Contacts of the strand formed by residues 224 - 231 (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 GLY 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B GLU* 3.5 2.3 - - - +
221B GLY 3.0 26.4 + - - +
222B GLY 3.4 3.4 - - - -
223B PHE* 1.3 91.0 - - - +
225B CYS* 1.3 63.4 + - - -
240B ARG 3.2 11.7 - - - -
242B LYS* 3.6 20.2 - - - -
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Residues in contact with CYS 225 (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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217B LYS* 3.5 30.5 - - + +
219B GLY 3.5 9.0 - - - +
220B GLU* 3.8 21.8 - - - +
223B PHE* 4.6 0.2 - - - -
224B GLY* 1.3 77.5 - - - -
226B VAL* 1.3 64.9 + - - +
227B TYR* 4.0 19.7 - - + -
238B VAL 3.7 0.9 - - - +
239B LYS* 3.4 3.8 - - - +
240B ARG* 2.8 36.0 + - + +
242B LYS* 4.3 9.0 - - - -
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Residues in contact with VAL 226 (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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217B LYS* 3.5 3.0 - - - -
218B ILE* 2.7 51.9 + - + +
219B GLY* 2.9 26.2 + - - +
223B PHE* 3.8 24.5 - - + -
225B CYS* 1.3 79.3 - - - +
227B TYR* 1.3 60.1 - - - +
237B ALA* 4.2 13.9 - - + -
238B VAL 3.4 11.0 - - - +
239B LYS* 4.3 9.0 - - + +
601B DL1 3.8 33.7 - - + +
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Residues in contact with TYR 227 (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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209B THR* 4.1 20.6 - - + -
212B PHE* 3.7 44.6 + + - +
213B SER 3.7 24.5 - - - -
214B GLU* 5.0 2.5 + - - -
216B LEU* 3.3 9.9 - - + +
217B LYS* 3.8 32.5 + - + -
218B ILE* 3.9 6.2 - - - +
225B CYS* 4.0 24.0 - - + +
226B VAL* 1.3 76.0 - - - +
228B ARG* 1.3 60.9 + - - +
237B ALA* 3.3 6.1 - - - -
238B VAL* 2.9 44.0 + - + +
240B ARG* 3.7 32.8 + - + -
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Residues in contact with ARG 228 (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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209B THR* 4.7 0.5 - - - -
216B LEU* 2.9 40.1 + - + +
218B ILE* 3.9 20.5 - - + +
227B TYR* 1.3 75.0 - - - +
229B ALA* 1.3 62.3 + - - +
230B VAL* 3.9 19.4 - - - +
235B VAL* 3.7 35.8 - - + +
236B TYR 3.6 3.1 - - - -
290B PHE* 3.8 34.8 - - + -
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Residues in contact with ALA 229 (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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208B GLY* 3.3 18.6 - - - +
209B THR* 3.7 18.4 - - + -
216B LEU* 5.2 0.2 - - - -
227B TYR 3.9 0.2 + - - -
228B ARG* 1.3 75.4 - - - +
230B VAL* 1.3 65.8 + - - +
231B MET* 4.1 9.6 - - + -
235B VAL* 3.5 6.1 - - - +
236B TYR* 2.9 35.1 + - + +
238B VAL* 3.8 21.1 - - + -
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Residues in contact with VAL 230 (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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207B ARG* 6.1 0.2 - - - -
208B GLY* 3.3 20.2 + - - +
228B ARG* 3.9 22.7 - - - +
229B ALA* 1.3 78.0 - - - +
231B MET* 1.3 68.1 + - - +
233B ASN* 4.6 9.0 - - - +
234B THR 3.4 18.2 - - - +
235B VAL* 4.5 13.0 - - + -
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Residues in contact with MET 231 (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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200B TRP* 3.8 32.5 - - + -
204B GLU* 3.5 31.6 - - + +
205B ILE* 3.7 24.2 - - + -
208B GLY* 4.2 4.3 - - - -
229B ALA* 4.1 4.7 - - + -
230B VAL* 1.3 81.5 - - - +
232B ARG* 1.3 71.3 - - - +
233B ASN 3.1 1.8 - - - +
234B THR* 2.9 26.5 + - - +
236B TYR* 3.4 27.6 - - + -
238B VAL* 4.5 7.0 - - + -
287B VAL* 3.8 24.9 - - + -
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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