Contacts of the strand formed by residues 234 - 241 (chain B) in PDB entry 6BFN
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 THR 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A HIS* 2.8 34.9 + - + +
269A PRO* 3.9 22.0 - - + -
324A ARG* 3.7 8.7 - - - +
328A PHE* 4.6 0.5 - - - -
230B VAL* 3.4 5.1 - - - +
231B MET 2.9 33.4 + - - +
232B ARG 3.0 12.5 + - - -
233B ASN* 1.3 78.9 + - - +
235B VAL* 1.3 66.1 + - - +
236B TYR* 3.4 29.8 + - + +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PRO* 4.9 3.1 - - - +
228B ARG* 3.7 39.9 - - + +
229B ALA 3.5 8.7 - - - +
230B VAL* 4.5 10.3 - - + +
233B ASN 5.9 0.7 - - - +
234B THR* 1.3 80.2 - - - +
236B TYR* 1.3 67.0 + - - +
289B GLY* 4.6 0.5 - - - -
290B PHE* 3.5 43.7 + - + +
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Residues in contact with TYR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG 5.1 1.8 + - - -
268A HIS* 3.7 5.5 - - - -
269A PRO* 4.7 9.6 - - + -
328A PHE* 3.5 27.9 - - - -
200B TRP* 3.7 17.6 - + - -
228B ARG* 3.6 4.2 - - - +
229B ALA* 2.9 33.7 + - - +
231B MET* 3.4 41.5 - - + -
234B THR* 3.4 40.5 - - + +
235B VAL* 1.3 76.1 - - - +
237B ALA* 1.3 61.7 + - - +
238B VAL* 4.7 2.5 - - + -
275B ALA* 3.7 21.0 - - + +
287B VAL* 3.6 21.5 - - + -
288B TYR 3.3 20.2 - - - +
289B GLY* 4.4 2.2 - - - -
290B PHE* 4.0 9.2 - - - -
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Residues in contact with ALA 237 (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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218B ILE* 4.6 0.9 - - + -
226B VAL* 4.2 8.5 - - + -
227B TYR 3.3 8.1 - - - +
236B TYR* 1.3 74.1 - - - +
238B VAL* 1.3 61.1 + - - +
239B LYS 4.1 0.4 - - - -
287B VAL* 3.6 2.9 - - - +
288B TYR* 2.9 38.0 + - + +
290B PHE* 4.1 9.1 - - + +
601B DL1 3.6 48.5 - - + +
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Residues in contact with VAL 238 (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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205B ILE* 4.1 24.5 - - + -
209B THR* 4.6 6.5 - - + -
212B PHE* 4.8 7.2 - - + -
226B VAL* 3.4 4.2 - - - -
227B TYR* 2.9 44.1 + - + +
229B ALA* 3.8 26.0 - - + -
231B MET* 4.5 6.3 - - + -
236B TYR* 4.7 0.9 - - + -
237B ALA* 1.3 77.9 - - - +
239B LYS* 1.3 64.8 - - - +
240B ARG 4.8 0.7 - - - +
285B CYS* 4.3 19.3 - - + -
286B LEU 3.4 8.1 - - - +
287B VAL* 4.4 18.8 - - + -
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Residues in contact with LYS 239 (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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223B PHE* 3.6 40.2 - - + +
225B CYS 3.4 4.5 - - - +
226B VAL* 4.3 8.2 - - + +
237B ALA 4.1 1.0 - - - -
238B VAL* 1.3 71.0 - - - +
240B ARG* 1.3 61.3 + - - +
241B LEU* 4.1 15.2 + - + +
259B GLU* 3.0 29.6 + - - -
284B TYR 3.5 1.4 - - - +
285B CYS* 3.3 4.0 - - - -
286B LEU* 2.9 46.9 + - + +
288B TYR* 3.4 30.3 + - + -
358B ASP* 2.8 28.1 + - - +
601B DL1 3.9 12.2 + - + +
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Residues in contact with ARG 240 (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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212B PHE* 3.9 31.6 - - + +
224B GLY* 3.2 3.1 - - - -
225B CYS* 2.8 39.4 + - - +
227B TYR* 3.7 33.4 + - + -
238B VAL* 3.7 1.4 + - + -
239B LYS* 1.3 72.9 - - - +
241B LEU* 1.3 72.5 + - - +
242B LYS* 5.1 0.2 - - - +
283B PHE* 3.2 40.3 - - + +
284B TYR 3.3 11.4 - - - +
285B CYS* 4.4 12.3 - - - +
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Residues in contact with LEU 241 (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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223B PHE* 3.4 21.8 - - + +
239B LYS* 4.2 30.5 - - + +
240B ARG* 1.3 84.2 + - - +
242B LYS* 1.3 60.7 + - - +
243B GLU* 4.4 6.6 + - - +
252B VAL* 4.1 26.2 - - + +
255B SER* 4.9 6.5 - - - -
256B PHE* 4.0 36.1 - - + +
259B GLU* 5.5 1.6 - - - +
284B TYR* 3.1 31.1 + - + +
286B LEU* 4.8 7.6 - - + -
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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