + - - -
264B ILE* 1.3 76.1 - - - +
266B PHE* 1.3 71.6 + - - +
267B HIS* 4.7 2.2 - - - +
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Residues in contact with PHE 266 (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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195B PHE* 3.4 26.9 - + + -
197B VAL* 3.7 26.0 - - + -
227B LEU* 3.7 32.3 - - + -
243B LEU* 4.2 1.0 - - - +
254B SER* 2.7 25.7 + - - -
255B VAL* 3.0 51.4 + - + +
256B TYR* 4.5 0.9 - - - -
257B CYS* 3.9 18.2 - - - -
264B ILE* 3.7 22.0 - - + -
265B MET* 1.3 80.6 - - - +
267B HIS* 1.3 65.8 + - - +
268B VAL* 3.7 1.3 - - + -
295B VAL* 4.5 4.0 - - + -
366B LEU* 3.9 11.7 - - + -
369B LEU* 4.0 12.8 - - + -
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Residues in contact with HIS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LYS* 3.6 19.0 - - + +
195B PHE 2.8 13.2 + - - +
197B VAL* 2.9 27.2 + - - +
241B GLY* 2.8 30.2 + - - -
243B LEU* 3.7 26.1 - - + +
265B MET* 4.7 1.7 - - + +
266B PHE* 1.3 79.8 - - - +
268B VAL* 1.3 62.0 + - - +
272B LEU* 4.1 9.6 - - + -
287B HIS* 3.4 20.6 + - + +
288B ILE* 3.6 22.2 - - + +
291B ASP* 2.7 36.5 + - - +
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 3.8 21.3 - - + +
220B PHE* 4.6 7.9 - - + -
224B LEU* 3.8 15.0 - - + -
254B SER* 4.6 4.0 + - - +
255B VAL* 3.5 31.4 - - + -
266B PHE* 3.7 5.1 + - + -
267B HIS* 1.3 72.1 - - - +
269B SER* 1.3 60.7 + - - +
270B THR* 3.3 25.6 - - - +
271B LYS* 3.0 27.3 + - + +
272B LEU* 2.8 32.7 + - - +
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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