Contacts of the strand formed by residues 245 - 250 (chain L) in PDB entry 6R8Y
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 VAL 245 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205L CYS* 3.5 13.3 - - - +
206L SER* 2.5 31.4 + - - +
219L GLY* 4.2 13.0 - - - -
220L ASP 3.2 17.5 + - - +
223L GLY* 4.6 7.2 - - - -
225L VAL* 4.4 14.1 - - + -
241L HIS* 4.2 19.7 - - + -
243L LYS 4.1 8.3 - - - +
244L LYS* 1.3 75.2 - - - +
246L THR* 1.3 54.4 + - - +
247L HIS 3.9 5.6 - - - +
248L VAL* 4.6 2.2 - - + -
260L THR* 3.5 16.8 - - - +
261L ALA 3.3 14.4 - - - +
262L SER* 4.1 6.3 - - - +
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Residues in contact with THR 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J A 4.2 10.6 + - - +
205L CYS* 4.2 19.0 - - - +
206L SER* 2.9 13.5 + - - -
244L LYS* 3.8 4.9 + - - +
245L VAL* 1.3 69.1 - - - +
247L HIS* 1.3 62.5 + - - +
261L ALA* 3.0 7.5 + - - -
262L SER 4.6 0.7 - - - -
263L VAL* 4.0 18.7 - - - +
291L VAL 3.7 18.7 + - - -
292L ASN* 3.2 34.9 + - - +
308L GLN* 5.5 0.3 + - - -
339L PRO* 5.3 9.2 - - + -
341L LYS* 5.0 11.0 + - - -
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Residues in contact with HIS 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L LYS* 5.7 4.7 - - - -
206L SER* 3.1 8.5 + - - -
207L LEU 5.0 8.2 + - - -
208L ASP* 5.5 2.5 - - - -
245L VAL* 3.9 0.7 - - - +
246L THR* 1.3 82.4 + - - +
248L VAL* 1.3 84.3 + - - +
249L ALA* 4.5 4.1 - - + +
260L THR* 3.7 1.0 + - - -
261L ALA* 2.9 31.4 + - + +
292L ASN 3.8 15.3 - - - +
293L ALA* 3.9 14.6 - - + -
294L ALA* 3.2 39.3 + - - +
295L CYS* 4.5 15.1 - - + +
341L LYS* 4.9 17.2 + - + +
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Residues in contact with VAL 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L SER* 3.7 24.0 - - - +
207L LEU 4.1 11.3 - - - +
208L ASP* 3.8 9.5 - - - +
217L VAL* 4.4 23.3 - - + +
218L THR* 5.0 0.9 - - - -
219L GLY 4.8 5.4 - - - +
225L VAL* 5.2 6.1 - - + -
245L VAL* 4.6 2.9 - - + -
247L HIS* 1.3 94.3 + - - +
249L ALA* 1.3 63.9 + - - +
258L LEU* 4.3 13.0 - - + -
259L ALA 2.9 22.7 - - - +
260L THR* 3.5 19.3 - - - +
294L ALA* 5.0 1.6 - - - -
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Residues in contact with ALA 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208L ASP* 3.5 19.1 - - - +
217L VAL* 5.3 0.2 - - - -
247L HIS* 4.5 6.5 - - - +
248L VAL* 1.3 77.8 - - - +
250L LEU* 1.3 62.5 + - - +
258L LEU* 2.9 20.5 - - - +
259L ALA* 2.9 22.7 + - - +
294L ALA 4.3 12.1 + - - +
295L CYS* 5.1 4.3 - - - -
296L PHE* 3.5 24.0 - - + +
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Residues in contact with LEU 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208L ASP* 4.0 5.8 + - + +
209L VAL* 3.5 17.5 - - - +
210L SER* 3.5 41.5 - - - +
213L SER* 5.9 0.7 - - - +
215L MET* 4.4 12.3 - - + +
217L VAL* 4.3 15.7 - - + -
227L LEU* 6.3 0.9 - - + -
249L ALA* 1.3 79.3 - - - +
251L ASN* 1.3 69.2 + - - +
252L PRO* 3.7 5.0 - - - +
255L ASP 5.2 6.3 - - - +
257L PHE 4.6 3.1 - - - +
258L LEU* 3.3 30.1 - - + -
272L LEU* 4.6 16.8 - - + -
296L PHE* 4.1 9.5 - - - +
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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