Contacts of the strand formed by residues 228 - 236 (chain B) in PDB entry 6CNC
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 LYS 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B VAL* 3.8 1.9 - - - -
221B THR 3.2 30.6 + - - +
222B SER* 3.8 1.4 + - - -
226B GLU* 3.2 25.2 + - - +
227B ARG* 1.3 81.3 - - - +
229B SER* 1.3 62.9 + - - +
244B HIS* 3.1 30.1 - - + +
245B ASN* 4.8 5.2 - - - +
246B SER* 3.6 19.3 - - - -
332B ILE* 2.8 42.3 + - - +
333B ALA* 3.5 15.9 - - + +
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Residues in contact with SER 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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220B VAL* 3.2 29.7 - - - +
227B ARG* 5.2 10.5 - - - +
228B LYS* 1.3 76.8 - - - +
230B LYS* 1.3 61.3 + - - +
231B THR* 3.9 19.5 - - - +
244B HIS* 2.9 23.8 + - - -
245B ASN* 3.7 11.0 + - - +
333B ALA* 4.8 0.2 - - - -
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLN* 3.9 2.2 - - - +
218B ALA* 3.7 2.3 - - - -
219B SER* 3.5 40.9 + - - +
221B THR* 6.3 0.2 - - + -
228B LYS 4.2 0.2 + - - -
229B SER* 1.3 75.5 + - - +
231B THR* 1.3 67.3 - - - +
232B TYR* 3.8 19.0 - - - +
242B LEU* 3.7 20.9 - - + +
244B HIS* 3.8 27.6 - - + +
332B ILE* 4.8 1.8 - - + -
333B ALA* 4.8 4.9 - - + +
334B HIS* 3.3 38.6 - - + -
349B ILE* 5.8 0.9 - - + -
352B MET* 3.3 33.9 - - - +
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Residues in contact with THR 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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216B VAL* 4.5 11.9 - - + -
217B GLN 3.6 5.8 - - - +
218B ALA* 4.5 11.9 - - + -
229B SER* 3.9 14.8 - - - +
230B LYS* 1.3 79.1 - - - +
232B TYR* 1.3 61.8 + - - +
233B VAL* 5.7 1.6 - - - -
242B LEU* 4.0 1.2 - - - -
243B LYS* 2.6 59.2 + - - +
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Residues in contact with TYR 232 (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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215B ILE 4.4 0.7 - - - +
216B VAL* 4.6 0.4 - - - +
217B GLN* 2.9 77.2 + - + +
230B LYS* 3.8 10.1 - - - +
231B THR* 1.3 75.9 - - - +
233B VAL* 1.3 65.8 + - - +
240B ILE* 3.1 41.9 - - + +
241B TYR* 2.9 34.8 - - - -
242B LEU* 3.3 17.3 - - + -
243B LYS 4.4 0.4 - - - +
253B ILE* 3.1 34.7 - - + +
352B MET* 5.9 0.2 - - + -
353B THR* 4.2 5.7 - - - +
356B VAL* 4.1 20.6 - - + -
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Residues in contact with VAL 233 (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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213B LYS* 4.3 8.3 - - + +
214B GLY 4.0 2.0 - - - +
215B ILE 4.7 2.2 - - - -
216B VAL* 3.5 39.7 - - + +
231B THR* 5.7 1.1 - - - +
232B TYR* 1.3 80.4 - - - +
234B ILE* 1.3 89.1 + - + +
235B THR* 4.8 0.8 + - - +
240B ILE* 4.2 3.6 - - - -
241B TYR* 2.7 38.7 + - + +
243B LYS* 4.3 34.1 - - + +
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Residues in contact with ILE 234 (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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213B LYS 3.3 12.9 - - - +
214B GLY* 3.3 40.1 + - - +
233B VAL* 1.3 92.7 - - + +
235B THR* 1.3 64.3 + - - +
236B LYS* 3.6 9.6 - - - +
237B ASN* 3.3 11.7 - - - +
238B GLY 3.1 27.8 - - - +
239B LYS 3.2 17.5 - - - +
240B ILE* 3.6 17.5 - - + +
243B LYS* 5.8 0.3 - - - -
360B MET* 3.7 15.7 - - + -
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Residues in contact with THR 235 (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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213B LYS 4.8 3.8 - - - +
233B VAL* 3.7 1.1 + - - +
234B ILE* 1.3 81.7 + - - +
236B LYS* 1.3 80.1 + - + +
239B LYS* 2.8 31.5 + - - +
241B TYR* 3.0 22.7 - - + +
243B LYS* 5.2 10.6 - - - +
250B GLU* 4.6 12.2 + - - +
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Residues in contact with LYS 236 (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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234B ILE* 3.8 2.0 - - - -
235B THR* 1.3 100.1 - - + +
237B ASN* 1.3 76.3 + - + +
238B GLY 3.7 1.1 - - - -
239B LYS* 2.9 33.4 + - - +
15Y T 4.3 21.2 + - - -
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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